From 4728e99fa3d009bc4c1fb5a8d0d42216b64eccfe Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Sat, 13 Mar 2021 18:28:46 +0100
Subject: [PATCH 001/139] Updated json importer and tests

---
 PyCTBN/PyCTBN/utility/json_importer.py     | 11 ++++++++---
 PyCTBN/tests/utility/test_json_importer.py |  4 ++--
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/PyCTBN/PyCTBN/utility/json_importer.py b/PyCTBN/PyCTBN/utility/json_importer.py
index edff212..2cadff4 100644
--- a/PyCTBN/PyCTBN/utility/json_importer.py
+++ b/PyCTBN/PyCTBN/utility/json_importer.py
@@ -49,10 +49,10 @@ class JsonImporter(AbstractImporter):
         super(JsonImporter, self).__init__(file_path)
         self._raw_data = self.read_json_file()
 
-    def import_data(self, indx: int) -> None:
+    def import_data(self, indx: int = 0) -> None:
         """Implements the abstract method of :class:`AbstractImporter`.
 
-        :param indx: the index of the outer JsonArray to extract the data from
+        :param indx: the index of the outer JsonArray to extract the data from, default to 0
         :type indx: int
         """
         self._array_indx = indx
@@ -101,7 +101,12 @@ class JsonImporter(AbstractImporter):
         """
         with open(self._file_path) as f:
             data = json.load(f)
-            return data
+
+            if (isinstance(data,list)):
+                return data
+            else:
+                return [data]
+         
 
     def one_level_normalizing(self, raw_data: typing.List, indx: int, key: str) -> pd.DataFrame:
         """Extracts the one-level nested data in the list ``raw_data`` at the index ``indx`` at the key ``key``.
diff --git a/PyCTBN/tests/utility/test_json_importer.py b/PyCTBN/tests/utility/test_json_importer.py
index 877805b..a4bb4c0 100644
--- a/PyCTBN/tests/utility/test_json_importer.py
+++ b/PyCTBN/tests/utility/test_json_importer.py
@@ -39,7 +39,7 @@ class TestJsonImporter(unittest.TestCase):
         path = os.getcwd()
         path = path + '/data.json'
         j1 = JsonImporter(path, '', '', '', '', '')
-        self.assertTrue(self.ordered(data_set) == self.ordered(j1._raw_data))
+        self.assertTrue(self.ordered([data_set]) == self.ordered(j1._raw_data))
         os.remove('data.json')
 
     def test_read_json_file_not_found(self):
@@ -155,7 +155,7 @@ class TestJsonImporter(unittest.TestCase):
         self.assertEqual(j1.file_path, "./PyCTBN/test_data/networks_and_trajectories_binary_data_01_3.json")
 
     def test_import_data(self):
-        j1 = JsonImporter("./PyCTBN/test_data/networks_and_trajectories_binary_data_01_3.json", 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        j1 = JsonImporter("./PyCTBN/test_data/networks_and_trajectories_binary_data_02_10_1.json", 'samples', 'dyn.str', 'variables', 'Time', 'Name')
         j1.import_data(0)
         self.assertEqual(list(j1.variables[j1._variables_key]),
                          list(j1.concatenated_samples.columns.values[1:len(j1.variables[j1._variables_key]) + 1]))

From 683780e555893eabd8d18927ac6c02849701b955 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 17:30:00 +0000
Subject: [PATCH 002/139] Update documentation

---
 .../doctrees/PyCTBN.PyCTBN.utility.doctree    | Bin 151587 -> 151908 bytes
 docs-out/_build/doctrees/environment.pickle   | Bin 148538 -> 148538 bytes
 .../_build/html/PyCTBN.PyCTBN.utility.html    |   4 ++--
 docs-out/_build/html/searchindex.js           |   2 +-
 docs/PyCTBN.PyCTBN.utility.html               |   4 ++--
 docs/searchindex.js                           |   2 +-
 6 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs-out/_build/doctrees/PyCTBN.PyCTBN.utility.doctree b/docs-out/_build/doctrees/PyCTBN.PyCTBN.utility.doctree
index 508570a1d4df367cdd853b345fe5bcdee5aeba94..a895732eb322969feb1f1757cdde2aedb703347b 100644
GIT binary patch
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diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 73cc95323e5747cdd9506eb85884df4a094b5971..a6906b6442bb5b721a2a813fef5543b79fd79de3 100644
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diff --git a/docs-out/_build/html/PyCTBN.PyCTBN.utility.html b/docs-out/_build/html/PyCTBN.PyCTBN.utility.html
index ba10218..5f834ce 100644
--- a/docs-out/_build/html/PyCTBN.PyCTBN.utility.html
+++ b/docs-out/_build/html/PyCTBN.PyCTBN.utility.html
@@ -391,11 +391,11 @@ dataset</p>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data">
-<code class="sig-name descname">import_data</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">indx</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">import_data</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">indx</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">0</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data" title="Permalink to this definition">¶</a></dt>
 <dd><p>Implements the abstract method of <code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractImporter</span></code>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>indx</strong> (<em>int</em>) – the index of the outer JsonArray to extract the data from</p>
+<dd class="field-odd"><p><strong>indx</strong> (<em>int</em>) – the index of the outer JsonArray to extract the data from, default to 0</p>
 </dd>
 </dl>
 </dd></dl>
diff --git a/docs-out/_build/html/searchindex.js b/docs-out/_build/html/searchindex.js
index c34509d..8061880 100644
--- a/docs-out/_build/html/searchindex.js
+++ b/docs-out/_build/html/searchindex.js
@@ -1 +1 @@
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diff --git a/docs/PyCTBN.PyCTBN.utility.html b/docs/PyCTBN.PyCTBN.utility.html
index ba10218..5f834ce 100644
--- a/docs/PyCTBN.PyCTBN.utility.html
+++ b/docs/PyCTBN.PyCTBN.utility.html
@@ -391,11 +391,11 @@ dataset</p>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data">
-<code class="sig-name descname">import_data</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">indx</span><span class="p">:</span> <span class="n">int</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">import_data</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">indx</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">0</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data" title="Permalink to this definition">¶</a></dt>
 <dd><p>Implements the abstract method of <code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractImporter</span></code>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>indx</strong> (<em>int</em>) – the index of the outer JsonArray to extract the data from</p>
+<dd class="field-odd"><p><strong>indx</strong> (<em>int</em>) – the index of the outer JsonArray to extract the data from, default to 0</p>
 </dd>
 </dl>
 </dd></dl>
diff --git a/docs/searchindex.js b/docs/searchindex.js
index c34509d..8061880 100644
--- a/docs/searchindex.js
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From 6cfa4b9d4da047004345af774596a7581460bec4 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 19:42:45 +0100
Subject: [PATCH 003/139] Create .gitattributes

---
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From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 18:43:56 +0000
Subject: [PATCH 004/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
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From 6a357d7331b8b24223f02b1b2f6b32e57803d848 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 19:45:11 +0100
Subject: [PATCH 005/139] Update .gitattributes

---
 .gitattributes | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.gitattributes b/.gitattributes
index da3301e..7c40d77 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1,3 +1,3 @@
-*.js linguist-vendored=false
-*.html linguist-vendored=false
-*.css linguist-vendored=false
+*.js linguist-vendored
+*.html linguist-vendored
+*.css linguist-vendored

From d2fe3f190cdadf29bc3e5140628872aba95d010b Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 18:46:12 +0000
Subject: [PATCH 006/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index c969b746c087cf8ceef70ba0b45ef83c9d2f5ec1..b661d54406cc7b2439c6303287f1233a832661af 100644
GIT binary patch
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From a4e3fd797ddd0d6ee89dd5bff277bf6c500f4d56 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 20:28:13 +0100
Subject: [PATCH 007/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 25 +++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 347b134..e86ae63 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -40,3 +40,28 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/
+        .
+        git config --local user.email "f.martini@campus.unimib.it"
+        git config --local user.name "philipMartini"
+        git add .
+        git commit -m "Create New Realease at dist/" -a || true
+        # The above command will fail if no changes were present, so we ignore
+        # that.
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        branch: master
+        github_token: ${{ secrets.PYCTBN_TOK }}

From 6a053e8458d1cf427b4361389fab3206a6fe798f Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 19:29:18 +0000
Subject: [PATCH 008/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index b661d54406cc7b2439c6303287f1233a832661af..c72e8ebc3595b94272ff8f812fe0715e4cab4727 100644
GIT binary patch
delta 6978
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From aff6727f9afd0e0ebc8cedfc6b7b35311067800b Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 20:57:58 +0100
Subject: [PATCH 009/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index e86ae63..3f70711 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -8,6 +8,8 @@ on:
     paths-ignore: 
       -'docs/**'
       -'docs-out/**'
+      -'dist/**'
+      -'build/**'
     branches: [ master ]
   pull_request:
     branches: [ master ]

From bfeec3fd4f3d85a2059d200d337b35f46bad506d Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 19:58:46 +0000
Subject: [PATCH 010/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index c72e8ebc3595b94272ff8f812fe0715e4cab4727..640055bd4d25efb7545c928d723970b2fbe1da6d 100644
GIT binary patch
delta 7098
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From 3182b9b114d23e9a82b8f51e46c50c4f53a6f38c Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 21:19:34 +0100
Subject: [PATCH 011/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 3f70711..21d19f5 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -62,6 +62,7 @@ jobs:
         git commit -m "Create New Realease at dist/" -a || true
         # The above command will fail if no changes were present, so we ignore
         # that.
+        git pull
     - name: Push changes
       uses: ad-m/github-push-action@master
       with:

From 801d653ede28cbf0ae562b45e3bb402e33f9c43d Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 20:20:36 +0000
Subject: [PATCH 012/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 640055bd4d25efb7545c928d723970b2fbe1da6d..32897a460317f3397147ac60cff64a8b7c37f4c7 100644
GIT binary patch
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From 6124d4a2410ec17e1cd6bb58e58e6d2230e286f5 Mon Sep 17 00:00:00 2001
From: Filippo Martini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 21:39:00 +0100
Subject: [PATCH 013/139] Add build and dist directories

---
 .gitignore                                    |   3 +-
 build/lib/PyCTBN/PyCTBN/__init__.py           |   8 +
 .../lib/PyCTBN/PyCTBN/estimators/__init__.py  |   5 +
 .../PyCTBN/estimators/fam_score_calculator.py | 265 ++++++++++++++++
 .../PyCTBN/estimators/parameters_estimator.py | 117 +++++++
 .../structure_constraint_based_estimator.py   | 246 +++++++++++++++
 .../PyCTBN/estimators/structure_estimator.py  | 183 +++++++++++
 .../structure_score_based_estimator.py        | 236 ++++++++++++++
 .../lib/PyCTBN/PyCTBN/optimizers/__init__.py  |   4 +
 .../optimizers/constraint_based_optimizer.py  |  84 +++++
 .../PyCTBN/optimizers/hill_climbing_search.py | 135 ++++++++
 .../lib/PyCTBN/PyCTBN/optimizers/optimizer.py |  39 +++
 .../PyCTBN/PyCTBN/optimizers/tabu_search.py   | 188 +++++++++++
 .../PyCTBN/PyCTBN/structure_graph/__init__.py |   6 +
 .../conditional_intensity_matrix.py           |  42 +++
 .../PyCTBN/structure_graph/network_graph.py   | 293 ++++++++++++++++++
 .../PyCTBN/structure_graph/sample_path.py     |  93 ++++++
 .../PyCTBN/structure_graph/set_of_cims.py     |  97 ++++++
 .../PyCTBN/structure_graph/structure.py       | 124 ++++++++
 .../PyCTBN/structure_graph/trajectory.py      |  45 +++
 build/lib/PyCTBN/PyCTBN/utility/__init__.py   |   4 +
 .../PyCTBN/utility/abstract_importer.py       | 163 ++++++++++
 build/lib/PyCTBN/PyCTBN/utility/cache.py      |  54 ++++
 .../PyCTBN/PyCTBN/utility/json_importer.py    | 181 +++++++++++
 .../PyCTBN/PyCTBN/utility/sample_importer.py  |  62 ++++
 build/lib/PyCTBN/__init__.py                  |   2 +
 build/lib/PyCTBN/basic_main.py                |  39 +++
 build/lib/PyCTBN/setup.py                     |  20 ++
 dist/PyCTBN-1.0-py3-none-any.whl              | Bin 0 -> 35618 bytes
 dist/PyCTBN-1.0.tar.gz                        | Bin 0 -> 24165 bytes
 30 files changed, 2736 insertions(+), 2 deletions(-)
 create mode 100644 build/lib/PyCTBN/PyCTBN/__init__.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/estimators/__init__.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/__init__.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/structure.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/utility/__init__.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/utility/cache.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/utility/json_importer.py
 create mode 100644 build/lib/PyCTBN/PyCTBN/utility/sample_importer.py
 create mode 100644 build/lib/PyCTBN/__init__.py
 create mode 100644 build/lib/PyCTBN/basic_main.py
 create mode 100644 build/lib/PyCTBN/setup.py
 create mode 100644 dist/PyCTBN-1.0-py3-none-any.whl
 create mode 100644 dist/PyCTBN-1.0.tar.gz

diff --git a/.gitignore b/.gitignore
index 7195554..9c3a923 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,7 +3,6 @@ __pycache__
 **/__pycache__
 **/data
 **/PyCTBN.egg-info
-**/dist
 **/results_data
 **/.scannerwork
-**/build
+
diff --git a/build/lib/PyCTBN/PyCTBN/__init__.py b/build/lib/PyCTBN/PyCTBN/__init__.py
new file mode 100644
index 0000000..faff79c
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/__init__.py
@@ -0,0 +1,8 @@
+import PyCTBN.PyCTBN.estimators
+from PyCTBN.PyCTBN.estimators import *
+import PyCTBN.PyCTBN.optimizers
+from PyCTBN.PyCTBN.optimizers import *
+import PyCTBN.PyCTBN.structure_graph
+from PyCTBN.PyCTBN.structure_graph import *
+import PyCTBN.PyCTBN.utility
+from PyCTBN.PyCTBN.utility import *
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/__init__.py b/build/lib/PyCTBN/PyCTBN/estimators/__init__.py
new file mode 100644
index 0000000..112086f
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/estimators/__init__.py
@@ -0,0 +1,5 @@
+from .fam_score_calculator import FamScoreCalculator
+from .parameters_estimator import ParametersEstimator
+from .structure_estimator import StructureEstimator
+from .structure_constraint_based_estimator import StructureConstraintBasedEstimator
+from .structure_score_based_estimator import StructureScoreBasedEstimator
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py b/build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
new file mode 100644
index 0000000..d8ec3a0
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
@@ -0,0 +1,265 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+from networkx.readwrite import json_graph
+
+from math import log
+
+from scipy.special import loggamma
+from random import choice
+
+from ..structure_graph.set_of_cims import SetOfCims
+from ..structure_graph.network_graph import NetworkGraph
+from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
+
+
+'''
+
+'''
+
+
+class FamScoreCalculator:
+    """
+    Has the task of calculating the FamScore of a node by using a Bayesian score function
+    """
+
+    def __init__(self):
+        #np.seterr('raise')
+        pass
+
+    # region theta
+
+    def marginal_likelihood_theta(self,
+                        cims: ConditionalIntensityMatrix,
+                        alpha_xu: float,
+                        alpha_xxu: float):
+        """
+        Calculate the FamScore value of the node identified by the label node_id
+
+        :param cims: np.array with all the node's cims
+        :type cims: np.array
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
+        :type alpha_xu: float
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta
+        :rtype: float
+        """
+        return np.sum(
+                        [self.variable_cim_xu_marginal_likelihood_theta(cim,
+                                                                    alpha_xu,
+                                                                    alpha_xxu)
+                        for cim in cims])
+
+    def variable_cim_xu_marginal_likelihood_theta(self,
+                        cim: ConditionalIntensityMatrix,
+                        alpha_xu: float,
+                        alpha_xxu: float):
+        """
+        Calculate the value of the marginal likelihood over theta given a cim
+
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
+        :type cim: class:'ConditionalIntensityMatrix'
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
+        :type alpha_xu: float
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta
+        :rtype: float
+        """
+
+        'get cim length'
+        values = len(cim._state_residence_times)
+
+        'compute the marginal likelihood for the current cim'
+        return np.sum([
+                    self.single_cim_xu_marginal_likelihood_theta(
+                                                index,
+                                                cim,
+                                                alpha_xu,
+                                                alpha_xxu)
+                    for index in range(values)])
+
+    def single_cim_xu_marginal_likelihood_theta(self,
+                    index: int,
+                    cim: ConditionalIntensityMatrix,
+                    alpha_xu: float,
+                    alpha_xxu: float):
+        """
+        Calculate the marginal likelihood on q of the node when assumes a specif value
+        and a specif parents's assignment
+
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
+        :type cim: class:'ConditionalIntensityMatrix'
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type alpha_xu: float
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta when the node assumes a specif value
+        :rtype: float
+        """
+
+        values = list(range(len(cim._state_residence_times)))
+
+        'remove the index because of the x != x^ condition in the summation '
+        values.remove(index)
+
+        'uncomment for alpha xx not uniform'
+        #alpha_xxu = alpha_xu * cim.state_transition_matrix[index,index_x_first] / cim.state_transition_matrix[index, index])
+
+        return (loggamma(alpha_xu) - loggamma(alpha_xu + cim.state_transition_matrix[index, index])) \
+                + \
+                np.sum([self.single_internal_cim_xxu_marginal_likelihood_theta(
+                                                                        cim.state_transition_matrix[index,index_x_first],
+                                                                        alpha_xxu)
+                for index_x_first in values])
+
+
+    def single_internal_cim_xxu_marginal_likelihood_theta(self,
+                                                M_xxu_suff_stats: float,
+                                                alpha_xxu: float=1):
+        """Calculate the second part of the marginal likelihood over theta formula
+        
+        :param M_xxu_suff_stats: value of the suffucient statistic M[xx'|u]
+        :type M_xxu_suff_stats: float
+        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
+        :type alpha_xxu: float
+
+        :return: the value of the marginal likelihood over theta when the node assumes a specif value
+        :rtype: float
+        """
+        return loggamma(alpha_xxu+M_xxu_suff_stats) - loggamma(alpha_xxu)
+
+    # endregion
+
+    # region q
+
+    def marginal_likelihood_q(self,
+                        cims: np.array,
+                        tau_xu: float=0.1,
+                        alpha_xu: float=1):
+        """
+        Calculate the value of the marginal likelihood over q of the node identified by the label node_id
+        
+        :param cims: np.array with all the node's cims
+        :type cims: np.array
+        :param tau_xu: hyperparameter over the CTBN’s q parameters
+        :type tau_xu: float
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type alpha_xu: float
+
+
+        :return: the value of the marginal likelihood over q
+        :rtype: float
+        """
+
+        return np.sum([self.variable_cim_xu_marginal_likelihood_q(cim, tau_xu, alpha_xu) for cim in cims])
+
+    def variable_cim_xu_marginal_likelihood_q(self,
+                        cim: ConditionalIntensityMatrix,
+                        tau_xu: float=0.1,
+                        alpha_xu: float=1):
+        """
+        Calculate the value of the marginal likelihood over q given a cim
+        
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
+        :type cim: class:'ConditionalIntensityMatrix'
+        :param tau_xu: hyperparameter over the CTBN’s q parameters
+        :type tau_xu: float
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type alpha_xu: float
+
+
+        :return: the value of the marginal likelihood over q
+        :rtype: float
+        """
+
+        'get cim length'
+        values=len(cim._state_residence_times)
+
+        'compute the marginal likelihood for the current cim'
+        return np.sum([
+                    self.single_cim_xu_marginal_likelihood_q(
+                                                cim.state_transition_matrix[index, index],
+                                                cim._state_residence_times[index],
+                                                tau_xu,
+                                                alpha_xu)
+                    for index in range(values)])
+
+
+    def single_cim_xu_marginal_likelihood_q(self,
+                        M_xu_suff_stats: float,
+                        T_xu_suff_stats: float,
+                        tau_xu: float=0.1,
+                        alpha_xu: float=1):
+        """
+        Calculate the marginal likelihood on q of the node when assumes a specif value
+        and a specif parents's assignment
+        
+        :param M_xu_suff_stats: value of the suffucient statistic M[x|u]
+        :type M_xxu_suff_stats: float
+        :param T_xu_suff_stats: value of the suffucient statistic T[x|u]
+        :type T_xu_suff_stats: float
+        :param cim: A conditional_intensity_matrix object with the sufficient statistics
+        :type cim: class:'ConditionalIntensityMatrix'
+        :param tau_xu: hyperparameter over the CTBN’s q parameters
+        :type tau_xu: float
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters
+        :type alpha_xu: float
+
+
+        :return: the value of the marginal likelihood of the node when assumes a specif value
+        :rtype: float
+        """
+        return (
+                loggamma(alpha_xu + M_xu_suff_stats + 1) + 
+                                                        (log(tau_xu)
+                                                        *
+                                                        (alpha_xu+1))
+                ) \
+                - \
+                (loggamma(alpha_xu + 1)+(
+                                    log(tau_xu + T_xu_suff_stats) 
+                                    *
+                                    (alpha_xu + M_xu_suff_stats + 1))
+                )
+
+    # end region
+
+    def get_fam_score(self,
+                cims: np.array,
+                tau_xu: float=0.1,
+                alpha_xu: float=1):
+        """
+        Calculate the FamScore value of the node
+        
+        
+        :param cims: np.array with all the node's cims
+        :type cims: np.array
+        :param tau_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
+        :type tau_xu: float, optional
+        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 1
+        :type alpha_xu: float, optional
+
+
+        :return: the FamScore value of the node
+        :rtype: float
+        """
+
+        'calculate alpha_xxu as a uniform distribution'                                
+        alpha_xxu = alpha_xu /(len(cims[0]._state_residence_times) - 1)
+
+        return self.marginal_likelihood_q(cims,
+                                    tau_xu,
+                                    alpha_xu) \
+               + \
+               self.marginal_likelihood_theta(cims, 
+                                        alpha_xu,
+                                        alpha_xxu)
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py
new file mode 100644
index 0000000..6b6883b
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py
@@ -0,0 +1,117 @@
+import sys
+sys.path.append('../')
+import numpy as np
+
+from ..structure_graph.network_graph import NetworkGraph
+from ..structure_graph.set_of_cims import SetOfCims
+from ..structure_graph.trajectory import Trajectory
+
+
+class ParametersEstimator(object):
+    """Has the task of computing the cims of particular node given the trajectories and the net structure
+    in the graph ``_net_graph``.
+
+    :param trajectories:  the trajectories
+    :type trajectories: Trajectory
+    :param net_graph: the net structure
+    :type net_graph: NetworkGraph
+    :_single_set_of_cims: the set of cims object that will hold the cims of the node
+    """
+
+    def __init__(self, trajectories: Trajectory, net_graph: NetworkGraph):
+        """Constructor Method
+        """
+        self._trajectories = trajectories
+        self._net_graph = net_graph
+        self._single_set_of_cims = None
+
+    def fast_init(self, node_id: str) -> None:
+        """Initializes all the necessary structures for the parameters estimation for the node ``node_id``.
+
+        :param node_id: the node label
+        :type node_id: string
+        """
+        p_vals = self._net_graph._aggregated_info_about_nodes_parents[2]
+        node_states_number = self._net_graph.get_states_number(node_id)
+        self._single_set_of_cims = SetOfCims(node_id, p_vals, node_states_number, self._net_graph.p_combs)
+
+    def compute_parameters_for_node(self, node_id: str) -> SetOfCims:
+        """Compute the CIMS of the node identified by the label ``node_id``.
+
+        :param node_id: the node label
+        :type node_id: string
+        :return: A SetOfCims object filled with the computed CIMS
+        :rtype: SetOfCims
+        """
+        node_indx = self._net_graph.get_node_indx(node_id)
+        state_res_times = self._single_set_of_cims._state_residence_times
+        transition_matrices = self._single_set_of_cims._transition_matrices
+        ParametersEstimator.compute_state_res_time_for_node(self._trajectories.times,
+                                             self._trajectories.trajectory,
+                                             self._net_graph.time_filtering,
+                                             self._net_graph.time_scalar_indexing_strucure,
+                                             state_res_times)
+        ParametersEstimator.compute_state_transitions_for_a_node(node_indx, self._trajectories.complete_trajectory,
+                                                                 self._net_graph.transition_filtering,
+                                                                 self._net_graph.transition_scalar_indexing_structure,
+                                                                 transition_matrices)
+        self._single_set_of_cims.build_cims(state_res_times, transition_matrices)
+        return self._single_set_of_cims
+
+    @staticmethod
+    def compute_state_res_time_for_node(times: np.ndarray, trajectory: np.ndarray,
+                                        cols_filter: np.ndarray, scalar_indexes_struct: np.ndarray,
+                                        T: np.ndarray) -> None:
+        """Compute the state residence times for a node and fill the matrix ``T`` with the results
+
+        :param node_indx: the index of the node
+        :type node_indx: int
+        :param times: the times deltas vector
+        :type times: numpy.array
+        :param trajectory: the trajectory
+        :type trajectory: numpy.ndArray
+        :param cols_filter: the columns filtering structure
+        :type cols_filter: numpy.array
+        :param scalar_indexes_struct: the indexing structure
+        :type scalar_indexes_struct: numpy.array
+        :param T: the state residence times vectors
+        :type T: numpy.ndArray
+        """
+        T[:] = np.bincount(np.sum(trajectory[:, cols_filter] * scalar_indexes_struct / scalar_indexes_struct[0], axis=1)
+                           .astype(np.int), \
+                           times,
+                           minlength=scalar_indexes_struct[-1]).reshape(-1, T.shape[1])
+
+    @staticmethod
+    def compute_state_transitions_for_a_node(node_indx: int, trajectory: np.ndarray, cols_filter: np.ndarray,
+                                             scalar_indexing: np.ndarray, M: np.ndarray) -> None:
+        """Compute the state residence times for a node and fill the matrices ``M`` with the results.
+
+        :param node_indx: the index of the node
+        :type node_indx: int
+        :param trajectory: the trajectory
+        :type trajectory: numpy.ndArray
+        :param cols_filter: the columns filtering structure
+        :type cols_filter: numpy.array
+        :param scalar_indexing: the indexing structure
+        :type scalar_indexing: numpy.array
+        :param M: the state transitions matrices
+        :type M: numpy.ndArray
+        """
+        diag_indices = np.array([x * M.shape[1] + x % M.shape[1] for x in range(M.shape[0] * M.shape[1])],
+                                dtype=np.int64)
+        trj_tmp = trajectory[trajectory[:, int(trajectory.shape[1] / 2) + node_indx].astype(np.int) >= 0]
+        M[:] = np.bincount(np.sum(trj_tmp[:, cols_filter] * scalar_indexing / scalar_indexing[0], axis=1).astype(np.int)
+                           , minlength=scalar_indexing[-1]).reshape(-1, M.shape[1], M.shape[2])
+        M_raveled = M.ravel()
+        M_raveled[diag_indices] = 0
+        M_raveled[diag_indices] = np.sum(M, axis=2).ravel()
+
+
+
+
+
+
+
+
+
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
new file mode 100644
index 0000000..0013d80
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
@@ -0,0 +1,246 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+from networkx.readwrite import json_graph
+import os
+from scipy.stats import chi2 as chi2_dist
+from scipy.stats import f as f_dist
+from tqdm import tqdm
+
+from ..utility.cache import Cache
+from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
+from ..structure_graph.network_graph import NetworkGraph
+from .parameters_estimator import ParametersEstimator
+from .structure_estimator import StructureEstimator
+from ..structure_graph.sample_path import SamplePath
+from ..structure_graph.structure import Structure
+from ..optimizers.constraint_based_optimizer import ConstraintBasedOptimizer
+
+import concurrent.futures
+
+
+
+import multiprocessing
+from multiprocessing import Pool
+
+
+class StructureConstraintBasedEstimator(StructureEstimator):
+    """
+    Has the task of estimating the network structure given the trajectories in samplepath by using a constraint-based approach.
+
+    :param sample_path: the _sample_path object containing the trajectories and the real structure
+    :type sample_path: SamplePath
+    :param exp_test_alfa: the significance level for the exponential Hp test
+    :type exp_test_alfa: float
+    :param chi_test_alfa: the significance level for the chi Hp test
+    :type chi_test_alfa: float
+    :param known_edges: the prior known edges in the net structure if present
+    :type known_edges: List
+    :param thumb_threshold: the threshold value to consider a valid independence test
+    :type thumb_threshold: int
+    :_nodes: the nodes labels
+    :_nodes_vals: the nodes cardinalities
+    :_nodes_indxs: the nodes indexes
+    :_complete_graph: the complete directed graph built using the nodes labels in ``_nodes``
+    :_cache: the Cache object
+    """
+
+    def __init__(self, sample_path: SamplePath, exp_test_alfa: float, chi_test_alfa: float,known_edges: typing.List= [],
+                 thumb_threshold:int = 25):
+        super().__init__(sample_path,known_edges)
+        self._exp_test_sign = exp_test_alfa
+        self._chi_test_alfa = chi_test_alfa
+        self._thumb_threshold = thumb_threshold
+        self._cache = Cache()
+
+    def complete_test(self, test_parent: str, test_child: str, parent_set: typing.List, child_states_numb: int,
+                      tot_vars_count: int, parent_indx, child_indx) -> bool:
+        """Performs a complete independence test on the directed graphs G1 = {test_child U parent_set}
+        G2 = {G1 U test_parent} (added as an additional parent of the test_child).
+        Generates all the necessary structures and datas to perform the tests.
+
+        :param test_parent: the node label of the test parent
+        :type test_parent: string
+        :param test_child: the node label of the child
+        :type test_child: string
+        :param parent_set: the common parent set
+        :type parent_set: List
+        :param child_states_numb: the cardinality of the ``test_child``
+        :type child_states_numb: int
+        :param tot_vars_count: the total number of variables in the net
+        :type tot_vars_count: int
+        :return: True iff test_child and test_parent are independent given the sep_set parent_set. False otherwise
+        :rtype: bool
+        """
+        p_set = parent_set[:]
+        complete_info = parent_set[:]
+        complete_info.append(test_child)
+
+        parents = np.array(parent_set)
+        parents = np.append(parents, test_parent)
+        sorted_parents = self._nodes[np.isin(self._nodes, parents)]
+        cims_filter = sorted_parents != test_parent
+
+        p_set.insert(0, test_parent)
+        sofc2 = self._cache.find(set(p_set))
+
+        if not sofc2:
+            complete_info.append(test_parent)
+            bool_mask2 = np.isin(self._nodes, complete_info)
+            l2 = list(self._nodes[bool_mask2])
+            indxs2 = self._nodes_indxs[bool_mask2]
+            vals2 = self._nodes_vals[bool_mask2]
+            eds2 = list(itertools.product(p_set, test_child))
+            s2 = Structure(l2, indxs2, vals2, eds2, tot_vars_count)
+            g2 = NetworkGraph(s2)
+            g2.fast_init(test_child)
+            p2 = ParametersEstimator(self._sample_path.trajectories, g2)
+            p2.fast_init(test_child)
+            sofc2 = p2.compute_parameters_for_node(test_child)
+            self._cache.put(set(p_set), sofc2)
+
+        del p_set[0]
+        sofc1 = self._cache.find(set(p_set))
+        if not sofc1:
+            g2.remove_node(test_parent)
+            g2.fast_init(test_child)
+            p2 = ParametersEstimator(self._sample_path.trajectories, g2)
+            p2.fast_init(test_child)
+            sofc1 = p2.compute_parameters_for_node(test_child)
+            self._cache.put(set(p_set), sofc1)
+        thumb_value = 0.0
+        if child_states_numb > 2:
+            parent_val = self._sample_path.structure.get_states_number(test_parent)
+            bool_mask_vals = np.isin(self._nodes, parent_set)
+            parents_vals = self._nodes_vals[bool_mask_vals]
+            thumb_value = self.compute_thumb_value(parent_val, child_states_numb, parents_vals)
+        for cim1, p_comb in zip(sofc1.actual_cims, sofc1.p_combs):
+            cond_cims = sofc2.filter_cims_with_mask(cims_filter, p_comb)
+            for cim2 in cond_cims:
+                if not self.independence_test(child_states_numb, cim1, cim2, thumb_value, parent_indx, child_indx):
+                    return False
+        return True
+
+    def independence_test(self, child_states_numb: int, cim1: ConditionalIntensityMatrix,
+                          cim2: ConditionalIntensityMatrix, thumb_value: float, parent_indx, child_indx) -> bool:
+        """Compute the actual independence test using two cims.
+        It is performed first the exponential test and if the null hypothesis is not rejected,
+        it is performed also the chi_test.
+
+        :param child_states_numb: the cardinality of the test child
+        :type child_states_numb: int
+        :param cim1: a cim belonging to the graph without test parent
+        :type cim1: ConditionalIntensityMatrix
+        :param cim2: a cim belonging to the graph with test parent
+        :type cim2: ConditionalIntensityMatrix
+        :return: True iff both tests do NOT reject the null hypothesis of independence. False otherwise.
+        :rtype: bool
+        """
+        M1 = cim1.state_transition_matrix
+        M2 = cim2.state_transition_matrix
+        r1s = M1.diagonal()
+        r2s = M2.diagonal()
+        C1 = cim1.cim
+        C2 = cim2.cim
+        if child_states_numb > 2 and (np.sum(np.diagonal(M1)) / thumb_value) < self._thumb_threshold:
+                self._removable_edges_matrix[parent_indx][child_indx] = False
+                return False
+        F_stats = C2.diagonal() / C1.diagonal()
+        exp_alfa = self._exp_test_sign
+        for val in range(0, child_states_numb):
+            if F_stats[val] < f_dist.ppf(exp_alfa / 2, r1s[val], r2s[val]) or \
+                    F_stats[val] > f_dist.ppf(1 - exp_alfa / 2, r1s[val], r2s[val]):
+                return False
+        M1_no_diag = M1[~np.eye(M1.shape[0], dtype=bool)].reshape(M1.shape[0], -1)
+        M2_no_diag = M2[~np.eye(M2.shape[0], dtype=bool)].reshape(
+            M2.shape[0], -1)
+        chi_2_quantile = chi2_dist.ppf(1 - self._chi_test_alfa, child_states_numb - 1)
+        Ks = np.sqrt(r1s / r2s)
+        Ls = np.sqrt(r2s / r1s)
+        for val in range(0, child_states_numb):
+            Chi = np.sum(np.power(Ks[val] * M2_no_diag[val] - Ls[val] *M1_no_diag[val], 2) /
+                         (M1_no_diag[val] + M2_no_diag[val]))
+            if Chi > chi_2_quantile:
+                return False
+        return True
+        
+    def compute_thumb_value(self, parent_val, child_val, parent_set_vals):
+        """Compute the value to test against the thumb_threshold.
+        
+        :param parent_val: test parent's variable cardinality
+        :type parent_val: int
+        :param child_val: test child's variable cardinality
+        :type child_val: int
+        :param parent_set_vals: the cardinalities of the nodes in the current sep-set
+        :type parent_set_vals: List
+        :return: the thumb value for the current independence test
+        :rtype: int
+        """
+        df = (child_val - 1) ** 2
+        df = df * parent_val
+        for v in parent_set_vals:
+            df = df * v
+        return df
+        
+    def one_iteration_of_CTPC_algorithm(self, var_id: str, tot_vars_count: int)-> typing.List:
+        """Performs an iteration of the CTPC algorithm using the node ``var_id`` as ``test_child``.
+
+        :param var_id: the node label of the test child
+        :type var_id: string
+        """
+        optimizer_obj = ConstraintBasedOptimizer(
+                                                            node_id = var_id,
+                                                            structure_estimator = self,
+                                                            tot_vars_count = tot_vars_count)
+        return optimizer_obj.optimize_structure()
+
+    
+    def ctpc_algorithm(self,disable_multiprocessing:bool= False ):
+        """Compute the CTPC algorithm over the entire net.
+        """
+        ctpc_algo = self.one_iteration_of_CTPC_algorithm
+        total_vars_numb = self._sample_path.total_variables_count
+
+        n_nodes= len(self._nodes)
+
+        total_vars_numb_array =  [total_vars_numb] *  n_nodes
+
+        'get the number of CPU'
+        cpu_count = multiprocessing.cpu_count()
+
+
+
+        'Remove all the edges from the structure'   
+        self._sample_path.structure.clean_structure_edges()
+
+        'Estimate the best parents for each node'
+        #with multiprocessing.Pool(processes=cpu_count) as pool:
+        #with get_context("spawn").Pool(processes=cpu_count) as pool:
+        if disable_multiprocessing:
+            print("DISABILITATO")
+            cpu_count = 1
+            list_edges_partial = [ctpc_algo(n,total_vars_numb) for n in self._nodes]
+        else:
+            with concurrent.futures.ProcessPoolExecutor(max_workers=cpu_count) as executor:
+                list_edges_partial = executor.map(ctpc_algo,
+                                                                 self._nodes,
+                                                                 total_vars_numb_array)
+            
+        'Update the graph'
+        edges = set(itertools.chain.from_iterable(list_edges_partial))
+        self._complete_graph = nx.DiGraph()
+        self._complete_graph.add_edges_from(edges)
+
+        return edges
+
+        
+    def estimate_structure(self,disable_multiprocessing:bool=False):
+        return self.ctpc_algorithm(disable_multiprocessing=disable_multiprocessing)
+
+    
+
+
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py
new file mode 100644
index 0000000..b77e21f
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py
@@ -0,0 +1,183 @@
+
+import itertools
+import json
+import typing
+
+import matplotlib.pyplot as plt
+import networkx as nx
+import numpy as np
+from networkx.readwrite import json_graph
+
+from abc import ABC
+import os
+import abc
+
+from ..utility.cache import Cache
+from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
+from ..structure_graph.network_graph import NetworkGraph
+from .parameters_estimator import ParametersEstimator
+from ..structure_graph.sample_path import SamplePath
+from ..structure_graph.structure import Structure
+
+
+class StructureEstimator(object):
+    """Has the task of estimating the network structure given the trajectories in ``samplepath``.
+
+    :param sample_path: the _sample_path object containing the trajectories and the real structure
+    :type sample_path: SamplePath
+    :param known_edges: the prior known edges in the net structure if present
+    :type known_edges: List
+    :_nodes: the nodes labels
+    :_nodes_vals: the nodes cardinalities
+    :_nodes_indxs: the nodes indexes
+    :_complete_graph: the complete directed graph built using the nodes labels in ``_nodes``
+    """
+
+    def __init__(self, sample_path: SamplePath, known_edges: typing.List = None):
+        self._sample_path = sample_path
+        self._nodes = np.array(self._sample_path.structure.nodes_labels)
+        self._nodes_vals = self._sample_path.structure.nodes_values
+        self._nodes_indxs = self._sample_path.structure.nodes_indexes
+        self._removable_edges_matrix = self.build_removable_edges_matrix(known_edges)
+        self._complete_graph = StructureEstimator.build_complete_graph(self._sample_path.structure.nodes_labels)
+        
+
+    def build_removable_edges_matrix(self, known_edges: typing.List):
+        """Builds a boolean matrix who shows if a edge could be removed or not, based on prior knowledge given:
+
+        :param known_edges: the list of nodes labels
+        :type known_edges: List
+        :return: a boolean matrix
+        :rtype: np.ndarray
+        """
+        tot_vars_count = self._sample_path.total_variables_count
+        complete_adj_matrix = np.full((tot_vars_count, tot_vars_count), True)
+        if known_edges:
+            for edge in known_edges:
+                i = self._sample_path.structure.get_node_indx(edge[0])
+                j = self._sample_path.structure.get_node_indx(edge[1])
+                complete_adj_matrix[i][j] = False
+        return complete_adj_matrix
+
+    @staticmethod
+    def build_complete_graph(node_ids: typing.List) -> nx.DiGraph:
+        """Builds a complete directed graph (no self loops) given the nodes labels in the list ``node_ids``:
+
+        :param node_ids: the list of nodes labels
+        :type node_ids: List
+        :return: a complete Digraph Object
+        :rtype: networkx.DiGraph
+        """
+        complete_graph = nx.DiGraph()
+        complete_graph.add_nodes_from(node_ids)
+        complete_graph.add_edges_from(itertools.permutations(node_ids, 2))
+        return complete_graph
+
+
+    @staticmethod
+    def generate_possible_sub_sets_of_size( u: typing.List, size: int, parent_label: str):
+        """Creates a list containing all possible subsets of the list ``u`` of size ``size``,
+        that do not contains a the node identified by ``parent_label``.
+
+        :param u: the list of nodes
+        :type u: List
+        :param size: the size of the subsets
+        :type size: int
+        :param parent_label: the node to exclude in the subsets generation
+        :type parent_label: string
+        :return: an Iterator Object containing a list of lists
+        :rtype: Iterator
+        """
+        list_without_test_parent = u[:]
+        list_without_test_parent.remove(parent_label)
+        return map(list, itertools.combinations(list_without_test_parent, size))
+
+    def save_results(self, file_path: str) -> None:
+        """Save the estimated Structure to a .json file in file_path.
+
+        :param file_path: the path including the file name with .json extension
+        :type file_path: string
+        """
+        res = json_graph.node_link_data(self._complete_graph)
+        with open(file_path, 'w') as f:
+            json.dump(res, f)
+
+
+    #def remove_diagonal_elements(self, matrix):
+    #   m = matrix.shape[0]
+    #    strided = np.lib.stride_tricks.as_strided
+    #    s0, s1 = matrix.strides
+    #    return strided(matrix.ravel()[1:], shape=(m - 1, m), strides=(s0 + s1, s1)).reshape(m, -1)
+
+
+    @abc.abstractmethod
+    def estimate_structure(self) -> typing.List:
+        """Abstract method to estimate the structure
+
+        :return: List of estimated edges
+        :rtype: Typing.List
+        """
+        pass
+
+    def adjacency_matrix(self) -> np.ndarray:
+        """Converts the estimated structure ``_complete_graph`` to a boolean adjacency matrix representation.
+
+        :return: The adjacency matrix of the graph ``_complete_graph``
+        :rtype: numpy.ndArray
+        """
+        return nx.adj_matrix(self._complete_graph, self._nodes).toarray().astype(bool)
+
+    def spurious_edges(self) -> typing.List:
+        """Return the spurious edges present in the estimated structure, if a prior net structure is present in
+            ``_sample_path.structure``.
+
+        :return: A list containing the spurious edges
+        :rtype: List
+        """
+        if not self._sample_path.has_prior_net_structure:
+            return []
+        real_graph = nx.DiGraph()
+        real_graph.add_nodes_from(self._sample_path.structure.nodes_labels)
+        real_graph.add_edges_from(self._sample_path.structure.edges)
+        return nx.difference(real_graph, self._complete_graph).edges
+
+    def save_plot_estimated_structure_graph(self, file_path: str) -> None:  
+            """Plot the estimated structure in a graphical model style, use .png extension.
+            Spurious edges are colored in red if a prior structure is present.
+
+            :param file_path: path to save the file to
+            :type: string
+            """
+            graph_to_draw = nx.DiGraph()
+            spurious_edges = self.spurious_edges()
+            non_spurious_edges = list(set(self._complete_graph.edges) - set(spurious_edges))
+            edges_colors = ['red' if edge in spurious_edges else 'black' for edge in self._complete_graph.edges]
+            graph_to_draw.add_edges_from(spurious_edges)
+            graph_to_draw.add_edges_from(non_spurious_edges)
+            pos = nx.spring_layout(graph_to_draw, k=0.5*1/np.sqrt(len(graph_to_draw.nodes())), iterations=50,scale=10)
+            options = {
+                "node_size": 2000,
+                "node_color": "white",
+                "edgecolors": "black",
+                'linewidths':2,
+                "with_labels":True,
+                "font_size":13,
+                'connectionstyle': 'arc3, rad = 0.1',
+                "arrowsize": 15,
+                "arrowstyle": '<|-',
+                "width": 1,
+                "edge_color":edges_colors,
+            }
+
+            nx.draw(graph_to_draw, pos, **options)
+            ax = plt.gca()
+            ax.margins(0.20)
+            plt.axis("off")
+            plt.savefig(file_path)
+            plt.clf()
+            print("Estimated Structure Plot Saved At: ", os.path.abspath(file_path))
+
+
+
+
+
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
new file mode 100644
index 0000000..12222f9
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
@@ -0,0 +1,236 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+from networkx.readwrite import json_graph
+
+from random import choice
+
+import concurrent.futures
+
+import copy
+
+from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
+from ..structure_graph.network_graph import NetworkGraph
+from .parameters_estimator import ParametersEstimator
+from .structure_estimator import StructureEstimator
+from ..structure_graph.sample_path import SamplePath
+from ..structure_graph.structure import Structure
+from .fam_score_calculator import FamScoreCalculator
+from ..optimizers.hill_climbing_search import HillClimbing
+from ..optimizers.tabu_search import TabuSearch
+
+
+import multiprocessing
+from multiprocessing import Pool
+
+
+
+
+class StructureScoreBasedEstimator(StructureEstimator):
+    """
+    Has the task of estimating the network structure given the trajectories in samplepath by
+    using a score based approach and differt kinds of optimization algorithms.
+
+    :param sample_path: the _sample_path object containing the trajectories and the real structure
+    :type sample_path: SamplePath
+    :param tau_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
+    :type tau_xu: float, optional
+    :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 1
+    :type alpha_xu: float, optional
+    :param known_edges: List of known edges, default to []
+    :type known_edges: List, optional
+
+    """
+
+    def __init__(self, sample_path: SamplePath, tau_xu:int=0.1, alpha_xu:int = 1,known_edges: typing.List= []):
+        super().__init__(sample_path,known_edges)
+        self.tau_xu=tau_xu
+        self.alpha_xu=alpha_xu
+
+
+    def estimate_structure(self, max_parents:int = None, iterations_number:int= 40,
+                         patience:int = None, tabu_length:int = None, tabu_rules_duration:int = None,
+                         optimizer: str = 'tabu',disable_multiprocessing:bool= False ):
+        """
+        Compute the score-based algorithm to find the optimal structure
+
+        :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
+        :type max_parents: int, optional
+        :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
+        :type iterations_number: int, optional
+        :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
+        :type patience: int, optional
+        :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
+        :type tabu_length: int, optional
+        :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
+        :type tabu_rules_duration: int, optional
+        :param optimizer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search), defualt to 'tabu'
+        :type optimizer: string, optional
+        :param disable_multiprocessing: true if you desire to disable the multiprocessing operations, default to False
+        :type disable_multiprocessing: Boolean, optional
+        """
+        'Save the true edges structure in tuples'
+        true_edges = copy.deepcopy(self._sample_path.structure.edges)
+        true_edges = set(map(tuple, true_edges))
+
+        'Remove all the edges from the structure'   
+        self._sample_path.structure.clean_structure_edges()
+
+        estimate_parents = self.estimate_parents
+
+        n_nodes= len(self._nodes)
+        
+        l_max_parents= [max_parents] * n_nodes
+        l_iterations_number = [iterations_number] * n_nodes
+        l_patience = [patience] * n_nodes
+        l_tabu_length = [tabu_length] * n_nodes
+        l_tabu_rules_duration = [tabu_rules_duration] * n_nodes
+        l_optimizer = [optimizer] * n_nodes
+
+
+        'get the number of CPU'
+        cpu_count = multiprocessing.cpu_count()
+        print(f"CPU COUNT: {cpu_count}")
+
+        if disable_multiprocessing:
+            cpu_count = 1
+
+        
+
+
+
+        #with get_context("spawn").Pool(processes=cpu_count) as pool:
+        #with multiprocessing.Pool(processes=cpu_count) as pool:
+
+        'Estimate the best parents for each node'
+        if disable_multiprocessing:
+            list_edges_partial = [estimate_parents(n,max_parents,iterations_number,patience,tabu_length,tabu_rules_duration,optimizer) for n in self._nodes]
+        else:
+            with concurrent.futures.ProcessPoolExecutor(max_workers=cpu_count) as executor:
+                list_edges_partial = executor.map(estimate_parents, 
+                                                            self._nodes,
+                                                            l_max_parents,
+                                                            l_iterations_number,
+                                                            l_patience,
+                                                            l_tabu_length,
+                                                            l_tabu_rules_duration,
+                                                            l_optimizer)
+
+
+        'Concatenate all the edges list'
+        set_list_edges =  set(itertools.chain.from_iterable(list_edges_partial))
+
+
+        'calculate precision and recall'
+        n_missing_edges = 0
+        n_added_fake_edges = 0
+
+        try:
+            n_added_fake_edges = len(set_list_edges.difference(true_edges))
+
+            n_missing_edges = len(true_edges.difference(set_list_edges))
+
+            n_true_positive = len(true_edges) - n_missing_edges
+
+            precision = n_true_positive / (n_true_positive + n_added_fake_edges)
+
+            recall = n_true_positive / (n_true_positive + n_missing_edges)
+        
+            print(true_edges)
+            print(set_list_edges)
+            print(f"precision: {precision} ")
+            print(f"recall: {recall} ")
+        except Exception as e: 
+            print(f"errore: {e}")
+
+
+        'Update the graph'
+        self._complete_graph = nx.DiGraph()
+        self._complete_graph.add_edges_from(set_list_edges)
+
+        return set_list_edges
+    
+
+    def estimate_parents(self,node_id:str, max_parents:int = None, iterations_number:int= 40,
+                            patience:int = 10, tabu_length:int = None, tabu_rules_duration:int=5, 
+                            optimizer:str = 'hill' ):
+        """
+        Use the FamScore of a node in order to find the best parent nodes
+        
+        :param node_id: current node's id
+        :type node_id: string
+        :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
+        :type max_parents: int, optional
+        :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
+        :type iterations_number: int, optional
+        :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
+        :type patience: int, optional
+        :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
+        :type tabu_length: int, optional
+        :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
+        :type tabu_rules_duration: int, optional
+        :param optimizer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search), defualt to 'tabu'
+        :type optimizer: string, optional
+
+        :return: A list of the best edges for the currente node
+        :rtype: List
+        """
+
+        "choose the optimizer algotithm"
+        if optimizer == 'tabu':
+            optimizer = TabuSearch(
+                        node_id = node_id,
+                        structure_estimator = self,
+                        max_parents = max_parents,
+                        iterations_number = iterations_number,
+                        patience = patience,
+                        tabu_length = tabu_length,
+                        tabu_rules_duration = tabu_rules_duration)
+        else: #if optimizer == 'hill':
+            optimizer = HillClimbing(
+                                    node_id = node_id,
+                                    structure_estimator = self,
+                                    max_parents = max_parents,
+                                    iterations_number = iterations_number,
+                                    patience = patience)
+
+        "call the optmizer's function that calculates the current node's parents"
+        return optimizer.optimize_structure()
+
+    
+    def get_score_from_graph(self,
+                            graph: NetworkGraph,
+                            node_id:str):
+        """
+        Get the FamScore of a node 
+        
+        :param node_id: current node's id
+        :type node_id: string
+        :param graph: current graph to be computed
+        :type graph: class:'NetworkGraph'
+
+
+        :return: The FamSCore for this graph structure
+        :rtype: float
+        """
+
+        'inizialize the graph for a single node'
+        graph.fast_init(node_id) 
+
+        params_estimation = ParametersEstimator(self._sample_path.trajectories, graph)
+
+        'Inizialize and compute parameters for node'
+        params_estimation.fast_init(node_id)
+        SoCims = params_estimation.compute_parameters_for_node(node_id)
+
+        'calculate the FamScore for the node'
+        fam_score_obj = FamScoreCalculator()
+
+        score = fam_score_obj.get_fam_score(SoCims.actual_cims,tau_xu = self.tau_xu,alpha_xu=self.alpha_xu)
+        
+        #print(f" lo score per {node_id} risulta: {score} ")
+        return score 
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/__init__.py b/build/lib/PyCTBN/PyCTBN/optimizers/__init__.py
new file mode 100644
index 0000000..4162bf1
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/optimizers/__init__.py
@@ -0,0 +1,4 @@
+from .optimizer import Optimizer
+from .tabu_search import TabuSearch
+from .hill_climbing_search import HillClimbing
+from .constraint_based_optimizer import ConstraintBasedOptimizer
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py b/build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
new file mode 100644
index 0000000..9ad05fc
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
@@ -0,0 +1,84 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+
+from random import choice
+
+from abc import ABC
+
+import copy
+
+
+from .optimizer import Optimizer
+from ..estimators.structure_estimator import StructureEstimator
+from ..structure_graph.network_graph import NetworkGraph
+
+
+class ConstraintBasedOptimizer(Optimizer):
+    """
+    Optimizer class that implement a CTPC Algorithm
+
+    :param node_id: current node's id
+    :type node_id: string
+    :param structure_estimator: a structure estimator object with the information about the net
+    :type structure_estimator: class:'StructureEstimator' 
+    :param tot_vars_count: number of variables in the dataset
+    :type tot_vars_count: int
+    """
+    def __init__(self,
+                node_id:str,
+                structure_estimator: StructureEstimator,
+                tot_vars_count:int
+                ):
+        """
+        Constructor
+        """
+        super().__init__(node_id, structure_estimator)
+        self.tot_vars_count = tot_vars_count
+        
+
+
+    def optimize_structure(self):
+        """
+        Compute Optimization process for a structure_estimator by using a CTPC Algorithm
+
+        :return: the estimated structure for the node
+        :rtype: List
+        """
+        print("##################TESTING VAR################", self.node_id)
+
+        graph = NetworkGraph(self.structure_estimator._sample_path.structure)
+
+        other_nodes =  [node for node in self.structure_estimator._sample_path.structure.nodes_labels if node != self.node_id]
+        
+        for possible_parent in other_nodes:
+            graph.add_edges([(possible_parent,self.node_id)])
+
+        
+        u = other_nodes
+        child_states_numb = self.structure_estimator._sample_path.structure.get_states_number(self.node_id)
+        b = 0
+        while b < len(u):
+            parent_indx = 0
+            while parent_indx < len(u):
+                removed = False
+                test_parent = u[parent_indx]
+               	i = self.structure_estimator._sample_path.structure.get_node_indx(test_parent)
+                j = self.structure_estimator._sample_path.structure.get_node_indx(self.node_id)
+                if self.structure_estimator._removable_edges_matrix[i][j]:
+                    S = StructureEstimator.generate_possible_sub_sets_of_size(u, b, test_parent)
+                    for parents_set in S:
+	                    if self.structure_estimator.complete_test(test_parent, self.node_id, parents_set, child_states_numb, self.tot_vars_count,i,j):
+	                        graph.remove_edges([(test_parent, self.node_id)])
+	                        u.remove(test_parent)
+	                        removed = True
+	                        break
+                if not removed:
+                    parent_indx += 1
+            b += 1
+        self.structure_estimator._cache.clear()
+        return graph.edges
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py b/build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
new file mode 100644
index 0000000..6783be0
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
@@ -0,0 +1,135 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+
+from random import choice
+
+from abc import ABC
+
+
+from .optimizer import Optimizer
+from ..estimators.structure_estimator import StructureEstimator
+from ..structure_graph.network_graph import NetworkGraph
+
+
+class HillClimbing(Optimizer):
+    """
+    Optimizer class that implement Hill Climbing Search
+    
+
+    :param node_id: current node's id
+    :type node_id: string
+    :param structure_estimator: a structure estimator object with the information about the net
+    :type structure_estimator: class:'StructureEstimator' 
+    :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
+    :type max_parents: int, optional
+    :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
+    :type iterations_number: int, optional
+    :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
+    :type patience: int, optional
+
+
+    
+    """
+    def __init__(self,
+                node_id:str,
+                structure_estimator: StructureEstimator,
+                max_parents:int = None,
+                iterations_number:int= 40,
+                patience:int = None
+                ):
+        """
+        Constructor
+        """
+        super().__init__(node_id, structure_estimator)
+        self.max_parents = max_parents
+        self.iterations_number = iterations_number
+        self.patience = patience
+        
+
+
+    def optimize_structure(self) -> typing.List:
+        """
+        Compute Optimization process for a structure_estimator by using a Hill Climbing Algorithm
+
+        :return: the estimated structure for the node
+        :rtype: List
+        """
+
+        #'Create the graph for the single node'
+        graph = NetworkGraph(self.structure_estimator._sample_path.structure)
+
+        'get the index for the current node'
+        node_index = self.structure_estimator._sample_path._structure.get_node_indx(self.node_id)
+
+        'list of prior edges'
+        prior_parents = set()
+
+        'Add the edges from prior knowledge'
+        for i in range(len(self.structure_estimator._removable_edges_matrix)):
+            if not self.structure_estimator._removable_edges_matrix[i][node_index]:
+                parent_id= self.structure_estimator._sample_path._structure.get_node_id(i)
+                prior_parents.add(parent_id)
+
+                'Add the node to the starting structure'
+                graph.add_edges([(parent_id, self.node_id)])
+
+
+
+        'get all the possible parents'
+        other_nodes =  [node for node in 
+                                            self.structure_estimator._sample_path.structure.nodes_labels if
+                                                                                            node != self.node_id and
+                                                                                            not prior_parents.__contains__(node)]
+        
+        actual_best_score = self.structure_estimator.get_score_from_graph(graph,self.node_id)
+
+        patince_count = 0
+        for i in range(self.iterations_number):
+            'choose a new random edge'
+            current_new_parent = choice(other_nodes)
+            current_edge =  (current_new_parent,self.node_id)
+            added = False
+            parent_removed = None 
+            
+
+            if graph.has_edge(current_edge):
+                graph.remove_edges([current_edge])
+            else:
+                'check the max_parents constraint'
+                if self.max_parents is not None:
+                    parents_list = graph.get_parents_by_id(self.node_id)
+                    if len(parents_list) >= self.max_parents :
+                        parent_removed = (choice(parents_list), self.node_id)
+                        graph.remove_edges([parent_removed])
+                graph.add_edges([current_edge])
+                added = True
+            #print('**************************')
+            current_score =  self.structure_estimator.get_score_from_graph(graph,self.node_id)
+
+
+            if current_score > actual_best_score:
+                'update current best score' 
+                actual_best_score = current_score
+                patince_count = 0
+            else:
+                'undo the last update'
+                if added:
+                    graph.remove_edges([current_edge])
+                    'If a parent was removed, add it again to the graph'
+                    if parent_removed is not None:
+                        graph.add_edges([parent_removed])
+                else:
+                    graph.add_edges([current_edge])
+                'update patience count'
+                patince_count += 1
+
+            if self.patience is not None and patince_count > self.patience:
+                break
+
+        print(f"finito variabile: {self.node_id}")
+        return graph.edges
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py b/build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py
new file mode 100644
index 0000000..1984f06
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py
@@ -0,0 +1,39 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+
+import abc 
+
+from ..estimators.structure_estimator import StructureEstimator
+
+
+
+class Optimizer(abc.ABC):
+    """
+    Interface class for all the optimizer's child PyCTBN
+
+    :param node_id: the node label
+    :type node_id: string
+    :param structure_estimator: A structureEstimator Object to predict the structure
+    :type structure_estimator: class:'StructureEstimator'
+    
+    """
+
+    def __init__(self, node_id:str, structure_estimator: StructureEstimator):
+        self.node_id = node_id
+        self.structure_estimator = structure_estimator
+        
+
+    @abc.abstractmethod
+    def optimize_structure(self) -> typing.List:
+        """
+        Compute Optimization process for a structure_estimator
+
+        :return: the estimated structure for the node
+        :rtype: List
+        """
+        pass
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py b/build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py
new file mode 100644
index 0000000..b7b2bc9
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py
@@ -0,0 +1,188 @@
+
+import itertools
+import json
+import typing
+
+import networkx as nx
+import numpy as np
+
+from random import choice,sample
+
+from abc import ABC
+
+
+from .optimizer import Optimizer
+from ..estimators.structure_estimator import StructureEstimator
+from ..structure_graph.network_graph import NetworkGraph
+
+import queue
+
+
+class TabuSearch(Optimizer):
+    """
+    Optimizer class that implement Tabu Search
+
+
+    :param node_id: current node's id
+    :type node_id: string
+    :param structure_estimator: a structure estimator object with the information about the net
+    :type structure_estimator: class:'StructureEstimator' 
+    :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
+    :type max_parents: int, optional
+    :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
+    :type iterations_number: int, optional
+    :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
+    :type patience: int, optional
+    :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
+    :type tabu_length: int, optional
+    :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
+    :type tabu_rules_duration: int, optional
+
+    
+    """
+    def __init__(self,
+                node_id:str,
+                structure_estimator: StructureEstimator,
+                max_parents:int = None,
+                iterations_number:int= 40,
+                patience:int = None,
+                tabu_length:int = None,
+                tabu_rules_duration = None
+                ):
+        """
+        Constructor
+        """
+        super().__init__(node_id, structure_estimator)
+        self.max_parents = max_parents
+        self.iterations_number = iterations_number
+        self.patience = patience
+        self.tabu_length = tabu_length
+        self.tabu_rules_duration = tabu_rules_duration
+
+
+    def optimize_structure(self) -> typing.List:
+        """
+        Compute Optimization process for a structure_estimator by using a Hill Climbing Algorithm
+
+        :return: the estimated structure for the node
+        :rtype: List
+        """
+        print(f"tabu search is processing the structure of {self.node_id}")
+
+        'Create the graph for the single node'
+        graph = NetworkGraph(self.structure_estimator._sample_path.structure)
+
+        'get the index for the current node'
+        node_index = self.structure_estimator._sample_path._structure.get_node_indx(self.node_id)
+
+        'list of prior edges'
+        prior_parents = set()
+
+        'Add the edges from prior knowledge'
+        for i in range(len(self.structure_estimator._removable_edges_matrix)):
+            if not self.structure_estimator._removable_edges_matrix[i][node_index]:
+                parent_id= self.structure_estimator._sample_path._structure.get_node_id(i)
+                prior_parents.add(parent_id)
+
+                'Add the node to the starting structure'
+                graph.add_edges([(parent_id, self.node_id)])
+
+
+
+        'get all the possible parents'
+        other_nodes =  set([node for node in 
+                                            self.structure_estimator._sample_path.structure.nodes_labels if
+                                                                                            node != self.node_id and
+                                                                                            not prior_parents.__contains__(node)])
+
+        'calculate the score for the node without parents'
+        actual_best_score = self.structure_estimator.get_score_from_graph(graph,self.node_id)
+
+
+        'initialize tabu_length and tabu_rules_duration if None'
+        if self.tabu_length is None:
+            self.tabu_length = len(other_nodes)
+
+        if self.tabu_rules_duration is None:
+            self.tabu_rules_duration = len(other_nodes)
+
+        'inizialize the data structures'
+        tabu_set = set()
+        tabu_queue = queue.Queue()
+
+        patince_count = 0
+        tabu_count = 0 
+        for i in range(self.iterations_number):
+            
+            current_possible_nodes = other_nodes.difference(tabu_set)
+
+            'choose a new random edge according to tabu restiction'
+            if(len(current_possible_nodes) > 0):
+                current_new_parent = sample(current_possible_nodes,k=1)[0]
+            else:
+                current_new_parent = tabu_queue.get()
+                tabu_set.remove(current_new_parent)
+
+
+            
+            current_edge =  (current_new_parent,self.node_id)
+            added = False
+            parent_removed = None 
+
+            if graph.has_edge(current_edge):
+                graph.remove_edges([current_edge])
+            else:
+                'check the max_parents constraint'
+                if self.max_parents is not None:
+                    parents_list = graph.get_parents_by_id(self.node_id)
+                    if len(parents_list) >= self.max_parents :
+                        parent_removed = (choice(parents_list), self.node_id)
+                        graph.remove_edges([parent_removed])
+                graph.add_edges([current_edge])
+                added = True
+           
+            current_score =  self.structure_estimator.get_score_from_graph(graph,self.node_id)
+
+            if current_score > actual_best_score:
+                'update current best score' 
+                actual_best_score = current_score
+                patince_count = 0
+                'update tabu list'
+
+
+            else:
+                'undo the last update'
+                if added:
+                    graph.remove_edges([current_edge])
+                    'If a parent was removed, add it again to the graph'
+                    if parent_removed is not None:
+                        graph.add_edges([parent_removed])
+                else:
+                    graph.add_edges([current_edge])
+                'update patience count'
+                patince_count += 1
+                
+            
+            if tabu_queue.qsize() >= self.tabu_length:
+                    current_removed = tabu_queue.get()
+                    tabu_set.remove(current_removed)
+            'Add the node on the tabu list'
+            tabu_queue.put(current_new_parent)
+            tabu_set.add(current_new_parent)
+
+            tabu_count += 1
+
+            'Every tabu_rules_duration step remove an item from the tabu list '
+            if tabu_count % self.tabu_rules_duration == 0:
+                if tabu_queue.qsize() > 0:
+                    current_removed = tabu_queue.get()
+                    tabu_set.remove(current_removed)
+                    tabu_count = 0
+                else:
+                    tabu_count = 0
+
+            if self.patience is not None and patince_count > self.patience:
+                break
+
+        print(f"finito variabile: {self.node_id}")
+        return graph.edges
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py b/build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py
new file mode 100644
index 0000000..85f18a2
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py
@@ -0,0 +1,6 @@
+from .conditional_intensity_matrix import ConditionalIntensityMatrix
+from .network_graph import NetworkGraph
+from .sample_path import SamplePath
+from .set_of_cims import SetOfCims
+from .structure import Structure
+from .trajectory import Trajectory
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py b/build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
new file mode 100644
index 0000000..4abfdd0
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
@@ -0,0 +1,42 @@
+import numpy as np
+
+
+class ConditionalIntensityMatrix(object):
+    """Abstracts the Conditional Intesity matrix of a node as aggregation of the state residence times vector
+    and state transition matrix and the actual CIM matrix.
+
+    :param state_residence_times: state residence times vector
+    :type state_residence_times: numpy.array
+    :param state_transition_matrix: the transitions count matrix
+    :type state_transition_matrix: numpy.ndArray
+    :_cim: the actual cim of the node
+    """
+    def __init__(self, state_residence_times: np.array, state_transition_matrix: np.array):
+        """Constructor Method
+        """
+        self._state_residence_times = state_residence_times
+        self._state_transition_matrix = state_transition_matrix
+        self._cim = self.state_transition_matrix.astype(np.float64)
+
+    def compute_cim_coefficients(self) -> None:
+        """Compute the coefficients of the matrix _cim by using the following equality q_xx' = M[x, x'] / T[x].
+        The class member ``_cim`` will contain the computed cim
+        """
+        np.fill_diagonal(self._cim, self._cim.diagonal() * -1)
+        self._cim = ((self._cim.T + 1) / (self._state_residence_times + 1)).T
+
+    @property
+    def state_residence_times(self) -> np.ndarray:
+        return self._state_residence_times
+
+    @property
+    def state_transition_matrix(self) -> np.ndarray:
+        return self._state_transition_matrix
+
+    @property
+    def cim(self) -> np.ndarray:
+        return self._cim
+
+    def __repr__(self):
+        return 'CIM:\n' + str(self.cim)
+
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py b/build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py
new file mode 100644
index 0000000..6fb3639
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py
@@ -0,0 +1,293 @@
+
+import typing
+
+import networkx as nx
+import numpy as np
+
+from .structure import Structure
+
+
+class NetworkGraph(object):
+    """Abstracts the infos contained in the Structure class in the form of a directed graph.
+    Has the task of creating all the necessary filtering and indexing structures for parameters estimation
+
+    :param graph_struct: the ``Structure`` object from which infos about the net will be extracted
+    :type graph_struct: Structure
+    :_graph: directed graph
+    :_aggregated_info_about_nodes_parents: a structure that contains all the necessary infos
+        about every parents of the node of which all the indexing and filtering structures will be constructed.
+    :_time_scalar_indexing_structure: the indexing structure for state res time estimation
+    :_transition_scalar_indexing_structure: the indexing structure for transition computation
+    :_time_filtering: the columns filtering structure used in the computation of the state res times
+    :_transition_filtering: the columns filtering structure used in the computation of the transition
+        from one state to another
+    :_p_combs_structure: all the possible parents states combination for the node of interest
+    """
+
+    def __init__(self, graph_struct: Structure):
+        """Constructor Method
+        """
+        self._graph_struct = graph_struct
+        self._graph = nx.DiGraph()
+        self._aggregated_info_about_nodes_parents = None
+        self._time_scalar_indexing_structure = None
+        self._transition_scalar_indexing_structure = None
+        self._time_filtering = None
+        self._transition_filtering = None
+        self._p_combs_structure = None
+
+    #def init_graph(self):
+    #    self.add_nodes(self._nodes_labels)
+    #    self.add_edges(self.graph_struct.edges)
+    #    self.aggregated_info_about_nodes_parents = self.get_ord_set_of_par_of_all_nodes()
+    #    self._fancy_indexing = self.build_fancy_indexing_structure(0)
+    #    self.build_scalar_indexing_structures()
+    #    self.build_time_columns_filtering_structure()
+    #    self.build_transition_columns_filtering_structure()
+    #    self._p_combs_structure = self.build_p_combs_structure()
+
+    def fast_init(self, node_id: str) -> None:
+        """Initializes all the necessary structures for parameters estimation of the node identified by the label
+        node_id
+
+        :param node_id: the label of the node
+        :type node_id: string
+        """
+        self.add_nodes(self._graph_struct.nodes_labels)
+        self.add_edges(self._graph_struct.edges)
+        self._aggregated_info_about_nodes_parents = self.get_ordered_by_indx_set_of_parents(node_id)
+        p_indxs = self._aggregated_info_about_nodes_parents[1]
+        p_vals = self._aggregated_info_about_nodes_parents[2]
+        node_states = self.get_states_number(node_id)
+        node_indx = self.get_node_indx(node_id)
+        cols_number = self._graph_struct.total_variables_number
+        self._time_scalar_indexing_structure = NetworkGraph.\
+            build_time_scalar_indexing_structure_for_a_node(node_states, p_vals)
+        self._transition_scalar_indexing_structure = NetworkGraph.\
+            build_transition_scalar_indexing_structure_for_a_node(node_states, p_vals)
+        self._time_filtering = NetworkGraph.build_time_columns_filtering_for_a_node(node_indx, p_indxs)
+        self._transition_filtering = NetworkGraph.build_transition_filtering_for_a_node(node_indx, p_indxs, cols_number)
+        self._p_combs_structure = NetworkGraph.build_p_comb_structure_for_a_node(p_vals)
+
+    def add_nodes(self, list_of_nodes: typing.List) -> None:
+        """Adds the nodes to the ``_graph`` contained in the list of nodes ``list_of_nodes``.
+        Sets all the properties that identify a nodes (index, positional index, cardinality)
+
+        :param list_of_nodes: the nodes to add to ``_graph``
+        :type list_of_nodes: List
+        """
+        nodes_indxs = self._graph_struct.nodes_indexes
+        nodes_vals = self._graph_struct.nodes_values
+        pos = 0
+        for id, node_indx, node_val in zip(list_of_nodes, nodes_indxs, nodes_vals):
+            self._graph.add_node(id, indx=node_indx, val=node_val, pos_indx=pos)
+            pos += 1
+
+    def has_edge(self,edge:tuple)-> bool:
+        """
+        Check if the graph contains a specific edge
+
+        Parameters:
+            edge: a tuple that rappresents the edge
+        Returns:
+            bool
+        """
+        return self._graph.has_edge(edge[0],edge[1])
+
+    def add_edges(self, list_of_edges: typing.List) -> None:
+        """Add the edges to the ``_graph`` contained in the list ``list_of_edges``.
+
+        :param list_of_edges: the list containing of tuples containing the edges
+        :type list_of_edges: List
+        """
+        self._graph.add_edges_from(list_of_edges)
+
+    def remove_node(self, node_id: str) -> None:
+        """Remove the node ``node_id`` from all the class members.
+        Initialize all the filtering/indexing structures.
+        """
+        self._graph.remove_node(node_id)
+        self._graph_struct.remove_node(node_id)
+        self.clear_indexing_filtering_structures()
+
+    def clear_indexing_filtering_structures(self) -> None:
+        """Initialize all the filtering/indexing structures.
+        """
+        self._aggregated_info_about_nodes_parents = None
+        self._time_scalar_indexing_structure = None
+        self._transition_scalar_indexing_structure = None
+        self._time_filtering = None
+        self._transition_filtering = None
+        self._p_combs_structure = None
+
+    def get_ordered_by_indx_set_of_parents(self, node: str) -> typing.Tuple:
+        """Builds the aggregated structure that holds all the infos relative to the parent set of the node, namely
+        (parents_labels, parents_indexes, parents_cardinalities).
+
+        :param node: the label of the node
+        :type node: string
+        :return: a tuple containing all the parent set infos
+        :rtype: Tuple
+        """
+        parents = self.get_parents_by_id(node)
+        nodes = self._graph_struct.nodes_labels
+        d = {v: i for i, v in enumerate(nodes)}
+        sorted_parents = sorted(parents, key=lambda v: d[v])
+        get_node_indx = self.get_node_indx
+        p_indxes = [get_node_indx(node) for node in sorted_parents]
+        p_values = [self.get_states_number(node) for node in sorted_parents]
+        return sorted_parents, p_indxes, p_values
+
+    def remove_edges(self, list_of_edges: typing.List) -> None:
+        """Remove the edges to the graph contained in the list list_of_edges.
+        
+        :param list_of_edges: The edges to remove from the graph
+        :type list_of_edges: List
+        """
+        self._graph.remove_edges_from(list_of_edges)
+
+    @staticmethod
+    def build_time_scalar_indexing_structure_for_a_node(node_states: int,
+                                                        parents_vals: typing.List) -> np.ndarray:
+        """Builds an indexing structure for the computation of state residence times values.
+
+        :param node_states: the node cardinality
+        :type node_states: int
+        :param parents_vals: the caridinalites of the node's parents
+        :type parents_vals: List
+        :return: The time indexing structure
+        :rtype: numpy.ndArray
+        """
+        T_vector = np.array([node_states])
+        T_vector = np.append(T_vector, parents_vals)
+        T_vector = T_vector.cumprod().astype(np.int)
+        return T_vector
+
+    @staticmethod
+    def build_transition_scalar_indexing_structure_for_a_node(node_states_number: int, parents_vals: typing.List) \
+            -> np.ndarray:
+        """Builds an indexing structure for the computation of state transitions values.
+
+        :param node_states_number: the node cardinality
+        :type node_states_number: int
+        :param parents_vals: the caridinalites of the node's parents
+        :type parents_vals: List
+        :return: The transition indexing structure
+        :rtype: numpy.ndArray
+        """
+        M_vector = np.array([node_states_number,
+                             node_states_number])
+        M_vector = np.append(M_vector, parents_vals)
+        M_vector = M_vector.cumprod().astype(np.int)
+        return M_vector
+
+    @staticmethod
+    def build_time_columns_filtering_for_a_node(node_indx: int, p_indxs: typing.List) -> np.ndarray:
+        """
+        Builds the necessary structure to filter the desired columns indicated by ``node_indx`` and ``p_indxs``
+        in the dataset.
+        This structute will be used in the computation of the state res times.
+        :param node_indx: the index of the node
+        :type node_indx: int
+        :param p_indxs: the indexes of the node's parents
+        :type p_indxs: List
+        :return: The filtering structure for times estimation
+        :rtype: numpy.ndArray
+        """
+        return np.append(np.array([node_indx], dtype=np.int), p_indxs).astype(np.int)
+
+    @staticmethod
+    def build_transition_filtering_for_a_node(node_indx: int, p_indxs: typing.List, nodes_number: int) \
+            -> np.ndarray:
+        """Builds the necessary structure to filter the desired columns indicated by ``node_indx`` and ``p_indxs``
+        in the dataset.
+        This structure will be used in the computation of the state transitions values.
+        :param node_indx: the index of the node
+        :type node_indx: int
+        :param p_indxs: the indexes of the node's parents
+        :type p_indxs: List
+        :param nodes_number: the total number of nodes in the dataset
+        :type nodes_number: int
+        :return: The filtering structure for transitions estimation
+        :rtype: numpy.ndArray
+        """
+        return np.array([node_indx + nodes_number, node_indx, *p_indxs], dtype=np.int)
+
+    @staticmethod
+    def build_p_comb_structure_for_a_node(parents_values: typing.List) -> np.ndarray:
+        """
+        Builds the combinatorial structure that contains the combinations of all the values contained in
+        ``parents_values``.
+
+        :param parents_values: the cardinalities of the nodes
+        :type parents_values: List
+        :return: A numpy matrix containing a grid of the combinations
+        :rtype: numpy.ndArray
+        """
+        tmp = []
+        for val in parents_values:
+            tmp.append([x for x in range(val)])
+        if len(parents_values) > 0:
+            parents_comb = np.array(np.meshgrid(*tmp)).T.reshape(-1, len(parents_values))
+            if len(parents_values) > 1:
+                tmp_comb = parents_comb[:, 1].copy()
+                parents_comb[:, 1] = parents_comb[:, 0].copy()
+                parents_comb[:, 0] = tmp_comb
+        else:
+            parents_comb = np.array([[]], dtype=np.int)
+        return parents_comb
+
+    def get_parents_by_id(self, node_id) -> typing.List:
+        """Returns a list of labels of the parents of the node ``node_id``
+
+        :param node_id: the node label
+        :type node_id: string
+        :return: a List of labels of the parents
+        :rtype: List
+        """
+        return list(self._graph.predecessors(node_id))
+
+    def get_states_number(self, node_id) -> int:
+        return self._graph.nodes[node_id]['val']
+
+    def get_node_indx(self, node_id) -> int:
+        return nx.get_node_attributes(self._graph, 'indx')[node_id]
+
+    def get_positional_node_indx(self, node_id) -> int:
+        return self._graph.nodes[node_id]['pos_indx']
+
+    @property
+    def nodes(self) -> typing.List:
+        return self._graph_struct.nodes_labels
+
+    @property
+    def edges(self) -> typing.List:
+        return list(self._graph.edges)
+
+    @property
+    def nodes_indexes(self) -> np.ndarray:
+        return self._graph_struct.nodes_indexes
+
+    @property
+    def nodes_values(self) -> np.ndarray:
+        return self._graph_struct.nodes_values
+
+    @property
+    def time_scalar_indexing_strucure(self) -> np.ndarray:
+        return self._time_scalar_indexing_structure
+
+    @property
+    def time_filtering(self) -> np.ndarray:
+        return self._time_filtering
+
+    @property
+    def transition_scalar_indexing_structure(self) -> np.ndarray:
+        return self._transition_scalar_indexing_structure
+
+    @property
+    def transition_filtering(self) -> np.ndarray:
+        return self._transition_filtering
+
+    @property
+    def p_combs(self) -> np.ndarray:
+        return self._p_combs_structure
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py b/build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py
new file mode 100644
index 0000000..88e9649
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py
@@ -0,0 +1,93 @@
+
+
+import numpy as np
+import pandas as pd
+
+from .structure import Structure
+from .trajectory import Trajectory
+from ..utility.abstract_importer import AbstractImporter
+
+
+MESSAGE_HAS_TO_CONTAIN_EXCEPTION = 'The importer object has to contain the all processed data!'
+
+
+class SamplePath(object):
+    """Aggregates all the informations about the trajectories, the real structure of the sampled net and variables
+    cardinalites. Has the task of creating the objects ``Trajectory`` and ``Structure`` that will
+    contain the mentioned data.
+
+    :param importer: the Importer object which contains the imported and processed data
+    :type importer: AbstractImporter
+    :_trajectories: the ``Trajectory`` object that will contain all the concatenated trajectories
+    :_structure: the ``Structure`` Object that will contain all the structural infos about the net
+    :_total_variables_count: the number of variables in the net
+    """
+    def __init__(self, importer: AbstractImporter):
+        """Constructor Method
+        """
+        self._importer = importer
+        if self._importer._df_variables is None or self._importer._concatenated_samples is None:
+            raise RuntimeError()
+        if self._importer._df_variables.empty:
+            raise RuntimeError(MESSAGE_HAS_TO_CONTAIN_EXCEPTION)
+        if isinstance(self._importer._concatenated_samples, pd.DataFrame) and\
+            self._importer._concatenated_samples.empty:
+                raise RuntimeError(MESSAGE_HAS_TO_CONTAIN_EXCEPTION)
+        if isinstance(self._importer._concatenated_samples, np.ndarray) and\
+            self._importer._concatenated_samples.size == 0:
+                raise RuntimeError(MESSAGE_HAS_TO_CONTAIN_EXCEPTION)
+        self._trajectories = None
+        self._structure = None
+        self._total_variables_count = None
+
+    def build_trajectories(self) -> None:
+        """Builds the Trajectory object that will contain all the trajectories.
+        Clears all the unused dataframes in ``_importer`` Object
+        """
+        self._trajectories = \
+            Trajectory(self._importer.build_list_of_samples_array(self._importer.concatenated_samples),
+                len(self._importer.sorter) + 1)
+        self._importer.clear_concatenated_frame()
+
+    def build_structure(self) -> None:
+        """
+        Builds the ``Structure`` object that aggregates all the infos about the net.
+        """
+        if self._importer.sorter != self._importer.variables.iloc[:, 0].to_list():
+            raise RuntimeError("The Dataset columns order have to match the order of labels in the variables Frame!")
+
+        self._total_variables_count = len(self._importer.sorter)
+        labels = self._importer.variables.iloc[:, 0].to_list()
+        indxs = self._importer.variables.index.to_numpy()
+        vals = self._importer.variables.iloc[:, 1].to_numpy()
+        if self._importer.structure is None or self._importer.structure.empty:
+            edges = []
+        else:
+            edges = list(self._importer.structure.to_records(index=False))
+        self._structure = Structure(labels, indxs, vals, edges,
+                                       self._total_variables_count)
+
+    def clear_memory(self):
+        self._importer._raw_data = [] 
+
+    @property
+    def trajectories(self) -> Trajectory:
+        return self._trajectories
+
+    @property
+    def structure(self) -> Structure:
+        return self._structure
+
+    @property
+    def total_variables_count(self) -> int:
+        return self._total_variables_count
+
+    @property
+    def has_prior_net_structure(self) -> bool:
+        return bool(self._structure.edges)
+
+
+
+
+
+
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py b/build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
new file mode 100644
index 0000000..81caff5
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
@@ -0,0 +1,97 @@
+
+
+import typing
+
+import numpy as np
+
+from .conditional_intensity_matrix import ConditionalIntensityMatrix
+
+
+class SetOfCims(object):
+    """Aggregates all the CIMS of the node identified by the label _node_id.
+
+    :param node_id: the node label
+    :type node_ind: string
+    :param parents_states_number: the cardinalities of the parents
+    :type parents_states_number: List
+    :param node_states_number: the caridinality of the node
+    :type node_states_number: int
+    :param p_combs: the p_comb structure bound to this node
+    :type p_combs: numpy.ndArray
+    :_state_residence_time: matrix containing all the state residence time vectors for the node
+    :_transition_matrices: matrix containing all the transition matrices for the node
+    :_actual_cims: the cims of the node
+    """
+
+    def __init__(self, node_id: str, parents_states_number: typing.List, node_states_number: int, p_combs: np.ndarray):
+        """Constructor Method
+        """
+        self._node_id = node_id
+        self._parents_states_number = parents_states_number
+        self._node_states_number = node_states_number
+        self._actual_cims = []
+        self._state_residence_times = None
+        self._transition_matrices = None
+        self._p_combs = p_combs
+        self.build_times_and_transitions_structures()
+
+    def build_times_and_transitions_structures(self) -> None:
+        """Initializes at the correct dimensions the state residence times matrix and the state transition matrices.
+        """
+        if not self._parents_states_number:
+            self._state_residence_times = np.zeros((1, self._node_states_number), dtype=np.float)
+            self._transition_matrices = np.zeros((1, self._node_states_number, self._node_states_number), dtype=np.int)
+        else:
+            self._state_residence_times = \
+                np.zeros((np.prod(self._parents_states_number), self._node_states_number), dtype=np.float)
+            self._transition_matrices = np.zeros([np.prod(self._parents_states_number), self._node_states_number,
+                                                  self._node_states_number], dtype=np.int)
+
+    def build_cims(self, state_res_times: np.ndarray, transition_matrices: np.ndarray) -> None:
+        """Build the ``ConditionalIntensityMatrix`` objects given the state residence times and transitions matrices.
+        Compute the cim coefficients.The class member ``_actual_cims`` will contain the computed cims.
+
+        :param state_res_times: the state residence times matrix
+        :type state_res_times: numpy.ndArray
+        :param transition_matrices: the transition matrices
+        :type transition_matrices: numpy.ndArray
+        """
+        for state_res_time_vector, transition_matrix in zip(state_res_times, transition_matrices):
+            cim_to_add = ConditionalIntensityMatrix(state_res_time_vector, transition_matrix)
+            cim_to_add.compute_cim_coefficients()
+            self._actual_cims.append(cim_to_add)
+        self._actual_cims = np.array(self._actual_cims)
+        self._transition_matrices = None
+        self._state_residence_times = None
+
+    def filter_cims_with_mask(self, mask_arr: np.ndarray, comb: typing.List) -> np.ndarray:
+        """Filter the cims contained in the array ``_actual_cims`` given the boolean mask ``mask_arr`` and the index
+        ``comb``.
+
+        :param mask_arr: the boolean mask that indicates which parent to consider
+        :type mask_arr: numpy.array
+        :param comb: the state/s of the filtered parents
+        :type comb: numpy.array
+        :return: Array of ``ConditionalIntensityMatrix`` objects
+        :rtype: numpy.array
+        """
+        if mask_arr.size <= 1:
+            return self._actual_cims
+        else:
+            flat_indxs = np.argwhere(np.all(self._p_combs[:, mask_arr] == comb, axis=1)).ravel()
+            return self._actual_cims[flat_indxs]
+
+    @property
+    def actual_cims(self) -> np.ndarray:
+        return self._actual_cims
+
+    @property
+    def p_combs(self) -> np.ndarray:
+        return self._p_combs
+
+    def get_cims_number(self):
+        return len(self._actual_cims)
+
+
+
+
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/structure.py b/build/lib/PyCTBN/PyCTBN/structure_graph/structure.py
new file mode 100644
index 0000000..f79c875
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/structure_graph/structure.py
@@ -0,0 +1,124 @@
+
+import typing as ty
+
+import numpy as np
+
+
+class Structure(object):
+    """Contains all the infos about the network structure(nodes labels, nodes caridinalites, edges, indexes)
+
+    :param nodes_labels_list: the symbolic names of the variables
+    :type nodes_labels_list: List
+    :param nodes_indexes_arr: the indexes of the nodes
+    :type nodes_indexes_arr: numpy.ndArray
+    :param nodes_vals_arr: the cardinalites of the nodes
+    :type nodes_vals_arr: numpy.ndArray
+    :param edges_list: the edges of the network
+    :type edges_list: List
+    :param total_variables_number: the total number of variables in the dataset
+    :type total_variables_number: int
+    """
+
+    def __init__(self, nodes_labels_list: ty.List, nodes_indexes_arr: np.ndarray, nodes_vals_arr: np.ndarray,
+                 edges_list: ty.List, total_variables_number: int):
+        """Constructor Method
+        """
+        self._nodes_labels_list = nodes_labels_list
+        self._nodes_indexes_arr = nodes_indexes_arr
+        self._nodes_vals_arr = nodes_vals_arr
+        self._edges_list = edges_list
+        self._total_variables_number = total_variables_number
+
+    def remove_node(self, node_id: str) -> None:
+        """Remove the node ``node_id`` from all the class members.
+        The class member ``_total_variables_number`` since it refers to the total number of variables in the dataset.
+        """
+        node_positional_indx = self._nodes_labels_list.index(node_id)
+        del self._nodes_labels_list[node_positional_indx]
+        self._nodes_indexes_arr = np.delete(self._nodes_indexes_arr, node_positional_indx)
+        self._nodes_vals_arr = np.delete(self._nodes_vals_arr, node_positional_indx)
+        self._edges_list = [(from_node, to_node) for (from_node, to_node) in self._edges_list if (from_node != node_id
+                                                                                        and to_node != node_id)]
+
+    @property
+    def edges(self) -> ty.List:
+        return self._edges_list
+
+    @property
+    def nodes_labels(self) -> ty.List:
+        return self._nodes_labels_list
+
+    @property
+    def nodes_indexes(self) -> np.ndarray:
+        return self._nodes_indexes_arr
+
+    @property
+    def nodes_values(self) -> np.ndarray:
+        return self._nodes_vals_arr
+
+    @property
+    def total_variables_number(self) -> int:
+        return self._total_variables_number
+
+    def get_node_id(self, node_indx: int) -> str:
+        """Given the ``node_index`` returns the node label.
+
+        :param node_indx: the node index
+        :type node_indx: int
+        :return: the node label
+        :rtype: string
+        """
+        return self._nodes_labels_list[node_indx]
+
+    def clean_structure_edges(self):
+        self._edges_list = list()
+
+    def add_edge(self,edge: tuple):
+        self._edges_list.append(edge)
+
+    
+    def remove_edge(self,edge: tuple):
+        self._edges_list.remove(edge)
+
+    def contains_edge(self,edge:tuple) -> bool:
+        return edge in self._edges_list
+
+    def get_node_indx(self, node_id: str) -> int:
+        """Given the ``node_index`` returns the node label.
+
+        :param node_id: the node label
+        :type node_id: string
+        :return: the node index
+        :rtype: int
+        """
+        pos_indx = self._nodes_labels_list.index(node_id)
+        return self._nodes_indexes_arr[pos_indx]
+
+    def get_positional_node_indx(self, node_id: str) -> int:
+        return self._nodes_labels_list.index(node_id)
+
+    def get_states_number(self, node: str) -> int:
+        """Given the node label ``node`` returns the cardinality of the node.
+
+        :param node: the node label
+        :type node: string
+        :return: the node cardinality
+        :rtype: int
+        """
+        pos_indx = self._nodes_labels_list.index(node)
+        return self._nodes_vals_arr[pos_indx]
+
+    def __repr__(self):
+        return "Variables:\n" + str(self._nodes_labels_list) +"\nValues:\n"+ str(self._nodes_vals_arr) +\
+               "\nEdges: \n" + str(self._edges_list)
+
+    def __eq__(self, other):
+        """Overrides the default implementation"""
+        if isinstance(other, Structure):
+            return set(self._nodes_labels_list) == set(other._nodes_labels_list) and \
+                   np.array_equal(self._nodes_vals_arr, other._nodes_vals_arr) and \
+                   np.array_equal(self._nodes_indexes_arr, other._nodes_indexes_arr) and \
+                   self._edges_list == other._edges_list
+
+        return False
+
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py b/build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py
new file mode 100644
index 0000000..36899b3
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py
@@ -0,0 +1,45 @@
+
+import typing
+
+import numpy as np
+
+
+class Trajectory(object):
+    """ Abstracts the infos about a complete set of trajectories, represented as a numpy array of doubles
+    (the time deltas) and a numpy matrix of ints (the changes of states).
+
+    :param list_of_columns: the list containing the times array and values matrix
+    :type list_of_columns: List
+    :param original_cols_number: total number of cols in the data
+    :type original_cols_number: int
+    :_actual_trajectory: the trajectory containing also the duplicated/shifted values
+    :_times: the array containing the time deltas
+    """
+
+    def __init__(self, list_of_columns: typing.List, original_cols_number: int):
+        """Constructor Method
+        """
+        self._times = list_of_columns[0]
+        self._actual_trajectory = list_of_columns[1]
+        self._original_cols_number = original_cols_number
+
+    @property
+    def trajectory(self) -> np.ndarray:
+        return self._actual_trajectory[:, :self._original_cols_number - 1]
+
+    @property
+    def complete_trajectory(self) -> np.ndarray:
+        return self._actual_trajectory
+
+    @property
+    def times(self):
+        return self._times
+
+    def size(self):
+        return self._actual_trajectory.shape[0]
+
+    def __repr__(self):
+        return "Complete Trajectory Rows: " + str(self.size()) + "\n" + self.complete_trajectory.__repr__() + \
+               "\nTimes Rows:" + str(self.times.size) + "\n" + self.times.__repr__()
+
+
diff --git a/build/lib/PyCTBN/PyCTBN/utility/__init__.py b/build/lib/PyCTBN/PyCTBN/utility/__init__.py
new file mode 100644
index 0000000..f79749c
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/utility/__init__.py
@@ -0,0 +1,4 @@
+from .abstract_importer import AbstractImporter
+from .cache import Cache
+from .json_importer import JsonImporter
+from .sample_importer import SampleImporter
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py b/build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py
new file mode 100644
index 0000000..8984b4d
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py
@@ -0,0 +1,163 @@
+
+import typing
+from abc import ABC, abstractmethod
+
+import numpy as np
+import pandas as pd
+
+import copy
+
+
+
+class AbstractImporter(ABC):
+    """Abstract class that exposes all the necessary methods to process the trajectories and the net structure.
+
+    :param file_path: the file path, or dataset name if you import already processed data
+    :type file_path: str
+    :param trajectory_list: Dataframe or numpy array containing the concatenation of all the processed trajectories
+    :type trajectory_list: typing.Union[pandas.DataFrame, numpy.ndarray]
+    :param variables: Dataframe containing the nodes labels and cardinalities
+    :type variables: pandas.DataFrame
+    :prior_net_structure: Dataframe containing the structure of the network (edges)
+    :type prior_net_structure: pandas.DataFrame
+    :_sorter: A list containing the variables labels in the SAME order as the columns in ``concatenated_samples``
+
+    .. warning::
+        The parameters ``variables`` and ``prior_net_structure`` HAVE to be properly constructed
+        as Pandas Dataframes with the following structure:
+        Header of _df_structure = [From_Node | To_Node]
+        Header of _df_variables = [Variable_Label | Variable_Cardinality]
+        See the tutorial on how to construct a correct ``concatenated_samples`` Dataframe/ndarray.
+
+    .. note::
+        See :class:``JsonImporter`` for an example implementation
+
+    """
+
+    def __init__(self, file_path: str = None, trajectory_list: typing.Union[pd.DataFrame, np.ndarray] = None,
+                 variables: pd.DataFrame = None, prior_net_structure: pd.DataFrame = None):
+        """Constructor
+        """
+        self._file_path = file_path
+        self._df_samples_list = trajectory_list
+        self._concatenated_samples = []
+        self._df_variables = variables
+        self._df_structure = prior_net_structure
+        self._sorter = None
+        super().__init__()
+
+    @abstractmethod
+    def build_sorter(self, trajecory_header: object) -> typing.List:
+        """Initializes the ``_sorter`` class member from a trajectory dataframe, exctracting the header of the frame
+        and keeping ONLY the variables symbolic labels, cutting out the time label in the header.
+
+        :param trajecory_header: an object that will be used to define the header
+        :type trajecory_header: object
+        :return: A list containing the processed header.
+        :rtype: List
+        """
+        pass
+
+    def compute_row_delta_sigle_samples_frame(self, sample_frame: pd.DataFrame,
+                                              columns_header: typing.List, shifted_cols_header: typing.List) \
+            -> pd.DataFrame:
+        """Computes the difference between each value present in th time column.
+        Copies and shift by one position up all the values present in the remaining columns.
+
+        :param sample_frame: the traj to be processed
+        :type sample_frame: pandas.Dataframe
+        :param columns_header: the original header of sample_frame
+        :type columns_header: List
+        :param shifted_cols_header: a copy of columns_header with changed names of the contents
+        :type shifted_cols_header: List
+        :return: The processed dataframe
+        :rtype: pandas.Dataframe
+
+        .. warning::
+            the Dataframe ``sample_frame`` has to follow the column structure of this header:
+            Header of sample_frame = [Time | Variable values]
+        """
+        sample_frame = copy.deepcopy(sample_frame)
+        sample_frame.iloc[:, 0] = sample_frame.iloc[:, 0].diff().shift(-1)
+        shifted_cols = sample_frame[columns_header].shift(-1).fillna(0).astype('int32')
+        shifted_cols.columns = shifted_cols_header
+        sample_frame = sample_frame.assign(**shifted_cols)
+        sample_frame.drop(sample_frame.tail(1).index, inplace=True)
+        return sample_frame
+
+    def compute_row_delta_in_all_samples_frames(self, df_samples_list: typing.List) -> None:
+        """Calls the method ``compute_row_delta_sigle_samples_frame`` on every dataframe present in the list
+        ``df_samples_list``.
+        Concatenates the result in the dataframe ``concatanated_samples``
+
+        :param df_samples_list: the datframe's list to be processed and concatenated
+        :type df_samples_list: List
+
+        .. warning::
+            The Dataframe sample_frame has to follow the column structure of this header:
+            Header of sample_frame = [Time | Variable values]
+            The class member self._sorter HAS to be properly INITIALIZED (See class members definition doc)
+        .. note::
+            After the call of this method the class member ``concatanated_samples`` will contain all processed
+            and merged trajectories
+        """
+        if not self._sorter:
+            raise RuntimeError("The class member self._sorter has to be INITIALIZED!")
+        shifted_cols_header = [s + "S" for s in self._sorter]
+        compute_row_delta = self.compute_row_delta_sigle_samples_frame
+        proc_samples_list = [compute_row_delta(sample, self._sorter, shifted_cols_header)
+                                for sample in df_samples_list]
+        self._concatenated_samples = pd.concat(proc_samples_list)
+
+        complete_header = self._sorter[:]
+        complete_header.insert(0,'Time')
+        complete_header.extend(shifted_cols_header)
+        self._concatenated_samples = self._concatenated_samples[complete_header]
+
+    def build_list_of_samples_array(self, concatenated_sample: pd.DataFrame) -> typing.List:
+        """Builds a List containing the the delta times numpy array, and the complete transitions matrix
+
+        :param concatenated_sample: the dataframe/array from which the time, and transitions matrix have to be extracted
+            and converted
+        :type concatenated_sample: pandas.Dataframe
+        :return: the resulting list of numpy arrays
+        :rtype: List
+        """
+        
+        concatenated_array = concatenated_sample.to_numpy()
+        columns_list = [concatenated_array[:, 0], concatenated_array[:, 1:].astype(int)]
+
+        return columns_list
+
+    def clear_concatenated_frame(self) -> None:
+        """Removes all values in the dataframe concatenated_samples.
+         """
+        if isinstance(self._concatenated_samples, pd.DataFrame):
+            self._concatenated_samples = self._concatenated_samples.iloc[0:0]
+
+    @abstractmethod
+    def dataset_id(self) -> object:
+        """If the original dataset contains multiple dataset, this method returns a unique id to identify the current
+        dataset
+        """
+        pass
+
+    @property
+    def concatenated_samples(self) -> pd.DataFrame:
+        return self._concatenated_samples
+
+    @property
+    def variables(self) -> pd.DataFrame:
+        return self._df_variables
+
+    @property
+    def structure(self) -> pd.DataFrame:
+        return self._df_structure
+
+    @property
+    def sorter(self) -> typing.List:
+        return self._sorter
+
+    @property
+    def file_path(self) -> str:
+        return self._file_path
diff --git a/build/lib/PyCTBN/PyCTBN/utility/cache.py b/build/lib/PyCTBN/PyCTBN/utility/cache.py
new file mode 100644
index 0000000..5191af3
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/utility/cache.py
@@ -0,0 +1,54 @@
+
+import typing
+
+from ..structure_graph.set_of_cims import SetOfCims 
+
+
+class Cache:
+    """This class acts as a cache of ``SetOfCims`` objects for a node.
+
+    :__list_of_sets_of_parents: a list of ``Sets`` objects of the parents to which the cim in cache at SAME
+        index is related
+    :__actual_cache: a list of setOfCims objects
+    """
+
+    def __init__(self):
+        """Constructor Method
+        """
+        self._list_of_sets_of_parents = []
+        self._actual_cache = []
+
+    def find(self, parents_comb: typing.Set): #typing.Union[typing.Set, str]
+        """
+        Tries to find in cache given the symbolic parents combination ``parents_comb`` the ``SetOfCims``
+        related to that ``parents_comb``.
+
+        :param parents_comb: the parents related to that ``SetOfCims``
+        :type parents_comb: Set
+        :return: A ``SetOfCims`` object if the ``parents_comb`` index is found in ``__list_of_sets_of_parents``.
+            None otherwise.
+        :rtype: SetOfCims
+        """
+        try:
+            result = self._actual_cache[self._list_of_sets_of_parents.index(parents_comb)]
+            return result
+        except ValueError:
+            return None
+
+    def put(self, parents_comb: typing.Set, socim: SetOfCims):
+        """Place in cache the ``SetOfCims`` object, and the related symbolic index ``parents_comb`` in
+        ``__list_of_sets_of_parents``.
+
+        :param parents_comb: the symbolic set index
+        :type parents_comb: Set
+        :param socim: the related SetOfCims object
+        :type socim: SetOfCims
+        """
+        self._list_of_sets_of_parents.append(parents_comb)
+        self._actual_cache.append(socim)
+
+    def clear(self):
+        """Clear the contents both of ``__actual_cache`` and ``__list_of_sets_of_parents``.
+        """
+        del self._list_of_sets_of_parents[:]
+        del self._actual_cache[:]
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/utility/json_importer.py b/build/lib/PyCTBN/PyCTBN/utility/json_importer.py
new file mode 100644
index 0000000..2cadff4
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/utility/json_importer.py
@@ -0,0 +1,181 @@
+import json
+import typing
+
+import pandas as pd
+
+
+from .abstract_importer import AbstractImporter
+
+
+class JsonImporter(AbstractImporter):
+    """Implements the abstracts methods of AbstractImporter and adds all the necessary methods to process and prepare
+    the data in json extension.
+
+    :param file_path: the path of the file that contains tha data to be imported
+    :type file_path: string
+    :param samples_label: the reference key for the samples in the trajectories
+    :type samples_label: string
+    :param structure_label: the reference key for the structure of the network data
+    :type structure_label: string
+    :param variables_label: the reference key for the cardinalites of the nodes data
+    :type variables_label: string
+    :param time_key: the key used to identify the timestamps in each trajectory
+    :type time_key: string
+    :param variables_key: the key used to identify the names of the variables in the net
+    :type variables_key: string
+    :_array_indx: the index of the outer JsonArray to extract the data from
+    :type _array_indx: int
+    :_df_samples_list: a Dataframe list in which every dataframe contains a trajectory
+    :_raw_data: The raw contents of the json file to import
+    :type _raw_data: List
+    """
+
+    def __init__(self, file_path: str, samples_label: str, structure_label: str, variables_label: str, time_key: str,
+                 variables_key: str):
+        """Constructor method
+
+        .. note::
+            This constructor calls also the method ``read_json_file()``, so after the construction of the object
+            the class member ``_raw_data`` will contain the raw imported json data.
+
+        """
+        self._samples_label = samples_label
+        self._structure_label = structure_label
+        self._variables_label = variables_label
+        self._time_key = time_key
+        self._variables_key = variables_key
+        self._df_samples_list = None
+        self._array_indx = None
+        super(JsonImporter, self).__init__(file_path)
+        self._raw_data = self.read_json_file()
+
+    def import_data(self, indx: int = 0) -> None:
+        """Implements the abstract method of :class:`AbstractImporter`.
+
+        :param indx: the index of the outer JsonArray to extract the data from, default to 0
+        :type indx: int
+        """
+        self._array_indx = indx
+        self._df_samples_list = self.import_trajectories(self._raw_data)
+        self._sorter = self.build_sorter(self._df_samples_list[0])
+        self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
+        self.clear_data_frame_list()
+        self._df_structure = self.import_structure(self._raw_data)
+        self._df_variables = self.import_variables(self._raw_data)
+
+    def import_trajectories(self, raw_data: typing.List) -> typing.List:
+        """Imports the trajectories from the list of dicts ``raw_data``.
+
+        :param raw_data: List of Dicts
+        :type raw_data: List
+        :return: List of dataframes containing all the trajectories
+        :rtype: List
+        """
+        return self.normalize_trajectories(raw_data, self._array_indx, self._samples_label)
+
+    def import_structure(self, raw_data: typing.List) -> pd.DataFrame:
+        """Imports in a dataframe the data in the list raw_data at the key ``_structure_label``
+
+        :param raw_data: List of Dicts
+        :type raw_data: List
+        :return: Dataframe containg the starting node a ending node of every arc of the network
+        :rtype: pandas.Dataframe
+        """
+        return self.one_level_normalizing(raw_data, self._array_indx, self._structure_label)
+
+    def import_variables(self, raw_data: typing.List) -> pd.DataFrame:
+        """Imports the data in ``raw_data`` at the key ``_variables_label``.
+
+        :param raw_data: List of Dicts
+        :type raw_data: List
+        :return: Datframe containg the variables simbolic labels and their cardinalities
+        :rtype: pandas.Dataframe
+        """
+        return self.one_level_normalizing(raw_data, self._array_indx, self._variables_label)
+
+    def read_json_file(self) -> typing.List:
+        """Reads the JSON file in the path self.filePath.
+
+        :return: The contents of the json file
+        :rtype: List
+        """
+        with open(self._file_path) as f:
+            data = json.load(f)
+
+            if (isinstance(data,list)):
+                return data
+            else:
+                return [data]
+         
+
+    def one_level_normalizing(self, raw_data: typing.List, indx: int, key: str) -> pd.DataFrame:
+        """Extracts the one-level nested data in the list ``raw_data`` at the index ``indx`` at the key ``key``.
+
+        :param raw_data: List of Dicts
+        :type raw_data: List
+        :param indx: The index of the array from which the data have to be extracted
+        :type indx: int
+        :param key: the key for the Dicts from which exctract data
+        :type key: string
+        :return: A normalized dataframe
+        :rtype: pandas.Datframe
+        """
+        return pd.DataFrame(raw_data[indx][key])
+
+    def normalize_trajectories(self, raw_data: typing.List, indx: int, trajectories_key: str) -> typing.List:
+        """
+        Extracts the trajectories in ``raw_data`` at the index ``index`` at the key ``trajectories key``.
+
+        :param raw_data: List of Dicts
+        :type raw_data: List
+        :param indx: The index of the array from which the data have to be extracted
+        :type indx: int
+        :param trajectories_key: the key of the trajectories objects
+        :type trajectories_key: string
+        :return: A list of daframes containg the trajectories
+        :rtype: List
+        """
+        dataframe = pd.DataFrame
+        smps = raw_data[indx][trajectories_key]
+        df_samples_list = [dataframe(sample) for sample in smps]
+        return df_samples_list
+
+    def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
+        """Implements the abstract method build_sorter of the :class:`AbstractImporter` for this dataset.
+        """
+        columns_header = list(sample_frame.columns.values)
+        columns_header.remove(self._time_key)
+        return columns_header
+
+    def clear_data_frame_list(self) -> None:
+        """Removes all values present in the dataframes in the list ``_df_samples_list``.
+        """
+        for indx in range(len(self._df_samples_list)):
+            self._df_samples_list[indx] = self._df_samples_list[indx].iloc[0:0]
+
+    def dataset_id(self) -> object:
+        return self._array_indx
+
+    def import_sampled_cims(self, raw_data: typing.List, indx: int, cims_key: str) -> typing.Dict:
+        """Imports the synthetic CIMS in the dataset in a dictionary, using variables labels
+        as keys for the set of CIMS of a particular node.
+
+        :param raw_data: List of Dicts
+        :type raw_data: List
+        :param indx: The index of the array from which the data have to be extracted
+        :type indx: int
+        :param cims_key: the key where the json object cims are placed
+        :type cims_key: string
+        :return: a dictionary containing the sampled CIMS for all the variables in the net
+        :rtype: Dictionary
+        """
+        cims_for_all_vars = {}
+        for var in raw_data[indx][cims_key]:
+            sampled_cims_list = []
+            cims_for_all_vars[var] = sampled_cims_list
+            for p_comb in raw_data[indx][cims_key][var]:
+                cims_for_all_vars[var].append(pd.DataFrame(raw_data[indx][cims_key][var][p_comb]).to_numpy())
+        return cims_for_all_vars
+
+
+
diff --git a/build/lib/PyCTBN/PyCTBN/utility/sample_importer.py b/build/lib/PyCTBN/PyCTBN/utility/sample_importer.py
new file mode 100644
index 0000000..b0b6e8f
--- /dev/null
+++ b/build/lib/PyCTBN/PyCTBN/utility/sample_importer.py
@@ -0,0 +1,62 @@
+import json
+import typing
+
+import pandas as pd
+import numpy as np
+
+from .abstract_importer import AbstractImporter
+
+
+
+class SampleImporter(AbstractImporter):
+    """Implements the abstracts methods of AbstractImporter and adds all the necessary methods to process and prepare
+    the data loaded directly by using DataFrame
+
+    :param trajectory_list: the data that describes the trajectories
+    :type trajectory_list: typing.Union[pd.DataFrame, np.ndarray, typing.List]
+    :param variables: the data that describes the variables with name and cardinality
+    :type variables: typing.Union[pd.DataFrame, np.ndarray, typing.List]
+    :param prior_net_structure: the data of the real structure, if it exists
+    :type prior_net_structure: typing.Union[pd.DataFrame, np.ndarray, typing.List]
+
+    :_df_samples_list: a Dataframe list in which every dataframe contains a trajectory
+    :_raw_data: The raw contents of the json file to import
+    :type _raw_data: List
+    """
+
+    def __init__(self, 
+                trajectory_list: typing.Union[pd.DataFrame, np.ndarray, typing.List] = None,
+                variables: typing.Union[pd.DataFrame, np.ndarray, typing.List] = None,
+                prior_net_structure: typing.Union[pd.DataFrame, np.ndarray,typing.List] = None):
+
+        'If the data are not DataFrame, it will be converted'
+        if isinstance(variables,list) or isinstance(variables,np.ndarray):
+            variables = pd.DataFrame(variables)
+        if isinstance(prior_net_structure,list) or isinstance(prior_net_structure,np.ndarray):
+            prior_net_structure=pd.DataFrame(prior_net_structure)
+
+        super(SampleImporter, self).__init__(trajectory_list =trajectory_list,
+                                        variables= variables,
+                                        prior_net_structure=prior_net_structure)
+
+    def import_data(self, header_column = None):
+
+        if header_column is not None:
+            self._sorter = header_column
+        else:    
+            self._sorter = self.build_sorter(self._df_samples_list[0])
+
+        samples_list= self._df_samples_list
+
+        self.compute_row_delta_in_all_samples_frames(samples_list)
+
+    def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
+        """Implements the abstract method build_sorter of the :class:`AbstractImporter` in order to get the ordered variables list.
+        """
+        columns_header = list(sample_frame.columns.values)
+        del columns_header[0]
+        return columns_header
+
+
+    def dataset_id(self) -> str:
+        return str("")
\ No newline at end of file
diff --git a/build/lib/PyCTBN/__init__.py b/build/lib/PyCTBN/__init__.py
new file mode 100644
index 0000000..7adf0d7
--- /dev/null
+++ b/build/lib/PyCTBN/__init__.py
@@ -0,0 +1,2 @@
+import PyCTBN.PyCTBN
+from PyCTBN.PyCTBN import *
diff --git a/build/lib/PyCTBN/basic_main.py b/build/lib/PyCTBN/basic_main.py
new file mode 100644
index 0000000..b1288db
--- /dev/null
+++ b/build/lib/PyCTBN/basic_main.py
@@ -0,0 +1,39 @@
+import glob
+import os
+
+import sys
+sys.path.append("./PyCTBN/")
+
+import structure_graph.network_graph as ng
+import structure_graph.sample_path as sp
+import structure_graph.set_of_cims as sofc
+import estimators.parameters_estimator as pe
+import utility.json_importer as ji
+
+
+def main():
+    read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
+    #import data
+    importer = ji.JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+    #Create a SamplePath Obj
+    s1 = sp.SamplePath(importer)
+    #Build The trajectries and the structural infos
+    s1.build_trajectories()
+    s1.build_structure()
+    #From The Structure Object build the Graph
+    g = ng.NetworkGraph(s1.structure)
+    #Select a node you want to estimate the parameters
+    node = g.nodes[1]
+    #Init the graph specifically for THIS node
+    g.fast_init(node)
+    #Use SamplePath and Grpah to create a ParametersEstimator Object
+    p1 = pe.ParametersEstimator(s1, g)
+    #Init the peEst specifically for THIS node
+    p1.fast_init(node)
+    #Compute the parameters
+    sofc1 = p1.compute_parameters_for_node(node)
+    #The est CIMS are inside the resultant SetOfCIms Obj
+    print(sofc1.actual_cims)
+
+if __name__ == "__main__":
+    main()
diff --git a/build/lib/PyCTBN/setup.py b/build/lib/PyCTBN/setup.py
new file mode 100644
index 0000000..56dd72f
--- /dev/null
+++ b/build/lib/PyCTBN/setup.py
@@ -0,0 +1,20 @@
+from setuptools import setup, find_packages
+
+
+setup(name='PyCTBN',
+      version='1.0',
+      url='https://github.com/philipMartini/PyCTBN',
+      license='MIT',
+      author=['Alessandro Bregoli', 'Filippo Martini','Luca Moretti'],
+      author_email=['a.bregoli1@campus.unimib.it', 'f.martini@campus.unimib.it','lucamoretti96@gmail.com'],
+      description='A Continuous Time Bayesian Networks Library',
+      packages=find_packages('.', exclude=['tests']),
+      #packages=['PyCTBN.PyCTBN'],
+      install_requires=[
+          'numpy', 'pandas', 'networkx', 'scipy', 'matplotlib', 'tqdm'],
+      dependency_links=['https://github.com/numpy/numpy', 'https://github.com/pandas-dev/pandas',
+                        'https://github.com/networkx/networkx', 'https://github.com/scipy/scipy',
+                        'https://github.com/tqdm/tqdm'],
+      #long_description=open('../README.md').read(),
+      zip_safe=False,
+      python_requires='>=3.6')
diff --git a/dist/PyCTBN-1.0-py3-none-any.whl b/dist/PyCTBN-1.0-py3-none-any.whl
new file mode 100644
index 0000000000000000000000000000000000000000..d2b496a1025fb4985feb27982534d70cb100bf67
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From df1d236cd12f796244141de0f88b42c3cc04ee7c Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 20:40:18 +0000
Subject: [PATCH 014/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 32897a460317f3397147ac60cff64a8b7c37f4c7..7b4e98c2502b88dfa372c31909776569ae31c8db 100644
GIT binary patch
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From 8fae012b663c0416f90a37cea0a56591b3018515 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 21:51:18 +0100
Subject: [PATCH 015/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 21d19f5..3f70711 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -62,7 +62,6 @@ jobs:
         git commit -m "Create New Realease at dist/" -a || true
         # The above command will fail if no changes were present, so we ignore
         # that.
-        git pull
     - name: Push changes
       uses: ad-m/github-push-action@master
       with:

From 53f79875827ab77b00a3cbbfdcc95bc8c143fa1e Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 20:52:23 +0000
Subject: [PATCH 016/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 7b4e98c2502b88dfa372c31909776569ae31c8db..6fcdb1402740ca4c6539d7977f4cb5ce965ee20b 100644
GIT binary patch
delta 6293
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From 3a9856dab1171305fb98b72699bb27fd15e9895c Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 22:09:32 +0100
Subject: [PATCH 017/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 3f70711..557f683 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -62,6 +62,7 @@ jobs:
         git commit -m "Create New Realease at dist/" -a || true
         # The above command will fail if no changes were present, so we ignore
         # that.
+        git pull origin
     - name: Push changes
       uses: ad-m/github-push-action@master
       with:

From bbe312d08f3a9c32ad04c667f64589b1ff5d7432 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 21:10:42 +0000
Subject: [PATCH 018/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 6fcdb1402740ca4c6539d7977f4cb5ce965ee20b..6addccd1a9b870344ff5e5275a2686907829645e 100644
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From be2bbae710d6b4c92e9fc37908659e5798483767 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 22:19:48 +0100
Subject: [PATCH 019/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 25 +--------------------
 1 file changed, 1 insertion(+), 24 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 557f683..3842459 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -42,29 +42,6 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
-    - name: Install pypa/build
-      run: >-
-        python -m
-        pip install
-        build
-        --user
-    - name: Build a binary wheel and a source tarball
-      run: >-
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/
-        .
-        git config --local user.email "f.martini@campus.unimib.it"
-        git config --local user.name "philipMartini"
-        git add .
-        git commit -m "Create New Realease at dist/" -a || true
-        # The above command will fail if no changes were present, so we ignore
-        # that.
-        git pull origin
-    - name: Push changes
-      uses: ad-m/github-push-action@master
-      with:
+   
         branch: master
         github_token: ${{ secrets.PYCTBN_TOK }}

From 6052877d1fd026cebffb881b2eb628d741357807 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 21:20:51 +0000
Subject: [PATCH 020/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 6addccd1a9b870344ff5e5275a2686907829645e..32fbbeb8cd6b62eb3a3689f27e9fe368fb5a31a4 100644
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From 97dd047b58197841102a6611f146b03907972fa7 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 22:23:03 +0100
Subject: [PATCH 021/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 3842459..c8d0ea6 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -42,6 +42,3 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
-   
-        branch: master
-        github_token: ${{ secrets.PYCTBN_TOK }}

From 4bfa81ed36c4fd09e2240c22010f39850fbceaf4 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 21:23:50 +0000
Subject: [PATCH 022/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 32fbbeb8cd6b62eb3a3689f27e9fe368fb5a31a4..3a63d5f15059bfbef1a5203d065ab2113f56c744 100644
GIT binary patch
delta 7219
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From 3629f4e488afdd114f23e7dc6c5b7331aeb1f677 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 23:25:01 +0100
Subject: [PATCH 023/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 26 +++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index c8d0ea6..aa1fa2d 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -42,3 +42,29 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
+    - name: Install pypa/build
+      run: >-
+        python -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: >-
+        git clone https://github.com/philipMartini/PyCTBN --branch master  --single-branch
+        python -m
+        build
+        --sdist
+        --wheel
+        --outdir dist/.
+        git config --local user.email "f.martini@campus.unimib.it"
+        git config --local user.name "philipMartini"
+        git add .
+        git commit -m "Create New Realease at dist/" -a || true
+        # The above command will fail if no changes were present, so we ignore
+        # that.
+        #git pull origin
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        branch: master
+        github_token: ${{ secrets.PYCTBN_TOK }}

From 21a600a91b6e976168c62b43160de2d1c49c3279 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 22:25:56 +0000
Subject: [PATCH 024/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 3a63d5f15059bfbef1a5203d065ab2113f56c744..d6f60c1fe465c5e190672dd4d00fa92d308dd0e6 100644
GIT binary patch
delta 7011
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From 76d963cb3f87846ac8ce8203a88491f68bc93815 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sat, 13 Mar 2021 23:55:17 +0100
Subject: [PATCH 025/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index aa1fa2d..1640330 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -43,13 +43,13 @@ jobs:
       run: |
         pytest PyCTBN/tests/
     - name: Install pypa/build
-      run: >-
+      run: |
         python -m
         pip install
         build
         --user
     - name: Build a binary wheel and a source tarball
-      run: >-
+      run: |
         git clone https://github.com/philipMartini/PyCTBN --branch master  --single-branch
         python -m
         build

From ed407573972bf1a6a771c7202ea0eda39c75c9d5 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 22:56:18 +0000
Subject: [PATCH 026/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index d6f60c1fe465c5e190672dd4d00fa92d308dd0e6..9e8e8953336a2c485568af9dae7693dbcd6dd7d1 100644
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From 28714b2ee0f328db26e565ad1e29e446a156c9b8 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 00:10:02 +0100
Subject: [PATCH 027/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 11 ++---------
 1 file changed, 2 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 1640330..ea7de22 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -44,18 +44,11 @@ jobs:
         pytest PyCTBN/tests/
     - name: Install pypa/build
       run: |
-        python -m
-        pip install
-        build
-        --user
+        python -m pip install build
     - name: Build a binary wheel and a source tarball
       run: |
         git clone https://github.com/philipMartini/PyCTBN --branch master  --single-branch
-        python -m
-        build
-        --sdist
-        --wheel
-        --outdir dist/.
+        python -m build --sdist --wheel --outdir dist/.
         git config --local user.email "f.martini@campus.unimib.it"
         git config --local user.name "philipMartini"
         git add .

From ec7c7fe89b6ff60ec19a779db7f5d85162b5c224 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sat, 13 Mar 2021 23:11:00 +0000
Subject: [PATCH 028/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 9e8e8953336a2c485568af9dae7693dbcd6dd7d1..7370d3b5d36d37df1624d68f508923a4c5136b94 100644
GIT binary patch
delta 6768
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From a9edaddb4ba991c648e34d044b0110f34858646c Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 01:17:06 +0100
Subject: [PATCH 029/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index ea7de22..c8d0ea6 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -42,22 +42,3 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
-    - name: Install pypa/build
-      run: |
-        python -m pip install build
-    - name: Build a binary wheel and a source tarball
-      run: |
-        git clone https://github.com/philipMartini/PyCTBN --branch master  --single-branch
-        python -m build --sdist --wheel --outdir dist/.
-        git config --local user.email "f.martini@campus.unimib.it"
-        git config --local user.name "philipMartini"
-        git add .
-        git commit -m "Create New Realease at dist/" -a || true
-        # The above command will fail if no changes were present, so we ignore
-        # that.
-        #git pull origin
-    - name: Push changes
-      uses: ad-m/github-push-action@master
-      with:
-        branch: master
-        github_token: ${{ secrets.PYCTBN_TOK }}

From 58d6961f8b680d4e7170aa52a1af8d65e38a8d14 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 00:18:05 +0000
Subject: [PATCH 030/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 7370d3b5d36d37df1624d68f508923a4c5136b94..a20ba121531b882612a7d6deb06d2fed672ab392 100644
GIT binary patch
delta 7016
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From aaec2574f7a4bb3d823f6eef0b0a19e655e0540b Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 11:42:07 +0100
Subject: [PATCH 031/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index c8d0ea6..de4697b 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -42,3 +42,20 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
+    - name: Install pypa/build
+      run: |
+        python -m pip install build
+    - name: Build a binary wheel and a source tarball
+      run: |
+        python -m build --sdist --wheel --outdir dist/.
+        git config --local user.email "f.martini@campus.unimib.it"
+        git config --local user.name "philipMartini"
+        git add .
+        git commit -m "Create New Realease at dist/" -a || true
+        # The above command will fail if no changes were present, so we ignore
+        # that.
+    - name: Push changes
+      uses: ad-m/github-push-action@master
+      with:
+        branch: master
+        github_token: ${{ secrets.PYCTBN_TOK }}

From 257c2538b05f845917e5444cc30122a326c0b4f3 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 10:50:53 +0000
Subject: [PATCH 032/139] Create New Realease at dist/

---
 dist/PyCTBN-1.0-py3-none-any.whl | Bin 35618 -> 35618 bytes
 dist/PyCTBN-1.0.tar.gz           | Bin 24165 -> 24271 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/dist/PyCTBN-1.0-py3-none-any.whl b/dist/PyCTBN-1.0-py3-none-any.whl
index d2b496a1025fb4985feb27982534d70cb100bf67..e229e0310fd9b42e3e655a303894742e886d4146 100644
GIT binary patch
delta 589
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diff --git a/dist/PyCTBN-1.0.tar.gz b/dist/PyCTBN-1.0.tar.gz
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From fc0f8635fc9f630439bb2c3ccf3493c554dce985 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 12:51:59 +0100
Subject: [PATCH 033/139] Update main.yml

---
 .github/workflows/main.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 21c11eb..cfbae9d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -4,13 +4,10 @@
 name: Sphinx Docs
 
 on:
-  push:
-    paths-ignore: 
-      -'docs/**'
-      -'docs-out/**'
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+  workflow_run:
+    workflows: ["Python package"]
+    types:
+      - completed
 
 jobs:
   build:

From 34c6e0283e4fa501a732e666605352c8d7619820 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 12:01:11 +0000
Subject: [PATCH 034/139] Create New Realease at dist/

---
 dist/PyCTBN-1.0-py3-none-any.whl | Bin 35618 -> 35618 bytes
 dist/PyCTBN-1.0.tar.gz           | Bin 24271 -> 24232 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)

diff --git a/dist/PyCTBN-1.0-py3-none-any.whl b/dist/PyCTBN-1.0-py3-none-any.whl
index e229e0310fd9b42e3e655a303894742e886d4146..974a54d6a50e564d5ea1efd9cb460bb8ab7243d7 100644
GIT binary patch
delta 485
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From d2c7577e946112f777f9401b004c67a0189fcc20 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 12:02:14 +0000
Subject: [PATCH 035/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
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From 4a16a7c5141e94db32d9221297221762bfb58f10 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 17:36:48 +0100
Subject: [PATCH 036/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index de4697b..43ea496 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -11,6 +11,8 @@ on:
       -'dist/**'
       -'build/**'
     branches: [ master ]
+    tags-ignore:
+      - 'v*'
   pull_request:
     branches: [ master ]
 

From 6fc38cce24689920e6c745c2ccd29b2bec0d392f Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 17:44:47 +0100
Subject: [PATCH 037/139] Create Build_Release.yml

---
 .github/workflows/Build_Release.yml | 61 +++++++++++++++++++++++++++++
 1 file changed, 61 insertions(+)
 create mode 100644 .github/workflows/Build_Release.yml

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
new file mode 100644
index 0000000..1947734
--- /dev/null
+++ b/.github/workflows/Build_Release.yml
@@ -0,0 +1,61 @@
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+	branches: [ master ]
+    tags:
+    - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+
+name: Upload Release Asset
+
+jobs:
+  build:
+    name: Upload Release Asset
+    runs-on: ubuntu-latest
+    steps:
+	  - uses: actions/checkout@v2
+	  - name: Set up Python ${{ matrix.python-version }}
+	    uses: actions/setup-python@v2
+	    with:
+	  	  python-version: ${{ matrix.python-version }}
+	  - name: Install dependencies
+		run: |
+		  python -m pip install --upgrade pip
+		  python -m pip install flake8 pytest
+		  if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+	  - name: Lint with flake8
+		run: |
+		  # stop the build if there are Python syntax errors or undefined names
+		  flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+		  # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+		  flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+	  - name: Test with pytest
+		run: |
+		  pytest PyCTBN/tests/
+	  - name: Install pypa/build
+      run: |
+        python -m pip install build
+      - name: Checkout code
+        uses: actions/checkout@v2
+      - name: Build project # This would actually build your project, using zip for an example artifact
+        run: |
+           python -m build --sdist --wheel --outdir dist/.
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          draft: false
+          prerelease: false
+      - name: Upload Release Asset
+        id: upload-release-asset 
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
+          asset_path: ./dist/Py
+          asset_name: PyCTBN-1.0.tar.gz
+          asset_content_type: application/tar+gzip

From 85e3ff588315c971b0622c057d3f370b50149999 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 16:46:52 +0000
Subject: [PATCH 038/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 3458ea09dd1b7dcff0b4a51c889143e4bf6f8bb6..7880f4000ec7aaccc4afde4dddcd46ac5caa5ff8 100644
GIT binary patch
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From f90f2afb5335d9c18ea6bda5117ea70bf0b9cdd4 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 16:54:58 +0000
Subject: [PATCH 039/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 7880f4000ec7aaccc4afde4dddcd46ac5caa5ff8..44a56ecdc50a35336bd2948a30f2aa846d482a56 100644
GIT binary patch
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zMJ(TF5^)S)nnViZ&@dN~!?4Un@YBQ~2GAuJQE4atWcUjm@DyXHZ3S<Yi7VLejRVCX
z`rK8Rc|r0}F@vFIsF=ghF;rAA%pWF@;pbsu3&UDBv5CRt&f(|KYwp4<EkLubcQ%!I
z2xp#O?I9L3bb5#t4CdjYf#LRWv6Z2I1aE*G^7RzYGVJq|l0jaauN)#TE<_G_d5fh6
z>Fz}rsz1olH+hSPnPKn|MGR#=BAwwqAMvmf>vW-%F7Er0zGABKr;CjCobQND`o-lZ
z?CDWI;Y^!0foo6y&Y`=$qLS5A`iXT6{rp9l(srwRi$A}Xul6Qi5kRf}!ka~|`iuW$
zSP&ozmE-_dbr^aieaR<K__0W8pjgFlFi=cm7&ua7Gt3{!doPEMj}#@U7;bcN96Q<c
zEF`Hq{541{V+oI7k*^B3I#?7a*#N3dVA&<lK{y?Fo*l~y5q8RpAXhSWa+1u?K`iYG
zkrmh%BBrT@VKii<h}OSc`HeqH7}RVeRgV+i6uAS2>8ucCZvQAztoU&@*M?D4sPLp!
zqlFW@RySIhmDMCy{Ze(O*Bc>?>b(SiRM3J@>Ho=4u|x??>2}TjWo|c3f8|%w3t?iA
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zsuZ*-@Q)H%JXszk?q}E+B_3pOj280^@_)8v-5zX+mMT7t=G~n2D+~}TU2WUWj#^?w
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zi9JU%<N3tB^bdXn`Xuydf5BCMt@4veUtO6X9C*$81m3n9{gJ?XQlpBoqEdOX%T@nY
z==LOhA2`wZy=*BbQ5clK>%G$;{bi}17qv#G6U9^|_@*lz@)5&n$ou?ct-TG7R5eb_
zXJco^iG@n!T~}KlOH%>t*SA<E{h1_;EID|*h+&vGUc~cv;FIHpSF-$<b-3}q`^+=U
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zp89)wB=@yG+~<37>5$TNUWWp@tzg6iNhK<n&5$e~(sN9`V`&;@^Hy>#eYhX>;?kSC
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z2@J{dUfR}2Pk(ot71_6+>%$$<i%VN{O*ynj!Epsw6bww2ykLf8c^2k#z3)}uoeSSx
XeaS8B!!7H@r8T-HZSTve;(75uE$NB}


From 1025f3ce86997fc2d429e76c7738f09411246b0d Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 17:57:27 +0100
Subject: [PATCH 040/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 43 ++++++++++-------------------
 1 file changed, 14 insertions(+), 29 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 1947734..a9b3ab3 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -1,7 +1,6 @@
 on:
   push:
     # Sequence of patterns matched against refs/tags
-	branches: [ master ]
     tags:
     - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
 
@@ -12,33 +11,19 @@ jobs:
     name: Upload Release Asset
     runs-on: ubuntu-latest
     steps:
-	  - uses: actions/checkout@v2
-	  - name: Set up Python ${{ matrix.python-version }}
-	    uses: actions/setup-python@v2
-	    with:
-	  	  python-version: ${{ matrix.python-version }}
-	  - name: Install dependencies
-		run: |
-		  python -m pip install --upgrade pip
-		  python -m pip install flake8 pytest
-		  if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-	  - name: Lint with flake8
-		run: |
-		  # stop the build if there are Python syntax errors or undefined names
-		  flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-		  # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-		  flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-	  - name: Test with pytest
-		run: |
-		  pytest PyCTBN/tests/
-	  - name: Install pypa/build
-      run: |
-        python -m pip install build
       - name: Checkout code
         uses: actions/checkout@v2
+      - name: Install dependencies
+        run: |
+            python -m pip install --upgrade pip
+            python -m pip install flake8 pytest
+            if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Install pypa/build
+        run: |
+            python -m pip install build
       - name: Build project # This would actually build your project, using zip for an example artifact
         run: |
-           python -m build --sdist --wheel --outdir dist/.
+          python -m build --sdist --wheel --outdir dist/.
       - name: Create Release
         id: create_release
         uses: actions/create-release@v1
@@ -53,9 +38,9 @@ jobs:
         id: upload-release-asset 
         uses: actions/upload-release-asset@v1
         env:
-          GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
+            GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
-          asset_path: ./dist/Py
-          asset_name: PyCTBN-1.0.tar.gz
-          asset_content_type: application/tar+gzip
+            upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
+            asset_path: ./dist/Py
+            asset_name: PyCTBN-1.0.tar.gz
+            asset_content_type: application/tar+gzip

From 53cc2cac960c692ab628d2bd3cdbf263b9322bc0 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 17:59:04 +0100
Subject: [PATCH 041/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index a9b3ab3..8684ae8 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -4,7 +4,7 @@ on:
     tags:
     - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
 
-name: Upload Release Asset
+name: Upload Release Asset 
 
 jobs:
   build:

From 9369f75db18dd2203a88e57ff22da770c6dfaf13 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:00:23 +0100
Subject: [PATCH 042/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 8684ae8..6d2fca5 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -1,9 +1,9 @@
 on:
   push:
     # Sequence of patterns matched against refs/tags
-    tags:
-    - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
-
+    #tags:
+    #- 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+    
 name: Upload Release Asset 
 
 jobs:

From 7bd6503a52d2606422d3450091660d384e82b20f Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:03:26 +0100
Subject: [PATCH 043/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 6d2fca5..4788655 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -41,6 +41,6 @@ jobs:
             GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
             upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
-            asset_path: ./dist/Py
+            asset_path: ./dist/PyCTBN-1.0.tar.gz
             asset_name: PyCTBN-1.0.tar.gz
             asset_content_type: application/tar+gzip

From 9e0f551fba73949a1a596e2a32b417d0aab99bc7 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:07:30 +0100
Subject: [PATCH 044/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 4788655..8a6cff0 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -30,8 +30,8 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
-          tag_name: ${{ github.ref }}
-          release_name: Release ${{ github.ref }}
+          tag_name: v.${{ github.ref }}
+          release_name: Release v ${{ github.ref }}
           draft: false
           prerelease: false
       - name: Upload Release Asset

From 2c853e7588585f802ae86bafd7c5e43a6c6170d1 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:16:53 +0100
Subject: [PATCH 045/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 8a6cff0..12cb5ca 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -1,4 +1,5 @@
-on:
+      
+      on:
   push:
     # Sequence of patterns matched against refs/tags
     #tags:
@@ -31,16 +32,13 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
           tag_name: v.${{ github.ref }}
-          release_name: Release v ${{ github.ref }}
+          release_name: Release v- ${{ github.ref }}
           draft: false
           prerelease: false
       - name: Upload Release Asset
         id: upload-release-asset 
-        uses: actions/upload-release-asset@v1
-        env:
-            GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
+        uses: AButler/upload-release-assets@v2.0
         with:
-            upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the CREATE RELEASE step above, referencing it's ID to get its outputs object, which include a `upload_url`. See this blog post for more info: https://jasonet.co/posts/new-features-of-github-actions/#passing-data-to-future-steps 
-            asset_path: ./dist/PyCTBN-1.0.tar.gz
-            asset_name: PyCTBN-1.0.tar.gz
-            asset_content_type: application/tar+gzip
+          files: 'dist/*;'
+          repo-token: ${{ secrets.PYCTBN_TOK }}
+

From 9375051bee460d83646689046c6468875493d034 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:21:19 +0100
Subject: [PATCH 046/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 12cb5ca..79be794 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -32,7 +32,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
           tag_name: v.${{ github.ref }}
-          release_name: Release v- ${{ github.ref }}
+          release_name: Release v. ${{ github.ref }}
           draft: false
           prerelease: false
       - name: Upload Release Asset

From 104b5170b7fa181b1b4dea45c3e23a972ea1bc9a Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:22:37 +0100
Subject: [PATCH 047/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 79be794..434d1fa 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -1,5 +1,5 @@
       
-      on:
+on:
   push:
     # Sequence of patterns matched against refs/tags
     #tags:

From cbab17e422a51c875cdf6cbf320ef79fddfc32f7 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:28:57 +0100
Subject: [PATCH 048/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 434d1fa..7bac19f 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -37,8 +37,9 @@ jobs:
           prerelease: false
       - name: Upload Release Asset
         id: upload-release-asset 
-        uses: AButler/upload-release-assets@v2.0
+        uses: dwenegar/upload-release-assets@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
-          files: 'dist/*;'
-          repo-token: ${{ secrets.PYCTBN_TOK }}
-
+          release_id: ${{ steps.create_release.outputs.id }}
+          assets_path: ./dist

From dd980902ffb1db0595f2f8d65db788eec4a65903 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:30:56 +0100
Subject: [PATCH 049/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 7bac19f..a7c17c0 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -31,8 +31,8 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
-          tag_name: v.${{ github.ref }}
-          release_name: Release v. ${{ github.ref }}
+          tag_name: ver.${{ github.ref }}
+          release_name: Release ver. ${{ github.ref }}
           draft: false
           prerelease: false
       - name: Upload Release Asset

From df2599f6350248cf7c28b4b4f1d50b6350b27210 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:35:51 +0100
Subject: [PATCH 050/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 23 +++++++++++++++++++++--
 1 file changed, 21 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index a7c17c0..8b99191 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -12,13 +12,32 @@ jobs:
     name: Upload Release Asset
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v2
+<     - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+            python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
             python -m pip install --upgrade pip
             python -m pip install flake8 pytest
             if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+            # stop the build if there are Python syntax errors or undefined names
+            flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+            # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+            flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with pytest
+        run: |
+            pytest PyCTBN/tests/>
+      - name: Checkout code
+            uses: actions/checkout@v2
+      - name: Install dependencies
+            run: |
+                python -m pip install --upgrade pip
+                python -m pip install flake8 pytest
+                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       - name: Install pypa/build
         run: |
             python -m pip install build

From 5e9144efe18fecd6f48a4f209890984569790003 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:36:41 +0100
Subject: [PATCH 051/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 8b99191..546f8ab 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -12,7 +12,7 @@ jobs:
     name: Upload Release Asset
     runs-on: ubuntu-latest
     steps:
-<     - uses: actions/checkout@v2
+      - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v2
         with:

From 2efdbe4ee91bdf31bbffe80361c6481f9c7230d5 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:37:15 +0100
Subject: [PATCH 052/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 546f8ab..38369f8 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -31,8 +31,6 @@ jobs:
       - name: Test with pytest
         run: |
             pytest PyCTBN/tests/>
-      - name: Checkout code
-            uses: actions/checkout@v2
       - name: Install dependencies
             run: |
                 python -m pip install --upgrade pip

From b088d6ddf622715f104e649f651c8d5a294bf85c Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:37:52 +0100
Subject: [PATCH 053/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 38369f8..625d492 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -32,7 +32,7 @@ jobs:
         run: |
             pytest PyCTBN/tests/>
       - name: Install dependencies
-            run: |
+        run: |
                 python -m pip install --upgrade pip
                 python -m pip install flake8 pytest
                 if [ -f requirements.txt ]; then pip install -r requirements.txt; fi

From 6c341138f3071e0ab5e5c3accdb272b3f83a8946 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:40:40 +0100
Subject: [PATCH 054/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 625d492..40e0bfe 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -31,11 +31,13 @@ jobs:
       - name: Test with pytest
         run: |
             pytest PyCTBN/tests/>
+      - name: Checkout code
+            uses: actions/checkout@v2
       - name: Install dependencies
         run: |
-                python -m pip install --upgrade pip
-                python -m pip install flake8 pytest
-                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+            python -m pip install --upgrade pip
+            python -m pip install flake8 pytest
+            if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
       - name: Install pypa/build
         run: |
             python -m pip install build

From c0dcc8ab2378af1ec7f14ead86f8f2b9acc6adbc Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:41:00 +0100
Subject: [PATCH 055/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 40e0bfe..43b35e4 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -31,8 +31,6 @@ jobs:
       - name: Test with pytest
         run: |
             pytest PyCTBN/tests/>
-      - name: Checkout code
-            uses: actions/checkout@v2
       - name: Install dependencies
         run: |
             python -m pip install --upgrade pip

From 918f0ab290024a642003e49ecd6ec3efb1647348 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:43:54 +0100
Subject: [PATCH 056/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 43b35e4..661733a 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -9,6 +9,12 @@ name: Upload Release Asset
 
 jobs:
   build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
     name: Upload Release Asset
     runs-on: ubuntu-latest
     steps:

From f9a9f17cf9a04da5a1514fe7d23aa261ff3a0609 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:44:32 +0100
Subject: [PATCH 057/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 661733a..76c6f24 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -16,7 +16,6 @@ jobs:
         python-version: [3.8]
 
     name: Upload Release Asset
-    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}

From c1a6f376e5ad7c53eb001d1356235603dbe1d2da Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:46:27 +0100
Subject: [PATCH 058/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 76c6f24..61f99f8 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -35,7 +35,7 @@ jobs:
             flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
       - name: Test with pytest
         run: |
-            pytest PyCTBN/tests/>
+            pytest PyCTBN/tests/
       - name: Install dependencies
         run: |
             python -m pip install --upgrade pip

From 70d15fb7540ca6f83ca574722378a4fc81496016 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:47:17 +0100
Subject: [PATCH 059/139] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index cfbae9d..2c1aa31 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -5,7 +5,7 @@ name: Sphinx Docs
 
 on:
   workflow_run:
-    workflows: ["Python package"]
+    workflows: ["Python package","Upload Release Asset"]
     types:
       - completed
 

From 01825691fa11f8e63dec39b922ad37477e674ff7 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:48:02 +0100
Subject: [PATCH 060/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 43ea496..5d3cf42 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -44,10 +44,6 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
-    - name: Install pypa/build
-      run: |
-        python -m pip install build
-    - name: Build a binary wheel and a source tarball
       run: |
         python -m build --sdist --wheel --outdir dist/.
         git config --local user.email "f.martini@campus.unimib.it"

From 36e12821afa8d30655e62288b248581db72440bc Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 17:53:23 +0000
Subject: [PATCH 061/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
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From 1f2dc51ab4abaf3e51fdd9769eb1298fc9f2266b Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 17:56:52 +0000
Subject: [PATCH 062/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index bfbb664e664fcf47d775ff042e52215a4b9832d6..ac18e18a57337cded8e386d80da1ca1b07d22267 100644
GIT binary patch
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From 986225405abfe4bde22acfb1039415610db6aa94 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 18:57:00 +0100
Subject: [PATCH 063/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 61f99f8..bc23a91 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -2,8 +2,8 @@
 on:
   push:
     # Sequence of patterns matched against refs/tags
-    #tags:
-    #- 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+    tags:
+    - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
     
 name: Upload Release Asset 
 

From 8546e8bc818e8350b719bf4da5d8221ec0b69484 Mon Sep 17 00:00:00 2001
From: Filippo Martini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 19:00:39 +0100
Subject: [PATCH 064/139] Delete basic_main

---
 PyCTBN/basic_main.py | 39 ---------------------------------------
 1 file changed, 39 deletions(-)
 delete mode 100644 PyCTBN/basic_main.py

diff --git a/PyCTBN/basic_main.py b/PyCTBN/basic_main.py
deleted file mode 100644
index b1288db..0000000
--- a/PyCTBN/basic_main.py
+++ /dev/null
@@ -1,39 +0,0 @@
-import glob
-import os
-
-import sys
-sys.path.append("./PyCTBN/")
-
-import structure_graph.network_graph as ng
-import structure_graph.sample_path as sp
-import structure_graph.set_of_cims as sofc
-import estimators.parameters_estimator as pe
-import utility.json_importer as ji
-
-
-def main():
-    read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
-    #import data
-    importer = ji.JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
-    #Create a SamplePath Obj
-    s1 = sp.SamplePath(importer)
-    #Build The trajectries and the structural infos
-    s1.build_trajectories()
-    s1.build_structure()
-    #From The Structure Object build the Graph
-    g = ng.NetworkGraph(s1.structure)
-    #Select a node you want to estimate the parameters
-    node = g.nodes[1]
-    #Init the graph specifically for THIS node
-    g.fast_init(node)
-    #Use SamplePath and Grpah to create a ParametersEstimator Object
-    p1 = pe.ParametersEstimator(s1, g)
-    #Init the peEst specifically for THIS node
-    p1.fast_init(node)
-    #Compute the parameters
-    sofc1 = p1.compute_parameters_for_node(node)
-    #The est CIMS are inside the resultant SetOfCIms Obj
-    print(sofc1.actual_cims)
-
-if __name__ == "__main__":
-    main()

From f4e1ec2194123063790aae68aad8487c13c3922d Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 19:05:43 +0100
Subject: [PATCH 065/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 5d3cf42..5b78767 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -44,16 +44,3 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/
-      run: |
-        python -m build --sdist --wheel --outdir dist/.
-        git config --local user.email "f.martini@campus.unimib.it"
-        git config --local user.name "philipMartini"
-        git add .
-        git commit -m "Create New Realease at dist/" -a || true
-        # The above command will fail if no changes were present, so we ignore
-        # that.
-    - name: Push changes
-      uses: ad-m/github-push-action@master
-      with:
-        branch: master
-        github_token: ${{ secrets.PYCTBN_TOK }}

From 37c5468e4cc6dbf1562a256cfe97e8cbba322b18 Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Sun, 14 Mar 2021 19:07:49 +0100
Subject: [PATCH 066/139] test commit

---
 PyCTBN/tests/utility/test_cache.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PyCTBN/tests/utility/test_cache.py b/PyCTBN/tests/utility/test_cache.py
index 5d9c766..087750d 100644
--- a/PyCTBN/tests/utility/test_cache.py
+++ b/PyCTBN/tests/utility/test_cache.py
@@ -53,5 +53,5 @@ class TestCache(unittest.TestCase):
         self.assertFalse(c1._actual_cache)
 
 
-if __name__ == '__main__':
+if __name__ == '__main__': 
     unittest.main()

From 9de3b2a3906797f3e7b7807aad6c727eb44459f3 Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Sun, 14 Mar 2021 19:10:16 +0100
Subject: [PATCH 067/139] test commit

---
 PyCTBN/tests/utility/test_cache.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PyCTBN/tests/utility/test_cache.py b/PyCTBN/tests/utility/test_cache.py
index 087750d..5d9c766 100644
--- a/PyCTBN/tests/utility/test_cache.py
+++ b/PyCTBN/tests/utility/test_cache.py
@@ -53,5 +53,5 @@ class TestCache(unittest.TestCase):
         self.assertFalse(c1._actual_cache)
 
 
-if __name__ == '__main__': 
+if __name__ == '__main__':
     unittest.main()

From f3ad55cb51d7df72798065724f169f6c29834e48 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 18:14:05 +0000
Subject: [PATCH 068/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index ac18e18a57337cded8e386d80da1ca1b07d22267..a706946cbb5b8583a9b81b78fc737c361edeb08c 100644
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From f7464e39d0089b3c2eddbfea4fbda74d8db4247a Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 18:23:40 +0000
Subject: [PATCH 069/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index a706946cbb5b8583a9b81b78fc737c361edeb08c..9627ce7c00df2706663d9285fc8a925324199e6c 100644
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From 09ef96a82d4925ab729f98df5b9b421adb5a263e Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 18:32:45 +0000
Subject: [PATCH 070/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 9627ce7c00df2706663d9285fc8a925324199e6c..143ccb404b8accff4f6d980090bd0c16b8fce134 100644
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From d0befd4d66bf8a46b350cc2a72f28ae34d0e3590 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 18:41:41 +0000
Subject: [PATCH 071/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 143ccb404b8accff4f6d980090bd0c16b8fce134..4c0bdf030f4d3659a39b5d0b0fd3962a40afd3fc 100644
GIT binary patch
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From 95102e464a54a4e7491ddf74420ed64738d283b2 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 19:41:45 +0100
Subject: [PATCH 072/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index bc23a91..3cc50f5 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -3,7 +3,7 @@ on:
   push:
     # Sequence of patterns matched against refs/tags
     tags:
-    - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
     
 name: Upload Release Asset 
 
@@ -53,8 +53,8 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
         with:
-          tag_name: ver.${{ github.ref }}
-          release_name: Release ver. ${{ github.ref }}
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
           draft: false
           prerelease: false
       - name: Upload Release Asset

From eb3cb170d804c25fdf3101954f2e6083ee3c4b50 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 18:44:11 +0000
Subject: [PATCH 073/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 4c0bdf030f4d3659a39b5d0b0fd3962a40afd3fc..f3b18a654f50fd524e59ff60275f88bdcbad35ce 100644
GIT binary patch
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From 24a20c93d7370f731441fb45eddd6c0de5305af6 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 18:52:40 +0000
Subject: [PATCH 074/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index f3b18a654f50fd524e59ff60275f88bdcbad35ce..b1e8c29df793d607e976258f16f4bdc94f3d5487 100644
GIT binary patch
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BD24z4


From 88aca0eadec05edacd414898f9ca6dc424168b1e Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 19:03:25 +0000
Subject: [PATCH 075/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index b1e8c29df793d607e976258f16f4bdc94f3d5487..34bde1614048bc97d6b94070e67939db3c0af912 100644
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From 6234146580878a13314f053e5433d830c4997bb6 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 14 Mar 2021 20:04:24 +0100
Subject: [PATCH 076/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 5b78767..6dc0e4d 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -43,4 +43,4 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest PyCTBN/tests/
+        pytest PyCTBN/tests/ 

From dc83603961170124ec58897202c71d6cc162d86d Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 19:16:36 +0000
Subject: [PATCH 077/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
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From 757873dc7deef4a19247966b4cc84ced9596accd Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 19:33:07 +0000
Subject: [PATCH 078/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 6c0c3fd4283a32d450a23b9015e00a0f2194a427..8cd95b96a04e420cdae6ec0638b47556df2a5985 100644
GIT binary patch
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From c53865fa1f0cd42898fc21ce84b7e586862ab25d Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 19:34:44 +0000
Subject: [PATCH 079/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 8cd95b96a04e420cdae6ec0638b47556df2a5985..85a7e68eb1651b0be974774d981674e9922bd6ff 100644
GIT binary patch
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From 6a80818fb617c0e73e6178c27445a25b7d19ac74 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 20:38:55 +0100
Subject: [PATCH 080/139] Update Build_Release.yml

---
 .github/workflows/Build_Release.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/Build_Release.yml b/.github/workflows/Build_Release.yml
index 3cc50f5..1c1f4ed 100644
--- a/.github/workflows/Build_Release.yml
+++ b/.github/workflows/Build_Release.yml
@@ -51,7 +51,7 @@ jobs:
         id: create_release
         uses: actions/create-release@v1
         env:
-          GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           tag_name: ${{ github.ref }}
           release_name: Release ${{ github.ref }}
@@ -61,7 +61,7 @@ jobs:
         id: upload-release-asset 
         uses: dwenegar/upload-release-assets@v1
         env:
-          GITHUB_TOKEN: ${{ secrets.PYCTBN_TOK }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           release_id: ${{ steps.create_release.outputs.id }}
           assets_path: ./dist

From 05fd7b777aa8e76634147572386a138f0ee8de82 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 19:49:20 +0000
Subject: [PATCH 081/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 85a7e68eb1651b0be974774d981674e9922bd6ff..4df301de88ac2543600cbaa2a0ea2df231dcfade 100644
GIT binary patch
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From db4826650ad540aa2d8ed4239fdcc2067b6aab1a Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 20:01:37 +0000
Subject: [PATCH 082/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 4df301de88ac2543600cbaa2a0ea2df231dcfade..ed925b9d96769f9c8ae553d3e191ff460135666b 100644
GIT binary patch
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From a797b9b5a3ad19fb1d97f28a7d8fcef0a4351bef Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 20:02:57 +0000
Subject: [PATCH 083/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index ed925b9d96769f9c8ae553d3e191ff460135666b..8ec1ce8daa4569bdec5862fc428cf0f237a7fa20 100644
GIT binary patch
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From e298fcb4f44d22a7c6e22704d954fed19fa63c46 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 21:07:05 +0100
Subject: [PATCH 084/139] Delete dist directory

---
 dist/PyCTBN-1.0-py3-none-any.whl | Bin 35618 -> 0 bytes
 dist/PyCTBN-1.0.tar.gz           | Bin 24232 -> 0 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 dist/PyCTBN-1.0-py3-none-any.whl
 delete mode 100644 dist/PyCTBN-1.0.tar.gz

diff --git a/dist/PyCTBN-1.0-py3-none-any.whl b/dist/PyCTBN-1.0-py3-none-any.whl
deleted file mode 100644
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literal 0
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From 1665c3ee06edf21301cf4fccbafbc704010b96c5 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 21:07:26 +0100
Subject: [PATCH 085/139] Delete build/lib/PyCTBN directory

---
 build/lib/PyCTBN/PyCTBN/__init__.py           |   8 -
 .../lib/PyCTBN/PyCTBN/estimators/__init__.py  |   5 -
 .../PyCTBN/estimators/fam_score_calculator.py | 265 ----------------
 .../PyCTBN/estimators/parameters_estimator.py | 117 -------
 .../structure_constraint_based_estimator.py   | 246 ---------------
 .../PyCTBN/estimators/structure_estimator.py  | 183 -----------
 .../structure_score_based_estimator.py        | 236 --------------
 .../lib/PyCTBN/PyCTBN/optimizers/__init__.py  |   4 -
 .../optimizers/constraint_based_optimizer.py  |  84 -----
 .../PyCTBN/optimizers/hill_climbing_search.py | 135 --------
 .../lib/PyCTBN/PyCTBN/optimizers/optimizer.py |  39 ---
 .../PyCTBN/PyCTBN/optimizers/tabu_search.py   | 188 -----------
 .../PyCTBN/PyCTBN/structure_graph/__init__.py |   6 -
 .../conditional_intensity_matrix.py           |  42 ---
 .../PyCTBN/structure_graph/network_graph.py   | 293 ------------------
 .../PyCTBN/structure_graph/sample_path.py     |  93 ------
 .../PyCTBN/structure_graph/set_of_cims.py     |  97 ------
 .../PyCTBN/structure_graph/structure.py       | 124 --------
 .../PyCTBN/structure_graph/trajectory.py      |  45 ---
 build/lib/PyCTBN/PyCTBN/utility/__init__.py   |   4 -
 .../PyCTBN/utility/abstract_importer.py       | 163 ----------
 build/lib/PyCTBN/PyCTBN/utility/cache.py      |  54 ----
 .../PyCTBN/PyCTBN/utility/json_importer.py    | 181 -----------
 .../PyCTBN/PyCTBN/utility/sample_importer.py  |  62 ----
 build/lib/PyCTBN/__init__.py                  |   2 -
 build/lib/PyCTBN/basic_main.py                |  39 ---
 build/lib/PyCTBN/setup.py                     |  20 --
 27 files changed, 2735 deletions(-)
 delete mode 100644 build/lib/PyCTBN/PyCTBN/__init__.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/estimators/__init__.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/__init__.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/structure.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/utility/__init__.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/utility/cache.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/utility/json_importer.py
 delete mode 100644 build/lib/PyCTBN/PyCTBN/utility/sample_importer.py
 delete mode 100644 build/lib/PyCTBN/__init__.py
 delete mode 100644 build/lib/PyCTBN/basic_main.py
 delete mode 100644 build/lib/PyCTBN/setup.py

diff --git a/build/lib/PyCTBN/PyCTBN/__init__.py b/build/lib/PyCTBN/PyCTBN/__init__.py
deleted file mode 100644
index faff79c..0000000
--- a/build/lib/PyCTBN/PyCTBN/__init__.py
+++ /dev/null
@@ -1,8 +0,0 @@
-import PyCTBN.PyCTBN.estimators
-from PyCTBN.PyCTBN.estimators import *
-import PyCTBN.PyCTBN.optimizers
-from PyCTBN.PyCTBN.optimizers import *
-import PyCTBN.PyCTBN.structure_graph
-from PyCTBN.PyCTBN.structure_graph import *
-import PyCTBN.PyCTBN.utility
-from PyCTBN.PyCTBN.utility import *
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/__init__.py b/build/lib/PyCTBN/PyCTBN/estimators/__init__.py
deleted file mode 100644
index 112086f..0000000
--- a/build/lib/PyCTBN/PyCTBN/estimators/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from .fam_score_calculator import FamScoreCalculator
-from .parameters_estimator import ParametersEstimator
-from .structure_estimator import StructureEstimator
-from .structure_constraint_based_estimator import StructureConstraintBasedEstimator
-from .structure_score_based_estimator import StructureScoreBasedEstimator
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py b/build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
deleted file mode 100644
index d8ec3a0..0000000
--- a/build/lib/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
+++ /dev/null
@@ -1,265 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import networkx as nx
-import numpy as np
-from networkx.readwrite import json_graph
-
-from math import log
-
-from scipy.special import loggamma
-from random import choice
-
-from ..structure_graph.set_of_cims import SetOfCims
-from ..structure_graph.network_graph import NetworkGraph
-from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
-
-
-'''
-
-'''
-
-
-class FamScoreCalculator:
-    """
-    Has the task of calculating the FamScore of a node by using a Bayesian score function
-    """
-
-    def __init__(self):
-        #np.seterr('raise')
-        pass
-
-    # region theta
-
-    def marginal_likelihood_theta(self,
-                        cims: ConditionalIntensityMatrix,
-                        alpha_xu: float,
-                        alpha_xxu: float):
-        """
-        Calculate the FamScore value of the node identified by the label node_id
-
-        :param cims: np.array with all the node's cims
-        :type cims: np.array
-        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
-        :type alpha_xu: float
-        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
-        :type alpha_xxu: float
-
-        :return: the value of the marginal likelihood over theta
-        :rtype: float
-        """
-        return np.sum(
-                        [self.variable_cim_xu_marginal_likelihood_theta(cim,
-                                                                    alpha_xu,
-                                                                    alpha_xxu)
-                        for cim in cims])
-
-    def variable_cim_xu_marginal_likelihood_theta(self,
-                        cim: ConditionalIntensityMatrix,
-                        alpha_xu: float,
-                        alpha_xxu: float):
-        """
-        Calculate the value of the marginal likelihood over theta given a cim
-
-        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-        :type cim: class:'ConditionalIntensityMatrix'
-        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
-        :type alpha_xu: float
-        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
-        :type alpha_xxu: float
-
-        :return: the value of the marginal likelihood over theta
-        :rtype: float
-        """
-
-        'get cim length'
-        values = len(cim._state_residence_times)
-
-        'compute the marginal likelihood for the current cim'
-        return np.sum([
-                    self.single_cim_xu_marginal_likelihood_theta(
-                                                index,
-                                                cim,
-                                                alpha_xu,
-                                                alpha_xxu)
-                    for index in range(values)])
-
-    def single_cim_xu_marginal_likelihood_theta(self,
-                    index: int,
-                    cim: ConditionalIntensityMatrix,
-                    alpha_xu: float,
-                    alpha_xxu: float):
-        """
-        Calculate the marginal likelihood on q of the node when assumes a specif value
-        and a specif parents's assignment
-
-        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-        :type cim: class:'ConditionalIntensityMatrix'
-        :param alpha_xu: hyperparameter over the CTBN’s q parameters
-        :type alpha_xu: float
-        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
-        :type alpha_xxu: float
-
-        :return: the value of the marginal likelihood over theta when the node assumes a specif value
-        :rtype: float
-        """
-
-        values = list(range(len(cim._state_residence_times)))
-
-        'remove the index because of the x != x^ condition in the summation '
-        values.remove(index)
-
-        'uncomment for alpha xx not uniform'
-        #alpha_xxu = alpha_xu * cim.state_transition_matrix[index,index_x_first] / cim.state_transition_matrix[index, index])
-
-        return (loggamma(alpha_xu) - loggamma(alpha_xu + cim.state_transition_matrix[index, index])) \
-                + \
-                np.sum([self.single_internal_cim_xxu_marginal_likelihood_theta(
-                                                                        cim.state_transition_matrix[index,index_x_first],
-                                                                        alpha_xxu)
-                for index_x_first in values])
-
-
-    def single_internal_cim_xxu_marginal_likelihood_theta(self,
-                                                M_xxu_suff_stats: float,
-                                                alpha_xxu: float=1):
-        """Calculate the second part of the marginal likelihood over theta formula
-        
-        :param M_xxu_suff_stats: value of the suffucient statistic M[xx'|u]
-        :type M_xxu_suff_stats: float
-        :param alpha_xxu: distribuited hyperparameter over the CTBN’s theta parameters
-        :type alpha_xxu: float
-
-        :return: the value of the marginal likelihood over theta when the node assumes a specif value
-        :rtype: float
-        """
-        return loggamma(alpha_xxu+M_xxu_suff_stats) - loggamma(alpha_xxu)
-
-    # endregion
-
-    # region q
-
-    def marginal_likelihood_q(self,
-                        cims: np.array,
-                        tau_xu: float=0.1,
-                        alpha_xu: float=1):
-        """
-        Calculate the value of the marginal likelihood over q of the node identified by the label node_id
-        
-        :param cims: np.array with all the node's cims
-        :type cims: np.array
-        :param tau_xu: hyperparameter over the CTBN’s q parameters
-        :type tau_xu: float
-        :param alpha_xu: hyperparameter over the CTBN’s q parameters
-        :type alpha_xu: float
-
-
-        :return: the value of the marginal likelihood over q
-        :rtype: float
-        """
-
-        return np.sum([self.variable_cim_xu_marginal_likelihood_q(cim, tau_xu, alpha_xu) for cim in cims])
-
-    def variable_cim_xu_marginal_likelihood_q(self,
-                        cim: ConditionalIntensityMatrix,
-                        tau_xu: float=0.1,
-                        alpha_xu: float=1):
-        """
-        Calculate the value of the marginal likelihood over q given a cim
-        
-        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-        :type cim: class:'ConditionalIntensityMatrix'
-        :param tau_xu: hyperparameter over the CTBN’s q parameters
-        :type tau_xu: float
-        :param alpha_xu: hyperparameter over the CTBN’s q parameters
-        :type alpha_xu: float
-
-
-        :return: the value of the marginal likelihood over q
-        :rtype: float
-        """
-
-        'get cim length'
-        values=len(cim._state_residence_times)
-
-        'compute the marginal likelihood for the current cim'
-        return np.sum([
-                    self.single_cim_xu_marginal_likelihood_q(
-                                                cim.state_transition_matrix[index, index],
-                                                cim._state_residence_times[index],
-                                                tau_xu,
-                                                alpha_xu)
-                    for index in range(values)])
-
-
-    def single_cim_xu_marginal_likelihood_q(self,
-                        M_xu_suff_stats: float,
-                        T_xu_suff_stats: float,
-                        tau_xu: float=0.1,
-                        alpha_xu: float=1):
-        """
-        Calculate the marginal likelihood on q of the node when assumes a specif value
-        and a specif parents's assignment
-        
-        :param M_xu_suff_stats: value of the suffucient statistic M[x|u]
-        :type M_xxu_suff_stats: float
-        :param T_xu_suff_stats: value of the suffucient statistic T[x|u]
-        :type T_xu_suff_stats: float
-        :param cim: A conditional_intensity_matrix object with the sufficient statistics
-        :type cim: class:'ConditionalIntensityMatrix'
-        :param tau_xu: hyperparameter over the CTBN’s q parameters
-        :type tau_xu: float
-        :param alpha_xu: hyperparameter over the CTBN’s q parameters
-        :type alpha_xu: float
-
-
-        :return: the value of the marginal likelihood of the node when assumes a specif value
-        :rtype: float
-        """
-        return (
-                loggamma(alpha_xu + M_xu_suff_stats + 1) + 
-                                                        (log(tau_xu)
-                                                        *
-                                                        (alpha_xu+1))
-                ) \
-                - \
-                (loggamma(alpha_xu + 1)+(
-                                    log(tau_xu + T_xu_suff_stats) 
-                                    *
-                                    (alpha_xu + M_xu_suff_stats + 1))
-                )
-
-    # end region
-
-    def get_fam_score(self,
-                cims: np.array,
-                tau_xu: float=0.1,
-                alpha_xu: float=1):
-        """
-        Calculate the FamScore value of the node
-        
-        
-        :param cims: np.array with all the node's cims
-        :type cims: np.array
-        :param tau_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
-        :type tau_xu: float, optional
-        :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 1
-        :type alpha_xu: float, optional
-
-
-        :return: the FamScore value of the node
-        :rtype: float
-        """
-
-        'calculate alpha_xxu as a uniform distribution'                                
-        alpha_xxu = alpha_xu /(len(cims[0]._state_residence_times) - 1)
-
-        return self.marginal_likelihood_q(cims,
-                                    tau_xu,
-                                    alpha_xu) \
-               + \
-               self.marginal_likelihood_theta(cims, 
-                                        alpha_xu,
-                                        alpha_xxu)
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py
deleted file mode 100644
index 6b6883b..0000000
--- a/build/lib/PyCTBN/PyCTBN/estimators/parameters_estimator.py
+++ /dev/null
@@ -1,117 +0,0 @@
-import sys
-sys.path.append('../')
-import numpy as np
-
-from ..structure_graph.network_graph import NetworkGraph
-from ..structure_graph.set_of_cims import SetOfCims
-from ..structure_graph.trajectory import Trajectory
-
-
-class ParametersEstimator(object):
-    """Has the task of computing the cims of particular node given the trajectories and the net structure
-    in the graph ``_net_graph``.
-
-    :param trajectories:  the trajectories
-    :type trajectories: Trajectory
-    :param net_graph: the net structure
-    :type net_graph: NetworkGraph
-    :_single_set_of_cims: the set of cims object that will hold the cims of the node
-    """
-
-    def __init__(self, trajectories: Trajectory, net_graph: NetworkGraph):
-        """Constructor Method
-        """
-        self._trajectories = trajectories
-        self._net_graph = net_graph
-        self._single_set_of_cims = None
-
-    def fast_init(self, node_id: str) -> None:
-        """Initializes all the necessary structures for the parameters estimation for the node ``node_id``.
-
-        :param node_id: the node label
-        :type node_id: string
-        """
-        p_vals = self._net_graph._aggregated_info_about_nodes_parents[2]
-        node_states_number = self._net_graph.get_states_number(node_id)
-        self._single_set_of_cims = SetOfCims(node_id, p_vals, node_states_number, self._net_graph.p_combs)
-
-    def compute_parameters_for_node(self, node_id: str) -> SetOfCims:
-        """Compute the CIMS of the node identified by the label ``node_id``.
-
-        :param node_id: the node label
-        :type node_id: string
-        :return: A SetOfCims object filled with the computed CIMS
-        :rtype: SetOfCims
-        """
-        node_indx = self._net_graph.get_node_indx(node_id)
-        state_res_times = self._single_set_of_cims._state_residence_times
-        transition_matrices = self._single_set_of_cims._transition_matrices
-        ParametersEstimator.compute_state_res_time_for_node(self._trajectories.times,
-                                             self._trajectories.trajectory,
-                                             self._net_graph.time_filtering,
-                                             self._net_graph.time_scalar_indexing_strucure,
-                                             state_res_times)
-        ParametersEstimator.compute_state_transitions_for_a_node(node_indx, self._trajectories.complete_trajectory,
-                                                                 self._net_graph.transition_filtering,
-                                                                 self._net_graph.transition_scalar_indexing_structure,
-                                                                 transition_matrices)
-        self._single_set_of_cims.build_cims(state_res_times, transition_matrices)
-        return self._single_set_of_cims
-
-    @staticmethod
-    def compute_state_res_time_for_node(times: np.ndarray, trajectory: np.ndarray,
-                                        cols_filter: np.ndarray, scalar_indexes_struct: np.ndarray,
-                                        T: np.ndarray) -> None:
-        """Compute the state residence times for a node and fill the matrix ``T`` with the results
-
-        :param node_indx: the index of the node
-        :type node_indx: int
-        :param times: the times deltas vector
-        :type times: numpy.array
-        :param trajectory: the trajectory
-        :type trajectory: numpy.ndArray
-        :param cols_filter: the columns filtering structure
-        :type cols_filter: numpy.array
-        :param scalar_indexes_struct: the indexing structure
-        :type scalar_indexes_struct: numpy.array
-        :param T: the state residence times vectors
-        :type T: numpy.ndArray
-        """
-        T[:] = np.bincount(np.sum(trajectory[:, cols_filter] * scalar_indexes_struct / scalar_indexes_struct[0], axis=1)
-                           .astype(np.int), \
-                           times,
-                           minlength=scalar_indexes_struct[-1]).reshape(-1, T.shape[1])
-
-    @staticmethod
-    def compute_state_transitions_for_a_node(node_indx: int, trajectory: np.ndarray, cols_filter: np.ndarray,
-                                             scalar_indexing: np.ndarray, M: np.ndarray) -> None:
-        """Compute the state residence times for a node and fill the matrices ``M`` with the results.
-
-        :param node_indx: the index of the node
-        :type node_indx: int
-        :param trajectory: the trajectory
-        :type trajectory: numpy.ndArray
-        :param cols_filter: the columns filtering structure
-        :type cols_filter: numpy.array
-        :param scalar_indexing: the indexing structure
-        :type scalar_indexing: numpy.array
-        :param M: the state transitions matrices
-        :type M: numpy.ndArray
-        """
-        diag_indices = np.array([x * M.shape[1] + x % M.shape[1] for x in range(M.shape[0] * M.shape[1])],
-                                dtype=np.int64)
-        trj_tmp = trajectory[trajectory[:, int(trajectory.shape[1] / 2) + node_indx].astype(np.int) >= 0]
-        M[:] = np.bincount(np.sum(trj_tmp[:, cols_filter] * scalar_indexing / scalar_indexing[0], axis=1).astype(np.int)
-                           , minlength=scalar_indexing[-1]).reshape(-1, M.shape[1], M.shape[2])
-        M_raveled = M.ravel()
-        M_raveled[diag_indices] = 0
-        M_raveled[diag_indices] = np.sum(M, axis=2).ravel()
-
-
-
-
-
-
-
-
-
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
deleted file mode 100644
index 0013d80..0000000
--- a/build/lib/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
+++ /dev/null
@@ -1,246 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import networkx as nx
-import numpy as np
-from networkx.readwrite import json_graph
-import os
-from scipy.stats import chi2 as chi2_dist
-from scipy.stats import f as f_dist
-from tqdm import tqdm
-
-from ..utility.cache import Cache
-from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
-from ..structure_graph.network_graph import NetworkGraph
-from .parameters_estimator import ParametersEstimator
-from .structure_estimator import StructureEstimator
-from ..structure_graph.sample_path import SamplePath
-from ..structure_graph.structure import Structure
-from ..optimizers.constraint_based_optimizer import ConstraintBasedOptimizer
-
-import concurrent.futures
-
-
-
-import multiprocessing
-from multiprocessing import Pool
-
-
-class StructureConstraintBasedEstimator(StructureEstimator):
-    """
-    Has the task of estimating the network structure given the trajectories in samplepath by using a constraint-based approach.
-
-    :param sample_path: the _sample_path object containing the trajectories and the real structure
-    :type sample_path: SamplePath
-    :param exp_test_alfa: the significance level for the exponential Hp test
-    :type exp_test_alfa: float
-    :param chi_test_alfa: the significance level for the chi Hp test
-    :type chi_test_alfa: float
-    :param known_edges: the prior known edges in the net structure if present
-    :type known_edges: List
-    :param thumb_threshold: the threshold value to consider a valid independence test
-    :type thumb_threshold: int
-    :_nodes: the nodes labels
-    :_nodes_vals: the nodes cardinalities
-    :_nodes_indxs: the nodes indexes
-    :_complete_graph: the complete directed graph built using the nodes labels in ``_nodes``
-    :_cache: the Cache object
-    """
-
-    def __init__(self, sample_path: SamplePath, exp_test_alfa: float, chi_test_alfa: float,known_edges: typing.List= [],
-                 thumb_threshold:int = 25):
-        super().__init__(sample_path,known_edges)
-        self._exp_test_sign = exp_test_alfa
-        self._chi_test_alfa = chi_test_alfa
-        self._thumb_threshold = thumb_threshold
-        self._cache = Cache()
-
-    def complete_test(self, test_parent: str, test_child: str, parent_set: typing.List, child_states_numb: int,
-                      tot_vars_count: int, parent_indx, child_indx) -> bool:
-        """Performs a complete independence test on the directed graphs G1 = {test_child U parent_set}
-        G2 = {G1 U test_parent} (added as an additional parent of the test_child).
-        Generates all the necessary structures and datas to perform the tests.
-
-        :param test_parent: the node label of the test parent
-        :type test_parent: string
-        :param test_child: the node label of the child
-        :type test_child: string
-        :param parent_set: the common parent set
-        :type parent_set: List
-        :param child_states_numb: the cardinality of the ``test_child``
-        :type child_states_numb: int
-        :param tot_vars_count: the total number of variables in the net
-        :type tot_vars_count: int
-        :return: True iff test_child and test_parent are independent given the sep_set parent_set. False otherwise
-        :rtype: bool
-        """
-        p_set = parent_set[:]
-        complete_info = parent_set[:]
-        complete_info.append(test_child)
-
-        parents = np.array(parent_set)
-        parents = np.append(parents, test_parent)
-        sorted_parents = self._nodes[np.isin(self._nodes, parents)]
-        cims_filter = sorted_parents != test_parent
-
-        p_set.insert(0, test_parent)
-        sofc2 = self._cache.find(set(p_set))
-
-        if not sofc2:
-            complete_info.append(test_parent)
-            bool_mask2 = np.isin(self._nodes, complete_info)
-            l2 = list(self._nodes[bool_mask2])
-            indxs2 = self._nodes_indxs[bool_mask2]
-            vals2 = self._nodes_vals[bool_mask2]
-            eds2 = list(itertools.product(p_set, test_child))
-            s2 = Structure(l2, indxs2, vals2, eds2, tot_vars_count)
-            g2 = NetworkGraph(s2)
-            g2.fast_init(test_child)
-            p2 = ParametersEstimator(self._sample_path.trajectories, g2)
-            p2.fast_init(test_child)
-            sofc2 = p2.compute_parameters_for_node(test_child)
-            self._cache.put(set(p_set), sofc2)
-
-        del p_set[0]
-        sofc1 = self._cache.find(set(p_set))
-        if not sofc1:
-            g2.remove_node(test_parent)
-            g2.fast_init(test_child)
-            p2 = ParametersEstimator(self._sample_path.trajectories, g2)
-            p2.fast_init(test_child)
-            sofc1 = p2.compute_parameters_for_node(test_child)
-            self._cache.put(set(p_set), sofc1)
-        thumb_value = 0.0
-        if child_states_numb > 2:
-            parent_val = self._sample_path.structure.get_states_number(test_parent)
-            bool_mask_vals = np.isin(self._nodes, parent_set)
-            parents_vals = self._nodes_vals[bool_mask_vals]
-            thumb_value = self.compute_thumb_value(parent_val, child_states_numb, parents_vals)
-        for cim1, p_comb in zip(sofc1.actual_cims, sofc1.p_combs):
-            cond_cims = sofc2.filter_cims_with_mask(cims_filter, p_comb)
-            for cim2 in cond_cims:
-                if not self.independence_test(child_states_numb, cim1, cim2, thumb_value, parent_indx, child_indx):
-                    return False
-        return True
-
-    def independence_test(self, child_states_numb: int, cim1: ConditionalIntensityMatrix,
-                          cim2: ConditionalIntensityMatrix, thumb_value: float, parent_indx, child_indx) -> bool:
-        """Compute the actual independence test using two cims.
-        It is performed first the exponential test and if the null hypothesis is not rejected,
-        it is performed also the chi_test.
-
-        :param child_states_numb: the cardinality of the test child
-        :type child_states_numb: int
-        :param cim1: a cim belonging to the graph without test parent
-        :type cim1: ConditionalIntensityMatrix
-        :param cim2: a cim belonging to the graph with test parent
-        :type cim2: ConditionalIntensityMatrix
-        :return: True iff both tests do NOT reject the null hypothesis of independence. False otherwise.
-        :rtype: bool
-        """
-        M1 = cim1.state_transition_matrix
-        M2 = cim2.state_transition_matrix
-        r1s = M1.diagonal()
-        r2s = M2.diagonal()
-        C1 = cim1.cim
-        C2 = cim2.cim
-        if child_states_numb > 2 and (np.sum(np.diagonal(M1)) / thumb_value) < self._thumb_threshold:
-                self._removable_edges_matrix[parent_indx][child_indx] = False
-                return False
-        F_stats = C2.diagonal() / C1.diagonal()
-        exp_alfa = self._exp_test_sign
-        for val in range(0, child_states_numb):
-            if F_stats[val] < f_dist.ppf(exp_alfa / 2, r1s[val], r2s[val]) or \
-                    F_stats[val] > f_dist.ppf(1 - exp_alfa / 2, r1s[val], r2s[val]):
-                return False
-        M1_no_diag = M1[~np.eye(M1.shape[0], dtype=bool)].reshape(M1.shape[0], -1)
-        M2_no_diag = M2[~np.eye(M2.shape[0], dtype=bool)].reshape(
-            M2.shape[0], -1)
-        chi_2_quantile = chi2_dist.ppf(1 - self._chi_test_alfa, child_states_numb - 1)
-        Ks = np.sqrt(r1s / r2s)
-        Ls = np.sqrt(r2s / r1s)
-        for val in range(0, child_states_numb):
-            Chi = np.sum(np.power(Ks[val] * M2_no_diag[val] - Ls[val] *M1_no_diag[val], 2) /
-                         (M1_no_diag[val] + M2_no_diag[val]))
-            if Chi > chi_2_quantile:
-                return False
-        return True
-        
-    def compute_thumb_value(self, parent_val, child_val, parent_set_vals):
-        """Compute the value to test against the thumb_threshold.
-        
-        :param parent_val: test parent's variable cardinality
-        :type parent_val: int
-        :param child_val: test child's variable cardinality
-        :type child_val: int
-        :param parent_set_vals: the cardinalities of the nodes in the current sep-set
-        :type parent_set_vals: List
-        :return: the thumb value for the current independence test
-        :rtype: int
-        """
-        df = (child_val - 1) ** 2
-        df = df * parent_val
-        for v in parent_set_vals:
-            df = df * v
-        return df
-        
-    def one_iteration_of_CTPC_algorithm(self, var_id: str, tot_vars_count: int)-> typing.List:
-        """Performs an iteration of the CTPC algorithm using the node ``var_id`` as ``test_child``.
-
-        :param var_id: the node label of the test child
-        :type var_id: string
-        """
-        optimizer_obj = ConstraintBasedOptimizer(
-                                                            node_id = var_id,
-                                                            structure_estimator = self,
-                                                            tot_vars_count = tot_vars_count)
-        return optimizer_obj.optimize_structure()
-
-    
-    def ctpc_algorithm(self,disable_multiprocessing:bool= False ):
-        """Compute the CTPC algorithm over the entire net.
-        """
-        ctpc_algo = self.one_iteration_of_CTPC_algorithm
-        total_vars_numb = self._sample_path.total_variables_count
-
-        n_nodes= len(self._nodes)
-
-        total_vars_numb_array =  [total_vars_numb] *  n_nodes
-
-        'get the number of CPU'
-        cpu_count = multiprocessing.cpu_count()
-
-
-
-        'Remove all the edges from the structure'   
-        self._sample_path.structure.clean_structure_edges()
-
-        'Estimate the best parents for each node'
-        #with multiprocessing.Pool(processes=cpu_count) as pool:
-        #with get_context("spawn").Pool(processes=cpu_count) as pool:
-        if disable_multiprocessing:
-            print("DISABILITATO")
-            cpu_count = 1
-            list_edges_partial = [ctpc_algo(n,total_vars_numb) for n in self._nodes]
-        else:
-            with concurrent.futures.ProcessPoolExecutor(max_workers=cpu_count) as executor:
-                list_edges_partial = executor.map(ctpc_algo,
-                                                                 self._nodes,
-                                                                 total_vars_numb_array)
-            
-        'Update the graph'
-        edges = set(itertools.chain.from_iterable(list_edges_partial))
-        self._complete_graph = nx.DiGraph()
-        self._complete_graph.add_edges_from(edges)
-
-        return edges
-
-        
-    def estimate_structure(self,disable_multiprocessing:bool=False):
-        return self.ctpc_algorithm(disable_multiprocessing=disable_multiprocessing)
-
-    
-
-
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py
deleted file mode 100644
index b77e21f..0000000
--- a/build/lib/PyCTBN/PyCTBN/estimators/structure_estimator.py
+++ /dev/null
@@ -1,183 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import matplotlib.pyplot as plt
-import networkx as nx
-import numpy as np
-from networkx.readwrite import json_graph
-
-from abc import ABC
-import os
-import abc
-
-from ..utility.cache import Cache
-from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
-from ..structure_graph.network_graph import NetworkGraph
-from .parameters_estimator import ParametersEstimator
-from ..structure_graph.sample_path import SamplePath
-from ..structure_graph.structure import Structure
-
-
-class StructureEstimator(object):
-    """Has the task of estimating the network structure given the trajectories in ``samplepath``.
-
-    :param sample_path: the _sample_path object containing the trajectories and the real structure
-    :type sample_path: SamplePath
-    :param known_edges: the prior known edges in the net structure if present
-    :type known_edges: List
-    :_nodes: the nodes labels
-    :_nodes_vals: the nodes cardinalities
-    :_nodes_indxs: the nodes indexes
-    :_complete_graph: the complete directed graph built using the nodes labels in ``_nodes``
-    """
-
-    def __init__(self, sample_path: SamplePath, known_edges: typing.List = None):
-        self._sample_path = sample_path
-        self._nodes = np.array(self._sample_path.structure.nodes_labels)
-        self._nodes_vals = self._sample_path.structure.nodes_values
-        self._nodes_indxs = self._sample_path.structure.nodes_indexes
-        self._removable_edges_matrix = self.build_removable_edges_matrix(known_edges)
-        self._complete_graph = StructureEstimator.build_complete_graph(self._sample_path.structure.nodes_labels)
-        
-
-    def build_removable_edges_matrix(self, known_edges: typing.List):
-        """Builds a boolean matrix who shows if a edge could be removed or not, based on prior knowledge given:
-
-        :param known_edges: the list of nodes labels
-        :type known_edges: List
-        :return: a boolean matrix
-        :rtype: np.ndarray
-        """
-        tot_vars_count = self._sample_path.total_variables_count
-        complete_adj_matrix = np.full((tot_vars_count, tot_vars_count), True)
-        if known_edges:
-            for edge in known_edges:
-                i = self._sample_path.structure.get_node_indx(edge[0])
-                j = self._sample_path.structure.get_node_indx(edge[1])
-                complete_adj_matrix[i][j] = False
-        return complete_adj_matrix
-
-    @staticmethod
-    def build_complete_graph(node_ids: typing.List) -> nx.DiGraph:
-        """Builds a complete directed graph (no self loops) given the nodes labels in the list ``node_ids``:
-
-        :param node_ids: the list of nodes labels
-        :type node_ids: List
-        :return: a complete Digraph Object
-        :rtype: networkx.DiGraph
-        """
-        complete_graph = nx.DiGraph()
-        complete_graph.add_nodes_from(node_ids)
-        complete_graph.add_edges_from(itertools.permutations(node_ids, 2))
-        return complete_graph
-
-
-    @staticmethod
-    def generate_possible_sub_sets_of_size( u: typing.List, size: int, parent_label: str):
-        """Creates a list containing all possible subsets of the list ``u`` of size ``size``,
-        that do not contains a the node identified by ``parent_label``.
-
-        :param u: the list of nodes
-        :type u: List
-        :param size: the size of the subsets
-        :type size: int
-        :param parent_label: the node to exclude in the subsets generation
-        :type parent_label: string
-        :return: an Iterator Object containing a list of lists
-        :rtype: Iterator
-        """
-        list_without_test_parent = u[:]
-        list_without_test_parent.remove(parent_label)
-        return map(list, itertools.combinations(list_without_test_parent, size))
-
-    def save_results(self, file_path: str) -> None:
-        """Save the estimated Structure to a .json file in file_path.
-
-        :param file_path: the path including the file name with .json extension
-        :type file_path: string
-        """
-        res = json_graph.node_link_data(self._complete_graph)
-        with open(file_path, 'w') as f:
-            json.dump(res, f)
-
-
-    #def remove_diagonal_elements(self, matrix):
-    #   m = matrix.shape[0]
-    #    strided = np.lib.stride_tricks.as_strided
-    #    s0, s1 = matrix.strides
-    #    return strided(matrix.ravel()[1:], shape=(m - 1, m), strides=(s0 + s1, s1)).reshape(m, -1)
-
-
-    @abc.abstractmethod
-    def estimate_structure(self) -> typing.List:
-        """Abstract method to estimate the structure
-
-        :return: List of estimated edges
-        :rtype: Typing.List
-        """
-        pass
-
-    def adjacency_matrix(self) -> np.ndarray:
-        """Converts the estimated structure ``_complete_graph`` to a boolean adjacency matrix representation.
-
-        :return: The adjacency matrix of the graph ``_complete_graph``
-        :rtype: numpy.ndArray
-        """
-        return nx.adj_matrix(self._complete_graph, self._nodes).toarray().astype(bool)
-
-    def spurious_edges(self) -> typing.List:
-        """Return the spurious edges present in the estimated structure, if a prior net structure is present in
-            ``_sample_path.structure``.
-
-        :return: A list containing the spurious edges
-        :rtype: List
-        """
-        if not self._sample_path.has_prior_net_structure:
-            return []
-        real_graph = nx.DiGraph()
-        real_graph.add_nodes_from(self._sample_path.structure.nodes_labels)
-        real_graph.add_edges_from(self._sample_path.structure.edges)
-        return nx.difference(real_graph, self._complete_graph).edges
-
-    def save_plot_estimated_structure_graph(self, file_path: str) -> None:  
-            """Plot the estimated structure in a graphical model style, use .png extension.
-            Spurious edges are colored in red if a prior structure is present.
-
-            :param file_path: path to save the file to
-            :type: string
-            """
-            graph_to_draw = nx.DiGraph()
-            spurious_edges = self.spurious_edges()
-            non_spurious_edges = list(set(self._complete_graph.edges) - set(spurious_edges))
-            edges_colors = ['red' if edge in spurious_edges else 'black' for edge in self._complete_graph.edges]
-            graph_to_draw.add_edges_from(spurious_edges)
-            graph_to_draw.add_edges_from(non_spurious_edges)
-            pos = nx.spring_layout(graph_to_draw, k=0.5*1/np.sqrt(len(graph_to_draw.nodes())), iterations=50,scale=10)
-            options = {
-                "node_size": 2000,
-                "node_color": "white",
-                "edgecolors": "black",
-                'linewidths':2,
-                "with_labels":True,
-                "font_size":13,
-                'connectionstyle': 'arc3, rad = 0.1',
-                "arrowsize": 15,
-                "arrowstyle": '<|-',
-                "width": 1,
-                "edge_color":edges_colors,
-            }
-
-            nx.draw(graph_to_draw, pos, **options)
-            ax = plt.gca()
-            ax.margins(0.20)
-            plt.axis("off")
-            plt.savefig(file_path)
-            plt.clf()
-            print("Estimated Structure Plot Saved At: ", os.path.abspath(file_path))
-
-
-
-
-
diff --git a/build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py b/build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
deleted file mode 100644
index 12222f9..0000000
--- a/build/lib/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
+++ /dev/null
@@ -1,236 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import networkx as nx
-import numpy as np
-from networkx.readwrite import json_graph
-
-from random import choice
-
-import concurrent.futures
-
-import copy
-
-from ..structure_graph.conditional_intensity_matrix import ConditionalIntensityMatrix
-from ..structure_graph.network_graph import NetworkGraph
-from .parameters_estimator import ParametersEstimator
-from .structure_estimator import StructureEstimator
-from ..structure_graph.sample_path import SamplePath
-from ..structure_graph.structure import Structure
-from .fam_score_calculator import FamScoreCalculator
-from ..optimizers.hill_climbing_search import HillClimbing
-from ..optimizers.tabu_search import TabuSearch
-
-
-import multiprocessing
-from multiprocessing import Pool
-
-
-
-
-class StructureScoreBasedEstimator(StructureEstimator):
-    """
-    Has the task of estimating the network structure given the trajectories in samplepath by
-    using a score based approach and differt kinds of optimization algorithms.
-
-    :param sample_path: the _sample_path object containing the trajectories and the real structure
-    :type sample_path: SamplePath
-    :param tau_xu: hyperparameter over the CTBN’s q parameters, default to 0.1
-    :type tau_xu: float, optional
-    :param alpha_xu: hyperparameter over the CTBN’s q parameters, default to 1
-    :type alpha_xu: float, optional
-    :param known_edges: List of known edges, default to []
-    :type known_edges: List, optional
-
-    """
-
-    def __init__(self, sample_path: SamplePath, tau_xu:int=0.1, alpha_xu:int = 1,known_edges: typing.List= []):
-        super().__init__(sample_path,known_edges)
-        self.tau_xu=tau_xu
-        self.alpha_xu=alpha_xu
-
-
-    def estimate_structure(self, max_parents:int = None, iterations_number:int= 40,
-                         patience:int = None, tabu_length:int = None, tabu_rules_duration:int = None,
-                         optimizer: str = 'tabu',disable_multiprocessing:bool= False ):
-        """
-        Compute the score-based algorithm to find the optimal structure
-
-        :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
-        :type max_parents: int, optional
-        :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
-        :type iterations_number: int, optional
-        :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
-        :type patience: int, optional
-        :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
-        :type tabu_length: int, optional
-        :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
-        :type tabu_rules_duration: int, optional
-        :param optimizer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search), defualt to 'tabu'
-        :type optimizer: string, optional
-        :param disable_multiprocessing: true if you desire to disable the multiprocessing operations, default to False
-        :type disable_multiprocessing: Boolean, optional
-        """
-        'Save the true edges structure in tuples'
-        true_edges = copy.deepcopy(self._sample_path.structure.edges)
-        true_edges = set(map(tuple, true_edges))
-
-        'Remove all the edges from the structure'   
-        self._sample_path.structure.clean_structure_edges()
-
-        estimate_parents = self.estimate_parents
-
-        n_nodes= len(self._nodes)
-        
-        l_max_parents= [max_parents] * n_nodes
-        l_iterations_number = [iterations_number] * n_nodes
-        l_patience = [patience] * n_nodes
-        l_tabu_length = [tabu_length] * n_nodes
-        l_tabu_rules_duration = [tabu_rules_duration] * n_nodes
-        l_optimizer = [optimizer] * n_nodes
-
-
-        'get the number of CPU'
-        cpu_count = multiprocessing.cpu_count()
-        print(f"CPU COUNT: {cpu_count}")
-
-        if disable_multiprocessing:
-            cpu_count = 1
-
-        
-
-
-
-        #with get_context("spawn").Pool(processes=cpu_count) as pool:
-        #with multiprocessing.Pool(processes=cpu_count) as pool:
-
-        'Estimate the best parents for each node'
-        if disable_multiprocessing:
-            list_edges_partial = [estimate_parents(n,max_parents,iterations_number,patience,tabu_length,tabu_rules_duration,optimizer) for n in self._nodes]
-        else:
-            with concurrent.futures.ProcessPoolExecutor(max_workers=cpu_count) as executor:
-                list_edges_partial = executor.map(estimate_parents, 
-                                                            self._nodes,
-                                                            l_max_parents,
-                                                            l_iterations_number,
-                                                            l_patience,
-                                                            l_tabu_length,
-                                                            l_tabu_rules_duration,
-                                                            l_optimizer)
-
-
-        'Concatenate all the edges list'
-        set_list_edges =  set(itertools.chain.from_iterable(list_edges_partial))
-
-
-        'calculate precision and recall'
-        n_missing_edges = 0
-        n_added_fake_edges = 0
-
-        try:
-            n_added_fake_edges = len(set_list_edges.difference(true_edges))
-
-            n_missing_edges = len(true_edges.difference(set_list_edges))
-
-            n_true_positive = len(true_edges) - n_missing_edges
-
-            precision = n_true_positive / (n_true_positive + n_added_fake_edges)
-
-            recall = n_true_positive / (n_true_positive + n_missing_edges)
-        
-            print(true_edges)
-            print(set_list_edges)
-            print(f"precision: {precision} ")
-            print(f"recall: {recall} ")
-        except Exception as e: 
-            print(f"errore: {e}")
-
-
-        'Update the graph'
-        self._complete_graph = nx.DiGraph()
-        self._complete_graph.add_edges_from(set_list_edges)
-
-        return set_list_edges
-    
-
-    def estimate_parents(self,node_id:str, max_parents:int = None, iterations_number:int= 40,
-                            patience:int = 10, tabu_length:int = None, tabu_rules_duration:int=5, 
-                            optimizer:str = 'hill' ):
-        """
-        Use the FamScore of a node in order to find the best parent nodes
-        
-        :param node_id: current node's id
-        :type node_id: string
-        :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
-        :type max_parents: int, optional
-        :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
-        :type iterations_number: int, optional
-        :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
-        :type patience: int, optional
-        :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
-        :type tabu_length: int, optional
-        :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
-        :type tabu_rules_duration: int, optional
-        :param optimizer: name of the optimizer algorithm. Possible values: 'hill' (Hill climbing),'tabu' (tabu search), defualt to 'tabu'
-        :type optimizer: string, optional
-
-        :return: A list of the best edges for the currente node
-        :rtype: List
-        """
-
-        "choose the optimizer algotithm"
-        if optimizer == 'tabu':
-            optimizer = TabuSearch(
-                        node_id = node_id,
-                        structure_estimator = self,
-                        max_parents = max_parents,
-                        iterations_number = iterations_number,
-                        patience = patience,
-                        tabu_length = tabu_length,
-                        tabu_rules_duration = tabu_rules_duration)
-        else: #if optimizer == 'hill':
-            optimizer = HillClimbing(
-                                    node_id = node_id,
-                                    structure_estimator = self,
-                                    max_parents = max_parents,
-                                    iterations_number = iterations_number,
-                                    patience = patience)
-
-        "call the optmizer's function that calculates the current node's parents"
-        return optimizer.optimize_structure()
-
-    
-    def get_score_from_graph(self,
-                            graph: NetworkGraph,
-                            node_id:str):
-        """
-        Get the FamScore of a node 
-        
-        :param node_id: current node's id
-        :type node_id: string
-        :param graph: current graph to be computed
-        :type graph: class:'NetworkGraph'
-
-
-        :return: The FamSCore for this graph structure
-        :rtype: float
-        """
-
-        'inizialize the graph for a single node'
-        graph.fast_init(node_id) 
-
-        params_estimation = ParametersEstimator(self._sample_path.trajectories, graph)
-
-        'Inizialize and compute parameters for node'
-        params_estimation.fast_init(node_id)
-        SoCims = params_estimation.compute_parameters_for_node(node_id)
-
-        'calculate the FamScore for the node'
-        fam_score_obj = FamScoreCalculator()
-
-        score = fam_score_obj.get_fam_score(SoCims.actual_cims,tau_xu = self.tau_xu,alpha_xu=self.alpha_xu)
-        
-        #print(f" lo score per {node_id} risulta: {score} ")
-        return score 
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/__init__.py b/build/lib/PyCTBN/PyCTBN/optimizers/__init__.py
deleted file mode 100644
index 4162bf1..0000000
--- a/build/lib/PyCTBN/PyCTBN/optimizers/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from .optimizer import Optimizer
-from .tabu_search import TabuSearch
-from .hill_climbing_search import HillClimbing
-from .constraint_based_optimizer import ConstraintBasedOptimizer
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py b/build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
deleted file mode 100644
index 9ad05fc..0000000
--- a/build/lib/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
+++ /dev/null
@@ -1,84 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import networkx as nx
-import numpy as np
-
-from random import choice
-
-from abc import ABC
-
-import copy
-
-
-from .optimizer import Optimizer
-from ..estimators.structure_estimator import StructureEstimator
-from ..structure_graph.network_graph import NetworkGraph
-
-
-class ConstraintBasedOptimizer(Optimizer):
-    """
-    Optimizer class that implement a CTPC Algorithm
-
-    :param node_id: current node's id
-    :type node_id: string
-    :param structure_estimator: a structure estimator object with the information about the net
-    :type structure_estimator: class:'StructureEstimator' 
-    :param tot_vars_count: number of variables in the dataset
-    :type tot_vars_count: int
-    """
-    def __init__(self,
-                node_id:str,
-                structure_estimator: StructureEstimator,
-                tot_vars_count:int
-                ):
-        """
-        Constructor
-        """
-        super().__init__(node_id, structure_estimator)
-        self.tot_vars_count = tot_vars_count
-        
-
-
-    def optimize_structure(self):
-        """
-        Compute Optimization process for a structure_estimator by using a CTPC Algorithm
-
-        :return: the estimated structure for the node
-        :rtype: List
-        """
-        print("##################TESTING VAR################", self.node_id)
-
-        graph = NetworkGraph(self.structure_estimator._sample_path.structure)
-
-        other_nodes =  [node for node in self.structure_estimator._sample_path.structure.nodes_labels if node != self.node_id]
-        
-        for possible_parent in other_nodes:
-            graph.add_edges([(possible_parent,self.node_id)])
-
-        
-        u = other_nodes
-        child_states_numb = self.structure_estimator._sample_path.structure.get_states_number(self.node_id)
-        b = 0
-        while b < len(u):
-            parent_indx = 0
-            while parent_indx < len(u):
-                removed = False
-                test_parent = u[parent_indx]
-               	i = self.structure_estimator._sample_path.structure.get_node_indx(test_parent)
-                j = self.structure_estimator._sample_path.structure.get_node_indx(self.node_id)
-                if self.structure_estimator._removable_edges_matrix[i][j]:
-                    S = StructureEstimator.generate_possible_sub_sets_of_size(u, b, test_parent)
-                    for parents_set in S:
-	                    if self.structure_estimator.complete_test(test_parent, self.node_id, parents_set, child_states_numb, self.tot_vars_count,i,j):
-	                        graph.remove_edges([(test_parent, self.node_id)])
-	                        u.remove(test_parent)
-	                        removed = True
-	                        break
-                if not removed:
-                    parent_indx += 1
-            b += 1
-        self.structure_estimator._cache.clear()
-        return graph.edges
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py b/build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
deleted file mode 100644
index 6783be0..0000000
--- a/build/lib/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
+++ /dev/null
@@ -1,135 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import networkx as nx
-import numpy as np
-
-from random import choice
-
-from abc import ABC
-
-
-from .optimizer import Optimizer
-from ..estimators.structure_estimator import StructureEstimator
-from ..structure_graph.network_graph import NetworkGraph
-
-
-class HillClimbing(Optimizer):
-    """
-    Optimizer class that implement Hill Climbing Search
-    
-
-    :param node_id: current node's id
-    :type node_id: string
-    :param structure_estimator: a structure estimator object with the information about the net
-    :type structure_estimator: class:'StructureEstimator' 
-    :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
-    :type max_parents: int, optional
-    :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
-    :type iterations_number: int, optional
-    :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
-    :type patience: int, optional
-
-
-    
-    """
-    def __init__(self,
-                node_id:str,
-                structure_estimator: StructureEstimator,
-                max_parents:int = None,
-                iterations_number:int= 40,
-                patience:int = None
-                ):
-        """
-        Constructor
-        """
-        super().__init__(node_id, structure_estimator)
-        self.max_parents = max_parents
-        self.iterations_number = iterations_number
-        self.patience = patience
-        
-
-
-    def optimize_structure(self) -> typing.List:
-        """
-        Compute Optimization process for a structure_estimator by using a Hill Climbing Algorithm
-
-        :return: the estimated structure for the node
-        :rtype: List
-        """
-
-        #'Create the graph for the single node'
-        graph = NetworkGraph(self.structure_estimator._sample_path.structure)
-
-        'get the index for the current node'
-        node_index = self.structure_estimator._sample_path._structure.get_node_indx(self.node_id)
-
-        'list of prior edges'
-        prior_parents = set()
-
-        'Add the edges from prior knowledge'
-        for i in range(len(self.structure_estimator._removable_edges_matrix)):
-            if not self.structure_estimator._removable_edges_matrix[i][node_index]:
-                parent_id= self.structure_estimator._sample_path._structure.get_node_id(i)
-                prior_parents.add(parent_id)
-
-                'Add the node to the starting structure'
-                graph.add_edges([(parent_id, self.node_id)])
-
-
-
-        'get all the possible parents'
-        other_nodes =  [node for node in 
-                                            self.structure_estimator._sample_path.structure.nodes_labels if
-                                                                                            node != self.node_id and
-                                                                                            not prior_parents.__contains__(node)]
-        
-        actual_best_score = self.structure_estimator.get_score_from_graph(graph,self.node_id)
-
-        patince_count = 0
-        for i in range(self.iterations_number):
-            'choose a new random edge'
-            current_new_parent = choice(other_nodes)
-            current_edge =  (current_new_parent,self.node_id)
-            added = False
-            parent_removed = None 
-            
-
-            if graph.has_edge(current_edge):
-                graph.remove_edges([current_edge])
-            else:
-                'check the max_parents constraint'
-                if self.max_parents is not None:
-                    parents_list = graph.get_parents_by_id(self.node_id)
-                    if len(parents_list) >= self.max_parents :
-                        parent_removed = (choice(parents_list), self.node_id)
-                        graph.remove_edges([parent_removed])
-                graph.add_edges([current_edge])
-                added = True
-            #print('**************************')
-            current_score =  self.structure_estimator.get_score_from_graph(graph,self.node_id)
-
-
-            if current_score > actual_best_score:
-                'update current best score' 
-                actual_best_score = current_score
-                patince_count = 0
-            else:
-                'undo the last update'
-                if added:
-                    graph.remove_edges([current_edge])
-                    'If a parent was removed, add it again to the graph'
-                    if parent_removed is not None:
-                        graph.add_edges([parent_removed])
-                else:
-                    graph.add_edges([current_edge])
-                'update patience count'
-                patince_count += 1
-
-            if self.patience is not None and patince_count > self.patience:
-                break
-
-        print(f"finito variabile: {self.node_id}")
-        return graph.edges
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py b/build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py
deleted file mode 100644
index 1984f06..0000000
--- a/build/lib/PyCTBN/PyCTBN/optimizers/optimizer.py
+++ /dev/null
@@ -1,39 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import networkx as nx
-import numpy as np
-
-import abc 
-
-from ..estimators.structure_estimator import StructureEstimator
-
-
-
-class Optimizer(abc.ABC):
-    """
-    Interface class for all the optimizer's child PyCTBN
-
-    :param node_id: the node label
-    :type node_id: string
-    :param structure_estimator: A structureEstimator Object to predict the structure
-    :type structure_estimator: class:'StructureEstimator'
-    
-    """
-
-    def __init__(self, node_id:str, structure_estimator: StructureEstimator):
-        self.node_id = node_id
-        self.structure_estimator = structure_estimator
-        
-
-    @abc.abstractmethod
-    def optimize_structure(self) -> typing.List:
-        """
-        Compute Optimization process for a structure_estimator
-
-        :return: the estimated structure for the node
-        :rtype: List
-        """
-        pass
diff --git a/build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py b/build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py
deleted file mode 100644
index b7b2bc9..0000000
--- a/build/lib/PyCTBN/PyCTBN/optimizers/tabu_search.py
+++ /dev/null
@@ -1,188 +0,0 @@
-
-import itertools
-import json
-import typing
-
-import networkx as nx
-import numpy as np
-
-from random import choice,sample
-
-from abc import ABC
-
-
-from .optimizer import Optimizer
-from ..estimators.structure_estimator import StructureEstimator
-from ..structure_graph.network_graph import NetworkGraph
-
-import queue
-
-
-class TabuSearch(Optimizer):
-    """
-    Optimizer class that implement Tabu Search
-
-
-    :param node_id: current node's id
-    :type node_id: string
-    :param structure_estimator: a structure estimator object with the information about the net
-    :type structure_estimator: class:'StructureEstimator' 
-    :param max_parents: maximum number of parents for each variable. If None, disabled, default to None
-    :type max_parents: int, optional
-    :param iterations_number: maximum number of optimization algorithm's iteration, default to 40
-    :type iterations_number: int, optional
-    :param patience: number of iteration without any improvement before to stop the search.If None, disabled, default to None
-    :type patience: int, optional
-    :param tabu_length: maximum lenght of the data structures used in the optimization process, default to None
-    :type tabu_length: int, optional
-    :param tabu_rules_duration: number of iterations in which each rule keeps its value, default to None
-    :type tabu_rules_duration: int, optional
-
-    
-    """
-    def __init__(self,
-                node_id:str,
-                structure_estimator: StructureEstimator,
-                max_parents:int = None,
-                iterations_number:int= 40,
-                patience:int = None,
-                tabu_length:int = None,
-                tabu_rules_duration = None
-                ):
-        """
-        Constructor
-        """
-        super().__init__(node_id, structure_estimator)
-        self.max_parents = max_parents
-        self.iterations_number = iterations_number
-        self.patience = patience
-        self.tabu_length = tabu_length
-        self.tabu_rules_duration = tabu_rules_duration
-
-
-    def optimize_structure(self) -> typing.List:
-        """
-        Compute Optimization process for a structure_estimator by using a Hill Climbing Algorithm
-
-        :return: the estimated structure for the node
-        :rtype: List
-        """
-        print(f"tabu search is processing the structure of {self.node_id}")
-
-        'Create the graph for the single node'
-        graph = NetworkGraph(self.structure_estimator._sample_path.structure)
-
-        'get the index for the current node'
-        node_index = self.structure_estimator._sample_path._structure.get_node_indx(self.node_id)
-
-        'list of prior edges'
-        prior_parents = set()
-
-        'Add the edges from prior knowledge'
-        for i in range(len(self.structure_estimator._removable_edges_matrix)):
-            if not self.structure_estimator._removable_edges_matrix[i][node_index]:
-                parent_id= self.structure_estimator._sample_path._structure.get_node_id(i)
-                prior_parents.add(parent_id)
-
-                'Add the node to the starting structure'
-                graph.add_edges([(parent_id, self.node_id)])
-
-
-
-        'get all the possible parents'
-        other_nodes =  set([node for node in 
-                                            self.structure_estimator._sample_path.structure.nodes_labels if
-                                                                                            node != self.node_id and
-                                                                                            not prior_parents.__contains__(node)])
-
-        'calculate the score for the node without parents'
-        actual_best_score = self.structure_estimator.get_score_from_graph(graph,self.node_id)
-
-
-        'initialize tabu_length and tabu_rules_duration if None'
-        if self.tabu_length is None:
-            self.tabu_length = len(other_nodes)
-
-        if self.tabu_rules_duration is None:
-            self.tabu_rules_duration = len(other_nodes)
-
-        'inizialize the data structures'
-        tabu_set = set()
-        tabu_queue = queue.Queue()
-
-        patince_count = 0
-        tabu_count = 0 
-        for i in range(self.iterations_number):
-            
-            current_possible_nodes = other_nodes.difference(tabu_set)
-
-            'choose a new random edge according to tabu restiction'
-            if(len(current_possible_nodes) > 0):
-                current_new_parent = sample(current_possible_nodes,k=1)[0]
-            else:
-                current_new_parent = tabu_queue.get()
-                tabu_set.remove(current_new_parent)
-
-
-            
-            current_edge =  (current_new_parent,self.node_id)
-            added = False
-            parent_removed = None 
-
-            if graph.has_edge(current_edge):
-                graph.remove_edges([current_edge])
-            else:
-                'check the max_parents constraint'
-                if self.max_parents is not None:
-                    parents_list = graph.get_parents_by_id(self.node_id)
-                    if len(parents_list) >= self.max_parents :
-                        parent_removed = (choice(parents_list), self.node_id)
-                        graph.remove_edges([parent_removed])
-                graph.add_edges([current_edge])
-                added = True
-           
-            current_score =  self.structure_estimator.get_score_from_graph(graph,self.node_id)
-
-            if current_score > actual_best_score:
-                'update current best score' 
-                actual_best_score = current_score
-                patince_count = 0
-                'update tabu list'
-
-
-            else:
-                'undo the last update'
-                if added:
-                    graph.remove_edges([current_edge])
-                    'If a parent was removed, add it again to the graph'
-                    if parent_removed is not None:
-                        graph.add_edges([parent_removed])
-                else:
-                    graph.add_edges([current_edge])
-                'update patience count'
-                patince_count += 1
-                
-            
-            if tabu_queue.qsize() >= self.tabu_length:
-                    current_removed = tabu_queue.get()
-                    tabu_set.remove(current_removed)
-            'Add the node on the tabu list'
-            tabu_queue.put(current_new_parent)
-            tabu_set.add(current_new_parent)
-
-            tabu_count += 1
-
-            'Every tabu_rules_duration step remove an item from the tabu list '
-            if tabu_count % self.tabu_rules_duration == 0:
-                if tabu_queue.qsize() > 0:
-                    current_removed = tabu_queue.get()
-                    tabu_set.remove(current_removed)
-                    tabu_count = 0
-                else:
-                    tabu_count = 0
-
-            if self.patience is not None and patince_count > self.patience:
-                break
-
-        print(f"finito variabile: {self.node_id}")
-        return graph.edges
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py b/build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py
deleted file mode 100644
index 85f18a2..0000000
--- a/build/lib/PyCTBN/PyCTBN/structure_graph/__init__.py
+++ /dev/null
@@ -1,6 +0,0 @@
-from .conditional_intensity_matrix import ConditionalIntensityMatrix
-from .network_graph import NetworkGraph
-from .sample_path import SamplePath
-from .set_of_cims import SetOfCims
-from .structure import Structure
-from .trajectory import Trajectory
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py b/build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
deleted file mode 100644
index 4abfdd0..0000000
--- a/build/lib/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
+++ /dev/null
@@ -1,42 +0,0 @@
-import numpy as np
-
-
-class ConditionalIntensityMatrix(object):
-    """Abstracts the Conditional Intesity matrix of a node as aggregation of the state residence times vector
-    and state transition matrix and the actual CIM matrix.
-
-    :param state_residence_times: state residence times vector
-    :type state_residence_times: numpy.array
-    :param state_transition_matrix: the transitions count matrix
-    :type state_transition_matrix: numpy.ndArray
-    :_cim: the actual cim of the node
-    """
-    def __init__(self, state_residence_times: np.array, state_transition_matrix: np.array):
-        """Constructor Method
-        """
-        self._state_residence_times = state_residence_times
-        self._state_transition_matrix = state_transition_matrix
-        self._cim = self.state_transition_matrix.astype(np.float64)
-
-    def compute_cim_coefficients(self) -> None:
-        """Compute the coefficients of the matrix _cim by using the following equality q_xx' = M[x, x'] / T[x].
-        The class member ``_cim`` will contain the computed cim
-        """
-        np.fill_diagonal(self._cim, self._cim.diagonal() * -1)
-        self._cim = ((self._cim.T + 1) / (self._state_residence_times + 1)).T
-
-    @property
-    def state_residence_times(self) -> np.ndarray:
-        return self._state_residence_times
-
-    @property
-    def state_transition_matrix(self) -> np.ndarray:
-        return self._state_transition_matrix
-
-    @property
-    def cim(self) -> np.ndarray:
-        return self._cim
-
-    def __repr__(self):
-        return 'CIM:\n' + str(self.cim)
-
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py b/build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py
deleted file mode 100644
index 6fb3639..0000000
--- a/build/lib/PyCTBN/PyCTBN/structure_graph/network_graph.py
+++ /dev/null
@@ -1,293 +0,0 @@
-
-import typing
-
-import networkx as nx
-import numpy as np
-
-from .structure import Structure
-
-
-class NetworkGraph(object):
-    """Abstracts the infos contained in the Structure class in the form of a directed graph.
-    Has the task of creating all the necessary filtering and indexing structures for parameters estimation
-
-    :param graph_struct: the ``Structure`` object from which infos about the net will be extracted
-    :type graph_struct: Structure
-    :_graph: directed graph
-    :_aggregated_info_about_nodes_parents: a structure that contains all the necessary infos
-        about every parents of the node of which all the indexing and filtering structures will be constructed.
-    :_time_scalar_indexing_structure: the indexing structure for state res time estimation
-    :_transition_scalar_indexing_structure: the indexing structure for transition computation
-    :_time_filtering: the columns filtering structure used in the computation of the state res times
-    :_transition_filtering: the columns filtering structure used in the computation of the transition
-        from one state to another
-    :_p_combs_structure: all the possible parents states combination for the node of interest
-    """
-
-    def __init__(self, graph_struct: Structure):
-        """Constructor Method
-        """
-        self._graph_struct = graph_struct
-        self._graph = nx.DiGraph()
-        self._aggregated_info_about_nodes_parents = None
-        self._time_scalar_indexing_structure = None
-        self._transition_scalar_indexing_structure = None
-        self._time_filtering = None
-        self._transition_filtering = None
-        self._p_combs_structure = None
-
-    #def init_graph(self):
-    #    self.add_nodes(self._nodes_labels)
-    #    self.add_edges(self.graph_struct.edges)
-    #    self.aggregated_info_about_nodes_parents = self.get_ord_set_of_par_of_all_nodes()
-    #    self._fancy_indexing = self.build_fancy_indexing_structure(0)
-    #    self.build_scalar_indexing_structures()
-    #    self.build_time_columns_filtering_structure()
-    #    self.build_transition_columns_filtering_structure()
-    #    self._p_combs_structure = self.build_p_combs_structure()
-
-    def fast_init(self, node_id: str) -> None:
-        """Initializes all the necessary structures for parameters estimation of the node identified by the label
-        node_id
-
-        :param node_id: the label of the node
-        :type node_id: string
-        """
-        self.add_nodes(self._graph_struct.nodes_labels)
-        self.add_edges(self._graph_struct.edges)
-        self._aggregated_info_about_nodes_parents = self.get_ordered_by_indx_set_of_parents(node_id)
-        p_indxs = self._aggregated_info_about_nodes_parents[1]
-        p_vals = self._aggregated_info_about_nodes_parents[2]
-        node_states = self.get_states_number(node_id)
-        node_indx = self.get_node_indx(node_id)
-        cols_number = self._graph_struct.total_variables_number
-        self._time_scalar_indexing_structure = NetworkGraph.\
-            build_time_scalar_indexing_structure_for_a_node(node_states, p_vals)
-        self._transition_scalar_indexing_structure = NetworkGraph.\
-            build_transition_scalar_indexing_structure_for_a_node(node_states, p_vals)
-        self._time_filtering = NetworkGraph.build_time_columns_filtering_for_a_node(node_indx, p_indxs)
-        self._transition_filtering = NetworkGraph.build_transition_filtering_for_a_node(node_indx, p_indxs, cols_number)
-        self._p_combs_structure = NetworkGraph.build_p_comb_structure_for_a_node(p_vals)
-
-    def add_nodes(self, list_of_nodes: typing.List) -> None:
-        """Adds the nodes to the ``_graph`` contained in the list of nodes ``list_of_nodes``.
-        Sets all the properties that identify a nodes (index, positional index, cardinality)
-
-        :param list_of_nodes: the nodes to add to ``_graph``
-        :type list_of_nodes: List
-        """
-        nodes_indxs = self._graph_struct.nodes_indexes
-        nodes_vals = self._graph_struct.nodes_values
-        pos = 0
-        for id, node_indx, node_val in zip(list_of_nodes, nodes_indxs, nodes_vals):
-            self._graph.add_node(id, indx=node_indx, val=node_val, pos_indx=pos)
-            pos += 1
-
-    def has_edge(self,edge:tuple)-> bool:
-        """
-        Check if the graph contains a specific edge
-
-        Parameters:
-            edge: a tuple that rappresents the edge
-        Returns:
-            bool
-        """
-        return self._graph.has_edge(edge[0],edge[1])
-
-    def add_edges(self, list_of_edges: typing.List) -> None:
-        """Add the edges to the ``_graph`` contained in the list ``list_of_edges``.
-
-        :param list_of_edges: the list containing of tuples containing the edges
-        :type list_of_edges: List
-        """
-        self._graph.add_edges_from(list_of_edges)
-
-    def remove_node(self, node_id: str) -> None:
-        """Remove the node ``node_id`` from all the class members.
-        Initialize all the filtering/indexing structures.
-        """
-        self._graph.remove_node(node_id)
-        self._graph_struct.remove_node(node_id)
-        self.clear_indexing_filtering_structures()
-
-    def clear_indexing_filtering_structures(self) -> None:
-        """Initialize all the filtering/indexing structures.
-        """
-        self._aggregated_info_about_nodes_parents = None
-        self._time_scalar_indexing_structure = None
-        self._transition_scalar_indexing_structure = None
-        self._time_filtering = None
-        self._transition_filtering = None
-        self._p_combs_structure = None
-
-    def get_ordered_by_indx_set_of_parents(self, node: str) -> typing.Tuple:
-        """Builds the aggregated structure that holds all the infos relative to the parent set of the node, namely
-        (parents_labels, parents_indexes, parents_cardinalities).
-
-        :param node: the label of the node
-        :type node: string
-        :return: a tuple containing all the parent set infos
-        :rtype: Tuple
-        """
-        parents = self.get_parents_by_id(node)
-        nodes = self._graph_struct.nodes_labels
-        d = {v: i for i, v in enumerate(nodes)}
-        sorted_parents = sorted(parents, key=lambda v: d[v])
-        get_node_indx = self.get_node_indx
-        p_indxes = [get_node_indx(node) for node in sorted_parents]
-        p_values = [self.get_states_number(node) for node in sorted_parents]
-        return sorted_parents, p_indxes, p_values
-
-    def remove_edges(self, list_of_edges: typing.List) -> None:
-        """Remove the edges to the graph contained in the list list_of_edges.
-        
-        :param list_of_edges: The edges to remove from the graph
-        :type list_of_edges: List
-        """
-        self._graph.remove_edges_from(list_of_edges)
-
-    @staticmethod
-    def build_time_scalar_indexing_structure_for_a_node(node_states: int,
-                                                        parents_vals: typing.List) -> np.ndarray:
-        """Builds an indexing structure for the computation of state residence times values.
-
-        :param node_states: the node cardinality
-        :type node_states: int
-        :param parents_vals: the caridinalites of the node's parents
-        :type parents_vals: List
-        :return: The time indexing structure
-        :rtype: numpy.ndArray
-        """
-        T_vector = np.array([node_states])
-        T_vector = np.append(T_vector, parents_vals)
-        T_vector = T_vector.cumprod().astype(np.int)
-        return T_vector
-
-    @staticmethod
-    def build_transition_scalar_indexing_structure_for_a_node(node_states_number: int, parents_vals: typing.List) \
-            -> np.ndarray:
-        """Builds an indexing structure for the computation of state transitions values.
-
-        :param node_states_number: the node cardinality
-        :type node_states_number: int
-        :param parents_vals: the caridinalites of the node's parents
-        :type parents_vals: List
-        :return: The transition indexing structure
-        :rtype: numpy.ndArray
-        """
-        M_vector = np.array([node_states_number,
-                             node_states_number])
-        M_vector = np.append(M_vector, parents_vals)
-        M_vector = M_vector.cumprod().astype(np.int)
-        return M_vector
-
-    @staticmethod
-    def build_time_columns_filtering_for_a_node(node_indx: int, p_indxs: typing.List) -> np.ndarray:
-        """
-        Builds the necessary structure to filter the desired columns indicated by ``node_indx`` and ``p_indxs``
-        in the dataset.
-        This structute will be used in the computation of the state res times.
-        :param node_indx: the index of the node
-        :type node_indx: int
-        :param p_indxs: the indexes of the node's parents
-        :type p_indxs: List
-        :return: The filtering structure for times estimation
-        :rtype: numpy.ndArray
-        """
-        return np.append(np.array([node_indx], dtype=np.int), p_indxs).astype(np.int)
-
-    @staticmethod
-    def build_transition_filtering_for_a_node(node_indx: int, p_indxs: typing.List, nodes_number: int) \
-            -> np.ndarray:
-        """Builds the necessary structure to filter the desired columns indicated by ``node_indx`` and ``p_indxs``
-        in the dataset.
-        This structure will be used in the computation of the state transitions values.
-        :param node_indx: the index of the node
-        :type node_indx: int
-        :param p_indxs: the indexes of the node's parents
-        :type p_indxs: List
-        :param nodes_number: the total number of nodes in the dataset
-        :type nodes_number: int
-        :return: The filtering structure for transitions estimation
-        :rtype: numpy.ndArray
-        """
-        return np.array([node_indx + nodes_number, node_indx, *p_indxs], dtype=np.int)
-
-    @staticmethod
-    def build_p_comb_structure_for_a_node(parents_values: typing.List) -> np.ndarray:
-        """
-        Builds the combinatorial structure that contains the combinations of all the values contained in
-        ``parents_values``.
-
-        :param parents_values: the cardinalities of the nodes
-        :type parents_values: List
-        :return: A numpy matrix containing a grid of the combinations
-        :rtype: numpy.ndArray
-        """
-        tmp = []
-        for val in parents_values:
-            tmp.append([x for x in range(val)])
-        if len(parents_values) > 0:
-            parents_comb = np.array(np.meshgrid(*tmp)).T.reshape(-1, len(parents_values))
-            if len(parents_values) > 1:
-                tmp_comb = parents_comb[:, 1].copy()
-                parents_comb[:, 1] = parents_comb[:, 0].copy()
-                parents_comb[:, 0] = tmp_comb
-        else:
-            parents_comb = np.array([[]], dtype=np.int)
-        return parents_comb
-
-    def get_parents_by_id(self, node_id) -> typing.List:
-        """Returns a list of labels of the parents of the node ``node_id``
-
-        :param node_id: the node label
-        :type node_id: string
-        :return: a List of labels of the parents
-        :rtype: List
-        """
-        return list(self._graph.predecessors(node_id))
-
-    def get_states_number(self, node_id) -> int:
-        return self._graph.nodes[node_id]['val']
-
-    def get_node_indx(self, node_id) -> int:
-        return nx.get_node_attributes(self._graph, 'indx')[node_id]
-
-    def get_positional_node_indx(self, node_id) -> int:
-        return self._graph.nodes[node_id]['pos_indx']
-
-    @property
-    def nodes(self) -> typing.List:
-        return self._graph_struct.nodes_labels
-
-    @property
-    def edges(self) -> typing.List:
-        return list(self._graph.edges)
-
-    @property
-    def nodes_indexes(self) -> np.ndarray:
-        return self._graph_struct.nodes_indexes
-
-    @property
-    def nodes_values(self) -> np.ndarray:
-        return self._graph_struct.nodes_values
-
-    @property
-    def time_scalar_indexing_strucure(self) -> np.ndarray:
-        return self._time_scalar_indexing_structure
-
-    @property
-    def time_filtering(self) -> np.ndarray:
-        return self._time_filtering
-
-    @property
-    def transition_scalar_indexing_structure(self) -> np.ndarray:
-        return self._transition_scalar_indexing_structure
-
-    @property
-    def transition_filtering(self) -> np.ndarray:
-        return self._transition_filtering
-
-    @property
-    def p_combs(self) -> np.ndarray:
-        return self._p_combs_structure
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py b/build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py
deleted file mode 100644
index 88e9649..0000000
--- a/build/lib/PyCTBN/PyCTBN/structure_graph/sample_path.py
+++ /dev/null
@@ -1,93 +0,0 @@
-
-
-import numpy as np
-import pandas as pd
-
-from .structure import Structure
-from .trajectory import Trajectory
-from ..utility.abstract_importer import AbstractImporter
-
-
-MESSAGE_HAS_TO_CONTAIN_EXCEPTION = 'The importer object has to contain the all processed data!'
-
-
-class SamplePath(object):
-    """Aggregates all the informations about the trajectories, the real structure of the sampled net and variables
-    cardinalites. Has the task of creating the objects ``Trajectory`` and ``Structure`` that will
-    contain the mentioned data.
-
-    :param importer: the Importer object which contains the imported and processed data
-    :type importer: AbstractImporter
-    :_trajectories: the ``Trajectory`` object that will contain all the concatenated trajectories
-    :_structure: the ``Structure`` Object that will contain all the structural infos about the net
-    :_total_variables_count: the number of variables in the net
-    """
-    def __init__(self, importer: AbstractImporter):
-        """Constructor Method
-        """
-        self._importer = importer
-        if self._importer._df_variables is None or self._importer._concatenated_samples is None:
-            raise RuntimeError()
-        if self._importer._df_variables.empty:
-            raise RuntimeError(MESSAGE_HAS_TO_CONTAIN_EXCEPTION)
-        if isinstance(self._importer._concatenated_samples, pd.DataFrame) and\
-            self._importer._concatenated_samples.empty:
-                raise RuntimeError(MESSAGE_HAS_TO_CONTAIN_EXCEPTION)
-        if isinstance(self._importer._concatenated_samples, np.ndarray) and\
-            self._importer._concatenated_samples.size == 0:
-                raise RuntimeError(MESSAGE_HAS_TO_CONTAIN_EXCEPTION)
-        self._trajectories = None
-        self._structure = None
-        self._total_variables_count = None
-
-    def build_trajectories(self) -> None:
-        """Builds the Trajectory object that will contain all the trajectories.
-        Clears all the unused dataframes in ``_importer`` Object
-        """
-        self._trajectories = \
-            Trajectory(self._importer.build_list_of_samples_array(self._importer.concatenated_samples),
-                len(self._importer.sorter) + 1)
-        self._importer.clear_concatenated_frame()
-
-    def build_structure(self) -> None:
-        """
-        Builds the ``Structure`` object that aggregates all the infos about the net.
-        """
-        if self._importer.sorter != self._importer.variables.iloc[:, 0].to_list():
-            raise RuntimeError("The Dataset columns order have to match the order of labels in the variables Frame!")
-
-        self._total_variables_count = len(self._importer.sorter)
-        labels = self._importer.variables.iloc[:, 0].to_list()
-        indxs = self._importer.variables.index.to_numpy()
-        vals = self._importer.variables.iloc[:, 1].to_numpy()
-        if self._importer.structure is None or self._importer.structure.empty:
-            edges = []
-        else:
-            edges = list(self._importer.structure.to_records(index=False))
-        self._structure = Structure(labels, indxs, vals, edges,
-                                       self._total_variables_count)
-
-    def clear_memory(self):
-        self._importer._raw_data = [] 
-
-    @property
-    def trajectories(self) -> Trajectory:
-        return self._trajectories
-
-    @property
-    def structure(self) -> Structure:
-        return self._structure
-
-    @property
-    def total_variables_count(self) -> int:
-        return self._total_variables_count
-
-    @property
-    def has_prior_net_structure(self) -> bool:
-        return bool(self._structure.edges)
-
-
-
-
-
-
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py b/build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
deleted file mode 100644
index 81caff5..0000000
--- a/build/lib/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
+++ /dev/null
@@ -1,97 +0,0 @@
-
-
-import typing
-
-import numpy as np
-
-from .conditional_intensity_matrix import ConditionalIntensityMatrix
-
-
-class SetOfCims(object):
-    """Aggregates all the CIMS of the node identified by the label _node_id.
-
-    :param node_id: the node label
-    :type node_ind: string
-    :param parents_states_number: the cardinalities of the parents
-    :type parents_states_number: List
-    :param node_states_number: the caridinality of the node
-    :type node_states_number: int
-    :param p_combs: the p_comb structure bound to this node
-    :type p_combs: numpy.ndArray
-    :_state_residence_time: matrix containing all the state residence time vectors for the node
-    :_transition_matrices: matrix containing all the transition matrices for the node
-    :_actual_cims: the cims of the node
-    """
-
-    def __init__(self, node_id: str, parents_states_number: typing.List, node_states_number: int, p_combs: np.ndarray):
-        """Constructor Method
-        """
-        self._node_id = node_id
-        self._parents_states_number = parents_states_number
-        self._node_states_number = node_states_number
-        self._actual_cims = []
-        self._state_residence_times = None
-        self._transition_matrices = None
-        self._p_combs = p_combs
-        self.build_times_and_transitions_structures()
-
-    def build_times_and_transitions_structures(self) -> None:
-        """Initializes at the correct dimensions the state residence times matrix and the state transition matrices.
-        """
-        if not self._parents_states_number:
-            self._state_residence_times = np.zeros((1, self._node_states_number), dtype=np.float)
-            self._transition_matrices = np.zeros((1, self._node_states_number, self._node_states_number), dtype=np.int)
-        else:
-            self._state_residence_times = \
-                np.zeros((np.prod(self._parents_states_number), self._node_states_number), dtype=np.float)
-            self._transition_matrices = np.zeros([np.prod(self._parents_states_number), self._node_states_number,
-                                                  self._node_states_number], dtype=np.int)
-
-    def build_cims(self, state_res_times: np.ndarray, transition_matrices: np.ndarray) -> None:
-        """Build the ``ConditionalIntensityMatrix`` objects given the state residence times and transitions matrices.
-        Compute the cim coefficients.The class member ``_actual_cims`` will contain the computed cims.
-
-        :param state_res_times: the state residence times matrix
-        :type state_res_times: numpy.ndArray
-        :param transition_matrices: the transition matrices
-        :type transition_matrices: numpy.ndArray
-        """
-        for state_res_time_vector, transition_matrix in zip(state_res_times, transition_matrices):
-            cim_to_add = ConditionalIntensityMatrix(state_res_time_vector, transition_matrix)
-            cim_to_add.compute_cim_coefficients()
-            self._actual_cims.append(cim_to_add)
-        self._actual_cims = np.array(self._actual_cims)
-        self._transition_matrices = None
-        self._state_residence_times = None
-
-    def filter_cims_with_mask(self, mask_arr: np.ndarray, comb: typing.List) -> np.ndarray:
-        """Filter the cims contained in the array ``_actual_cims`` given the boolean mask ``mask_arr`` and the index
-        ``comb``.
-
-        :param mask_arr: the boolean mask that indicates which parent to consider
-        :type mask_arr: numpy.array
-        :param comb: the state/s of the filtered parents
-        :type comb: numpy.array
-        :return: Array of ``ConditionalIntensityMatrix`` objects
-        :rtype: numpy.array
-        """
-        if mask_arr.size <= 1:
-            return self._actual_cims
-        else:
-            flat_indxs = np.argwhere(np.all(self._p_combs[:, mask_arr] == comb, axis=1)).ravel()
-            return self._actual_cims[flat_indxs]
-
-    @property
-    def actual_cims(self) -> np.ndarray:
-        return self._actual_cims
-
-    @property
-    def p_combs(self) -> np.ndarray:
-        return self._p_combs
-
-    def get_cims_number(self):
-        return len(self._actual_cims)
-
-
-
-
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/structure.py b/build/lib/PyCTBN/PyCTBN/structure_graph/structure.py
deleted file mode 100644
index f79c875..0000000
--- a/build/lib/PyCTBN/PyCTBN/structure_graph/structure.py
+++ /dev/null
@@ -1,124 +0,0 @@
-
-import typing as ty
-
-import numpy as np
-
-
-class Structure(object):
-    """Contains all the infos about the network structure(nodes labels, nodes caridinalites, edges, indexes)
-
-    :param nodes_labels_list: the symbolic names of the variables
-    :type nodes_labels_list: List
-    :param nodes_indexes_arr: the indexes of the nodes
-    :type nodes_indexes_arr: numpy.ndArray
-    :param nodes_vals_arr: the cardinalites of the nodes
-    :type nodes_vals_arr: numpy.ndArray
-    :param edges_list: the edges of the network
-    :type edges_list: List
-    :param total_variables_number: the total number of variables in the dataset
-    :type total_variables_number: int
-    """
-
-    def __init__(self, nodes_labels_list: ty.List, nodes_indexes_arr: np.ndarray, nodes_vals_arr: np.ndarray,
-                 edges_list: ty.List, total_variables_number: int):
-        """Constructor Method
-        """
-        self._nodes_labels_list = nodes_labels_list
-        self._nodes_indexes_arr = nodes_indexes_arr
-        self._nodes_vals_arr = nodes_vals_arr
-        self._edges_list = edges_list
-        self._total_variables_number = total_variables_number
-
-    def remove_node(self, node_id: str) -> None:
-        """Remove the node ``node_id`` from all the class members.
-        The class member ``_total_variables_number`` since it refers to the total number of variables in the dataset.
-        """
-        node_positional_indx = self._nodes_labels_list.index(node_id)
-        del self._nodes_labels_list[node_positional_indx]
-        self._nodes_indexes_arr = np.delete(self._nodes_indexes_arr, node_positional_indx)
-        self._nodes_vals_arr = np.delete(self._nodes_vals_arr, node_positional_indx)
-        self._edges_list = [(from_node, to_node) for (from_node, to_node) in self._edges_list if (from_node != node_id
-                                                                                        and to_node != node_id)]
-
-    @property
-    def edges(self) -> ty.List:
-        return self._edges_list
-
-    @property
-    def nodes_labels(self) -> ty.List:
-        return self._nodes_labels_list
-
-    @property
-    def nodes_indexes(self) -> np.ndarray:
-        return self._nodes_indexes_arr
-
-    @property
-    def nodes_values(self) -> np.ndarray:
-        return self._nodes_vals_arr
-
-    @property
-    def total_variables_number(self) -> int:
-        return self._total_variables_number
-
-    def get_node_id(self, node_indx: int) -> str:
-        """Given the ``node_index`` returns the node label.
-
-        :param node_indx: the node index
-        :type node_indx: int
-        :return: the node label
-        :rtype: string
-        """
-        return self._nodes_labels_list[node_indx]
-
-    def clean_structure_edges(self):
-        self._edges_list = list()
-
-    def add_edge(self,edge: tuple):
-        self._edges_list.append(edge)
-
-    
-    def remove_edge(self,edge: tuple):
-        self._edges_list.remove(edge)
-
-    def contains_edge(self,edge:tuple) -> bool:
-        return edge in self._edges_list
-
-    def get_node_indx(self, node_id: str) -> int:
-        """Given the ``node_index`` returns the node label.
-
-        :param node_id: the node label
-        :type node_id: string
-        :return: the node index
-        :rtype: int
-        """
-        pos_indx = self._nodes_labels_list.index(node_id)
-        return self._nodes_indexes_arr[pos_indx]
-
-    def get_positional_node_indx(self, node_id: str) -> int:
-        return self._nodes_labels_list.index(node_id)
-
-    def get_states_number(self, node: str) -> int:
-        """Given the node label ``node`` returns the cardinality of the node.
-
-        :param node: the node label
-        :type node: string
-        :return: the node cardinality
-        :rtype: int
-        """
-        pos_indx = self._nodes_labels_list.index(node)
-        return self._nodes_vals_arr[pos_indx]
-
-    def __repr__(self):
-        return "Variables:\n" + str(self._nodes_labels_list) +"\nValues:\n"+ str(self._nodes_vals_arr) +\
-               "\nEdges: \n" + str(self._edges_list)
-
-    def __eq__(self, other):
-        """Overrides the default implementation"""
-        if isinstance(other, Structure):
-            return set(self._nodes_labels_list) == set(other._nodes_labels_list) and \
-                   np.array_equal(self._nodes_vals_arr, other._nodes_vals_arr) and \
-                   np.array_equal(self._nodes_indexes_arr, other._nodes_indexes_arr) and \
-                   self._edges_list == other._edges_list
-
-        return False
-
diff --git a/build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py b/build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py
deleted file mode 100644
index 36899b3..0000000
--- a/build/lib/PyCTBN/PyCTBN/structure_graph/trajectory.py
+++ /dev/null
@@ -1,45 +0,0 @@
-
-import typing
-
-import numpy as np
-
-
-class Trajectory(object):
-    """ Abstracts the infos about a complete set of trajectories, represented as a numpy array of doubles
-    (the time deltas) and a numpy matrix of ints (the changes of states).
-
-    :param list_of_columns: the list containing the times array and values matrix
-    :type list_of_columns: List
-    :param original_cols_number: total number of cols in the data
-    :type original_cols_number: int
-    :_actual_trajectory: the trajectory containing also the duplicated/shifted values
-    :_times: the array containing the time deltas
-    """
-
-    def __init__(self, list_of_columns: typing.List, original_cols_number: int):
-        """Constructor Method
-        """
-        self._times = list_of_columns[0]
-        self._actual_trajectory = list_of_columns[1]
-        self._original_cols_number = original_cols_number
-
-    @property
-    def trajectory(self) -> np.ndarray:
-        return self._actual_trajectory[:, :self._original_cols_number - 1]
-
-    @property
-    def complete_trajectory(self) -> np.ndarray:
-        return self._actual_trajectory
-
-    @property
-    def times(self):
-        return self._times
-
-    def size(self):
-        return self._actual_trajectory.shape[0]
-
-    def __repr__(self):
-        return "Complete Trajectory Rows: " + str(self.size()) + "\n" + self.complete_trajectory.__repr__() + \
-               "\nTimes Rows:" + str(self.times.size) + "\n" + self.times.__repr__()
-
-
diff --git a/build/lib/PyCTBN/PyCTBN/utility/__init__.py b/build/lib/PyCTBN/PyCTBN/utility/__init__.py
deleted file mode 100644
index f79749c..0000000
--- a/build/lib/PyCTBN/PyCTBN/utility/__init__.py
+++ /dev/null
@@ -1,4 +0,0 @@
-from .abstract_importer import AbstractImporter
-from .cache import Cache
-from .json_importer import JsonImporter
-from .sample_importer import SampleImporter
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py b/build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py
deleted file mode 100644
index 8984b4d..0000000
--- a/build/lib/PyCTBN/PyCTBN/utility/abstract_importer.py
+++ /dev/null
@@ -1,163 +0,0 @@
-
-import typing
-from abc import ABC, abstractmethod
-
-import numpy as np
-import pandas as pd
-
-import copy
-
-
-
-class AbstractImporter(ABC):
-    """Abstract class that exposes all the necessary methods to process the trajectories and the net structure.
-
-    :param file_path: the file path, or dataset name if you import already processed data
-    :type file_path: str
-    :param trajectory_list: Dataframe or numpy array containing the concatenation of all the processed trajectories
-    :type trajectory_list: typing.Union[pandas.DataFrame, numpy.ndarray]
-    :param variables: Dataframe containing the nodes labels and cardinalities
-    :type variables: pandas.DataFrame
-    :prior_net_structure: Dataframe containing the structure of the network (edges)
-    :type prior_net_structure: pandas.DataFrame
-    :_sorter: A list containing the variables labels in the SAME order as the columns in ``concatenated_samples``
-
-    .. warning::
-        The parameters ``variables`` and ``prior_net_structure`` HAVE to be properly constructed
-        as Pandas Dataframes with the following structure:
-        Header of _df_structure = [From_Node | To_Node]
-        Header of _df_variables = [Variable_Label | Variable_Cardinality]
-        See the tutorial on how to construct a correct ``concatenated_samples`` Dataframe/ndarray.
-
-    .. note::
-        See :class:``JsonImporter`` for an example implementation
-
-    """
-
-    def __init__(self, file_path: str = None, trajectory_list: typing.Union[pd.DataFrame, np.ndarray] = None,
-                 variables: pd.DataFrame = None, prior_net_structure: pd.DataFrame = None):
-        """Constructor
-        """
-        self._file_path = file_path
-        self._df_samples_list = trajectory_list
-        self._concatenated_samples = []
-        self._df_variables = variables
-        self._df_structure = prior_net_structure
-        self._sorter = None
-        super().__init__()
-
-    @abstractmethod
-    def build_sorter(self, trajecory_header: object) -> typing.List:
-        """Initializes the ``_sorter`` class member from a trajectory dataframe, exctracting the header of the frame
-        and keeping ONLY the variables symbolic labels, cutting out the time label in the header.
-
-        :param trajecory_header: an object that will be used to define the header
-        :type trajecory_header: object
-        :return: A list containing the processed header.
-        :rtype: List
-        """
-        pass
-
-    def compute_row_delta_sigle_samples_frame(self, sample_frame: pd.DataFrame,
-                                              columns_header: typing.List, shifted_cols_header: typing.List) \
-            -> pd.DataFrame:
-        """Computes the difference between each value present in th time column.
-        Copies and shift by one position up all the values present in the remaining columns.
-
-        :param sample_frame: the traj to be processed
-        :type sample_frame: pandas.Dataframe
-        :param columns_header: the original header of sample_frame
-        :type columns_header: List
-        :param shifted_cols_header: a copy of columns_header with changed names of the contents
-        :type shifted_cols_header: List
-        :return: The processed dataframe
-        :rtype: pandas.Dataframe
-
-        .. warning::
-            the Dataframe ``sample_frame`` has to follow the column structure of this header:
-            Header of sample_frame = [Time | Variable values]
-        """
-        sample_frame = copy.deepcopy(sample_frame)
-        sample_frame.iloc[:, 0] = sample_frame.iloc[:, 0].diff().shift(-1)
-        shifted_cols = sample_frame[columns_header].shift(-1).fillna(0).astype('int32')
-        shifted_cols.columns = shifted_cols_header
-        sample_frame = sample_frame.assign(**shifted_cols)
-        sample_frame.drop(sample_frame.tail(1).index, inplace=True)
-        return sample_frame
-
-    def compute_row_delta_in_all_samples_frames(self, df_samples_list: typing.List) -> None:
-        """Calls the method ``compute_row_delta_sigle_samples_frame`` on every dataframe present in the list
-        ``df_samples_list``.
-        Concatenates the result in the dataframe ``concatanated_samples``
-
-        :param df_samples_list: the datframe's list to be processed and concatenated
-        :type df_samples_list: List
-
-        .. warning::
-            The Dataframe sample_frame has to follow the column structure of this header:
-            Header of sample_frame = [Time | Variable values]
-            The class member self._sorter HAS to be properly INITIALIZED (See class members definition doc)
-        .. note::
-            After the call of this method the class member ``concatanated_samples`` will contain all processed
-            and merged trajectories
-        """
-        if not self._sorter:
-            raise RuntimeError("The class member self._sorter has to be INITIALIZED!")
-        shifted_cols_header = [s + "S" for s in self._sorter]
-        compute_row_delta = self.compute_row_delta_sigle_samples_frame
-        proc_samples_list = [compute_row_delta(sample, self._sorter, shifted_cols_header)
-                                for sample in df_samples_list]
-        self._concatenated_samples = pd.concat(proc_samples_list)
-
-        complete_header = self._sorter[:]
-        complete_header.insert(0,'Time')
-        complete_header.extend(shifted_cols_header)
-        self._concatenated_samples = self._concatenated_samples[complete_header]
-
-    def build_list_of_samples_array(self, concatenated_sample: pd.DataFrame) -> typing.List:
-        """Builds a List containing the the delta times numpy array, and the complete transitions matrix
-
-        :param concatenated_sample: the dataframe/array from which the time, and transitions matrix have to be extracted
-            and converted
-        :type concatenated_sample: pandas.Dataframe
-        :return: the resulting list of numpy arrays
-        :rtype: List
-        """
-        
-        concatenated_array = concatenated_sample.to_numpy()
-        columns_list = [concatenated_array[:, 0], concatenated_array[:, 1:].astype(int)]
-
-        return columns_list
-
-    def clear_concatenated_frame(self) -> None:
-        """Removes all values in the dataframe concatenated_samples.
-         """
-        if isinstance(self._concatenated_samples, pd.DataFrame):
-            self._concatenated_samples = self._concatenated_samples.iloc[0:0]
-
-    @abstractmethod
-    def dataset_id(self) -> object:
-        """If the original dataset contains multiple dataset, this method returns a unique id to identify the current
-        dataset
-        """
-        pass
-
-    @property
-    def concatenated_samples(self) -> pd.DataFrame:
-        return self._concatenated_samples
-
-    @property
-    def variables(self) -> pd.DataFrame:
-        return self._df_variables
-
-    @property
-    def structure(self) -> pd.DataFrame:
-        return self._df_structure
-
-    @property
-    def sorter(self) -> typing.List:
-        return self._sorter
-
-    @property
-    def file_path(self) -> str:
-        return self._file_path
diff --git a/build/lib/PyCTBN/PyCTBN/utility/cache.py b/build/lib/PyCTBN/PyCTBN/utility/cache.py
deleted file mode 100644
index 5191af3..0000000
--- a/build/lib/PyCTBN/PyCTBN/utility/cache.py
+++ /dev/null
@@ -1,54 +0,0 @@
-
-import typing
-
-from ..structure_graph.set_of_cims import SetOfCims 
-
-
-class Cache:
-    """This class acts as a cache of ``SetOfCims`` objects for a node.
-
-    :__list_of_sets_of_parents: a list of ``Sets`` objects of the parents to which the cim in cache at SAME
-        index is related
-    :__actual_cache: a list of setOfCims objects
-    """
-
-    def __init__(self):
-        """Constructor Method
-        """
-        self._list_of_sets_of_parents = []
-        self._actual_cache = []
-
-    def find(self, parents_comb: typing.Set): #typing.Union[typing.Set, str]
-        """
-        Tries to find in cache given the symbolic parents combination ``parents_comb`` the ``SetOfCims``
-        related to that ``parents_comb``.
-
-        :param parents_comb: the parents related to that ``SetOfCims``
-        :type parents_comb: Set
-        :return: A ``SetOfCims`` object if the ``parents_comb`` index is found in ``__list_of_sets_of_parents``.
-            None otherwise.
-        :rtype: SetOfCims
-        """
-        try:
-            result = self._actual_cache[self._list_of_sets_of_parents.index(parents_comb)]
-            return result
-        except ValueError:
-            return None
-
-    def put(self, parents_comb: typing.Set, socim: SetOfCims):
-        """Place in cache the ``SetOfCims`` object, and the related symbolic index ``parents_comb`` in
-        ``__list_of_sets_of_parents``.
-
-        :param parents_comb: the symbolic set index
-        :type parents_comb: Set
-        :param socim: the related SetOfCims object
-        :type socim: SetOfCims
-        """
-        self._list_of_sets_of_parents.append(parents_comb)
-        self._actual_cache.append(socim)
-
-    def clear(self):
-        """Clear the contents both of ``__actual_cache`` and ``__list_of_sets_of_parents``.
-        """
-        del self._list_of_sets_of_parents[:]
-        del self._actual_cache[:]
\ No newline at end of file
diff --git a/build/lib/PyCTBN/PyCTBN/utility/json_importer.py b/build/lib/PyCTBN/PyCTBN/utility/json_importer.py
deleted file mode 100644
index 2cadff4..0000000
--- a/build/lib/PyCTBN/PyCTBN/utility/json_importer.py
+++ /dev/null
@@ -1,181 +0,0 @@
-import json
-import typing
-
-import pandas as pd
-
-
-from .abstract_importer import AbstractImporter
-
-
-class JsonImporter(AbstractImporter):
-    """Implements the abstracts methods of AbstractImporter and adds all the necessary methods to process and prepare
-    the data in json extension.
-
-    :param file_path: the path of the file that contains tha data to be imported
-    :type file_path: string
-    :param samples_label: the reference key for the samples in the trajectories
-    :type samples_label: string
-    :param structure_label: the reference key for the structure of the network data
-    :type structure_label: string
-    :param variables_label: the reference key for the cardinalites of the nodes data
-    :type variables_label: string
-    :param time_key: the key used to identify the timestamps in each trajectory
-    :type time_key: string
-    :param variables_key: the key used to identify the names of the variables in the net
-    :type variables_key: string
-    :_array_indx: the index of the outer JsonArray to extract the data from
-    :type _array_indx: int
-    :_df_samples_list: a Dataframe list in which every dataframe contains a trajectory
-    :_raw_data: The raw contents of the json file to import
-    :type _raw_data: List
-    """
-
-    def __init__(self, file_path: str, samples_label: str, structure_label: str, variables_label: str, time_key: str,
-                 variables_key: str):
-        """Constructor method
-
-        .. note::
-            This constructor calls also the method ``read_json_file()``, so after the construction of the object
-            the class member ``_raw_data`` will contain the raw imported json data.
-
-        """
-        self._samples_label = samples_label
-        self._structure_label = structure_label
-        self._variables_label = variables_label
-        self._time_key = time_key
-        self._variables_key = variables_key
-        self._df_samples_list = None
-        self._array_indx = None
-        super(JsonImporter, self).__init__(file_path)
-        self._raw_data = self.read_json_file()
-
-    def import_data(self, indx: int = 0) -> None:
-        """Implements the abstract method of :class:`AbstractImporter`.
-
-        :param indx: the index of the outer JsonArray to extract the data from, default to 0
-        :type indx: int
-        """
-        self._array_indx = indx
-        self._df_samples_list = self.import_trajectories(self._raw_data)
-        self._sorter = self.build_sorter(self._df_samples_list[0])
-        self.compute_row_delta_in_all_samples_frames(self._df_samples_list)
-        self.clear_data_frame_list()
-        self._df_structure = self.import_structure(self._raw_data)
-        self._df_variables = self.import_variables(self._raw_data)
-
-    def import_trajectories(self, raw_data: typing.List) -> typing.List:
-        """Imports the trajectories from the list of dicts ``raw_data``.
-
-        :param raw_data: List of Dicts
-        :type raw_data: List
-        :return: List of dataframes containing all the trajectories
-        :rtype: List
-        """
-        return self.normalize_trajectories(raw_data, self._array_indx, self._samples_label)
-
-    def import_structure(self, raw_data: typing.List) -> pd.DataFrame:
-        """Imports in a dataframe the data in the list raw_data at the key ``_structure_label``
-
-        :param raw_data: List of Dicts
-        :type raw_data: List
-        :return: Dataframe containg the starting node a ending node of every arc of the network
-        :rtype: pandas.Dataframe
-        """
-        return self.one_level_normalizing(raw_data, self._array_indx, self._structure_label)
-
-    def import_variables(self, raw_data: typing.List) -> pd.DataFrame:
-        """Imports the data in ``raw_data`` at the key ``_variables_label``.
-
-        :param raw_data: List of Dicts
-        :type raw_data: List
-        :return: Datframe containg the variables simbolic labels and their cardinalities
-        :rtype: pandas.Dataframe
-        """
-        return self.one_level_normalizing(raw_data, self._array_indx, self._variables_label)
-
-    def read_json_file(self) -> typing.List:
-        """Reads the JSON file in the path self.filePath.
-
-        :return: The contents of the json file
-        :rtype: List
-        """
-        with open(self._file_path) as f:
-            data = json.load(f)
-
-            if (isinstance(data,list)):
-                return data
-            else:
-                return [data]
-         
-
-    def one_level_normalizing(self, raw_data: typing.List, indx: int, key: str) -> pd.DataFrame:
-        """Extracts the one-level nested data in the list ``raw_data`` at the index ``indx`` at the key ``key``.
-
-        :param raw_data: List of Dicts
-        :type raw_data: List
-        :param indx: The index of the array from which the data have to be extracted
-        :type indx: int
-        :param key: the key for the Dicts from which exctract data
-        :type key: string
-        :return: A normalized dataframe
-        :rtype: pandas.Datframe
-        """
-        return pd.DataFrame(raw_data[indx][key])
-
-    def normalize_trajectories(self, raw_data: typing.List, indx: int, trajectories_key: str) -> typing.List:
-        """
-        Extracts the trajectories in ``raw_data`` at the index ``index`` at the key ``trajectories key``.
-
-        :param raw_data: List of Dicts
-        :type raw_data: List
-        :param indx: The index of the array from which the data have to be extracted
-        :type indx: int
-        :param trajectories_key: the key of the trajectories objects
-        :type trajectories_key: string
-        :return: A list of daframes containg the trajectories
-        :rtype: List
-        """
-        dataframe = pd.DataFrame
-        smps = raw_data[indx][trajectories_key]
-        df_samples_list = [dataframe(sample) for sample in smps]
-        return df_samples_list
-
-    def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
-        """Implements the abstract method build_sorter of the :class:`AbstractImporter` for this dataset.
-        """
-        columns_header = list(sample_frame.columns.values)
-        columns_header.remove(self._time_key)
-        return columns_header
-
-    def clear_data_frame_list(self) -> None:
-        """Removes all values present in the dataframes in the list ``_df_samples_list``.
-        """
-        for indx in range(len(self._df_samples_list)):
-            self._df_samples_list[indx] = self._df_samples_list[indx].iloc[0:0]
-
-    def dataset_id(self) -> object:
-        return self._array_indx
-
-    def import_sampled_cims(self, raw_data: typing.List, indx: int, cims_key: str) -> typing.Dict:
-        """Imports the synthetic CIMS in the dataset in a dictionary, using variables labels
-        as keys for the set of CIMS of a particular node.
-
-        :param raw_data: List of Dicts
-        :type raw_data: List
-        :param indx: The index of the array from which the data have to be extracted
-        :type indx: int
-        :param cims_key: the key where the json object cims are placed
-        :type cims_key: string
-        :return: a dictionary containing the sampled CIMS for all the variables in the net
-        :rtype: Dictionary
-        """
-        cims_for_all_vars = {}
-        for var in raw_data[indx][cims_key]:
-            sampled_cims_list = []
-            cims_for_all_vars[var] = sampled_cims_list
-            for p_comb in raw_data[indx][cims_key][var]:
-                cims_for_all_vars[var].append(pd.DataFrame(raw_data[indx][cims_key][var][p_comb]).to_numpy())
-        return cims_for_all_vars
-
-
-
diff --git a/build/lib/PyCTBN/PyCTBN/utility/sample_importer.py b/build/lib/PyCTBN/PyCTBN/utility/sample_importer.py
deleted file mode 100644
index b0b6e8f..0000000
--- a/build/lib/PyCTBN/PyCTBN/utility/sample_importer.py
+++ /dev/null
@@ -1,62 +0,0 @@
-import json
-import typing
-
-import pandas as pd
-import numpy as np
-
-from .abstract_importer import AbstractImporter
-
-
-
-class SampleImporter(AbstractImporter):
-    """Implements the abstracts methods of AbstractImporter and adds all the necessary methods to process and prepare
-    the data loaded directly by using DataFrame
-
-    :param trajectory_list: the data that describes the trajectories
-    :type trajectory_list: typing.Union[pd.DataFrame, np.ndarray, typing.List]
-    :param variables: the data that describes the variables with name and cardinality
-    :type variables: typing.Union[pd.DataFrame, np.ndarray, typing.List]
-    :param prior_net_structure: the data of the real structure, if it exists
-    :type prior_net_structure: typing.Union[pd.DataFrame, np.ndarray, typing.List]
-
-    :_df_samples_list: a Dataframe list in which every dataframe contains a trajectory
-    :_raw_data: The raw contents of the json file to import
-    :type _raw_data: List
-    """
-
-    def __init__(self, 
-                trajectory_list: typing.Union[pd.DataFrame, np.ndarray, typing.List] = None,
-                variables: typing.Union[pd.DataFrame, np.ndarray, typing.List] = None,
-                prior_net_structure: typing.Union[pd.DataFrame, np.ndarray,typing.List] = None):
-
-        'If the data are not DataFrame, it will be converted'
-        if isinstance(variables,list) or isinstance(variables,np.ndarray):
-            variables = pd.DataFrame(variables)
-        if isinstance(prior_net_structure,list) or isinstance(prior_net_structure,np.ndarray):
-            prior_net_structure=pd.DataFrame(prior_net_structure)
-
-        super(SampleImporter, self).__init__(trajectory_list =trajectory_list,
-                                        variables= variables,
-                                        prior_net_structure=prior_net_structure)
-
-    def import_data(self, header_column = None):
-
-        if header_column is not None:
-            self._sorter = header_column
-        else:    
-            self._sorter = self.build_sorter(self._df_samples_list[0])
-
-        samples_list= self._df_samples_list
-
-        self.compute_row_delta_in_all_samples_frames(samples_list)
-
-    def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List:
-        """Implements the abstract method build_sorter of the :class:`AbstractImporter` in order to get the ordered variables list.
-        """
-        columns_header = list(sample_frame.columns.values)
-        del columns_header[0]
-        return columns_header
-
-
-    def dataset_id(self) -> str:
-        return str("")
\ No newline at end of file
diff --git a/build/lib/PyCTBN/__init__.py b/build/lib/PyCTBN/__init__.py
deleted file mode 100644
index 7adf0d7..0000000
--- a/build/lib/PyCTBN/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-import PyCTBN.PyCTBN
-from PyCTBN.PyCTBN import *
diff --git a/build/lib/PyCTBN/basic_main.py b/build/lib/PyCTBN/basic_main.py
deleted file mode 100644
index b1288db..0000000
--- a/build/lib/PyCTBN/basic_main.py
+++ /dev/null
@@ -1,39 +0,0 @@
-import glob
-import os
-
-import sys
-sys.path.append("./PyCTBN/")
-
-import structure_graph.network_graph as ng
-import structure_graph.sample_path as sp
-import structure_graph.set_of_cims as sofc
-import estimators.parameters_estimator as pe
-import utility.json_importer as ji
-
-
-def main():
-    read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
-    #import data
-    importer = ji.JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
-    #Create a SamplePath Obj
-    s1 = sp.SamplePath(importer)
-    #Build The trajectries and the structural infos
-    s1.build_trajectories()
-    s1.build_structure()
-    #From The Structure Object build the Graph
-    g = ng.NetworkGraph(s1.structure)
-    #Select a node you want to estimate the parameters
-    node = g.nodes[1]
-    #Init the graph specifically for THIS node
-    g.fast_init(node)
-    #Use SamplePath and Grpah to create a ParametersEstimator Object
-    p1 = pe.ParametersEstimator(s1, g)
-    #Init the peEst specifically for THIS node
-    p1.fast_init(node)
-    #Compute the parameters
-    sofc1 = p1.compute_parameters_for_node(node)
-    #The est CIMS are inside the resultant SetOfCIms Obj
-    print(sofc1.actual_cims)
-
-if __name__ == "__main__":
-    main()
diff --git a/build/lib/PyCTBN/setup.py b/build/lib/PyCTBN/setup.py
deleted file mode 100644
index 56dd72f..0000000
--- a/build/lib/PyCTBN/setup.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from setuptools import setup, find_packages
-
-
-setup(name='PyCTBN',
-      version='1.0',
-      url='https://github.com/philipMartini/PyCTBN',
-      license='MIT',
-      author=['Alessandro Bregoli', 'Filippo Martini','Luca Moretti'],
-      author_email=['a.bregoli1@campus.unimib.it', 'f.martini@campus.unimib.it','lucamoretti96@gmail.com'],
-      description='A Continuous Time Bayesian Networks Library',
-      packages=find_packages('.', exclude=['tests']),
-      #packages=['PyCTBN.PyCTBN'],
-      install_requires=[
-          'numpy', 'pandas', 'networkx', 'scipy', 'matplotlib', 'tqdm'],
-      dependency_links=['https://github.com/numpy/numpy', 'https://github.com/pandas-dev/pandas',
-                        'https://github.com/networkx/networkx', 'https://github.com/scipy/scipy',
-                        'https://github.com/tqdm/tqdm'],
-      #long_description=open('../README.md').read(),
-      zip_safe=False,
-      python_requires='>=3.6')

From cdb8ec6291cba4abce2aae5b25cb103bc0b8b259 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 14 Mar 2021 21:11:02 +0100
Subject: [PATCH 086/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 6dc0e4d..08fb056 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -5,11 +5,8 @@ name: Python package
 
 on:
   push:
-    paths-ignore: 
-      -'docs/**'
-      -'docs-out/**'
-      -'dist/**'
-      -'build/**'
+    paths:
+      - 'PyCTBN/**'
     branches: [ master ]
     tags-ignore:
       - 'v*'

From db4dc33d7d595bd48f172d906ee5cc9742ede24d Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 20:17:01 +0000
Subject: [PATCH 087/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 8ec1ce8daa4569bdec5862fc428cf0f237a7fa20..3dd7f1c59768c6bee3569a552cee904f81605d17 100644
GIT binary patch
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From 294a80cf94fc6caea7a7c2f96f8a091e2e0b1f19 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 20:18:37 +0000
Subject: [PATCH 088/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 3dd7f1c59768c6bee3569a552cee904f81605d17..3f17084507786e0a1c3524c850a9d63f2e8093bd 100644
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From 3d1ca886c291af97a3a776866705936766975853 Mon Sep 17 00:00:00 2001
From: Filippo Martini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 21:22:48 +0100
Subject: [PATCH 089/139] Update README

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 27773ca..13b939c 100644
--- a/README.rst
+++ b/README.rst
@@ -92,7 +92,7 @@ Parameters Estimation Example
         #The est CIMS are inside the resultant SetOfCIms Obj
         print(sofc1.actual_cims)
 
-Structure Estimation Example
+Structure Estimation Examples
 ****************************
 
 .. code-block:: python

From c8257394901529564ab5f3aac4e1e30d5c6ca9af Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 20:34:48 +0000
Subject: [PATCH 090/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
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From bf1c154658c3188e0b9aad3119376b95c68a4495 Mon Sep 17 00:00:00 2001
From: Filippo Martini <f.martini@campus.unimib.it>
Date: Mon, 15 Mar 2021 00:00:07 +0100
Subject: [PATCH 091/139] Modify plot graph method

---
 .gitignore                                    |  1 +
 .../PyCTBN/estimators/structure_estimator.py  | 62 +++++++++----------
 PyCTBN/setup.py                               | 20 ------
 setup.py                                      |  2 +-
 4 files changed, 30 insertions(+), 55 deletions(-)
 delete mode 100644 PyCTBN/setup.py

diff --git a/.gitignore b/.gitignore
index 9c3a923..34f5167 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,5 @@ __pycache__
 **/PyCTBN.egg-info
 **/results_data
 **/.scannerwork
+.idea
 
diff --git a/PyCTBN/PyCTBN/estimators/structure_estimator.py b/PyCTBN/PyCTBN/estimators/structure_estimator.py
index b77e21f..e6da5a7 100644
--- a/PyCTBN/PyCTBN/estimators/structure_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_estimator.py
@@ -142,40 +142,34 @@ class StructureEstimator(object):
         return nx.difference(real_graph, self._complete_graph).edges
 
     def save_plot_estimated_structure_graph(self, file_path: str) -> None:  
-            """Plot the estimated structure in a graphical model style, use .png extension.
-            Spurious edges are colored in red if a prior structure is present.
-
-            :param file_path: path to save the file to
-            :type: string
-            """
-            graph_to_draw = nx.DiGraph()
-            spurious_edges = self.spurious_edges()
-            non_spurious_edges = list(set(self._complete_graph.edges) - set(spurious_edges))
-            edges_colors = ['red' if edge in spurious_edges else 'black' for edge in self._complete_graph.edges]
-            graph_to_draw.add_edges_from(spurious_edges)
-            graph_to_draw.add_edges_from(non_spurious_edges)
-            pos = nx.spring_layout(graph_to_draw, k=0.5*1/np.sqrt(len(graph_to_draw.nodes())), iterations=50,scale=10)
-            options = {
-                "node_size": 2000,
-                "node_color": "white",
-                "edgecolors": "black",
-                'linewidths':2,
-                "with_labels":True,
-                "font_size":13,
-                'connectionstyle': 'arc3, rad = 0.1',
-                "arrowsize": 15,
-                "arrowstyle": '<|-',
-                "width": 1,
-                "edge_color":edges_colors,
-            }
-
-            nx.draw(graph_to_draw, pos, **options)
-            ax = plt.gca()
-            ax.margins(0.20)
-            plt.axis("off")
-            plt.savefig(file_path)
-            plt.clf()
-            print("Estimated Structure Plot Saved At: ", os.path.abspath(file_path))
+        """Plot the estimated structure in a graphical model style, use .png extension.
+
+        :param file_path: path to save the file to
+        :type: string
+        """
+        pos = nx.spring_layout(self._complete_graph, k=0.5*1/np.sqrt(len(self._complete_graph.nodes)),
+                               iterations=50,scale=10)
+        options = {
+            "node_size": 2000,
+            "node_color": "white",
+            "edgecolors": "black",
+            'linewidths':2,
+            "with_labels":True,
+            "font_size":13,
+            'connectionstyle': 'arc3, rad = 0.1',
+            "arrowsize": 15,
+            #"arrowstyle": '<|-',
+            "width": 1,
+            #"edge_color":edges_colors,
+        }
+
+        nx.draw(self._complete_graph, pos, **options)
+        ax = plt.gca()
+        ax.margins(0.20)
+        plt.axis("off")
+        plt.savefig(file_path)
+        plt.clf()
+        print("Estimated Structure Plot Saved At: ", os.path.abspath(file_path))
 
 
 
diff --git a/PyCTBN/setup.py b/PyCTBN/setup.py
deleted file mode 100644
index 56dd72f..0000000
--- a/PyCTBN/setup.py
+++ /dev/null
@@ -1,20 +0,0 @@
-from setuptools import setup, find_packages
-
-
-setup(name='PyCTBN',
-      version='1.0',
-      url='https://github.com/philipMartini/PyCTBN',
-      license='MIT',
-      author=['Alessandro Bregoli', 'Filippo Martini','Luca Moretti'],
-      author_email=['a.bregoli1@campus.unimib.it', 'f.martini@campus.unimib.it','lucamoretti96@gmail.com'],
-      description='A Continuous Time Bayesian Networks Library',
-      packages=find_packages('.', exclude=['tests']),
-      #packages=['PyCTBN.PyCTBN'],
-      install_requires=[
-          'numpy', 'pandas', 'networkx', 'scipy', 'matplotlib', 'tqdm'],
-      dependency_links=['https://github.com/numpy/numpy', 'https://github.com/pandas-dev/pandas',
-                        'https://github.com/networkx/networkx', 'https://github.com/scipy/scipy',
-                        'https://github.com/tqdm/tqdm'],
-      #long_description=open('../README.md').read(),
-      zip_safe=False,
-      python_requires='>=3.6')
diff --git a/setup.py b/setup.py
index 7cad4ea..58f0226 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 
 setup(name='PyCTBN',
-      version='1.0',
+      version='2.1',
       url='https://github.com/philipMartini/PyCTBN',
       license='MIT',
       author=['Alessandro Bregoli', 'Filippo Martini','Luca Moretti'],

From 528a4436b126f15ea26199874e15614711b1e163 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 23:11:08 +0000
Subject: [PATCH 092/139] Update documentation

---
 .../doctrees/PyCTBN.PyCTBN.estimators.doctree | Bin 253064 -> 252930 bytes
 docs-out/_build/doctrees/environment.pickle   | Bin 148538 -> 148538 bytes
 .../_build/html/PyCTBN.PyCTBN.estimators.html |   3 +--
 docs-out/_build/html/searchindex.js           |   2 +-
 docs/PyCTBN.PyCTBN.estimators.html            |   3 +--
 docs/searchindex.js                           |   2 +-
 6 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/docs-out/_build/doctrees/PyCTBN.PyCTBN.estimators.doctree b/docs-out/_build/doctrees/PyCTBN.PyCTBN.estimators.doctree
index 94d843830b612e391b8ce9eb5f75f9dcd94a542b..7524a26f25624b179527a2c99cacee51d8ce0e81 100644
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index cbb732589d3014dd0ea31cdaf7433151f96352f7..3dc100e9ca4905909a8344a30c8824b166260fa1 100644
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diff --git a/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html b/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html
index b76ff0c..cc28d0c 100644
--- a/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html
+++ b/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html
@@ -636,8 +636,7 @@ that do not contains a the node identified by <code class="docutils literal notr
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph">
 <code class="sig-name descname">save_plot_estimated_structure_graph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">file_path</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph" title="Permalink to this definition">¶</a></dt>
-<dd><p>Plot the estimated structure in a graphical model style, use .png extension.
-Spurious edges are colored in red if a prior structure is present.</p>
+<dd><p>Plot the estimated structure in a graphical model style, use .png extension.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><p><strong>file_path</strong> – path to save the file to</p>
diff --git a/docs-out/_build/html/searchindex.js b/docs-out/_build/html/searchindex.js
index 8061880..051c818 100644
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\ No newline at end of file
diff --git a/docs/PyCTBN.PyCTBN.estimators.html b/docs/PyCTBN.PyCTBN.estimators.html
index b76ff0c..cc28d0c 100644
--- a/docs/PyCTBN.PyCTBN.estimators.html
+++ b/docs/PyCTBN.PyCTBN.estimators.html
@@ -636,8 +636,7 @@ that do not contains a the node identified by <code class="docutils literal notr
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph">
 <code class="sig-name descname">save_plot_estimated_structure_graph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">file_path</span><span class="p">:</span> <span class="n">str</span></em><span class="sig-paren">)</span> &#x2192; None<a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph" title="Permalink to this definition">¶</a></dt>
-<dd><p>Plot the estimated structure in a graphical model style, use .png extension.
-Spurious edges are colored in red if a prior structure is present.</p>
+<dd><p>Plot the estimated structure in a graphical model style, use .png extension.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
 <dd class="field-odd"><p><strong>file_path</strong> – path to save the file to</p>
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 8061880..051c818 100644
--- a/docs/searchindex.js
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\ No newline at end of file

From 02611b4545458d4424cdc537e1b8b9c319b6478e Mon Sep 17 00:00:00 2001
From: Filippo Martini <f.martini@campus.unimib.it>
Date: Mon, 15 Mar 2021 00:12:24 +0100
Subject: [PATCH 093/139] Modify README

---
 README.rst | 61 +++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 44 insertions(+), 17 deletions(-)

diff --git a/README.rst b/README.rst
index 13b939c..5655d54 100644
--- a/README.rst
+++ b/README.rst
@@ -94,32 +94,59 @@ Parameters Estimation Example
 
 Structure Estimation Examples
 ****************************
+This example shows how to estimate the structure given a series of trajectories using a constraint based approach.
+The first three instructions import all the necessary data (trajectories, nodes cardinalities, nodes labels),
+and are contextual to the dataset that is been used, in the code comments are marked as optional <>.
+If your data has a different structure or format you should implement your own importer (see Implementing your own importer example).
+The other instructions are not optional and should follow the same order.
+A SamplePath object is been created, passing an AbstractImporter object that contains the  correct class members filled
+with the data that are necessary to estimate the structure.
+Next the build_trajectories  and build_structure methods are called to instantiate the objects that will contain
+the processed trajectories and all the net infos.
+Then an estimator object is created, in this case a constraint based estimator, it necessary to pass a SamplePath object
+where build_trajectories and build_structure methods have already been called.
+If you have prior knowledge about the net structure pass it to the constructor with the known_edges parameter.
+The other three parameters are contextual to the StructureConstraintBasedEstimator, see the documentation for more details.
+To estimate the structure simply call the estimate_structure method.
+You can obtain the estimated structure as a boolean adjacency matrix with the method adjacency_matrix, or save it as a json file
+that contains all the nodes labels, and obviously the estimated edges.
+You can also save a graphical model representation of the estimated structure with the save_plot_estimated_structure_graph.
 
 .. code-block:: python
 
+    import glob
+    import os
+
     from PyCTBN import JsonImporter
     from PyCTBN import SamplePath
-    from PyCTBN import StructureEstimator
-    
-    def structure_estimation_example():
+    from PyCTBN import StructureConstraintBasedEstimator
+
 
-        # read the json files in ./data path
+    def structure_constraint_based_estimation_example():
+        # <read the json files in ./data path>
         read_files = glob.glob(os.path.join('./data', "*.json"))
-        # initialize a JsonImporter object for the first file
-        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
-        # import the data at index 0 of the outer json array
+        # <initialize a JsonImporter object for the first file>
+        importer = JsonImporter(file_path=read_files[0], samples_label='samples',
+                                structure_label='dyn.str', variables_label='variables',
+                                time_key='Time', variables_key='Name')
+        # <import the data at index 0 of the outer json array>
         importer.import_data(0)
-        # construct a SamplePath Object passing a filled AbstractImporter
-        s1 = SamplePath(importer)
+        # construct a SamplePath Object passing a filled AbstractImporter object
+        s1 = SamplePath(importer=importer)
         # build the trajectories
         s1.build_trajectories()
-        # build the real structure
+        # build the information about the net
         s1.build_structure()
-        # construct a StructureEstimator object
-        se1 = StructureEstimator(s1, 0.1, 0.1)
-        # call the ctpc algorithm
-        se1.ctpc_algorithm()
-        # the adjacency matrix of the estimated structure
+        # construct a StructureEstimator object passing a correctly build SamplePath object and the
+        # independence tests significance, if you have prior knowledge about the net structure create a list of tuples
+        # that contains them and pass it as known_edges parameter
+        se1 = StructureConstraintBasedEstimator(sample_path=s1, exp_test_alfa=0.1, chi_test_alfa=0.1,
+                                                known_edges=[], thumb_threshold=25)
+        # call the algorithm to estimate the structure
+        se1.estimate_structure()
+        # obtain the adjacency matrix of the estimated structure
         print(se1.adjacency_matrix())
-        # save results to a json file
-        se1.save_results()
+        # save the estimated structure  to a json file (remember to specify the path AND the .json extension)....
+        se1.save_results('./results0.json')
+        # ...or save it also in a graphical model fashion (remember to specify the path AND the .png extension)
+        se1.save_plot_estimated_structure_graph('./result0.png')
\ No newline at end of file

From aa93f1d405ffbaf0b235fa60ceb3cff0489b3b9e Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 14 Mar 2021 23:23:28 +0000
Subject: [PATCH 094/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 3dc100e9ca4905909a8344a30c8824b166260fa1..8cc4c1348c3171a88300839aa7cbb05c6a7aeb98 100644
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From 0da3dc20c6d255c816cf87e999721989b0fb838d Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 21 Mar 2021 12:08:59 +0100
Subject: [PATCH 095/139] Update README.rst

---
 README.rst | 49 +++++++++++++++++++++++++++----------------------
 1 file changed, 27 insertions(+), 22 deletions(-)

diff --git a/README.rst b/README.rst
index 5655d54..9ddc4d2 100644
--- a/README.rst
+++ b/README.rst
@@ -94,23 +94,25 @@ Parameters Estimation Example
 
 Structure Estimation Examples
 ****************************
-This example shows how to estimate the structure given a series of trajectories using a constraint based approach.
-The first three instructions import all the necessary data (trajectories, nodes cardinalities, nodes labels),
-and are contextual to the dataset that is been used, in the code comments are marked as optional <>.
-If your data has a different structure or format you should implement your own importer (see Implementing your own importer example).
-The other instructions are not optional and should follow the same order.
-A SamplePath object is been created, passing an AbstractImporter object that contains the  correct class members filled
-with the data that are necessary to estimate the structure.
-Next the build_trajectories  and build_structure methods are called to instantiate the objects that will contain
-the processed trajectories and all the net infos.
-Then an estimator object is created, in this case a constraint based estimator, it necessary to pass a SamplePath object
-where build_trajectories and build_structure methods have already been called.
-If you have prior knowledge about the net structure pass it to the constructor with the known_edges parameter.
-The other three parameters are contextual to the StructureConstraintBasedEstimator, see the documentation for more details.
-To estimate the structure simply call the estimate_structure method.
-You can obtain the estimated structure as a boolean adjacency matrix with the method adjacency_matrix, or save it as a json file
-that contains all the nodes labels, and obviously the estimated edges.
-You can also save a graphical model representation of the estimated structure with the save_plot_estimated_structure_graph.
+| This example shows how to estimate the structure given a series of trajectories using a constraint based approach.
+| The first three instructions import all the necessary data (trajectories, nodes cardinalities, nodes labels),
+| and are contextual to the dataset that is been used, in the code comments are marked as optional <>.
+| If your data has a different structure or format you should implement your own importer 
+| (see Implementing your own importer example).
+| The other instructions are not optional and should follow the same order.
+| A SamplePath object is been created, passing an AbstractImporter object that contains the  correct class members 
+| filled with the data that are necessary to estimate the structure.
+| Next the build_trajectories  and build_structure methods are called to instantiate the objects that will contain
+| the processed trajectories and all the net information.
+| Then an estimator object is created, in this case a constraint based estimator, 
+| it necessary to pass a SamplePath object where build_trajectories and build_structure methods have already been called.
+| If you have prior knowledge about the net structure pass it to the constructor with the known_edges parameter.
+| The other three parameters are contextual to the StructureConstraintBasedEstimator, see the documentation for more details.
+| To estimate the structure simply call the estimate_structure method.
+| You can obtain the estimated structure as a boolean adjacency matrix with the method adjacency_matrix, 
+| or save it as a json file that contains all the nodes labels, and obviously the estimated edges.
+| You can also save a graphical model representation of the estimated structure 
+| with the save_plot_estimated_structure_graph.
 
 .. code-block:: python
 
@@ -137,8 +139,9 @@ You can also save a graphical model representation of the estimated structure wi
         s1.build_trajectories()
         # build the information about the net
         s1.build_structure()
-        # construct a StructureEstimator object passing a correctly build SamplePath object and the
-        # independence tests significance, if you have prior knowledge about the net structure create a list of tuples
+        # construct a StructureEstimator object passing a correctly build SamplePath object
+        # and the independence tests significance, if you have prior knowledge about 
+        # the net structure create a list of tuples
         # that contains them and pass it as known_edges parameter
         se1 = StructureConstraintBasedEstimator(sample_path=s1, exp_test_alfa=0.1, chi_test_alfa=0.1,
                                                 known_edges=[], thumb_threshold=25)
@@ -146,7 +149,9 @@ You can also save a graphical model representation of the estimated structure wi
         se1.estimate_structure()
         # obtain the adjacency matrix of the estimated structure
         print(se1.adjacency_matrix())
-        # save the estimated structure  to a json file (remember to specify the path AND the .json extension)....
+        # save the estimated structure  to a json file 
+        # (remember to specify the path AND the .json extension)....
         se1.save_results('./results0.json')
-        # ...or save it also in a graphical model fashion (remember to specify the path AND the .png extension)
-        se1.save_plot_estimated_structure_graph('./result0.png')
\ No newline at end of file
+        # ...or save it also in a graphical model fashion 
+        # (remember to specify the path AND the .png extension)
+        se1.save_plot_estimated_structure_graph('./result0.png')

From 3fbbc80881da8c1301165975143925f5a21abead Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 21 Mar 2021 12:57:36 +0100
Subject: [PATCH 096/139] Add files via upload

---
 docs-out/esempio_dataset.png | Bin 0 -> 15144 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 docs-out/esempio_dataset.png

diff --git a/docs-out/esempio_dataset.png b/docs-out/esempio_dataset.png
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From 79dfd5d6ff8811697936f26eb2ca30a9ffa1ae93 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 21 Mar 2021 12:58:53 +0100
Subject: [PATCH 097/139] Update README.rst

---
 README.rst | 33 +++++++++++++++++++++++++++++----
 1 file changed, 29 insertions(+), 4 deletions(-)

diff --git a/README.rst b/README.rst
index 9ddc4d2..959cef0 100644
--- a/README.rst
+++ b/README.rst
@@ -15,11 +15,24 @@ Please refer to https://philipmartini.github.io/PyCTBN/ for the full project doc
 
 Implementing your own data importer
 ***********************************
-.. code-block:: python
+| This example demonstrates the implementation of a simple data importer the extends the class AbstractImporter 
+| to import data in csv format. The net in exam has three ternary nodes and no prior net structure.
+| Suppose the trajectories that have to be inported have this structure:
+.. image:: docs-out/esempio_dataset.png
+  :width: 400
+  :alt: An example trajectory to be imported.
+| In the read_csv_file method the data are imported in memory, put in a list and  assigned to the _df_samples_list class
+| member, so that it contains all the trajectories to be processed.
+| In the import_variables method the dataframe containing the nodes labels and the cardinalities of the nodes 
+|is assigned to the _df_variables class member. 
+| The class member _sorter has to contain the nodes labels in the same order of the trajectory columns,
+| just override the build_sorter method to do that.
+| If your datasets names have particular id, you can keep it using the dataset_id method to assign the id to a new class member. 
+| Finally the import_data method call all the previously implemented methods and calls the compute_row_delta_in_all_samples_frames
+| to process all the trajectories in _df_samples_list.
+| For more information about the class memebers and methods of AbstractImporter please refer to the documentation.
 
-    """This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.
-    The net in exam has three ternary nodes and no prior net structure.
-    """
+.. code-block:: python
 
     from PyCTBN import AbstractImporter
 
@@ -53,6 +66,18 @@ Implementing your own data importer
         def dataset_id(self) -> object:
             pass
 
+    def main():
+        # create the importer object
+        csvimp = CSVImporter('/dataset_example.csv')
+        # call the wrapping method that wil import and process the data
+        csvimp.import_data()
+        # pass the AbstractImporter object to the SamplePath constructor
+        s1 = SamplePath(csvimp)
+        # SamplePath will contain the Trajecotry object...
+        s1.build_trajectories()
+        #...and the Structure object with all the process data
+        s1.build_structure()
+
 Parameters Estimation Example
 *****************************
 

From da3e943dfb7e9f676e276e2af5297b2bbabca868 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 21 Mar 2021 13:02:37 +0100
Subject: [PATCH 098/139] Update README.rst

---
 README.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 959cef0..02ccd6e 100644
--- a/README.rst
+++ b/README.rst
@@ -19,7 +19,7 @@ Implementing your own data importer
 | to import data in csv format. The net in exam has three ternary nodes and no prior net structure.
 | Suppose the trajectories that have to be inported have this structure:
 .. image:: docs-out/esempio_dataset.png
-  :width: 400
+  :width: 600
   :alt: An example trajectory to be imported.
 | In the read_csv_file method the data are imported in memory, put in a list and  assigned to the _df_samples_list class
 | member, so that it contains all the trajectories to be processed.
@@ -34,7 +34,11 @@ Implementing your own data importer
 
 .. code-block:: python
 
+    import pandas as pd
+    import typing
+    
     from PyCTBN import AbstractImporter
+    from PyCTBN import SamplePath
 
     class CSVImporter(AbstractImporter):
 

From a179dd3498b53a24804fb09d961466dd5303a89d Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 21 Mar 2021 13:03:57 +0100
Subject: [PATCH 099/139] Update README.rst

---
 README.rst | 41 ++---------------------------------------
 1 file changed, 2 insertions(+), 39 deletions(-)

diff --git a/README.rst b/README.rst
index 02ccd6e..df54db8 100644
--- a/README.rst
+++ b/README.rst
@@ -18,9 +18,11 @@ Implementing your own data importer
 | This example demonstrates the implementation of a simple data importer the extends the class AbstractImporter 
 | to import data in csv format. The net in exam has three ternary nodes and no prior net structure.
 | Suppose the trajectories that have to be inported have this structure:
+
 .. image:: docs-out/esempio_dataset.png
   :width: 600
   :alt: An example trajectory to be imported.
+ 
 | In the read_csv_file method the data are imported in memory, put in a list and  assigned to the _df_samples_list class
 | member, so that it contains all the trajectories to be processed.
 | In the import_variables method the dataframe containing the nodes labels and the cardinalities of the nodes 
@@ -82,45 +84,6 @@ Implementing your own data importer
         #...and the Structure object with all the process data
         s1.build_structure()
 
-Parameters Estimation Example
-*****************************
-
-.. code-block:: python
-
-    from PyCTBN import JsonImporter
-    from PyCTBN import SamplePath
-    from PyCTBN import NetworkGraph
-    from PyCTBN import ParametersEstimator
-
-
-    def main():
-        read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
-        #import data
-        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
-        importer.import_data(0)
-        #Create a SamplePath Obj passing an already filled AbstractImporter object
-        s1 = SamplePath(importer)
-        #Build The trajectries and the structural infos
-        s1.build_trajectories()
-        s1.build_structure()
-        print(s1.structure.edges)
-        print(s1.structure.nodes_values)
-        #From The Structure Object build the Graph
-        g = NetworkGraph(s1.structure)
-        #Select a node you want to estimate the parameters
-        node = g.nodes[2]
-        print("Node", node)
-        #Init the _graph specifically for THIS node
-        g.fast_init(node)
-        #Use SamplePath and Grpah to create a ParametersEstimator Object
-        p1 = ParametersEstimator(s1.trajectories, g)
-        #Init the peEst specifically for THIS node
-        p1.fast_init(node)
-        #Compute the parameters
-        sofc1 = p1.compute_parameters_for_node(node)
-        #The est CIMS are inside the resultant SetOfCIms Obj
-        print(sofc1.actual_cims)
-
 Structure Estimation Examples
 ****************************
 | This example shows how to estimate the structure given a series of trajectories using a constraint based approach.

From e173978bf42707c90cd23709b934a98aef8d4f44 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 21 Mar 2021 13:05:59 +0100
Subject: [PATCH 100/139] Update README.rst

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index df54db8..a7c5573 100644
--- a/README.rst
+++ b/README.rst
@@ -26,7 +26,7 @@ Implementing your own data importer
 | In the read_csv_file method the data are imported in memory, put in a list and  assigned to the _df_samples_list class
 | member, so that it contains all the trajectories to be processed.
 | In the import_variables method the dataframe containing the nodes labels and the cardinalities of the nodes 
-|is assigned to the _df_variables class member. 
+| is assigned to the _df_variables class member. 
 | The class member _sorter has to contain the nodes labels in the same order of the trajectory columns,
 | just override the build_sorter method to do that.
 | If your datasets names have particular id, you can keep it using the dataset_id method to assign the id to a new class member. 

From 02dc6abd275381e2bd0029b63f68c552b07cd4c2 Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Sun, 28 Mar 2021 17:37:38 +0200
Subject: [PATCH 101/139] Updated examples file

---
 README.rst | 178 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 178 insertions(+)

diff --git a/README.rst b/README.rst
index a7c5573..f9fcb54 100644
--- a/README.rst
+++ b/README.rst
@@ -84,7 +84,14 @@ Implementing your own data importer
         #...and the Structure object with all the process data
         s1.build_structure()
 
+
 Structure Estimation Examples
+##############################
+
+| In this section some examples will be shown in order to provide some useful information about the usage of the library
+
+
+Constraint based estimation
 ****************************
 | This example shows how to estimate the structure given a series of trajectories using a constraint based approach.
 | The first three instructions import all the necessary data (trajectories, nodes cardinalities, nodes labels),
@@ -147,3 +154,174 @@ Structure Estimation Examples
         # ...or save it also in a graphical model fashion 
         # (remember to specify the path AND the .png extension)
         se1.save_plot_estimated_structure_graph('./result0.png')
+
+
+
+Score based estimation with Hill Climbing
+*****************************************
+
+| This example shows how to estimate the structure given a series of trajectories using a score based approach
+| and the Hill Climbing algorithm as optimization strategy.
+| The structure of the code is the same as the previus example, but an explanation of the Structure score based estimator 
+| will be provided.
+| Then an estimator object is created, in this case a score based estimator, 
+| it necessary to pass a SamplePath object where build_trajectories and build_structure methods have already been called.
+| If you have prior knowledge about the net structure pass it to the constructor with the known_edges parameter.
+| The other parameters are contextual to the StructureScoreBasedEstimator, see the documentation for more details.
+| To estimate the structure simply call the estimate_structure method passing the desidered parameters, such as the 
+| optimization strategy, or simply use the default configuration. 
+| In this case an Hill Climbing approch is choosen.
+
+.. code-block:: python
+
+    import glob
+    import os
+
+    from PyCTBN import JsonImporter
+    from PyCTBN import SamplePath
+    from PyCTBN import StructureScoreBasedEstimator
+
+
+    def structure_constraint_based_estimation_example():
+        # <read the json files in ./data path>
+        read_files = glob.glob(os.path.join('./data', "*.json"))
+        # <initialize a JsonImporter object for the first file>
+        importer = JsonImporter(file_path=read_files[0], samples_label='samples',
+                                structure_label='dyn.str', variables_label='variables',
+                                time_key='Time', variables_key='Name')
+        # <import the data at index 0 of the outer json array>
+        importer.import_data(0)
+        # construct a SamplePath Object passing a filled AbstractImporter object
+        s1 = SamplePath(importer=importer)
+        # build the trajectories
+        s1.build_trajectories()
+        # build the information about the net
+        s1.build_structure()
+        # construct a StructureEstimator object passing a correctly build SamplePath object
+        # and hyperparameters tau and alpha, if you have prior knowledge about 
+        # the net structure create a list of tuples
+        # that contains them and pass it as known_edges parameter
+        se1 = StructureScoreBasedEstimator(sample_path=s1, tau_xu = 0.1, alpha_xu = 1,
+                                          known_edges=[])
+        # call the algorithm to estimate the structure
+        # and pass all the desidered parameters, in this case an Hill Climbing approach 
+        # will be selected as optimization strategy. 
+        se1.estimate_structure(
+                            max_parents = None,
+                            iterations_number = 40,
+                            patience = None,
+                            optimizer = 'hill'
+                            )
+        # obtain the adjacency matrix of the estimated structure
+        print(se1.adjacency_matrix())
+        # save the estimated structure  to a json file 
+        # (remember to specify the path AND the .json extension)....
+        se1.save_results('./results0.json')
+        # ...or save it also in a graphical model fashion 
+        # (remember to specify the path AND the .png extension)
+        se1.save_plot_estimated_structure_graph('./result0.png')
+
+
+Score based estimation with Tabu Search and Data Augmentation
+**************************************************************
+
+| This example shows how to estimate the structure given a series of trajectories using a score based approach
+| and the Tabu Search algorithm as optimization strategy and how to use a data augmentation strategy to increase the 
+| number of data available. 
+| The structure of the code is the same as the previus example, but an explanation of the data augmentation technique
+| will be provided.
+| In this case a SampleImporter is used to import the data instead of a JsonImporter.
+| Using a SampleImporter requires the user to read the data and put it into different lists or DataFrames before to 
+| inizialize the SampleImporter instance.
+| Then it is possible to increase the amount of data by using one of the external libraries who provide data augmentation 
+| approaches, in this example sklearn is used.
+| Then all the information can be passed to the SampleImporter constructor and the import_data method can be used to provide
+| the preprossing operations of the PyCTBN library.
+| Then an estimator object is created, in this case a score based estimator, 
+| it necessary to pass a SamplePath object where build_trajectories and build_structure methods have already been called.
+| If you have prior knowledge about the net structure pass it to the constructor with the known_edges parameter.
+| The other parameters are contextual to the StructureScoreBasedEstimator, see the documentation for more details.
+| To estimate the structure simply call the estimate_structure method passing the desidered parameters, such as the 
+| optimization strategy, or simply use the default configuration. 
+| In this case an Hill Climbing approch is choosen.
+
+
+.. code-block:: python
+
+    import glob
+    import os
+
+    from sklearn.utils import resample
+
+    from PyCTBN import SampleImporter
+    from PyCTBN import SamplePath
+    from PyCTBN import StructureScoreBasedEstimator
+
+
+    def structure_constraint_based_estimation_example():
+        # <read the json files in ./data path>
+        read_files = glob.glob(os.path.join('./data', "*.json"))
+
+        # read the first file in the directory (or pass the file path)
+        with open(file_path=read_files[0]) as f:
+                    raw_data = json.load(f)
+
+                    # read the variables information
+                    variables= pd.DataFrame(raw_data[0]["variables"])
+
+                    # read the prior information if they are given
+                    prior_net_structure = pd.DataFrame(raw_data[0]["dyn.str"])
+
+                    #read the samples
+                    trajectory_list_raw= raw_data[0]["samples"]
+
+                    #convert them in DataFrame
+                    trajectory_list = [pd.DataFrame(sample) for sample in trajectory_list_raw]
+
+                    # use an external library in order to provide the data augmentation operations, in this case
+                    # sklearn.utils is used
+                    augmented_trajectory_list = resample (trajectory_list, replace = True, n_samples = 300 )
+
+
+        # <initialize a SampleImporter object using the data read before>
+        importer = SampleImporter(
+                                        trajectory_list = augmented_trajectory_list,
+                                        variables=variables,
+                                        prior_net_structure=prior_net_structure
+                                    )
+
+        # <import the data>
+        importer.import_data()
+        # construct a SamplePath Object passing a filled AbstractImporter object
+
+        s1 = SamplePath(importer=importer)
+        # build the trajectories
+        s1.build_trajectories()
+        # build the information about the net
+        s1.build_structure()
+        # construct a StructureEstimator object passing a correctly build SamplePath object
+        # and hyperparameters tau and alpha, if you have prior knowledge about 
+        # the net structure create a list of tuples
+        # that contains them and pass it as known_edges parameter
+        se1 = StructureScoreBasedEstimator(sample_path=s1, tau_xu = 0.1, alpha_xu = 1,
+                                          known_edges=[])
+        # call the algorithm to estimate the structure
+        # and pass all the desidered parameters, in this case a Tabu Search approach 
+        # will be selected as optimization strategy. It is possible to select the tabu list length and 
+        # the tabu rules duration, and the other parameters as in the previus example. 
+        se1.estimate_structure(
+                            max_parents = None,
+                            iterations_number = 100,
+                            patience = 20,
+                            optimizer = 'tabu',
+                            tabu_length = 10,
+                            tabu_rules_duration = 10
+                            )
+        # obtain the adjacency matrix of the estimated structure
+        print(se1.adjacency_matrix())
+        # save the estimated structure  to a json file 
+        # (remember to specify the path AND the .json extension)....
+        se1.save_results('./results0.json')
+        # ...or save it also in a graphical model fashion 
+        # (remember to specify the path AND the .png extension)
+        se1.save_plot_estimated_structure_graph('./result0.png')
\ No newline at end of file

From c0b45e4631de816e979fa8709cbfd7c948ff7330 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 28 Mar 2021 18:07:09 +0200
Subject: [PATCH 102/139] Create codecov.yml

---
 codecov.yml | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 codecov.yml

diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1 @@
+

From fa0c33642155103c9955795053ec479bc8da380e Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 28 Mar 2021 18:07:42 +0200
Subject: [PATCH 103/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 23 +++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 08fb056..857ddea 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -41,3 +41,26 @@ jobs:
     - name: Test with pytest
       run: |
         pytest PyCTBN/tests/ 
+    - name: Generate coverage report
+      run: |
+        pip install pytest
+        pip install pytest-cov
+        pytest --cov=./PyCTBN/tests/ --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        token: ${{ secrets.GITHUB_TOKEN }}
+        files: ./coverage1.xml,./coverage2.xml
+        directory: ./coverage/reports/
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: true
+        path_to_write_report: ./coverage/codecov_report.txt
+        verbose: true
+        
+        
+        
+        
+        
+        

From 24844be838e752b1f09452e1ae0025d99e47aff0 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 28 Mar 2021 18:08:55 +0200
Subject: [PATCH 104/139] Update test_tabu_search.py

---
 PyCTBN/tests/optimizers/test_tabu_search.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/PyCTBN/tests/optimizers/test_tabu_search.py b/PyCTBN/tests/optimizers/test_tabu_search.py
index 54f6a2f..301a52c 100644
--- a/PyCTBN/tests/optimizers/test_tabu_search.py
+++ b/PyCTBN/tests/optimizers/test_tabu_search.py
@@ -75,7 +75,8 @@ class TestTabuSearch(unittest.TestCase):
     def test_structure_3(self):
         with open("./PyCTBN/test_data/networks_and_trajectories_ternary_data_01_6_1.json") as f:
                     raw_data = json.load(f)
-
+                
+                    # read the samples
                     trajectory_list_raw= raw_data["samples"]
 
                     trajectory_list = [pd.DataFrame(sample) for sample in trajectory_list_raw]

From 6d3412460fa59bd6a5f90809992fae16a0dd726c Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 28 Mar 2021 16:28:03 +0000
Subject: [PATCH 105/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 8cc4c1348c3171a88300839aa7cbb05c6a7aeb98..95f49796d8b93838ef415e4e9e16d0854b848e5b 100644
GIT binary patch
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From 3fa1a546ccf30a9bf16820a9928eb1daf2e5174a Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 28 Mar 2021 19:02:18 +0200
Subject: [PATCH 106/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index 857ddea..cdecbc9 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -45,18 +45,15 @@ jobs:
       run: |
         pip install pytest
         pip install pytest-cov
-        pytest --cov=./PyCTBN/tests/ --cov-report=xml
+        pytest PyCTBN/tests/ --cov='./' --cov-report=xml
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
       with:
-        token: ${{ secrets.GITHUB_TOKEN }}
-        files: ./coverage1.xml,./coverage2.xml
-        directory: ./coverage/reports/
+        files: ./coverage.xml
         flags: unittests
         env_vars: OS,PYTHON
         name: codecov-umbrella
         fail_ci_if_error: true
-        path_to_write_report: ./coverage/codecov_report.txt
         verbose: true
         
         

From 1f7c0d5e594222ad0dbf6c31e74d4e368e272840 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 28 Mar 2021 19:02:45 +0200
Subject: [PATCH 107/139] Update python-PyCTBN-package.yml

---
 .github/workflows/python-PyCTBN-package.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/python-PyCTBN-package.yml b/.github/workflows/python-PyCTBN-package.yml
index cdecbc9..4d624d0 100644
--- a/.github/workflows/python-PyCTBN-package.yml
+++ b/.github/workflows/python-PyCTBN-package.yml
@@ -38,9 +38,6 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest
-      run: |
-        pytest PyCTBN/tests/ 
     - name: Generate coverage report
       run: |
         pip install pytest

From 8ed694fb280cce12daf3df5e4a79bc367f25b3d1 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 28 Mar 2021 19:04:18 +0200
Subject: [PATCH 108/139] Update test_sample_importer.py

---
 PyCTBN/tests/utility/test_sample_importer.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/PyCTBN/tests/utility/test_sample_importer.py b/PyCTBN/tests/utility/test_sample_importer.py
index aa9a5a7..8e96778 100644
--- a/PyCTBN/tests/utility/test_sample_importer.py
+++ b/PyCTBN/tests/utility/test_sample_importer.py
@@ -17,9 +17,10 @@ class TestSampleImporter(unittest.TestCase):
     def setUpClass(cls) -> None:
         with open("./PyCTBN/test_data/networks_and_trajectories_binary_data_01_3.json") as f:
             raw_data = json.load(f)
-
+            
+            #read the samples
             trajectory_list_raw= raw_data[0]["samples"]
-
+            
             cls.trajectory_list = [pd.DataFrame(sample) for sample in trajectory_list_raw]
 
             cls.variables= pd.DataFrame(raw_data[0]["variables"])

From f8938e1aaee11e231b1fe0eed50630a0e8ac1246 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 28 Mar 2021 17:15:05 +0000
Subject: [PATCH 109/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 95f49796d8b93838ef415e4e9e16d0854b848e5b..6b5ebe3d9c8cf98b6f64fd58350d1513406081bf 100644
GIT binary patch
delta 7426
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From 36f135b35a69eec2fc7a98f737d6f337b9068c14 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Sun, 28 Mar 2021 19:36:36 +0200
Subject: [PATCH 110/139] Update README.rst

---
 README.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index f9fcb54..422aed7 100644
--- a/README.rst
+++ b/README.rst
@@ -8,6 +8,10 @@ Installation/Usage
 Download the release in .tar.gz or .whl format and simply use pip install to install it::
 
     $ pip install PyCTBN-1.0.tar.gz
+    
+Coverage
+********
+Please refer to https://app.codecov.io/gh/philipMartini/PyCTBN for a detailed report of test coverage.
 
 Documentation
 *************
@@ -324,4 +328,4 @@ Score based estimation with Tabu Search and Data Augmentation
         se1.save_results('./results0.json')
         # ...or save it also in a graphical model fashion 
         # (remember to specify the path AND the .png extension)
-        se1.save_plot_estimated_structure_graph('./result0.png')
\ No newline at end of file
+        se1.save_plot_estimated_structure_graph('./result0.png')

From 0088b449ce6c3db7262fbd0c70be91eba607c37e Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 28 Mar 2021 19:39:34 +0200
Subject: [PATCH 111/139] Update test_hill_climbing_search.py

---
 PyCTBN/tests/optimizers/test_hill_climbing_search.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PyCTBN/tests/optimizers/test_hill_climbing_search.py b/PyCTBN/tests/optimizers/test_hill_climbing_search.py
index 1ca8f8c..84fa023 100644
--- a/PyCTBN/tests/optimizers/test_hill_climbing_search.py
+++ b/PyCTBN/tests/optimizers/test_hill_climbing_search.py
@@ -54,9 +54,9 @@ class TestHillClimbingSearch(unittest.TestCase):
     def test_structure_3(self):
         with open("./PyCTBN/test_data/networks_and_trajectories_ternary_data_01_6_1.json") as f:
                     raw_data = json.load(f)
-
+                    
                     trajectory_list_raw= raw_data["samples"]
-
+                    # Convert to DataFrame
                     trajectory_list = [pd.DataFrame(sample) for sample in trajectory_list_raw]
 
                     variables= raw_data["variables"]

From 63f403a03cd84d0a5cb2379af7cabfdc03e3e7c3 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 28 Mar 2021 17:50:55 +0000
Subject: [PATCH 112/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 6b5ebe3d9c8cf98b6f64fd58350d1513406081bf..2e9ad9eb2634c25ad905628966f6b0487488da18 100644
GIT binary patch
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From 1592afe8ee7c0ebe921ad2fd822c1533489821c3 Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Tue, 27 Apr 2021 21:13:49 +0200
Subject: [PATCH 113/139] Added Processes number parameter

---
 .../structure_constraint_based_estimator.py   | 27 +++++++++++++++----
 .../structure_score_based_estimator.py        |  7 ++++-
 ...st_structure_constraint_based_estimator.py |  2 +-
 .../test_structure_score_based_estimator.py   |  4 ++-
 4 files changed, 32 insertions(+), 8 deletions(-)

diff --git a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
index 0013d80..2fa255e 100644
--- a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
@@ -199,8 +199,14 @@ class StructureConstraintBasedEstimator(StructureEstimator):
         return optimizer_obj.optimize_structure()
 
     
-    def ctpc_algorithm(self,disable_multiprocessing:bool= False ):
+    def ctpc_algorithm(self, disable_multiprocessing:bool= False, processes_number:int= None):
         """Compute the CTPC algorithm over the entire net.
+
+        :param disable_multiprocessing: true if you desire to disable the multiprocessing operations, default to False
+        :type disable_multiprocessing: Boolean, optional
+        :param processes_number: if disable_multiprocessing is false indicates 
+        the maximum number of process; if None it will be automatically set, default to None
+        :type processes_number: int, optional
         """
         ctpc_algo = self.one_iteration_of_CTPC_algorithm
         total_vars_numb = self._sample_path.total_variables_count
@@ -212,8 +218,6 @@ class StructureConstraintBasedEstimator(StructureEstimator):
         'get the number of CPU'
         cpu_count = multiprocessing.cpu_count()
 
-
-
         'Remove all the edges from the structure'   
         self._sample_path.structure.clean_structure_edges()
 
@@ -225,6 +229,9 @@ class StructureConstraintBasedEstimator(StructureEstimator):
             cpu_count = 1
             list_edges_partial = [ctpc_algo(n,total_vars_numb) for n in self._nodes]
         else:
+            if processes_number is not None and cpu_count < processes_number:
+                cpu_count = processes_number
+
             with concurrent.futures.ProcessPoolExecutor(max_workers=cpu_count) as executor:
                 list_edges_partial = executor.map(ctpc_algo,
                                                                  self._nodes,
@@ -238,8 +245,18 @@ class StructureConstraintBasedEstimator(StructureEstimator):
         return edges
 
         
-    def estimate_structure(self,disable_multiprocessing:bool=False):
-        return self.ctpc_algorithm(disable_multiprocessing=disable_multiprocessing)
+    def estimate_structure(self, disable_multiprocessing:bool=False, processes_number:int= None):
+        """
+        Compute the constraint-based algorithm to find the optimal structure
+
+        :param disable_multiprocessing: true if you desire to disable the multiprocessing operations, default to False
+        :type disable_multiprocessing: Boolean, optional
+        :param processes_number: if disable_multiprocessing is false indicates 
+        the maximum number of process; if None it will be automatically set, default to None
+        :type processes_number: int, optional
+        """
+        return self.ctpc_algorithm(disable_multiprocessing=disable_multiprocessing,
+                                    processes_number=processes_number)
 
     
 
diff --git a/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py b/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
index 12222f9..5763739 100644
--- a/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
@@ -54,7 +54,7 @@ class StructureScoreBasedEstimator(StructureEstimator):
 
     def estimate_structure(self, max_parents:int = None, iterations_number:int= 40,
                          patience:int = None, tabu_length:int = None, tabu_rules_duration:int = None,
-                         optimizer: str = 'tabu',disable_multiprocessing:bool= False ):
+                         optimizer: str = 'tabu', disable_multiprocessing:bool= False, processes_number:int= None):
         """
         Compute the score-based algorithm to find the optimal structure
 
@@ -72,6 +72,9 @@ class StructureScoreBasedEstimator(StructureEstimator):
         :type optimizer: string, optional
         :param disable_multiprocessing: true if you desire to disable the multiprocessing operations, default to False
         :type disable_multiprocessing: Boolean, optional
+        :param processes_number: if disable_multiprocessing is false indicates 
+        the maximum number of process; if None it will be automatically set, default to None
+        :type processes_number: int, optional
         """
         'Save the true edges structure in tuples'
         true_edges = copy.deepcopy(self._sample_path.structure.edges)
@@ -98,6 +101,8 @@ class StructureScoreBasedEstimator(StructureEstimator):
 
         if disable_multiprocessing:
             cpu_count = 1
+        elif processes_number is not None and cpu_count < processes_number:
+            cpu_count = processes_number
 
         
 
diff --git a/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py b/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py
index b69d445..3e9d2b0 100644
--- a/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py
+++ b/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py
@@ -54,7 +54,7 @@ class TestStructureConstraintBasedEstimator(unittest.TestCase):
         true_edges = set(map(tuple, true_edges))
 
         se1 = StructureConstraintBasedEstimator(self.s1,0.1,0.1)
-        edges = se1.estimate_structure(True)
+        edges = se1.estimate_structure(processes_number=2)
         
         self.assertFalse(se1.spurious_edges())
         self.assertEqual(edges, true_edges)
diff --git a/PyCTBN/tests/estimators/test_structure_score_based_estimator.py b/PyCTBN/tests/estimators/test_structure_score_based_estimator.py
index 8cbbcb5..407201e 100644
--- a/PyCTBN/tests/estimators/test_structure_score_based_estimator.py
+++ b/PyCTBN/tests/estimators/test_structure_score_based_estimator.py
@@ -111,7 +111,8 @@ class TestStructureScoreBasedEstimator(unittest.TestCase):
                                     tabu_length = 15,
                                     tabu_rules_duration = 15,
                                     optimizer = 'hill',
-                                    disable_multiprocessing=False
+                                    disable_multiprocessing=False,
+                                    processes_number=2
                                     )
         
 
@@ -240,6 +241,7 @@ class TestStructureScoreBasedEstimator(unittest.TestCase):
         self.assertGreaterEqual(recall,0.75)      
 
 
+
 if __name__ == '__main__':
     unittest.main()
 

From 0a94eb19451ba60153d775d224578fa85a5cbb98 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Tue, 27 Apr 2021 19:24:39 +0000
Subject: [PATCH 114/139] Update documentation

---
 .../_build/doctrees/PyCTBN.PyCTBN.doctree     | Bin 3658 -> 3707 bytes
 .../doctrees/PyCTBN.PyCTBN.estimators.doctree | Bin 252930 -> 272060 bytes
 .../doctrees/PyCTBN.PyCTBN.optimizers.doctree | Bin 58866 -> 60965 bytes
 .../PyCTBN.PyCTBN.structure_graph.doctree     | Bin 196000 -> 201462 bytes
 .../doctrees/PyCTBN.PyCTBN.utility.doctree    | Bin 151908 -> 157217 bytes
 docs-out/_build/doctrees/PyCTBN.doctree       | Bin 3685 -> 3734 bytes
 docs-out/_build/doctrees/PyCTBN.tests.doctree | Bin 3642 -> 3691 bytes
 .../doctrees/PyCTBN.tests.estimators.doctree  | Bin 51696 -> 51965 bytes
 .../doctrees/PyCTBN.tests.optimizers.doctree  | Bin 18388 -> 18517 bytes
 .../PyCTBN.tests.structure_graph.doctree      | Bin 95711 -> 96380 bytes
 .../doctrees/PyCTBN.tests.utility.doctree     | Bin 45421 -> 45630 bytes
 docs-out/_build/doctrees/basic_main.doctree   | Bin 2324 -> 2373 bytes
 docs-out/_build/doctrees/environment.pickle   | Bin 148538 -> 148538 bytes
 docs-out/_build/doctrees/examples.doctree     | Bin 11353 -> 11402 bytes
 docs-out/_build/doctrees/index.doctree        | Bin 4864 -> 4946 bytes
 docs-out/_build/doctrees/modules.doctree      | Bin 2608 -> 2657 bytes
 docs-out/_build/doctrees/setup.doctree        | Bin 2278 -> 2327 bytes
 docs-out/_build/html/.buildinfo               |   2 +-
 .../_build/html/PyCTBN.PyCTBN.estimators.html |  67 +++++++++++-------
 docs-out/_build/html/PyCTBN.PyCTBN.html       |  14 ++--
 .../_build/html/PyCTBN.PyCTBN.optimizers.html |  30 ++++----
 .../html/PyCTBN.PyCTBN.structure_graph.html   |  38 +++++-----
 .../_build/html/PyCTBN.PyCTBN.utility.html    |  30 ++++----
 docs-out/_build/html/PyCTBN.html              |  18 ++---
 .../_build/html/PyCTBN.tests.estimators.html  |  30 ++++----
 docs-out/_build/html/PyCTBN.tests.html        |  14 ++--
 .../_build/html/PyCTBN.tests.optimizers.html  |  22 +++---
 .../html/PyCTBN.tests.structure_graph.html    |  38 +++++-----
 .../_build/html/PyCTBN.tests.utility.html     |  26 +++----
 docs-out/_build/html/basic_main.html          |   6 +-
 docs-out/_build/html/examples.html            |  22 +++---
 docs-out/_build/html/genindex.html            |   2 +-
 docs-out/_build/html/index.html               |  12 ++--
 docs-out/_build/html/modules.html             |   6 +-
 docs-out/_build/html/py-modindex.html         |   2 +-
 docs-out/_build/html/search.html              |   2 +-
 docs-out/_build/html/searchindex.js           |   2 +-
 docs-out/_build/html/setup.html               |   6 +-
 docs/PyCTBN.PyCTBN.estimators.html            |  67 +++++++++++-------
 docs/PyCTBN.PyCTBN.html                       |  14 ++--
 docs/PyCTBN.PyCTBN.optimizers.html            |  30 ++++----
 docs/PyCTBN.PyCTBN.structure_graph.html       |  38 +++++-----
 docs/PyCTBN.PyCTBN.utility.html               |  30 ++++----
 docs/PyCTBN.html                              |  18 ++---
 docs/PyCTBN.tests.estimators.html             |  30 ++++----
 docs/PyCTBN.tests.html                        |  14 ++--
 docs/PyCTBN.tests.optimizers.html             |  22 +++---
 docs/PyCTBN.tests.structure_graph.html        |  38 +++++-----
 docs/PyCTBN.tests.utility.html                |  26 +++----
 docs/basic_main.html                          |   6 +-
 docs/examples.html                            |  22 +++---
 docs/genindex.html                            |   2 +-
 docs/index.html                               |  12 ++--
 docs/modules.html                             |   6 +-
 docs/py-modindex.html                         |   2 +-
 docs/search.html                              |   2 +-
 docs/searchindex.js                           |   2 +-
 docs/setup.html                               |   6 +-
 58 files changed, 403 insertions(+), 373 deletions(-)

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diff --git a/docs-out/_build/doctrees/PyCTBN.doctree b/docs-out/_build/doctrees/PyCTBN.doctree
index e2888030d6b8466c91c3183b83350d85fae31cd2..dc97e78ef3ffd9fcc69cd1f6f81fac222ca4717c 100644
GIT binary patch
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diff --git a/docs-out/_build/doctrees/PyCTBN.tests.doctree b/docs-out/_build/doctrees/PyCTBN.tests.doctree
index 207b2ebf77f08e5436ab3ab393e47f9b77bc295b..a108437136f1ce7516764208a8947dce5cbd990a 100644
GIT binary patch
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diff --git a/docs-out/_build/doctrees/PyCTBN.tests.estimators.doctree b/docs-out/_build/doctrees/PyCTBN.tests.estimators.doctree
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GIT binary patch
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diff --git a/docs-out/_build/doctrees/basic_main.doctree b/docs-out/_build/doctrees/basic_main.doctree
index 20d38876e839a06b41079a2d4f39524c68d3751a..bf49862c0e4ed141ae4757196b35fcb4aa2862fd 100644
GIT binary patch
delta 281
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diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 2e9ad9eb2634c25ad905628966f6b0487488da18..9b766b2abb8786a1ac554518b28c8bfa96e36f51 100644
GIT binary patch
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delta 7452
zcmbVQdt6t=wr`EX4*`MSkGJv?5Rf-0AR+=jFhN8QWvR)-L}1HL^a4e`(DJB1ghU5j
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diff --git a/docs-out/_build/doctrees/examples.doctree b/docs-out/_build/doctrees/examples.doctree
index b6048067d57a4559b5010904309433682452dc30..07c7eded18fa66d0749883fdf29734776cb360f0 100644
GIT binary patch
delta 1211
zcmbu9O=}ZT6o#2*64Mw-?4lr(L_$*X*;Yywv`~u_U8J4bu3Ae-CzEN;z+@(E=892D
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bRZ&3&`lwbU)TO5&iQ1~Qw1hX|P=4qShh3rC

delta 1179
zcmeB*ycxmLz&h1$BFkZ>491C<3t1U6m@{N1doo%w%X%|S-oPR^c`>7<oneM_hJFTE
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zei@JbN;4Edf-itsDhXIF^a1n5c3{ju$k@BtTw9+}gexUAIlm~eBomlO{6KyvP0|AZ
D%cYZ9

diff --git a/docs-out/_build/doctrees/index.doctree b/docs-out/_build/doctrees/index.doctree
index c5dcf41f0720de587b6f530c4138590274a2f289..ae88b93ee58ab0584179608282cd9ec080ce7516 100644
GIT binary patch
delta 917
zcma))&ui0Q7{{AsNt<R}+BrK)SG)P6?b@;0jVYd{A}Wk!ARa^+rETJ#lr(|bpcipN
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zZbY&L5qdfu#><m*Db@PBP?k9=YDP)76f)3UbQT=juc#%nTBvEJ;mCAzR&nAd?-nV%

delta 867
zcmcbl)}Y4Pz&iD-&_>pUOiUS!lQ%Kl;5W(;%P`1b%wWz?^UKiio5ZcauLl&;h6rV-
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GIT binary patch
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diff --git a/docs-out/_build/html/.buildinfo b/docs-out/_build/html/.buildinfo
index 7fb3e3f..cf48ae4 100644
--- a/docs-out/_build/html/.buildinfo
+++ b/docs-out/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: b22e9cd1b245962cc8b033cb6fcce1d2
+config: bd0f22f9d3c91fa8612ea653c4096172
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html b/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html
index cc28d0c..744c567 100644
--- a/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html
+++ b/docs-out/_build/html/PyCTBN.PyCTBN.estimators.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-estimators-package">
+  <section id="pyctbn-pyctbn-estimators-package">
 <h1>PyCTBN.PyCTBN.estimators package<a class="headerlink" href="#pyctbn-pyctbn-estimators-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.fam_score_calculator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.fam_score_calculator">
 <span id="pyctbn-pyctbn-estimators-fam-score-calculator-module"></span><h2>PyCTBN.PyCTBN.estimators.fam_score_calculator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.fam_score_calculator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.fam_score_calculator.FamScoreCalculator">
@@ -300,8 +300,8 @@ and a specif parents’s assignment</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.parameters_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.parameters_estimator">
 <span id="pyctbn-pyctbn-estimators-parameters-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.parameters_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.parameters_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.parameters_estimator.ParametersEstimator">
@@ -385,8 +385,8 @@ in the graph <code class="docutils literal notranslate"><span class="pre">_net_g
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator">
 <span id="pyctbn-pyctbn-estimators-structure-constraint-based-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator">
@@ -467,22 +467,34 @@ Generates all the necessary structures and datas to perform the tests.</p>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm">
-<code class="sig-name descname">ctpc_algorithm</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ctpc_algorithm</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em>, <em class="sig-param"><span class="n">processes_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm" title="Permalink to this definition">¶</a></dt>
 <dd><p>Compute the CTPC algorithm over the entire net.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>disable_multiprocessing</strong> (<em>Boolean</em><em>, </em><em>optional</em>) – true if you desire to disable the multiprocessing operations, default to False</p></li>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
+</ul>
+</dd>
+</dl>
+<p>the maximum number of process; if None it will be automatically set, default to None
+:type processes_number: int, optional</p>
 </dd></dl>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure">
-<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
-<dd><p>Abstract method to estimate the structure</p>
+<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em>, <em class="sig-param"><span class="n">processes_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
+<dd><p>Compute the constraint-based algorithm to find the optimal structure</p>
 <dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>List of estimated edges</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p>Typing.List</p>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>disable_multiprocessing</strong> (<em>Boolean</em><em>, </em><em>optional</em>) – true if you desire to disable the multiprocessing operations, default to False</p></li>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
+</ul>
 </dd>
 </dl>
+<p>the maximum number of process; if None it will be automatically set, default to None
+:type processes_number: int, optional</p>
 </dd></dl>
 
 <dl class="py method">
@@ -521,8 +533,8 @@ it is performed also the chi_test.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.structure_estimator">
 <span id="pyctbn-pyctbn-estimators-structure-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.structure_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.structure_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator">
@@ -677,8 +689,8 @@ that do not contains a the node identified by <code class="docutils literal notr
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator">
 <span id="pyctbn-pyctbn-estimators-structure-score-based-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.structure_score_based_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator">
@@ -723,7 +735,7 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure">
-<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">max_parents</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">iterations_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">40</span></em>, <em class="sig-param"><span class="n">patience</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_length</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_rules_duration</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="p">:</span> <span class="n">str</span> <span class="o">=</span> <span class="default_value">'tabu'</span></em>, <em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">max_parents</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">iterations_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">40</span></em>, <em class="sig-param"><span class="n">patience</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_length</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_rules_duration</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="p">:</span> <span class="n">str</span> <span class="o">=</span> <span class="default_value">'tabu'</span></em>, <em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em>, <em class="sig-param"><span class="n">processes_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
 <dd><p>Compute the score-based algorithm to find the optimal structure</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
@@ -735,9 +747,12 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 <li><p><strong>tabu_rules_duration</strong> (<em>int</em><em>, </em><em>optional</em>) – number of iterations in which each rule keeps its value, default to None</p></li>
 <li><p><strong>optimizer</strong> (<em>string</em><em>, </em><em>optional</em>) – name of the optimizer algorithm. Possible values: ‘hill’ (Hill climbing),’tabu’ (tabu search), defualt to ‘tabu’</p></li>
 <li><p><strong>disable_multiprocessing</strong> (<em>Boolean</em><em>, </em><em>optional</em>) – true if you desire to disable the multiprocessing operations, default to False</p></li>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
 </ul>
 </dd>
 </dl>
+<p>the maximum number of process; if None it will be automatically set, default to None
+:type processes_number: int, optional</p>
 </dd></dl>
 
 <dl class="py method">
@@ -762,11 +777,11 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.PyCTBN.html b/docs-out/_build/html/PyCTBN.PyCTBN.html
index 6e4fde1..bd6313d 100644
--- a/docs-out/_build/html/PyCTBN.PyCTBN.html
+++ b/docs-out/_build/html/PyCTBN.PyCTBN.html
@@ -60,7 +60,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#subpackages">Subpackages</a></li>
@@ -114,9 +114,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-package">
+  <section id="pyctbn-pyctbn-package">
 <h1>PyCTBN.PyCTBN package<a class="headerlink" href="#pyctbn-pyctbn-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="subpackages">
+<section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -161,11 +161,11 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN">
+</section>
+<section id="module-PyCTBN.PyCTBN">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.PyCTBN.optimizers.html b/docs-out/_build/html/PyCTBN.PyCTBN.optimizers.html
index be9cd55..58423f2 100644
--- a/docs-out/_build/html/PyCTBN.PyCTBN.optimizers.html
+++ b/docs-out/_build/html/PyCTBN.PyCTBN.optimizers.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-optimizers-package">
+  <section id="pyctbn-pyctbn-optimizers-package">
 <h1>PyCTBN.PyCTBN.optimizers package<a class="headerlink" href="#pyctbn-pyctbn-optimizers-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer">
 <span id="pyctbn-pyctbn-optimizers-constraint-based-optimizer-module"></span><h2>PyCTBN.PyCTBN.optimizers.constraint_based_optimizer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.constraint_based_optimizer.ConstraintBasedOptimizer">
@@ -152,8 +152,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.hill_climbing_search">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.hill_climbing_search">
 <span id="pyctbn-pyctbn-optimizers-hill-climbing-search-module"></span><h2>PyCTBN.PyCTBN.optimizers.hill_climbing_search module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.hill_climbing_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.hill_climbing_search.HillClimbing">
@@ -187,8 +187,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.optimizer">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.optimizer">
 <span id="pyctbn-pyctbn-optimizers-optimizer-module"></span><h2>PyCTBN.PyCTBN.optimizers.optimizer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.optimizer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.optimizer.Optimizer">
@@ -219,8 +219,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.tabu_search">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.tabu_search">
 <span id="pyctbn-pyctbn-optimizers-tabu-search-module"></span><h2>PyCTBN.PyCTBN.optimizers.tabu_search module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.tabu_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.tabu_search.TabuSearch">
@@ -256,11 +256,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.PyCTBN.structure_graph.html b/docs-out/_build/html/PyCTBN.PyCTBN.structure_graph.html
index 6080755..9ff99e7 100644
--- a/docs-out/_build/html/PyCTBN.PyCTBN.structure_graph.html
+++ b/docs-out/_build/html/PyCTBN.PyCTBN.structure_graph.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-structure-graph-package">
+  <section id="pyctbn-pyctbn-structure-graph-package">
 <h1>PyCTBN.PyCTBN.structure_graph package<a class="headerlink" href="#pyctbn-pyctbn-structure-graph-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix">
 <span id="pyctbn-pyctbn-structure-graph-conditional-intensity-matrix-module"></span><h2>PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix">
@@ -163,8 +163,8 @@ The class member <code class="docutils literal notranslate"><span class="pre">_c
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.network_graph">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.network_graph">
 <span id="pyctbn-pyctbn-structure-graph-network-graph-module"></span><h2>PyCTBN.PyCTBN.structure_graph.network_graph module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.network_graph" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.network_graph.NetworkGraph">
@@ -456,8 +456,8 @@ Initialize all the filtering/indexing structures.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.sample_path">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.sample_path">
 <span id="pyctbn-pyctbn-structure-graph-sample-path-module"></span><h2>PyCTBN.PyCTBN.structure_graph.sample_path module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.sample_path" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.sample_path.SamplePath">
@@ -520,8 +520,8 @@ Clears all the unused dataframes in <code class="docutils literal notranslate"><
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.set_of_cims">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.set_of_cims">
 <span id="pyctbn-pyctbn-structure-graph-set-of-cims-module"></span><h2>PyCTBN.PyCTBN.structure_graph.set_of_cims module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.set_of_cims" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.set_of_cims.SetOfCims">
@@ -606,8 +606,8 @@ Compute the cim coefficients.The class member <code class="docutils literal notr
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.structure">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.structure">
 <span id="pyctbn-pyctbn-structure-graph-structure-module"></span><h2>PyCTBN.PyCTBN.structure_graph.structure module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.structure" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.structure.Structure">
@@ -735,8 +735,8 @@ The class member <code class="docutils literal notranslate"><span class="pre">_t
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.trajectory">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.trajectory">
 <span id="pyctbn-pyctbn-structure-graph-trajectory-module"></span><h2>PyCTBN.PyCTBN.structure_graph.trajectory module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.trajectory" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.trajectory.Trajectory">
@@ -780,11 +780,11 @@ The class member <code class="docutils literal notranslate"><span class="pre">_t
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.PyCTBN.utility.html b/docs-out/_build/html/PyCTBN.PyCTBN.utility.html
index 5f834ce..50c6ce2 100644
--- a/docs-out/_build/html/PyCTBN.PyCTBN.utility.html
+++ b/docs-out/_build/html/PyCTBN.PyCTBN.utility.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-utility-package">
+  <section id="pyctbn-pyctbn-utility-package">
 <h1>PyCTBN.PyCTBN.utility package<a class="headerlink" href="#pyctbn-pyctbn-utility-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.abstract_importer">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.abstract_importer">
 <span id="pyctbn-pyctbn-utility-abstract-importer-module"></span><h2>PyCTBN.PyCTBN.utility.abstract_importer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.abstract_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter">
@@ -281,8 +281,8 @@ dataset</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.cache">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.cache">
 <span id="pyctbn-pyctbn-utility-cache-module"></span><h2>PyCTBN.PyCTBN.utility.cache module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.cache" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.cache.Cache">
@@ -340,8 +340,8 @@ None otherwise.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.json_importer">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.json_importer">
 <span id="pyctbn-pyctbn-utility-json-importer-module"></span><h2>PyCTBN.PyCTBN.utility.json_importer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.json_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.json_importer.JsonImporter">
@@ -531,8 +531,8 @@ as keys for the set of CIMS of a particular node.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.sample_importer">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.sample_importer">
 <span id="pyctbn-pyctbn-utility-sample-importer-module"></span><h2>PyCTBN.PyCTBN.utility.sample_importer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.sample_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.sample_importer.SampleImporter">
@@ -575,11 +575,11 @@ dataset</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.html b/docs-out/_build/html/PyCTBN.html
index 1faa738..8f6f17f 100644
--- a/docs-out/_build/html/PyCTBN.html
+++ b/docs-out/_build/html/PyCTBN.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-package">
+  <section id="pyctbn-package">
 <h1>PyCTBN package<a class="headerlink" href="#pyctbn-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="subpackages">
+<section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -166,14 +166,14 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="submodules">
+</section>
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN">
+</section>
+<section id="module-PyCTBN">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.tests.estimators.html b/docs-out/_build/html/PyCTBN.tests.estimators.html
index ab1bfc8..8a63d1f 100644
--- a/docs-out/_build/html/PyCTBN.tests.estimators.html
+++ b/docs-out/_build/html/PyCTBN.tests.estimators.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-estimators-package">
+  <section id="pyctbn-tests-estimators-package">
 <h1>PyCTBN.tests.estimators package<a class="headerlink" href="#pyctbn-tests-estimators-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_parameters_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_parameters_estimator">
 <span id="pyctbn-tests-estimators-test-parameters-estimator-module"></span><h2>PyCTBN.tests.estimators.test_parameters_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_parameters_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_parameters_estimator.TestParametersEstimatior">
@@ -156,8 +156,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator">
 <span id="pyctbn-tests-estimators-test-structure-constraint-based-estimator-module"></span><h2>PyCTBN.tests.estimators.test_structure_constraint_based_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator">
@@ -186,8 +186,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_structure_estimator">
 <span id="pyctbn-tests-estimators-test-structure-estimator-module"></span><h2>PyCTBN.tests.estimators.test_structure_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_structure_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_structure_estimator.TestStructureEstimator">
@@ -241,8 +241,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_score_based_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_structure_score_based_estimator">
 <span id="pyctbn-tests-estimators-test-structure-score-based-estimator-module"></span><h2>PyCTBN.tests.estimators.test_structure_score_based_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_structure_score_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator">
@@ -276,11 +276,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators">
+</section>
+<section id="module-PyCTBN.tests.estimators">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.estimators" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.tests.html b/docs-out/_build/html/PyCTBN.tests.html
index dc6280d..83be260 100644
--- a/docs-out/_build/html/PyCTBN.tests.html
+++ b/docs-out/_build/html/PyCTBN.tests.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-package">
+  <section id="pyctbn-tests-package">
 <h1>PyCTBN.tests package<a class="headerlink" href="#pyctbn-tests-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="subpackages">
+<section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -155,11 +155,11 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="module-PyCTBN.tests">
+</section>
+<section id="module-PyCTBN.tests">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.tests.optimizers.html b/docs-out/_build/html/PyCTBN.tests.optimizers.html
index 20e937a..96038cc 100644
--- a/docs-out/_build/html/PyCTBN.tests.optimizers.html
+++ b/docs-out/_build/html/PyCTBN.tests.optimizers.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-optimizers-package">
+  <section id="pyctbn-tests-optimizers-package">
 <h1>PyCTBN.tests.optimizers package<a class="headerlink" href="#pyctbn-tests-optimizers-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.optimizers.test_hill_climbing_search">
+</section>
+<section id="module-PyCTBN.tests.optimizers.test_hill_climbing_search">
 <span id="pyctbn-tests-optimizers-test-hill-climbing-search-module"></span><h2>PyCTBN.tests.optimizers.test_hill_climbing_search module<a class="headerlink" href="#module-PyCTBN.tests.optimizers.test_hill_climbing_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.optimizers.test_hill_climbing_search.TestHillClimbingSearch">
@@ -141,8 +141,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.optimizers.test_tabu_search">
+</section>
+<section id="module-PyCTBN.tests.optimizers.test_tabu_search">
 <span id="pyctbn-tests-optimizers-test-tabu-search-module"></span><h2>PyCTBN.tests.optimizers.test_tabu_search module<a class="headerlink" href="#module-PyCTBN.tests.optimizers.test_tabu_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.optimizers.test_tabu_search.TestTabuSearch">
@@ -166,11 +166,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.optimizers">
+</section>
+<section id="module-PyCTBN.tests.optimizers">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.optimizers" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.tests.structure_graph.html b/docs-out/_build/html/PyCTBN.tests.structure_graph.html
index f87e7db..f3dae53 100644
--- a/docs-out/_build/html/PyCTBN.tests.structure_graph.html
+++ b/docs-out/_build/html/PyCTBN.tests.structure_graph.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-structure-graph-package">
+  <section id="pyctbn-tests-structure-graph-package">
 <h1>PyCTBN.tests.structure_graph package<a class="headerlink" href="#pyctbn-tests-structure-graph-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_cim">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_cim">
 <span id="pyctbn-tests-structure-graph-test-cim-module"></span><h2>PyCTBN.tests.structure_graph.test_cim module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_cim" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_cim.TestConditionalIntensityMatrix">
@@ -146,8 +146,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_networkgraph">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_networkgraph">
 <span id="pyctbn-tests-structure-graph-test-networkgraph-module"></span><h2>PyCTBN.tests.structure_graph.test_networkgraph module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_networkgraph" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_networkgraph.TestNetworkGraph">
@@ -251,8 +251,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_sample_path">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_sample_path">
 <span id="pyctbn-tests-structure-graph-test-sample-path-module"></span><h2>PyCTBN.tests.structure_graph.test_sample_path module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_sample_path" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_sample_path.TestSamplePath">
@@ -311,8 +311,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_setofcims">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_setofcims">
 <span id="pyctbn-tests-structure-graph-test-setofcims-module"></span><h2>PyCTBN.tests.structure_graph.test_setofcims module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_setofcims" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_setofcims.TestSetOfCims">
@@ -368,8 +368,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_structure">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_structure">
 <span id="pyctbn-tests-structure-graph-test-structure-module"></span><h2>PyCTBN.tests.structure_graph.test_structure module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_structure" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_structure.TestStructure">
@@ -423,8 +423,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_trajectory">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_trajectory">
 <span id="pyctbn-tests-structure-graph-test-trajectory-module"></span><h2>PyCTBN.tests.structure_graph.test_trajectory module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_trajectory" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_trajectory.TestTrajectory">
@@ -443,11 +443,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph">
+</section>
+<section id="module-PyCTBN.tests.structure_graph">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.structure_graph" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/PyCTBN.tests.utility.html b/docs-out/_build/html/PyCTBN.tests.utility.html
index 0cd5380..606ce71 100644
--- a/docs-out/_build/html/PyCTBN.tests.utility.html
+++ b/docs-out/_build/html/PyCTBN.tests.utility.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-utility-package">
+  <section id="pyctbn-tests-utility-package">
 <h1>PyCTBN.tests.utility package<a class="headerlink" href="#pyctbn-tests-utility-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.utility.test_cache">
+</section>
+<section id="module-PyCTBN.tests.utility.test_cache">
 <span id="pyctbn-tests-utility-test-cache-module"></span><h2>PyCTBN.tests.utility.test_cache module<a class="headerlink" href="#module-PyCTBN.tests.utility.test_cache" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.utility.test_cache.TestCache">
@@ -145,8 +145,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.utility.test_json_importer">
+</section>
+<section id="module-PyCTBN.tests.utility.test_json_importer">
 <span id="pyctbn-tests-utility-test-json-importer-module"></span><h2>PyCTBN.tests.utility.test_json_importer module<a class="headerlink" href="#module-PyCTBN.tests.utility.test_json_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.utility.test_json_importer.TestJsonImporter">
@@ -255,8 +255,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.utility.test_sample_importer">
+</section>
+<section id="module-PyCTBN.tests.utility.test_sample_importer">
 <span id="pyctbn-tests-utility-test-sample-importer-module"></span><h2>PyCTBN.tests.utility.test_sample_importer module<a class="headerlink" href="#module-PyCTBN.tests.utility.test_sample_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.utility.test_sample_importer.TestSampleImporter">
@@ -285,11 +285,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.utility">
+</section>
+<section id="module-PyCTBN.tests.utility">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.utility" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/basic_main.html b/docs-out/_build/html/basic_main.html
index 1ba75f4..a74fa74 100644
--- a/docs-out/_build/html/basic_main.html
+++ b/docs-out/_build/html/basic_main.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="basic-main-module">
+  <section id="basic-main-module">
 <h1>basic_main module<a class="headerlink" href="#basic-main-module" title="Permalink to this headline">¶</a></h1>
-</div>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/examples.html b/docs-out/_build/html/examples.html
index 8bf8f53..94a79a7 100644
--- a/docs-out/_build/html/examples.html
+++ b/docs-out/_build/html/examples.html
@@ -59,7 +59,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -113,16 +113,16 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="examples">
+  <section id="examples">
 <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="installation-usage">
+<section id="installation-usage">
 <h2>Installation/Usage<a class="headerlink" href="#installation-usage" title="Permalink to this headline">¶</a></h2>
 <p>Download the release in .tar.gz or .whl format and simply use pip install to install it:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$pip install PyCTBN-1.0.tar.gz
 </pre></div>
 </div>
-</div>
-<div class="section" id="implementing-your-own-data-importer">
+</section>
+<section id="implementing-your-own-data-importer">
 <h2>Implementing your own data importer<a class="headerlink" href="#implementing-your-own-data-importer" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="sd">&quot;&quot;&quot;This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.</span>
 <span class="sd">The net in exam has three ternary nodes and no prior net structure.</span>
@@ -161,8 +161,8 @@
         <span class="k">pass</span>
 </pre></div>
 </div>
-</div>
-<div class="section" id="parameters-estimation-example">
+</section>
+<section id="parameters-estimation-example">
 <h2>Parameters Estimation Example<a class="headerlink" href="#parameters-estimation-example" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">JsonImporter</span>
 <span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">SamplePath</span>
@@ -199,8 +199,8 @@
     <span class="nb">print</span><span class="p">(</span><span class="n">sofc1</span><span class="o">.</span><span class="n">actual_cims</span><span class="p">)</span>
 </pre></div>
 </div>
-</div>
-<div class="section" id="structure-estimation-example">
+</section>
+<section id="structure-estimation-example">
 <h2>Structure Estimation Example<a class="headerlink" href="#structure-estimation-example" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">JsonImporter</span>
 <span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">SamplePath</span>
@@ -230,8 +230,8 @@
     <span class="n">se1</span><span class="o">.</span><span class="n">save_results</span><span class="p">()</span>
 </pre></div>
 </div>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/genindex.html b/docs-out/_build/html/genindex.html
index 0dea95f..bd2996c 100644
--- a/docs-out/_build/html/genindex.html
+++ b/docs-out/_build/html/genindex.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
diff --git a/docs-out/_build/html/index.html b/docs-out/_build/html/index.html
index f262fe7..996979e 100644
--- a/docs-out/_build/html/index.html
+++ b/docs-out/_build/html/index.html
@@ -59,7 +59,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -113,10 +113,10 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="welcome-to-pyctbn-s-documentation">
+  <section id="welcome-to-pyctbn-s-documentation">
 <h1>Welcome to PyCTBN’s documentation!<a class="headerlink" href="#welcome-to-pyctbn-s-documentation" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
-<p class="caption"><span class="caption-text">Contents:</span></p>
+<p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a><ul>
@@ -173,15 +173,15 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="indices-and-tables">
+</section>
+<section id="indices-and-tables">
 <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
 <ul class="simple">
 <li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
 <li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
 <li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
 </ul>
-</div>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/modules.html b/docs-out/_build/html/modules.html
index 28d3d3b..2540d43 100644
--- a/docs-out/_build/html/modules.html
+++ b/docs-out/_build/html/modules.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,7 +112,7 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn">
+  <section id="pyctbn">
 <h1>PyCTBN<a class="headerlink" href="#pyctbn" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
@@ -171,7 +171,7 @@
 </li>
 </ul>
 </div>
-</div>
+</section>
 
 
 	    </div>
diff --git a/docs-out/_build/html/py-modindex.html b/docs-out/_build/html/py-modindex.html
index 809febd..d729367 100644
--- a/docs-out/_build/html/py-modindex.html
+++ b/docs-out/_build/html/py-modindex.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
diff --git a/docs-out/_build/html/search.html b/docs-out/_build/html/search.html
index b9884b3..21fd6c9 100644
--- a/docs-out/_build/html/search.html
+++ b/docs-out/_build/html/search.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
diff --git a/docs-out/_build/html/searchindex.js b/docs-out/_build/html/searchindex.js
index 051c818..7d0597c 100644
--- a/docs-out/_build/html/searchindex.js
+++ b/docs-out/_build/html/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/docs-out/_build/html/setup.html b/docs-out/_build/html/setup.html
index d942353..8f74cf7 100644
--- a/docs-out/_build/html/setup.html
+++ b/docs-out/_build/html/setup.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="setup-module">
+  <section id="setup-module">
 <h1>setup module<a class="headerlink" href="#setup-module" title="Permalink to this headline">¶</a></h1>
-</div>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.PyCTBN.estimators.html b/docs/PyCTBN.PyCTBN.estimators.html
index cc28d0c..744c567 100644
--- a/docs/PyCTBN.PyCTBN.estimators.html
+++ b/docs/PyCTBN.PyCTBN.estimators.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-estimators-package">
+  <section id="pyctbn-pyctbn-estimators-package">
 <h1>PyCTBN.PyCTBN.estimators package<a class="headerlink" href="#pyctbn-pyctbn-estimators-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.fam_score_calculator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.fam_score_calculator">
 <span id="pyctbn-pyctbn-estimators-fam-score-calculator-module"></span><h2>PyCTBN.PyCTBN.estimators.fam_score_calculator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.fam_score_calculator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.fam_score_calculator.FamScoreCalculator">
@@ -300,8 +300,8 @@ and a specif parents’s assignment</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.parameters_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.parameters_estimator">
 <span id="pyctbn-pyctbn-estimators-parameters-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.parameters_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.parameters_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.parameters_estimator.ParametersEstimator">
@@ -385,8 +385,8 @@ in the graph <code class="docutils literal notranslate"><span class="pre">_net_g
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator">
 <span id="pyctbn-pyctbn-estimators-structure-constraint-based-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator">
@@ -467,22 +467,34 @@ Generates all the necessary structures and datas to perform the tests.</p>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm">
-<code class="sig-name descname">ctpc_algorithm</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">ctpc_algorithm</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em>, <em class="sig-param"><span class="n">processes_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm" title="Permalink to this definition">¶</a></dt>
 <dd><p>Compute the CTPC algorithm over the entire net.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>disable_multiprocessing</strong> (<em>Boolean</em><em>, </em><em>optional</em>) – true if you desire to disable the multiprocessing operations, default to False</p></li>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
+</ul>
+</dd>
+</dl>
+<p>the maximum number of process; if None it will be automatically set, default to None
+:type processes_number: int, optional</p>
 </dd></dl>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure">
-<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
-<dd><p>Abstract method to estimate the structure</p>
+<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em>, <em class="sig-param"><span class="n">processes_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
+<dd><p>Compute the constraint-based algorithm to find the optimal structure</p>
 <dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p>List of estimated edges</p>
-</dd>
-<dt class="field-even">Return type</dt>
-<dd class="field-even"><p>Typing.List</p>
+<dt class="field-odd">Parameters</dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>disable_multiprocessing</strong> (<em>Boolean</em><em>, </em><em>optional</em>) – true if you desire to disable the multiprocessing operations, default to False</p></li>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
+</ul>
 </dd>
 </dl>
+<p>the maximum number of process; if None it will be automatically set, default to None
+:type processes_number: int, optional</p>
 </dd></dl>
 
 <dl class="py method">
@@ -521,8 +533,8 @@ it is performed also the chi_test.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.structure_estimator">
 <span id="pyctbn-pyctbn-estimators-structure-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.structure_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.structure_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator">
@@ -677,8 +689,8 @@ that do not contains a the node identified by <code class="docutils literal notr
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator">
 <span id="pyctbn-pyctbn-estimators-structure-score-based-estimator-module"></span><h2>PyCTBN.PyCTBN.estimators.structure_score_based_estimator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator">
@@ -723,7 +735,7 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 
 <dl class="py method">
 <dt id="PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure">
-<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">max_parents</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">iterations_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">40</span></em>, <em class="sig-param"><span class="n">patience</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_length</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_rules_duration</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="p">:</span> <span class="n">str</span> <span class="o">=</span> <span class="default_value">'tabu'</span></em>, <em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">estimate_structure</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">max_parents</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">iterations_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">40</span></em>, <em class="sig-param"><span class="n">patience</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_length</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">tabu_rules_duration</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="p">:</span> <span class="n">str</span> <span class="o">=</span> <span class="default_value">'tabu'</span></em>, <em class="sig-param"><span class="n">disable_multiprocessing</span><span class="p">:</span> <span class="n">bool</span> <span class="o">=</span> <span class="default_value">False</span></em>, <em class="sig-param"><span class="n">processes_number</span><span class="p">:</span> <span class="n">int</span> <span class="o">=</span> <span class="default_value">None</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure" title="Permalink to this definition">¶</a></dt>
 <dd><p>Compute the score-based algorithm to find the optimal structure</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
@@ -735,9 +747,12 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 <li><p><strong>tabu_rules_duration</strong> (<em>int</em><em>, </em><em>optional</em>) – number of iterations in which each rule keeps its value, default to None</p></li>
 <li><p><strong>optimizer</strong> (<em>string</em><em>, </em><em>optional</em>) – name of the optimizer algorithm. Possible values: ‘hill’ (Hill climbing),’tabu’ (tabu search), defualt to ‘tabu’</p></li>
 <li><p><strong>disable_multiprocessing</strong> (<em>Boolean</em><em>, </em><em>optional</em>) – true if you desire to disable the multiprocessing operations, default to False</p></li>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
 </ul>
 </dd>
 </dl>
+<p>the maximum number of process; if None it will be automatically set, default to None
+:type processes_number: int, optional</p>
 </dd></dl>
 
 <dl class="py method">
@@ -762,11 +777,11 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators">
+</section>
+<section id="module-PyCTBN.PyCTBN.estimators">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.estimators" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.PyCTBN.html b/docs/PyCTBN.PyCTBN.html
index 6e4fde1..bd6313d 100644
--- a/docs/PyCTBN.PyCTBN.html
+++ b/docs/PyCTBN.PyCTBN.html
@@ -60,7 +60,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="current reference internal" href="#">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#subpackages">Subpackages</a></li>
@@ -114,9 +114,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-package">
+  <section id="pyctbn-pyctbn-package">
 <h1>PyCTBN.PyCTBN package<a class="headerlink" href="#pyctbn-pyctbn-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="subpackages">
+<section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -161,11 +161,11 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN">
+</section>
+<section id="module-PyCTBN.PyCTBN">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.PyCTBN.optimizers.html b/docs/PyCTBN.PyCTBN.optimizers.html
index be9cd55..58423f2 100644
--- a/docs/PyCTBN.PyCTBN.optimizers.html
+++ b/docs/PyCTBN.PyCTBN.optimizers.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-optimizers-package">
+  <section id="pyctbn-pyctbn-optimizers-package">
 <h1>PyCTBN.PyCTBN.optimizers package<a class="headerlink" href="#pyctbn-pyctbn-optimizers-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer">
 <span id="pyctbn-pyctbn-optimizers-constraint-based-optimizer-module"></span><h2>PyCTBN.PyCTBN.optimizers.constraint_based_optimizer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.constraint_based_optimizer.ConstraintBasedOptimizer">
@@ -152,8 +152,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.hill_climbing_search">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.hill_climbing_search">
 <span id="pyctbn-pyctbn-optimizers-hill-climbing-search-module"></span><h2>PyCTBN.PyCTBN.optimizers.hill_climbing_search module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.hill_climbing_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.hill_climbing_search.HillClimbing">
@@ -187,8 +187,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.optimizer">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.optimizer">
 <span id="pyctbn-pyctbn-optimizers-optimizer-module"></span><h2>PyCTBN.PyCTBN.optimizers.optimizer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.optimizer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.optimizer.Optimizer">
@@ -219,8 +219,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.tabu_search">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers.tabu_search">
 <span id="pyctbn-pyctbn-optimizers-tabu-search-module"></span><h2>PyCTBN.PyCTBN.optimizers.tabu_search module<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers.tabu_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.optimizers.tabu_search.TabuSearch">
@@ -256,11 +256,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers">
+</section>
+<section id="module-PyCTBN.PyCTBN.optimizers">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.optimizers" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.PyCTBN.structure_graph.html b/docs/PyCTBN.PyCTBN.structure_graph.html
index 6080755..9ff99e7 100644
--- a/docs/PyCTBN.PyCTBN.structure_graph.html
+++ b/docs/PyCTBN.PyCTBN.structure_graph.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-structure-graph-package">
+  <section id="pyctbn-pyctbn-structure-graph-package">
 <h1>PyCTBN.PyCTBN.structure_graph package<a class="headerlink" href="#pyctbn-pyctbn-structure-graph-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix">
 <span id="pyctbn-pyctbn-structure-graph-conditional-intensity-matrix-module"></span><h2>PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix">
@@ -163,8 +163,8 @@ The class member <code class="docutils literal notranslate"><span class="pre">_c
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.network_graph">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.network_graph">
 <span id="pyctbn-pyctbn-structure-graph-network-graph-module"></span><h2>PyCTBN.PyCTBN.structure_graph.network_graph module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.network_graph" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.network_graph.NetworkGraph">
@@ -456,8 +456,8 @@ Initialize all the filtering/indexing structures.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.sample_path">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.sample_path">
 <span id="pyctbn-pyctbn-structure-graph-sample-path-module"></span><h2>PyCTBN.PyCTBN.structure_graph.sample_path module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.sample_path" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.sample_path.SamplePath">
@@ -520,8 +520,8 @@ Clears all the unused dataframes in <code class="docutils literal notranslate"><
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.set_of_cims">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.set_of_cims">
 <span id="pyctbn-pyctbn-structure-graph-set-of-cims-module"></span><h2>PyCTBN.PyCTBN.structure_graph.set_of_cims module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.set_of_cims" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.set_of_cims.SetOfCims">
@@ -606,8 +606,8 @@ Compute the cim coefficients.The class member <code class="docutils literal notr
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.structure">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.structure">
 <span id="pyctbn-pyctbn-structure-graph-structure-module"></span><h2>PyCTBN.PyCTBN.structure_graph.structure module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.structure" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.structure.Structure">
@@ -735,8 +735,8 @@ The class member <code class="docutils literal notranslate"><span class="pre">_t
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.trajectory">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph.trajectory">
 <span id="pyctbn-pyctbn-structure-graph-trajectory-module"></span><h2>PyCTBN.PyCTBN.structure_graph.trajectory module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.trajectory" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.structure_graph.trajectory.Trajectory">
@@ -780,11 +780,11 @@ The class member <code class="docutils literal notranslate"><span class="pre">_t
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph">
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.PyCTBN.utility.html b/docs/PyCTBN.PyCTBN.utility.html
index 5f834ce..50c6ce2 100644
--- a/docs/PyCTBN.PyCTBN.utility.html
+++ b/docs/PyCTBN.PyCTBN.utility.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1 current"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -115,12 +115,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-pyctbn-utility-package">
+  <section id="pyctbn-pyctbn-utility-package">
 <h1>PyCTBN.PyCTBN.utility package<a class="headerlink" href="#pyctbn-pyctbn-utility-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.abstract_importer">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.abstract_importer">
 <span id="pyctbn-pyctbn-utility-abstract-importer-module"></span><h2>PyCTBN.PyCTBN.utility.abstract_importer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.abstract_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter">
@@ -281,8 +281,8 @@ dataset</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.cache">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.cache">
 <span id="pyctbn-pyctbn-utility-cache-module"></span><h2>PyCTBN.PyCTBN.utility.cache module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.cache" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.cache.Cache">
@@ -340,8 +340,8 @@ None otherwise.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.json_importer">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.json_importer">
 <span id="pyctbn-pyctbn-utility-json-importer-module"></span><h2>PyCTBN.PyCTBN.utility.json_importer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.json_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.json_importer.JsonImporter">
@@ -531,8 +531,8 @@ as keys for the set of CIMS of a particular node.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.sample_importer">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility.sample_importer">
 <span id="pyctbn-pyctbn-utility-sample-importer-module"></span><h2>PyCTBN.PyCTBN.utility.sample_importer module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.sample_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.PyCTBN.utility.sample_importer.SampleImporter">
@@ -575,11 +575,11 @@ dataset</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility">
+</section>
+<section id="module-PyCTBN.PyCTBN.utility">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.html b/docs/PyCTBN.html
index 1faa738..8f6f17f 100644
--- a/docs/PyCTBN.html
+++ b/docs/PyCTBN.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-package">
+  <section id="pyctbn-package">
 <h1>PyCTBN package<a class="headerlink" href="#pyctbn-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="subpackages">
+<section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -166,14 +166,14 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="submodules">
+</section>
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN">
+</section>
+<section id="module-PyCTBN">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.tests.estimators.html b/docs/PyCTBN.tests.estimators.html
index ab1bfc8..8a63d1f 100644
--- a/docs/PyCTBN.tests.estimators.html
+++ b/docs/PyCTBN.tests.estimators.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-estimators-package">
+  <section id="pyctbn-tests-estimators-package">
 <h1>PyCTBN.tests.estimators package<a class="headerlink" href="#pyctbn-tests-estimators-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_parameters_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_parameters_estimator">
 <span id="pyctbn-tests-estimators-test-parameters-estimator-module"></span><h2>PyCTBN.tests.estimators.test_parameters_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_parameters_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_parameters_estimator.TestParametersEstimatior">
@@ -156,8 +156,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator">
 <span id="pyctbn-tests-estimators-test-structure-constraint-based-estimator-module"></span><h2>PyCTBN.tests.estimators.test_structure_constraint_based_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator">
@@ -186,8 +186,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_structure_estimator">
 <span id="pyctbn-tests-estimators-test-structure-estimator-module"></span><h2>PyCTBN.tests.estimators.test_structure_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_structure_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_structure_estimator.TestStructureEstimator">
@@ -241,8 +241,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_score_based_estimator">
+</section>
+<section id="module-PyCTBN.tests.estimators.test_structure_score_based_estimator">
 <span id="pyctbn-tests-estimators-test-structure-score-based-estimator-module"></span><h2>PyCTBN.tests.estimators.test_structure_score_based_estimator module<a class="headerlink" href="#module-PyCTBN.tests.estimators.test_structure_score_based_estimator" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator">
@@ -276,11 +276,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.estimators">
+</section>
+<section id="module-PyCTBN.tests.estimators">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.estimators" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.tests.html b/docs/PyCTBN.tests.html
index dc6280d..83be260 100644
--- a/docs/PyCTBN.tests.html
+++ b/docs/PyCTBN.tests.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-package">
+  <section id="pyctbn-tests-package">
 <h1>PyCTBN.tests package<a class="headerlink" href="#pyctbn-tests-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="subpackages">
+<section id="subpackages">
 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -155,11 +155,11 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="module-PyCTBN.tests">
+</section>
+<section id="module-PyCTBN.tests">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.tests.optimizers.html b/docs/PyCTBN.tests.optimizers.html
index 20e937a..96038cc 100644
--- a/docs/PyCTBN.tests.optimizers.html
+++ b/docs/PyCTBN.tests.optimizers.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-optimizers-package">
+  <section id="pyctbn-tests-optimizers-package">
 <h1>PyCTBN.tests.optimizers package<a class="headerlink" href="#pyctbn-tests-optimizers-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.optimizers.test_hill_climbing_search">
+</section>
+<section id="module-PyCTBN.tests.optimizers.test_hill_climbing_search">
 <span id="pyctbn-tests-optimizers-test-hill-climbing-search-module"></span><h2>PyCTBN.tests.optimizers.test_hill_climbing_search module<a class="headerlink" href="#module-PyCTBN.tests.optimizers.test_hill_climbing_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.optimizers.test_hill_climbing_search.TestHillClimbingSearch">
@@ -141,8 +141,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.optimizers.test_tabu_search">
+</section>
+<section id="module-PyCTBN.tests.optimizers.test_tabu_search">
 <span id="pyctbn-tests-optimizers-test-tabu-search-module"></span><h2>PyCTBN.tests.optimizers.test_tabu_search module<a class="headerlink" href="#module-PyCTBN.tests.optimizers.test_tabu_search" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.optimizers.test_tabu_search.TestTabuSearch">
@@ -166,11 +166,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.optimizers">
+</section>
+<section id="module-PyCTBN.tests.optimizers">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.optimizers" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.tests.structure_graph.html b/docs/PyCTBN.tests.structure_graph.html
index f87e7db..f3dae53 100644
--- a/docs/PyCTBN.tests.structure_graph.html
+++ b/docs/PyCTBN.tests.structure_graph.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-structure-graph-package">
+  <section id="pyctbn-tests-structure-graph-package">
 <h1>PyCTBN.tests.structure_graph package<a class="headerlink" href="#pyctbn-tests-structure-graph-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_cim">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_cim">
 <span id="pyctbn-tests-structure-graph-test-cim-module"></span><h2>PyCTBN.tests.structure_graph.test_cim module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_cim" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_cim.TestConditionalIntensityMatrix">
@@ -146,8 +146,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_networkgraph">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_networkgraph">
 <span id="pyctbn-tests-structure-graph-test-networkgraph-module"></span><h2>PyCTBN.tests.structure_graph.test_networkgraph module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_networkgraph" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_networkgraph.TestNetworkGraph">
@@ -251,8 +251,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_sample_path">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_sample_path">
 <span id="pyctbn-tests-structure-graph-test-sample-path-module"></span><h2>PyCTBN.tests.structure_graph.test_sample_path module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_sample_path" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_sample_path.TestSamplePath">
@@ -311,8 +311,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_setofcims">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_setofcims">
 <span id="pyctbn-tests-structure-graph-test-setofcims-module"></span><h2>PyCTBN.tests.structure_graph.test_setofcims module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_setofcims" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_setofcims.TestSetOfCims">
@@ -368,8 +368,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_structure">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_structure">
 <span id="pyctbn-tests-structure-graph-test-structure-module"></span><h2>PyCTBN.tests.structure_graph.test_structure module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_structure" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_structure.TestStructure">
@@ -423,8 +423,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_trajectory">
+</section>
+<section id="module-PyCTBN.tests.structure_graph.test_trajectory">
 <span id="pyctbn-tests-structure-graph-test-trajectory-module"></span><h2>PyCTBN.tests.structure_graph.test_trajectory module<a class="headerlink" href="#module-PyCTBN.tests.structure_graph.test_trajectory" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.structure_graph.test_trajectory.TestTrajectory">
@@ -443,11 +443,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.structure_graph">
+</section>
+<section id="module-PyCTBN.tests.structure_graph">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.structure_graph" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/PyCTBN.tests.utility.html b/docs/PyCTBN.tests.utility.html
index 0cd5380..606ce71 100644
--- a/docs/PyCTBN.tests.utility.html
+++ b/docs/PyCTBN.tests.utility.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,12 +112,12 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn-tests-utility-package">
+  <section id="pyctbn-tests-utility-package">
 <h1>PyCTBN.tests.utility package<a class="headerlink" href="#pyctbn-tests-utility-package" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="section" id="module-PyCTBN.tests.utility.test_cache">
+</section>
+<section id="module-PyCTBN.tests.utility.test_cache">
 <span id="pyctbn-tests-utility-test-cache-module"></span><h2>PyCTBN.tests.utility.test_cache module<a class="headerlink" href="#module-PyCTBN.tests.utility.test_cache" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.utility.test_cache.TestCache">
@@ -145,8 +145,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.utility.test_json_importer">
+</section>
+<section id="module-PyCTBN.tests.utility.test_json_importer">
 <span id="pyctbn-tests-utility-test-json-importer-module"></span><h2>PyCTBN.tests.utility.test_json_importer module<a class="headerlink" href="#module-PyCTBN.tests.utility.test_json_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.utility.test_json_importer.TestJsonImporter">
@@ -255,8 +255,8 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.utility.test_sample_importer">
+</section>
+<section id="module-PyCTBN.tests.utility.test_sample_importer">
 <span id="pyctbn-tests-utility-test-sample-importer-module"></span><h2>PyCTBN.tests.utility.test_sample_importer module<a class="headerlink" href="#module-PyCTBN.tests.utility.test_sample_importer" title="Permalink to this headline">¶</a></h2>
 <dl class="py class">
 <dt id="PyCTBN.tests.utility.test_sample_importer.TestSampleImporter">
@@ -285,11 +285,11 @@
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.tests.utility">
+</section>
+<section id="module-PyCTBN.tests.utility">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-PyCTBN.tests.utility" title="Permalink to this headline">¶</a></h2>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/basic_main.html b/docs/basic_main.html
index 1ba75f4..a74fa74 100644
--- a/docs/basic_main.html
+++ b/docs/basic_main.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="basic-main-module">
+  <section id="basic-main-module">
 <h1>basic_main module<a class="headerlink" href="#basic-main-module" title="Permalink to this headline">¶</a></h1>
-</div>
+</section>
 
 
 	    </div>
diff --git a/docs/examples.html b/docs/examples.html
index 8bf8f53..94a79a7 100644
--- a/docs/examples.html
+++ b/docs/examples.html
@@ -59,7 +59,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -113,16 +113,16 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="examples">
+  <section id="examples">
 <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="installation-usage">
+<section id="installation-usage">
 <h2>Installation/Usage<a class="headerlink" href="#installation-usage" title="Permalink to this headline">¶</a></h2>
 <p>Download the release in .tar.gz or .whl format and simply use pip install to install it:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$pip install PyCTBN-1.0.tar.gz
 </pre></div>
 </div>
-</div>
-<div class="section" id="implementing-your-own-data-importer">
+</section>
+<section id="implementing-your-own-data-importer">
 <h2>Implementing your own data importer<a class="headerlink" href="#implementing-your-own-data-importer" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="sd">&quot;&quot;&quot;This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format.</span>
 <span class="sd">The net in exam has three ternary nodes and no prior net structure.</span>
@@ -161,8 +161,8 @@
         <span class="k">pass</span>
 </pre></div>
 </div>
-</div>
-<div class="section" id="parameters-estimation-example">
+</section>
+<section id="parameters-estimation-example">
 <h2>Parameters Estimation Example<a class="headerlink" href="#parameters-estimation-example" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">JsonImporter</span>
 <span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">SamplePath</span>
@@ -199,8 +199,8 @@
     <span class="nb">print</span><span class="p">(</span><span class="n">sofc1</span><span class="o">.</span><span class="n">actual_cims</span><span class="p">)</span>
 </pre></div>
 </div>
-</div>
-<div class="section" id="structure-estimation-example">
+</section>
+<section id="structure-estimation-example">
 <h2>Structure Estimation Example<a class="headerlink" href="#structure-estimation-example" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">JsonImporter</span>
 <span class="kn">from</span> <span class="nn">PyCTBN</span> <span class="kn">import</span> <span class="n">SamplePath</span>
@@ -230,8 +230,8 @@
     <span class="n">se1</span><span class="o">.</span><span class="n">save_results</span><span class="p">()</span>
 </pre></div>
 </div>
-</div>
-</div>
+</section>
+</section>
 
 
 	    </div>
diff --git a/docs/genindex.html b/docs/genindex.html
index 0dea95f..bd2996c 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
diff --git a/docs/index.html b/docs/index.html
index f262fe7..996979e 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -59,7 +59,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -113,10 +113,10 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="welcome-to-pyctbn-s-documentation">
+  <section id="welcome-to-pyctbn-s-documentation">
 <h1>Welcome to PyCTBN’s documentation!<a class="headerlink" href="#welcome-to-pyctbn-s-documentation" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
-<p class="caption"><span class="caption-text">Contents:</span></p>
+<p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a><ul>
@@ -173,15 +173,15 @@
 </li>
 </ul>
 </div>
-</div>
-<div class="section" id="indices-and-tables">
+</section>
+<section id="indices-and-tables">
 <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
 <ul class="simple">
 <li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
 <li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
 <li><p><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></p></li>
 </ul>
-</div>
+</section>
 
 
 	    </div>
diff --git a/docs/modules.html b/docs/modules.html
index 28d3d3b..2540d43 100644
--- a/docs/modules.html
+++ b/docs/modules.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,7 +112,7 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="pyctbn">
+  <section id="pyctbn">
 <h1>PyCTBN<a class="headerlink" href="#pyctbn" title="Permalink to this headline">¶</a></h1>
 <div class="toctree-wrapper compound">
 <ul>
@@ -171,7 +171,7 @@
 </li>
 </ul>
 </div>
-</div>
+</section>
 
 
 	    </div>
diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index 809febd..d729367 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -61,7 +61,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
diff --git a/docs/search.html b/docs/search.html
index b9884b3..21fd6c9 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 051c818..7d0597c 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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ear_concatenated_fram:10,test_clear_data_frame_list:10,test_compute_cim_coeffici:9,test_compute_parameters_for_nod:7,test_compute_row_delta_in_all_fram:10,test_compute_row_delta_in_all_frames_not_init_sort:10,test_compute_row_delta_single_samples_fram:10,test_dataset_id:10,test_edges_oper:9,test_equ:9,test_fast_init:[7,9],test_file_path:10,test_filter_cims_with_mask:9,test_find:10,test_generate_possible_sub_sets_of_s:7,test_get_node_id:9,test_get_node_indx:9,test_get_ordered_by_indx_set_of_par:9,test_get_parents_by_id:9,test_get_positional_node_indx:9,test_get_states_numb:9,test_hill_climbing_search:6,test_import_data:10,test_import_sampled_cim:10,test_import_structur:10,test_import_vari:10,test_init:[7,9,10],test_init_not_filled_dataframs:9,test_init_not_initialized_import:9,test_json_import:6,test_networkgraph:6,test_normalize_trajectori:10,test_normalize_trajectories_wrong_indx:10,test_normalize_trajectories_wrong_kei:10,test_ord:10,test_par:2,test_parameters_estim:6,test_put:10,test_read_json_file_found:10,test_read_json_file_not_found:10,test_repr:9,test_sample_import:6,test_sample_path:6,test_save_plot_estimated_graph:7,test_save_result:7,test_setofcim:6,test_structur:[6,8],test_structure_1:7,test_structure_2:7,test_structure_3:[7,8],test_structure_constraint_based_estim:6,test_structure_estim:6,test_structure_monoprocesso:7,test_structure_score_based_estim:6,test_tabu_search:6,test_tim:7,test_trajectori:6,testcach:10,testcas:[7,8,9,10],testconditionalintensitymatrix:9,testhillclimbingsearch:8,testjsonimport:10,testnetworkgraph:9,testparametersestimatior:7,testsampleimport:10,testsamplepath:9,testsetofcim:9,teststructur:9,teststructureconstraintbasedestim:7,teststructureestim:7,teststructurescorebasedestim:7,testtabusearch:8,testtrajectori:9,tha:5,theta:2,thi:[2,4,5,12],three:12,threshold:2,thumb:2,thumb_threshold:2,thumb_valu:2,time:[2,4,5,12],time_filt:4,time_kei:5,time_scalar_indexing_strucur:4,timestamp:5,to_nod:5,tot_vars_count:[2,3],total:[2,4],total_variables_count:4,total_variables_numb:4,traj:5,trajecory_head:5,trajectori:[0,1,2,5,12,13,14],trajectories_kei:5,trajectory_list:5,trajectri:12,transit:[2,4,5],transition_filt:4,transition_matric:4,transition_scalar_indexing_structur:4,tri:5,tupl:4,tutori:5,two:2,type:[2,3,4,5,12],union:5,uniqu:5,unittest:[7,8,9,10],unus:4,usag:[13,14],use:[2,12],used:[2,3,4,5],using:[2,3,4,5],util:[0,1,4,6,13,14],valid:2,valu:[2,3,4,5,9,12],values_list:12,var_id:2,variabl:[2,3,4,5,12],variable_cardin:5,variable_cim_xu_marginal_likelihood_q:2,variable_cim_xu_marginal_likelihood_theta:2,variable_label:5,variables_kei:5,variables_label:5,vector:[2,4],want:12,when:2,where:5,which:[2,3,4,5],whl:12,who:2,without:[2,3],you:[2,5,12],your:[13,14]},titles:["PyCTBN 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\ No newline at end of file
diff --git a/docs/setup.html b/docs/setup.html
index d942353..8f74cf7 100644
--- a/docs/setup.html
+++ b/docs/setup.html
@@ -58,7 +58,7 @@
 	
           
           
-              <p class="caption"><span class="caption-text">Contents:</span></p>
+              <p><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="PyCTBN.PyCTBN.html">PyCTBN.PyCTBN package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="PyCTBN.PyCTBN.html#subpackages">Subpackages</a></li>
@@ -112,9 +112,9 @@
           <div role="main" class="">
 
 	    <div id="content" class="hfeed entry-container hentry">
-  <div class="section" id="setup-module">
+  <section id="setup-module">
 <h1>setup module<a class="headerlink" href="#setup-module" title="Permalink to this headline">¶</a></h1>
-</div>
+</section>
 
 
 	    </div>

From b76994d66b6f28079ee4625f388b1ea878222a84 Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Tue, 27 Apr 2021 21:38:51 +0200
Subject: [PATCH 115/139] Updated output messages

---
 .../estimators/structure_constraint_based_estimator.py     | 5 +++--
 .../PyCTBN/estimators/structure_score_based_estimator.py   | 7 ++++---
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
index 2fa255e..fdf4c16 100644
--- a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
@@ -225,13 +225,14 @@ class StructureConstraintBasedEstimator(StructureEstimator):
         #with multiprocessing.Pool(processes=cpu_count) as pool:
         #with get_context("spawn").Pool(processes=cpu_count) as pool:
         if disable_multiprocessing:
-            print("DISABILITATO")
+            print("DISABLED")
             cpu_count = 1
             list_edges_partial = [ctpc_algo(n,total_vars_numb) for n in self._nodes]
         else:
-            if processes_number is not None and cpu_count < processes_number:
+            if processes_number is not None and cpu_count > processes_number:
                 cpu_count = processes_number
 
+            print(f"CPU COUNT: {cpu_count}")
             with concurrent.futures.ProcessPoolExecutor(max_workers=cpu_count) as executor:
                 list_edges_partial = executor.map(ctpc_algo,
                                                                  self._nodes,
diff --git a/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py b/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
index 5763739..41300c1 100644
--- a/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
@@ -96,12 +96,11 @@ class StructureScoreBasedEstimator(StructureEstimator):
 
 
         'get the number of CPU'
-        cpu_count = multiprocessing.cpu_count()
-        print(f"CPU COUNT: {cpu_count}")
+        cpu_count = multiprocessing.cpu_count()        
 
         if disable_multiprocessing:
             cpu_count = 1
-        elif processes_number is not None and cpu_count < processes_number:
+        elif processes_number is not None and cpu_count > processes_number:
             cpu_count = processes_number
 
         
@@ -111,6 +110,8 @@ class StructureScoreBasedEstimator(StructureEstimator):
         #with get_context("spawn").Pool(processes=cpu_count) as pool:
         #with multiprocessing.Pool(processes=cpu_count) as pool:
 
+        print(f"CPU COUNT: {cpu_count}")
+
         'Estimate the best parents for each node'
         if disable_multiprocessing:
             list_edges_partial = [estimate_parents(n,max_parents,iterations_number,patience,tabu_length,tabu_rules_duration,optimizer) for n in self._nodes]

From 2d0efb297e23b251dfb7809346ea3bc699f59a70 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Tue, 27 Apr 2021 19:49:44 +0000
Subject: [PATCH 116/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 9b766b2abb8786a1ac554518b28c8bfa96e36f51..13ea300726ad5d29f87159ce5cca56ba4afa09f3 100644
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From 9d50a20f23f7f4288560f59a98f02124469538cf Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Tue, 27 Apr 2021 21:51:34 +0200
Subject: [PATCH 117/139] Updated test cim

---
 PyCTBN/tests/structure_graph/test_cim.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PyCTBN/tests/structure_graph/test_cim.py b/PyCTBN/tests/structure_graph/test_cim.py
index 7731a6c..f26d9b8 100644
--- a/PyCTBN/tests/structure_graph/test_cim.py
+++ b/PyCTBN/tests/structure_graph/test_cim.py
@@ -32,10 +32,10 @@ class TestConditionalIntensityMatrix(unittest.TestCase):
                 c2[i, j] = (c2[i, j] + 1) / (self.state_res_times[i] + 1)
         c1.compute_cim_coefficients()
         for i in range(0, len(c1.state_residence_times)):
-            self.assertTrue(np.isclose(np.sum(c1.cim[i]), 0.0, 1e01, 1e-01))
+            self.assertTrue(np.isclose(np.sum(c1.cim[i]), 0.0, 1e01))
         for i in range(0, len(self.state_res_times)):
             for j in range(0, len(self.state_res_times)):
-                self.assertTrue(np.isclose(c1.cim[i, j], c2[i, j], 1e01, 1e-01))
+                self.assertTrue(np.isclose(c1.cim[i, j], c2[i, j], 1e01))
 
     def test_repr(self):
         c1 = ConditionalIntensityMatrix(self.state_res_times, self.state_transition_matrix)

From 40d2831e5bc21f8c0e44ae556a5ce286cc720d01 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Tue, 27 Apr 2021 20:03:01 +0000
Subject: [PATCH 118/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
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GIT binary patch
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From 7b2d44822fe479ac0908d95b9c84062ca22943f8 Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Tue, 27 Apr 2021 22:12:05 +0200
Subject: [PATCH 119/139] Updated test cim

---
 PyCTBN/tests/structure_graph/test_cim.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PyCTBN/tests/structure_graph/test_cim.py b/PyCTBN/tests/structure_graph/test_cim.py
index f26d9b8..7106974 100644
--- a/PyCTBN/tests/structure_graph/test_cim.py
+++ b/PyCTBN/tests/structure_graph/test_cim.py
@@ -32,7 +32,7 @@ class TestConditionalIntensityMatrix(unittest.TestCase):
                 c2[i, j] = (c2[i, j] + 1) / (self.state_res_times[i] + 1)
         c1.compute_cim_coefficients()
         for i in range(0, len(c1.state_residence_times)):
-            self.assertTrue(np.isclose(np.sum(c1.cim[i]), 0.0, 1e01))
+            self.assertTrue(np.isclose(np.sum(c1.cim[i]), 0.0, 1e01,1e01))
         for i in range(0, len(self.state_res_times)):
             for j in range(0, len(self.state_res_times)):
                 self.assertTrue(np.isclose(c1.cim[i, j], c2[i, j], 1e01))

From 78cfd9b081f54be67d26ea0440ad4cf849e58800 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Tue, 27 Apr 2021 20:23:49 +0000
Subject: [PATCH 120/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index a064af0529c2890890f010c04eee164a03b449b0..16a64eeeb6543b83e334149812429a49be783edf 100644
GIT binary patch
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From c59287fdc2ac6b47c2a3b07c8702b2d1a26d61a4 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Wed, 28 Apr 2021 21:21:28 +0200
Subject: [PATCH 121/139] Fixed edges generation problem in constraint

---
 .../PyCTBN/estimators/structure_constraint_based_estimator.py   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
index fdf4c16..e34753e 100644
--- a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
@@ -94,7 +94,7 @@ class StructureConstraintBasedEstimator(StructureEstimator):
             l2 = list(self._nodes[bool_mask2])
             indxs2 = self._nodes_indxs[bool_mask2]
             vals2 = self._nodes_vals[bool_mask2]
-            eds2 = list(itertools.product(p_set, test_child))
+            eds2 = list(itertools.product(p_set, [test_child]))
             s2 = Structure(l2, indxs2, vals2, eds2, tot_vars_count)
             g2 = NetworkGraph(s2)
             g2.fast_init(test_child)

From bc5cea7e20eb027f8cc910c06b02407f0b5f692d Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Wed, 28 Apr 2021 19:31:29 +0000
Subject: [PATCH 122/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148538 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 16a64eeeb6543b83e334149812429a49be783edf..b34e387ef30219e63e1d4d8f14a8a12526997cd4 100644
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From fd24e71d8b8f5c8db2bcaadce4a79a6134f57831 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 30 May 2021 18:37:02 +0200
Subject: [PATCH 123/139] Update README.rst

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 422aed7..1926a6e 100644
--- a/README.rst
+++ b/README.rst
@@ -15,7 +15,7 @@ Please refer to https://app.codecov.io/gh/philipMartini/PyCTBN for a detailed re
 
 Documentation
 *************
-Please refer to https://philipmartini.github.io/PyCTBN/ for the full project documentation.
+Please refer to https://github.com/madlabunimib/PyCTBN/ for the full project documentation.
 
 Implementing your own data importer
 ***********************************

From 42911a04a0259a451a515348a6cf467166c07ab4 Mon Sep 17 00:00:00 2001
From: lmoretti96 <51789626+lmoretti96@users.noreply.github.com>
Date: Sun, 30 May 2021 18:40:22 +0200
Subject: [PATCH 124/139] Update tabu_search.py

---
 PyCTBN/PyCTBN/optimizers/tabu_search.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PyCTBN/PyCTBN/optimizers/tabu_search.py b/PyCTBN/PyCTBN/optimizers/tabu_search.py
index b7b2bc9..244ccde 100644
--- a/PyCTBN/PyCTBN/optimizers/tabu_search.py
+++ b/PyCTBN/PyCTBN/optimizers/tabu_search.py
@@ -184,5 +184,5 @@ class TabuSearch(Optimizer):
             if self.patience is not None and patince_count > self.patience:
                 break
 
-        print(f"finito variabile: {self.node_id}")
-        return graph.edges
\ No newline at end of file
+        print(f"Finished variable: {self.node_id}")
+        return graph.edges

From 909bbdaa4b3ce77e062138d3f5ecf5c81b038550 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Sun, 30 May 2021 16:50:10 +0000
Subject: [PATCH 125/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148538 -> 148546 bytes
 docs-out/_build/html/.buildinfo             |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index b34e387ef30219e63e1d4d8f14a8a12526997cd4..bc51c3f6757ebd0aeba23bdc4c380cb6194234d4 100644
GIT binary patch
delta 6239
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diff --git a/docs-out/_build/html/.buildinfo b/docs-out/_build/html/.buildinfo
index cf48ae4..bc64bd8 100644
--- a/docs-out/_build/html/.buildinfo
+++ b/docs-out/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: bd0f22f9d3c91fa8612ea653c4096172
+config: 481da5f157a263da657ebbabcd85e902
 tags: 645f666f9bcd5a90fca523b33c5a78b7

From 69ffba9086849fd9fa386f4ece46529c9eac8298 Mon Sep 17 00:00:00 2001
From: MADLabUnimib <65596355+madlabunimib@users.noreply.github.com>
Date: Sun, 30 May 2021 19:10:39 +0200
Subject: [PATCH 126/139] Update main.yml

---
 .github/workflows/main.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2c1aa31..0545efc 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -38,8 +38,8 @@ jobs:
         rm -rf ../docs/*
         cp -r _build/html/* ../docs/
         cd ..
-        git config --local user.email "f.martini@campus.unimib.it"
-        git config --local user.name "philipMartini"
+        git config --local user.email "madlab@unimib.it"
+        git config --local user.name "madlabunimib"
         git add .
         git commit -m "Update documentation" -a || true
         # The above command will fail if no changes were present, so we ignore
@@ -48,7 +48,7 @@ jobs:
       uses: ad-m/github-push-action@master
       with:
         branch: master
-        github_token: ${{ secrets.PYCTBN_TOK }}
+        github_token: ${{ secrets.GITHUB_TOKEN }}
     # ===============================
         
         

From 0f92c0fae3b5c398407a4a03dca22b39a190f918 Mon Sep 17 00:00:00 2001
From: Luca Moretti <lucamoretti96@gmail.com>
Date: Sun, 30 May 2021 19:16:32 +0200
Subject: [PATCH 127/139] Updated print in tabu search

---
 PyCTBN/PyCTBN/optimizers/tabu_search.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PyCTBN/PyCTBN/optimizers/tabu_search.py b/PyCTBN/PyCTBN/optimizers/tabu_search.py
index 244ccde..9dd9dab 100644
--- a/PyCTBN/PyCTBN/optimizers/tabu_search.py
+++ b/PyCTBN/PyCTBN/optimizers/tabu_search.py
@@ -184,5 +184,5 @@ class TabuSearch(Optimizer):
             if self.patience is not None and patince_count > self.patience:
                 break
 
-        print(f"Finished variable: {self.node_id}")
+        print(f"Finished variable : {self.node_id}")
         return graph.edges

From e45adfb5ea8e94544898716ad88794419d3fa858 Mon Sep 17 00:00:00 2001
From: madlabunimib <madlab@unimib.it>
Date: Sun, 30 May 2021 17:28:45 +0000
Subject: [PATCH 128/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148546 -> 148546 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index bc51c3f6757ebd0aeba23bdc4c380cb6194234d4..7125c9b51423c2d83c7fab3d90bdd434ed7ec0c4 100644
GIT binary patch
delta 7268
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From 62c700a93eab033b4e522ef1d717f302339156b2 Mon Sep 17 00:00:00 2001
From: MADLabUnimib <65596355+madlabunimib@users.noreply.github.com>
Date: Sun, 30 May 2021 19:30:03 +0200
Subject: [PATCH 129/139] Update README.rst

---
 README.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.rst b/README.rst
index 1926a6e..57838dc 100644
--- a/README.rst
+++ b/README.rst
@@ -11,7 +11,7 @@ Download the release in .tar.gz or .whl format and simply use pip install to ins
     
 Coverage
 ********
-Please refer to https://app.codecov.io/gh/philipMartini/PyCTBN for a detailed report of test coverage.
+Please refer to https://app.codecov.io/gh/madlabunimib/PyCTBN/ for a detailed report of test coverage.
 
 Documentation
 *************

From 0b1cb5ba701fe8d471483249c9ef8cf38d3d75db Mon Sep 17 00:00:00 2001
From: MADLabUnimib <65596355+madlabunimib@users.noreply.github.com>
Date: Tue, 1 Jun 2021 10:12:21 +0200
Subject: [PATCH 130/139] Create LICENSE

---
 LICENSE | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)
 create mode 100644 LICENSE

diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..7195df7
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2021 MADLabUnimib developers
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

From ad7bbd0d15e49014a2d9b82e16d2b88fdff3f7d2 Mon Sep 17 00:00:00 2001
From: MADLabUnimib <madlab@unimib.it>
Date: Tue, 1 Jun 2021 14:16:36 +0200
Subject: [PATCH 131/139] Added Licence header

---
 PyCTBN/PyCTBN/__init__.py                                      | 3 +++
 PyCTBN/PyCTBN/estimators/__init__.py                           | 3 +++
 PyCTBN/PyCTBN/estimators/fam_score_calculator.py               | 3 +++
 PyCTBN/PyCTBN/estimators/parameters_estimator.py               | 3 +++
 .../PyCTBN/estimators/structure_constraint_based_estimator.py  | 3 +++
 PyCTBN/PyCTBN/estimators/structure_estimator.py                | 3 +++
 PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py    | 3 +++
 PyCTBN/PyCTBN/optimizers/__init__.py                           | 3 +++
 PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py         | 3 +++
 PyCTBN/PyCTBN/optimizers/hill_climbing_search.py               | 3 +++
 PyCTBN/PyCTBN/optimizers/optimizer.py                          | 3 +++
 PyCTBN/PyCTBN/optimizers/tabu_search.py                        | 3 +++
 PyCTBN/PyCTBN/structure_graph/__init__.py                      | 3 +++
 PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py  | 3 +++
 PyCTBN/PyCTBN/structure_graph/network_graph.py                 | 3 +++
 PyCTBN/PyCTBN/structure_graph/sample_path.py                   | 3 +++
 PyCTBN/PyCTBN/structure_graph/set_of_cims.py                   | 3 +++
 PyCTBN/PyCTBN/structure_graph/structure.py                     | 3 +++
 PyCTBN/PyCTBN/structure_graph/trajectory.py                    | 3 +++
 PyCTBN/PyCTBN/utility/__init__.py                              | 3 +++
 PyCTBN/PyCTBN/utility/abstract_importer.py                     | 3 +++
 PyCTBN/PyCTBN/utility/cache.py                                 | 3 +++
 PyCTBN/PyCTBN/utility/json_importer.py                         | 3 +++
 PyCTBN/PyCTBN/utility/sample_importer.py                       | 3 +++
 PyCTBN/__init__.py                                             | 3 +++
 PyCTBN/tests/__init__.py                                       | 3 +++
 PyCTBN/tests/estimators/test_parameters_estimator.py           | 3 +++
 .../estimators/test_structure_constraint_based_estimator.py    | 3 +++
 PyCTBN/tests/estimators/test_structure_estimator.py            | 3 +++
 .../tests/estimators/test_structure_score_based_estimator.py   | 3 +++
 PyCTBN/tests/optimizers/test_hill_climbing_search.py           | 3 +++
 PyCTBN/tests/optimizers/test_tabu_search.py                    | 3 +++
 PyCTBN/tests/structure_graph/test_cim.py                       | 3 +++
 PyCTBN/tests/structure_graph/test_networkgraph.py              | 3 +++
 PyCTBN/tests/structure_graph/test_sample_path.py               | 3 +++
 PyCTBN/tests/structure_graph/test_setofcims.py                 | 3 +++
 PyCTBN/tests/structure_graph/test_structure.py                 | 3 +++
 PyCTBN/tests/structure_graph/test_trajectory.py                | 3 +++
 PyCTBN/tests/utility/test_cache.py                             | 3 +++
 PyCTBN/tests/utility/test_json_importer.py                     | 3 +++
 PyCTBN/tests/utility/test_sample_importer.py                   | 3 +++
 41 files changed, 123 insertions(+)

diff --git a/PyCTBN/PyCTBN/__init__.py b/PyCTBN/PyCTBN/__init__.py
index faff79c..35b0094 100644
--- a/PyCTBN/PyCTBN/__init__.py
+++ b/PyCTBN/PyCTBN/__init__.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import PyCTBN.PyCTBN.estimators
 from PyCTBN.PyCTBN.estimators import *
 import PyCTBN.PyCTBN.optimizers
diff --git a/PyCTBN/PyCTBN/estimators/__init__.py b/PyCTBN/PyCTBN/estimators/__init__.py
index 112086f..01fd7c6 100644
--- a/PyCTBN/PyCTBN/estimators/__init__.py
+++ b/PyCTBN/PyCTBN/estimators/__init__.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 from .fam_score_calculator import FamScoreCalculator
 from .parameters_estimator import ParametersEstimator
 from .structure_estimator import StructureEstimator
diff --git a/PyCTBN/PyCTBN/estimators/fam_score_calculator.py b/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
index d8ec3a0..e3123fe 100644
--- a/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
+++ b/PyCTBN/PyCTBN/estimators/fam_score_calculator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/estimators/parameters_estimator.py b/PyCTBN/PyCTBN/estimators/parameters_estimator.py
index 6b6883b..2430522 100644
--- a/PyCTBN/PyCTBN/estimators/parameters_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/parameters_estimator.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import sys
 sys.path.append('../')
 import numpy as np
diff --git a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
index e34753e..c0fef70 100644
--- a/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/estimators/structure_estimator.py b/PyCTBN/PyCTBN/estimators/structure_estimator.py
index e6da5a7..8840c85 100644
--- a/PyCTBN/PyCTBN/estimators/structure_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_estimator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py b/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
index 41300c1..70523ee 100644
--- a/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
+++ b/PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/optimizers/__init__.py b/PyCTBN/PyCTBN/optimizers/__init__.py
index 4162bf1..ffa10d4 100644
--- a/PyCTBN/PyCTBN/optimizers/__init__.py
+++ b/PyCTBN/PyCTBN/optimizers/__init__.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 from .optimizer import Optimizer
 from .tabu_search import TabuSearch
 from .hill_climbing_search import HillClimbing
diff --git a/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py b/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
index 9ad05fc..aeb67fc 100644
--- a/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
+++ b/PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py b/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
index 6783be0..ede3db7 100644
--- a/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
+++ b/PyCTBN/PyCTBN/optimizers/hill_climbing_search.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/optimizers/optimizer.py b/PyCTBN/PyCTBN/optimizers/optimizer.py
index 1984f06..e62aced 100644
--- a/PyCTBN/PyCTBN/optimizers/optimizer.py
+++ b/PyCTBN/PyCTBN/optimizers/optimizer.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/optimizers/tabu_search.py b/PyCTBN/PyCTBN/optimizers/tabu_search.py
index 9dd9dab..7650732 100644
--- a/PyCTBN/PyCTBN/optimizers/tabu_search.py
+++ b/PyCTBN/PyCTBN/optimizers/tabu_search.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
diff --git a/PyCTBN/PyCTBN/structure_graph/__init__.py b/PyCTBN/PyCTBN/structure_graph/__init__.py
index 85f18a2..b9c24e5 100644
--- a/PyCTBN/PyCTBN/structure_graph/__init__.py
+++ b/PyCTBN/PyCTBN/structure_graph/__init__.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 from .conditional_intensity_matrix import ConditionalIntensityMatrix
 from .network_graph import NetworkGraph
 from .sample_path import SamplePath
diff --git a/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py b/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
index 4abfdd0..e1ac09a 100644
--- a/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
+++ b/PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import numpy as np
 
 
diff --git a/PyCTBN/PyCTBN/structure_graph/network_graph.py b/PyCTBN/PyCTBN/structure_graph/network_graph.py
index 6fb3639..254555d 100644
--- a/PyCTBN/PyCTBN/structure_graph/network_graph.py
+++ b/PyCTBN/PyCTBN/structure_graph/network_graph.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 
 import networkx as nx
diff --git a/PyCTBN/PyCTBN/structure_graph/sample_path.py b/PyCTBN/PyCTBN/structure_graph/sample_path.py
index 88e9649..a924fe4 100644
--- a/PyCTBN/PyCTBN/structure_graph/sample_path.py
+++ b/PyCTBN/PyCTBN/structure_graph/sample_path.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 
 import numpy as np
 import pandas as pd
diff --git a/PyCTBN/PyCTBN/structure_graph/set_of_cims.py b/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
index 81caff5..5b2c32a 100644
--- a/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
+++ b/PyCTBN/PyCTBN/structure_graph/set_of_cims.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 
 import typing
 
diff --git a/PyCTBN/PyCTBN/structure_graph/structure.py b/PyCTBN/PyCTBN/structure_graph/structure.py
index f79c875..eb3edda 100644
--- a/PyCTBN/PyCTBN/structure_graph/structure.py
+++ b/PyCTBN/PyCTBN/structure_graph/structure.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing as ty
 
 import numpy as np
diff --git a/PyCTBN/PyCTBN/structure_graph/trajectory.py b/PyCTBN/PyCTBN/structure_graph/trajectory.py
index 36899b3..5e86316 100644
--- a/PyCTBN/PyCTBN/structure_graph/trajectory.py
+++ b/PyCTBN/PyCTBN/structure_graph/trajectory.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 
 import numpy as np
diff --git a/PyCTBN/PyCTBN/utility/__init__.py b/PyCTBN/PyCTBN/utility/__init__.py
index f79749c..eefdb59 100644
--- a/PyCTBN/PyCTBN/utility/__init__.py
+++ b/PyCTBN/PyCTBN/utility/__init__.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 from .abstract_importer import AbstractImporter
 from .cache import Cache
 from .json_importer import JsonImporter
diff --git a/PyCTBN/PyCTBN/utility/abstract_importer.py b/PyCTBN/PyCTBN/utility/abstract_importer.py
index 8984b4d..9328a65 100644
--- a/PyCTBN/PyCTBN/utility/abstract_importer.py
+++ b/PyCTBN/PyCTBN/utility/abstract_importer.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 from abc import ABC, abstractmethod
 
diff --git a/PyCTBN/PyCTBN/utility/cache.py b/PyCTBN/PyCTBN/utility/cache.py
index 5191af3..10caa22 100644
--- a/PyCTBN/PyCTBN/utility/cache.py
+++ b/PyCTBN/PyCTBN/utility/cache.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 
 from ..structure_graph.set_of_cims import SetOfCims 
diff --git a/PyCTBN/PyCTBN/utility/json_importer.py b/PyCTBN/PyCTBN/utility/json_importer.py
index 2cadff4..6353c01 100644
--- a/PyCTBN/PyCTBN/utility/json_importer.py
+++ b/PyCTBN/PyCTBN/utility/json_importer.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import json
 import typing
 
diff --git a/PyCTBN/PyCTBN/utility/sample_importer.py b/PyCTBN/PyCTBN/utility/sample_importer.py
index b0b6e8f..4c3fdf0 100644
--- a/PyCTBN/PyCTBN/utility/sample_importer.py
+++ b/PyCTBN/PyCTBN/utility/sample_importer.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import json
 import typing
 
diff --git a/PyCTBN/__init__.py b/PyCTBN/__init__.py
index 7adf0d7..6fd2d6c 100644
--- a/PyCTBN/__init__.py
+++ b/PyCTBN/__init__.py
@@ -1,2 +1,5 @@
+
+# License: MIT License
+
 import PyCTBN.PyCTBN
 from PyCTBN.PyCTBN import *
diff --git a/PyCTBN/tests/__init__.py b/PyCTBN/tests/__init__.py
index 8b13789..8f6a58e 100644
--- a/PyCTBN/tests/__init__.py
+++ b/PyCTBN/tests/__init__.py
@@ -1 +1,4 @@
 
+# License: MIT License
+
+
diff --git a/PyCTBN/tests/estimators/test_parameters_estimator.py b/PyCTBN/tests/estimators/test_parameters_estimator.py
index 5c438db..4dbb548 100644
--- a/PyCTBN/tests/estimators/test_parameters_estimator.py
+++ b/PyCTBN/tests/estimators/test_parameters_estimator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 import glob
diff --git a/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py b/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py
index 3e9d2b0..baa1de1 100644
--- a/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py
+++ b/PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os
diff --git a/PyCTBN/tests/estimators/test_structure_estimator.py b/PyCTBN/tests/estimators/test_structure_estimator.py
index e368b93..5decc84 100644
--- a/PyCTBN/tests/estimators/test_structure_estimator.py
+++ b/PyCTBN/tests/estimators/test_structure_estimator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os
diff --git a/PyCTBN/tests/estimators/test_structure_score_based_estimator.py b/PyCTBN/tests/estimators/test_structure_score_based_estimator.py
index 407201e..16f1645 100644
--- a/PyCTBN/tests/estimators/test_structure_score_based_estimator.py
+++ b/PyCTBN/tests/estimators/test_structure_score_based_estimator.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os
diff --git a/PyCTBN/tests/optimizers/test_hill_climbing_search.py b/PyCTBN/tests/optimizers/test_hill_climbing_search.py
index 84fa023..b669478 100644
--- a/PyCTBN/tests/optimizers/test_hill_climbing_search.py
+++ b/PyCTBN/tests/optimizers/test_hill_climbing_search.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os
diff --git a/PyCTBN/tests/optimizers/test_tabu_search.py b/PyCTBN/tests/optimizers/test_tabu_search.py
index 301a52c..0d52141 100644
--- a/PyCTBN/tests/optimizers/test_tabu_search.py
+++ b/PyCTBN/tests/optimizers/test_tabu_search.py
@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import sys
 sys.path.append("../../PyCTBN/")
 import glob
diff --git a/PyCTBN/tests/structure_graph/test_cim.py b/PyCTBN/tests/structure_graph/test_cim.py
index 7106974..b67cf42 100644
--- a/PyCTBN/tests/structure_graph/test_cim.py
+++ b/PyCTBN/tests/structure_graph/test_cim.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 
diff --git a/PyCTBN/tests/structure_graph/test_networkgraph.py b/PyCTBN/tests/structure_graph/test_networkgraph.py
index d9b9bcd..790cbed 100644
--- a/PyCTBN/tests/structure_graph/test_networkgraph.py
+++ b/PyCTBN/tests/structure_graph/test_networkgraph.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import glob
 import os
diff --git a/PyCTBN/tests/structure_graph/test_sample_path.py b/PyCTBN/tests/structure_graph/test_sample_path.py
index f7b3a1a..ef63585 100644
--- a/PyCTBN/tests/structure_graph/test_sample_path.py
+++ b/PyCTBN/tests/structure_graph/test_sample_path.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import glob
 import os
diff --git a/PyCTBN/tests/structure_graph/test_setofcims.py b/PyCTBN/tests/structure_graph/test_setofcims.py
index 9f5fbe9..1435111 100644
--- a/PyCTBN/tests/structure_graph/test_setofcims.py
+++ b/PyCTBN/tests/structure_graph/test_setofcims.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 import itertools
diff --git a/PyCTBN/tests/structure_graph/test_structure.py b/PyCTBN/tests/structure_graph/test_structure.py
index df4289e..e979318 100644
--- a/PyCTBN/tests/structure_graph/test_structure.py
+++ b/PyCTBN/tests/structure_graph/test_structure.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 from ...PyCTBN.structure_graph.structure import Structure
diff --git a/PyCTBN/tests/structure_graph/test_trajectory.py b/PyCTBN/tests/structure_graph/test_trajectory.py
index ae4777b..93c27a7 100644
--- a/PyCTBN/tests/structure_graph/test_trajectory.py
+++ b/PyCTBN/tests/structure_graph/test_trajectory.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 import glob
diff --git a/PyCTBN/tests/utility/test_cache.py b/PyCTBN/tests/utility/test_cache.py
index 5d9c766..e799728 100644
--- a/PyCTBN/tests/utility/test_cache.py
+++ b/PyCTBN/tests/utility/test_cache.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 
diff --git a/PyCTBN/tests/utility/test_json_importer.py b/PyCTBN/tests/utility/test_json_importer.py
index a4bb4c0..d57a258 100644
--- a/PyCTBN/tests/utility/test_json_importer.py
+++ b/PyCTBN/tests/utility/test_json_importer.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import os
 import glob
diff --git a/PyCTBN/tests/utility/test_sample_importer.py b/PyCTBN/tests/utility/test_sample_importer.py
index 8e96778..ad2ddda 100644
--- a/PyCTBN/tests/utility/test_sample_importer.py
+++ b/PyCTBN/tests/utility/test_sample_importer.py
@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import os
 import glob

From 598dc17ad8c5c7516ea0306bb8fda5ccd46bab07 Mon Sep 17 00:00:00 2001
From: madlabunimib <madlab@unimib.it>
Date: Tue, 1 Jun 2021 12:27:02 +0000
Subject: [PATCH 132/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148546 -> 148546 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 7125c9b51423c2d83c7fab3d90bdd434ed7ec0c4..26081d4950b0aa5957ff783ca49143331b0d8ffe 100644
GIT binary patch
delta 7278
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delta 7306
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From 5e314f9342e39e8e3533bb9df8793e863749e669 Mon Sep 17 00:00:00 2001
From: MADLabUnimib <65596355+madlabunimib@users.noreply.github.com>
Date: Tue, 1 Jun 2021 16:23:02 +0200
Subject: [PATCH 133/139] Update README.rst

---
 README.rst | 26 ++++++++++++++++++++------
 1 file changed, 20 insertions(+), 6 deletions(-)

diff --git a/README.rst b/README.rst
index 57838dc..de6f10f 100644
--- a/README.rst
+++ b/README.rst
@@ -1,21 +1,35 @@
 PyCTBN
 ======
 
+.. image:: https://codecov.io/gh/madlabunimib/PyCTBN/branch/master/graph/badge.svg
+    :target: https://codecov.io/gh/madlabunimib/PyCTBN
+    
+    
+
+
 A Continuous Time Bayesian Networks Library
 
 Installation/Usage
 *******************
-Download the release in .tar.gz or .whl format and simply use pip install to install it::
+
+The library has been tested on Linux and Windows with Python 3.8 and it relies on the following Python modules:
+
+- numpy
+- pandas
+- networkx
+- scipy
+- matplotlib
+- tqdm
+
+**Pip installation**
+
+Download the release in .tar.gz or .whl format and simply use pip install to install it:
 
     $ pip install PyCTBN-1.0.tar.gz
     
-Coverage
-********
-Please refer to https://app.codecov.io/gh/madlabunimib/PyCTBN/ for a detailed report of test coverage.
-
 Documentation
 *************
-Please refer to https://github.com/madlabunimib/PyCTBN/ for the full project documentation.
+Please refer to https://madlabunimib.github.io/PyCTBN/ for the full project documentation.
 
 Implementing your own data importer
 ***********************************

From b81b4110dda286cc38aef019df329113aece3d41 Mon Sep 17 00:00:00 2001
From: madlabunimib <madlab@unimib.it>
Date: Fri, 2 Jul 2021 09:51:06 +0000
Subject: [PATCH 134/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148546 -> 148546 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
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From 65f8c3f794ddd48cd72796dacff44478637c228d Mon Sep 17 00:00:00 2001
From: madlabunimib <madlab@unimib.it>
Date: Fri, 2 Jul 2021 10:39:14 +0000
Subject: [PATCH 135/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle | Bin 148546 -> 148546 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index 2425ce09152466faec923f1e64041cdc7feb6053..cc31d3c46fea3f7853e4e5c99c53d0520b008687 100644
GIT binary patch
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From 0f1605ced6e5723f322e493d4a4b7df9f61a99be Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Fri, 2 Jul 2021 12:40:19 +0200
Subject: [PATCH 136/139] Update README.rst

---
 README.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.rst b/README.rst
index de6f10f..c6636bc 100644
--- a/README.rst
+++ b/README.rst
@@ -23,9 +23,9 @@ The library has been tested on Linux and Windows with Python 3.8 and it relies o
 
 **Pip installation**
 
-Download the release in .tar.gz or .whl format and simply use pip install to install it:
+Download the latest release in .tar.gz or .whl format and simply use pip install to install it:
 
-    $ pip install PyCTBN-1.0.tar.gz
+    $ pip install PyCTBN-2.2.tar.gz
     
 Documentation
 *************

From 3b0843aef676a6b6bd24dba7a5fc32c5e8a01a86 Mon Sep 17 00:00:00 2001
From: philipMartini <45294280+philipMartini@users.noreply.github.com>
Date: Fri, 2 Jul 2021 13:29:21 +0200
Subject: [PATCH 137/139] Update examples.rst

---
 docs-out/examples.rst | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs-out/examples.rst b/docs-out/examples.rst
index b1e07c5..5386451 100644
--- a/docs-out/examples.rst
+++ b/docs-out/examples.rst
@@ -3,9 +3,9 @@ Examples
 
 Installation/Usage
 ******************
-Download the release in .tar.gz or .whl format and simply use pip install to install it::
+Download the latest release in .tar.gz or .whl format and simply use pip install to install it::
 
-    $pip install PyCTBN-1.0.tar.gz
+    $pip install PyCTBN-2.2.tar.gz
 
 
 Implementing your own data importer

From 19862b894278addc38f34eed44f46efdcbef9ac8 Mon Sep 17 00:00:00 2001
From: philipMartini <f.martini@campus.unimib.it>
Date: Fri, 2 Jul 2021 13:36:56 +0200
Subject: [PATCH 138/139] Modify imports order insample_importer_test file

---
 PyCTBN/tests/utility/test_sample_importer.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/PyCTBN/tests/utility/test_sample_importer.py b/PyCTBN/tests/utility/test_sample_importer.py
index ad2ddda..f938c70 100644
--- a/PyCTBN/tests/utility/test_sample_importer.py
+++ b/PyCTBN/tests/utility/test_sample_importer.py
@@ -5,12 +5,15 @@
 import unittest
 import os
 import glob
+import json
 import numpy as np
 import pandas as pd
+
+
 from ...PyCTBN.utility.sample_importer import SampleImporter
 from ...PyCTBN.structure_graph.sample_path import SamplePath
 
-import json
+
 
 
 

From d10e8b3e706d694e1b7519ffb1dc818fa387b1c5 Mon Sep 17 00:00:00 2001
From: madlabunimib <madlab@unimib.it>
Date: Fri, 2 Jul 2021 11:46:42 +0000
Subject: [PATCH 139/139] Update documentation

---
 docs-out/_build/doctrees/environment.pickle   | Bin 148546 -> 148546 bytes
 docs-out/_build/doctrees/examples.doctree     | Bin 11402 -> 11423 bytes
 .../_build/html/_sources/examples.rst.txt     |   4 ++--
 docs-out/_build/html/examples.html            |   4 ++--
 docs-out/_build/html/searchindex.js           |   2 +-
 docs/_sources/examples.rst.txt                |   4 ++--
 docs/examples.html                            |   4 ++--
 docs/searchindex.js                           |   2 +-
 8 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/docs-out/_build/doctrees/environment.pickle b/docs-out/_build/doctrees/environment.pickle
index cc31d3c46fea3f7853e4e5c99c53d0520b008687..8c0b1628cb6dcbf57817ca27820b0847b0ca0284 100644
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diff --git a/docs-out/_build/doctrees/examples.doctree b/docs-out/_build/doctrees/examples.doctree
index 07c7eded18fa66d0749883fdf29734776cb360f0..72a32a6d973d9bb22202bb10deaeaff1bd88a863 100644
GIT binary patch
delta 119
zcmeB*oFB>3z&drxMiyfxkp!3g^1Ph<#1w^+j8ui3#FEtFlF3}mK9eUfaf-xam-Llu
hozgg^c8W#@YYz@32bhiYj3%FDRsqqQzc5eJ0074qDUJXD

delta 103
zcmbOq*%issz&f>lBa1N;Z=_3pd0tL_Vv0gZM(SjFW*;%DDH-gsQ!>PQBG9CK#apK|
dPN|)uk->@~cYxVY&tUQ+W)%><nUiIj1^_y<BEJ9t

diff --git a/docs-out/_build/html/_sources/examples.rst.txt b/docs-out/_build/html/_sources/examples.rst.txt
index b1e07c5..5386451 100644
--- a/docs-out/_build/html/_sources/examples.rst.txt
+++ b/docs-out/_build/html/_sources/examples.rst.txt
@@ -3,9 +3,9 @@ Examples
 
 Installation/Usage
 ******************
-Download the release in .tar.gz or .whl format and simply use pip install to install it::
+Download the latest release in .tar.gz or .whl format and simply use pip install to install it::
 
-    $pip install PyCTBN-1.0.tar.gz
+    $pip install PyCTBN-2.2.tar.gz
 
 
 Implementing your own data importer
diff --git a/docs-out/_build/html/examples.html b/docs-out/_build/html/examples.html
index 94a79a7..2755cf0 100644
--- a/docs-out/_build/html/examples.html
+++ b/docs-out/_build/html/examples.html
@@ -117,8 +117,8 @@
 <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h1>
 <section id="installation-usage">
 <h2>Installation/Usage<a class="headerlink" href="#installation-usage" title="Permalink to this headline">¶</a></h2>
-<p>Download the release in .tar.gz or .whl format and simply use pip install to install it:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$pip install PyCTBN-1.0.tar.gz
+<p>Download the latest release in .tar.gz or .whl format and simply use pip install to install it:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$pip install PyCTBN-2.2.tar.gz
 </pre></div>
 </div>
 </section>
diff --git a/docs-out/_build/html/searchindex.js b/docs-out/_build/html/searchindex.js
index 7d0597c..22a6a83 100644
--- a/docs-out/_build/html/searchindex.js
+++ b/docs-out/_build/html/searchindex.js
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\ No newline at end of file
diff --git a/docs/_sources/examples.rst.txt b/docs/_sources/examples.rst.txt
index b1e07c5..5386451 100644
--- a/docs/_sources/examples.rst.txt
+++ b/docs/_sources/examples.rst.txt
@@ -3,9 +3,9 @@ Examples
 
 Installation/Usage
 ******************
-Download the release in .tar.gz or .whl format and simply use pip install to install it::
+Download the latest release in .tar.gz or .whl format and simply use pip install to install it::
 
-    $pip install PyCTBN-1.0.tar.gz
+    $pip install PyCTBN-2.2.tar.gz
 
 
 Implementing your own data importer
diff --git a/docs/examples.html b/docs/examples.html
index 94a79a7..2755cf0 100644
--- a/docs/examples.html
+++ b/docs/examples.html
@@ -117,8 +117,8 @@
 <h1>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h1>
 <section id="installation-usage">
 <h2>Installation/Usage<a class="headerlink" href="#installation-usage" title="Permalink to this headline">¶</a></h2>
-<p>Download the release in .tar.gz or .whl format and simply use pip install to install it:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$pip install PyCTBN-1.0.tar.gz
+<p>Download the latest release in .tar.gz or .whl format and simply use pip install to install it:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$pip install PyCTBN-2.2.tar.gz
 </pre></div>
 </div>
 </section>
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 7d0597c..22a6a83 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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