Merge branch 'master' into trajectory-generation

.gitattributes

@@ -0,0 +1,3 @@
+*.js linguist-vendored
+*.html linguist-vendored
+*.css linguist-vendored

.github/workflows/Build_Release.yml

@@ -0,0 +1,67 @@
+      
+on:
+  push:
+    # Sequence of patterns matched against refs/tags
+    tags:
+      - 'v*' # Push events to matching v*, i.e. v1.0, v20.15.10
+    
+name: Upload Release Asset 
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    name: Upload Release Asset
+    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 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/.
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Release ${{ github.ref }}
+          draft: false
+          prerelease: false
+      - name: Upload Release Asset
+        id: upload-release-asset 
+        uses: dwenegar/upload-release-assets@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          release_id: ${{ steps.create_release.outputs.id }}
+          assets_path: ./dist

.github/workflows/main.yml

@@ -4,13 +4,10 @@
 name: Sphinx Docs
 
 on:
-  push:
+  workflow_run:
-    paths-ignore: 
+    workflows: ["Python package","Upload Release Asset"]
-      -'docs/**'
+    types:
-      -'docs-out/**'
+      - completed
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
 
 jobs:
   build:
@@ -41,8 +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.email "madlab@unimib.it"
-        git config --local user.name "philipMartini"
+        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
@@ -51,7 +48,7 @@ jobs:
       uses: ad-m/github-push-action@master
       with:
         branch: master
-        github_token: ${{ secrets.PYCTBN_TOK }}
+        github_token: ${{ secrets.GITHUB_TOKEN }}
     # ===============================
         
         

.github/workflows/python-PyCTBN-package.yml

@@ -5,10 +5,11 @@ name: Python package
 
 on:
   push:
-    paths-ignore: 
+    paths:
-      -'docs/**'
+      - 'PyCTBN/**'
-      -'docs-out/**'
     branches: [ master ]
+    tags-ignore:
+      - 'v*'
   pull_request:
     branches: [ master ]
 
@@ -37,6 +38,23 @@ 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
+    - name: Generate coverage report
       run: |
-        pytest PyCTBN/tests/
+        pip install pytest
+        pip install pytest-cov
+        pytest PyCTBN/tests/ --cov='./' --cov-report=xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1
+      with:
+        files: ./coverage.xml
+        flags: unittests
+        env_vars: OS,PYTHON
+        name: codecov-umbrella
+        fail_ci_if_error: true
+        verbose: true
+        
+        
+        
+        
+        
+        

.gitignore

@@ -3,7 +3,6 @@ __pycache__
 **/__pycache__
 **/data
 **/PyCTBN.egg-info
-**/dist
 **/results_data
 **/.scannerwork
 **/build
@@ -15,3 +14,4 @@ test3.json
 result0.png
 example.json
 test_time.py
+.idea

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.

PyCTBN/PyCTBN/__init__.py

@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import PyCTBN.PyCTBN.estimators
 from PyCTBN.PyCTBN.estimators import *
 import PyCTBN.PyCTBN.optimizers

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

PyCTBN/PyCTBN/estimators/fam_score_calculator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing

PyCTBN/PyCTBN/estimators/parameters_estimator.py

@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import sys
 sys.path.append('../')
 import numpy as np

PyCTBN/PyCTBN/estimators/structure_constraint_based_estimator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
@@ -94,7 +97,7 @@ 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)
@@ -199,8 +202,14 @@ 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 +221,6 @@ 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()
 
@@ -221,10 +228,14 @@ 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:
+                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,
@@ -238,8 +249,18 @@ class StructureConstraintBasedEstimator(StructureEstimator):
         return edges
 
         
-    def estimate_structure(self,disable_multiprocessing:bool=False):
+    def estimate_structure(self, disable_multiprocessing:bool=False, processes_number:int= None):
-        return self.ctpc_algorithm(disable_multiprocessing=disable_multiprocessing)
+        """
+        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)
 
     
 

PyCTBN/PyCTBN/estimators/structure_estimator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
@@ -142,40 +145,34 @@ 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.
+        """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
-            :param file_path: path to save the file to
+        :type: string
-            :type: string
+        """
-            """
+        pos = nx.spring_layout(self._complete_graph, k=0.5*1/np.sqrt(len(self._complete_graph.nodes)),
-            graph_to_draw = nx.DiGraph()
+                               iterations=50,scale=10)
-            spurious_edges = self.spurious_edges()
+        options = {
-            non_spurious_edges = list(set(self._complete_graph.edges) - set(spurious_edges))
+            "node_size": 2000,
-            edges_colors = ['red' if edge in spurious_edges else 'black' for edge in self._complete_graph.edges]
+            "node_color": "white",
-            graph_to_draw.add_edges_from(spurious_edges)
+            "edgecolors": "black",
-            graph_to_draw.add_edges_from(non_spurious_edges)
+            'linewidths':2,
-            pos = nx.spring_layout(graph_to_draw, k=0.5*1/np.sqrt(len(graph_to_draw.nodes())), iterations=50,scale=10)
+            "with_labels":True,
-            options = {
+            "font_size":13,
-                "node_size": 2000,
+            'connectionstyle': 'arc3, rad = 0.1',
-                "node_color": "white",
+            "arrowsize": 15,
-                "edgecolors": "black",
+            #"arrowstyle": '<|-',
-                'linewidths':2,
+            "width": 1,
-                "with_labels":True,
+            #"edge_color":edges_colors,
-                "font_size":13,
+        }
-                'connectionstyle': 'arc3, rad = 0.1',
+
-                "arrowsize": 15,
+        nx.draw(self._complete_graph, pos, **options)
-                "arrowstyle": '<|-',
+        ax = plt.gca()
-                "width": 1,
+        ax.margins(0.20)
-                "edge_color":edges_colors,
+        plt.axis("off")
-            }
+        plt.savefig(file_path)
-
+        plt.clf()
-            nx.draw(graph_to_draw, pos, **options)
+        print("Estimated Structure Plot Saved At: ", os.path.abspath(file_path))
-            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))
 
 
 

PyCTBN/PyCTBN/estimators/structure_score_based_estimator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
@@ -54,7 +57,7 @@ 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 +75,9 @@ 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)
@@ -93,11 +99,12 @@ class StructureScoreBasedEstimator(StructureEstimator):
 
 
         'get the number of CPU'
-        cpu_count = multiprocessing.cpu_count()
+        cpu_count = multiprocessing.cpu_count()        
-        print(f"CPU COUNT: {cpu_count}")
 
         if disable_multiprocessing:
             cpu_count = 1
+        elif processes_number is not None and cpu_count > processes_number:
+            cpu_count = processes_number
 
         
 
@@ -106,6 +113,8 @@ 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]

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

PyCTBN/PyCTBN/optimizers/constraint_based_optimizer.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing

PyCTBN/PyCTBN/optimizers/hill_climbing_search.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing

PyCTBN/PyCTBN/optimizers/optimizer.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing

PyCTBN/PyCTBN/optimizers/tabu_search.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import itertools
 import json
 import typing
@@ -184,5 +187,5 @@ class TabuSearch(Optimizer):
             if self.patience is not None and patince_count > self.patience:
                 break
 
-        print(f"finito variabile: {self.node_id}")
+        print(f"Finished variable : {self.node_id}")
-        return graph.edges
+        return graph.edges

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

PyCTBN/PyCTBN/structure_graph/conditional_intensity_matrix.py

@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import numpy as np
 
 

PyCTBN/PyCTBN/structure_graph/network_graph.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 
 import networkx as nx

PyCTBN/PyCTBN/structure_graph/sample_path.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 
 import numpy as np
 import pandas as pd

PyCTBN/PyCTBN/structure_graph/set_of_cims.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 
 import typing
 

PyCTBN/PyCTBN/structure_graph/structure.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing as ty
 
 import numpy as np

PyCTBN/PyCTBN/structure_graph/trajectory.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 
 import numpy as np

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

PyCTBN/PyCTBN/utility/abstract_importer.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 from abc import ABC, abstractmethod
 

PyCTBN/PyCTBN/utility/cache.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import typing
 
 from ..structure_graph.set_of_cims import SetOfCims 

PyCTBN/PyCTBN/utility/json_importer.py

@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import json
 import typing
 
@@ -50,10 +53,10 @@ 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
@@ -105,7 +108,12 @@ 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``.

PyCTBN/PyCTBN/utility/sample_importer.py

@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import json
 import typing
 

PyCTBN/__init__.py

@@ -1,2 +1,5 @@
+
+# License: MIT License
+
 import PyCTBN.PyCTBN
 from PyCTBN.PyCTBN import *

PyCTBN/basic_main.py

@@ -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()

PyCTBN/setup.py

@@ -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')

PyCTBN/tests/__init__.py

@@ -1 +1,4 @@
 
+# License: MIT License
+
+

PyCTBN/tests/estimators/test_parameters_estimator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 import glob

PyCTBN/tests/estimators/test_structure_constraint_based_estimator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os
@@ -54,7 +57,7 @@ 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)

PyCTBN/tests/estimators/test_structure_estimator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os

PyCTBN/tests/estimators/test_structure_score_based_estimator.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os
@@ -111,7 +114,8 @@ class TestStructureScoreBasedEstimator(unittest.TestCase):
                                     tabu_length = 15,
                                     tabu_rules_duration = 15,
                                     optimizer = 'hill',
-                                    disable_multiprocessing=False
+                                    disable_multiprocessing=False,
+                                    processes_number=2
                                     )
         
 
@@ -240,6 +244,7 @@ class TestStructureScoreBasedEstimator(unittest.TestCase):
         self.assertGreaterEqual(recall,0.75)      
 
 
+
 if __name__ == '__main__':
     unittest.main()
 

PyCTBN/tests/optimizers/test_hill_climbing_search.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import glob
 import math
 import os
@@ -54,9 +57,9 @@ 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"]

PyCTBN/tests/optimizers/test_tabu_search.py

@@ -1,3 +1,6 @@
+
+# License: MIT License
+
 import sys
 sys.path.append("../../PyCTBN/")
 import glob
@@ -75,7 +78,8 @@ 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]

PyCTBN/tests/structure_graph/test_cim.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 
@@ -34,10 +37,10 @@ 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, 1e01,1e01))
         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(state_residence_times = self.state_res_times, 

PyCTBN/tests/structure_graph/test_networkgraph.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import glob
 import os

PyCTBN/tests/structure_graph/test_sample_path.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import glob
 import os

PyCTBN/tests/structure_graph/test_setofcims.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 import itertools

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

PyCTBN/tests/structure_graph/test_trajectory.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 import glob

PyCTBN/tests/utility/test_cache.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import numpy as np
 

PyCTBN/tests/utility/test_json_importer.py

@@ -1,4 +1,7 @@
 
+# License: MIT License
+
+
 import unittest
 import os
 import glob
@@ -39,7 +42,7 @@ 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 +158,7 @@ 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]))

PyCTBN/tests/utility/test_sample_importer.py

@@ -1,13 +1,19 @@
 
+# License: MIT License
+
+
 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
+
 
 
 
@@ -17,9 +23,10 @@ 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"])

README.rst

@@ -1,27 +1,64 @@
 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::
 
-    $ pip install PyCTBN-1.0.tar.gz
+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 latest release in .tar.gz or .whl format and simply use pip install to install it:
+
+    $ pip install PyCTBN-2.2.tar.gz
+    
 Documentation
 *************
-Please refer to https://philipmartini.github.io/PyCTBN/ for the full project documentation.
+Please refer to https://madlabunimib.github.io/PyCTBN/ for the full project documentation.
 
 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: 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 
+| 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.
+.. code-block:: python
-    The net in exam has three ternary nodes and no prior net structure.
-    """
 
+    import pandas as pd
+    import typing
+    
     from PyCTBN import AbstractImporter
+    from PyCTBN import SamplePath
 
     class CSVImporter(AbstractImporter):
 
@@ -53,73 +90,256 @@ Implementing your own data importer
         def dataset_id(self) -> object:
             pass
 
-Parameters Estimation Example
+    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()
+
+
+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),
+| 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
 
+    import glob
+    import os
+
     from PyCTBN import JsonImporter
     from PyCTBN import SamplePath
-    from PyCTBN import NetworkGraph
+    from PyCTBN import StructureConstraintBasedEstimator
-    from PyCTBN import ParametersEstimator
 
 
-    def main():
+    def structure_constraint_based_estimation_example():
-        read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir
+        # <read the json files in ./data path>
-        #import data
+        read_files = glob.glob(os.path.join('./data', "*.json"))
-        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        # <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)
-        #Create a SamplePath Obj passing an already filled AbstractImporter object
+        # construct a SamplePath Object passing a filled AbstractImporter object
-        s1 = SamplePath(importer)
+        s1 = SamplePath(importer=importer)
-        #Build The trajectries and the structural infos
+        # build the trajectories
         s1.build_trajectories()
+        # build the information about the net
         s1.build_structure()
-        print(s1.structure.edges)
+        # construct a StructureEstimator object passing a correctly build SamplePath object
-        print(s1.structure.nodes_values)
+        # and the independence tests significance, if you have prior knowledge about 
-        #From The Structure Object build the Graph
+        # the net structure create a list of tuples
-        g = NetworkGraph(s1.structure)
+        # that contains them and pass it as known_edges parameter
-        #Select a node you want to estimate the parameters
+        se1 = StructureConstraintBasedEstimator(sample_path=s1, exp_test_alfa=0.1, chi_test_alfa=0.1,
-        node = g.nodes[2]
+                                                known_edges=[], thumb_threshold=25)
-        print("Node", node)
+        # call the algorithm to estimate the structure
-        #Init the _graph specifically for THIS node
+        se1.estimate_structure()
-        g.fast_init(node)
+        # obtain the adjacency matrix of the estimated structure
-        #Use SamplePath and Grpah to create a ParametersEstimator Object
+        print(se1.adjacency_matrix())
-        p1 = ParametersEstimator(s1.trajectories, g)
+        # save the estimated structure  to a json file 
-        #Init the peEst specifically for THIS node
+        # (remember to specify the path AND the .json extension)....
-        p1.fast_init(node)
+        se1.save_results('./results0.json')
-        #Compute the parameters
+        # ...or save it also in a graphical model fashion 
-        sofc1 = p1.compute_parameters_for_node(node)
+        # (remember to specify the path AND the .png extension)
-        #The est CIMS are inside the resultant SetOfCIms Obj
+        se1.save_plot_estimated_structure_graph('./result0.png')
-        print(sofc1.actual_cims)
+
-
+
-Structure Estimation Example
+
-****************************
+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 StructureEstimator
+    from PyCTBN import StructureScoreBasedEstimator
-    
+
-    def structure_estimation_example():
 
-        # 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
+        # <initialize a JsonImporter object for the first file>
-        importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name')
+        importer = JsonImporter(file_path=read_files[0], samples_label='samples',
-        # import the data at index 0 of the outer json array
+                                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
+        # construct a SamplePath Object passing a filled AbstractImporter object
-        s1 = SamplePath(importer)
+        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 real structure
+        # build the information about the net
         s1.build_structure()
-        # construct a StructureEstimator object
+        # construct a StructureEstimator object passing a correctly build SamplePath object
-        se1 = StructureEstimator(s1, 0.1, 0.1)
+        # and hyperparameters tau and alpha, if you have prior knowledge about 
-        # call the ctpc algorithm
+        # the net structure create a list of tuples
-        se1.ctpc_algorithm()
+        # that contains them and pass it as known_edges parameter
-        # the adjacency matrix of the estimated structure
+        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 results to a json file
+        # save the estimated structure  to a json file 
-        se1.save_results()
+        # (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')

codecov.yml

@@ -0,0 +1 @@
+

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: 481da5f157a263da657ebbabcd85e902
 tags: 645f666f9bcd5a90fca523b33c5a78b7

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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.fam_score_calculator">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.parameters_estimator">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator">
+<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>
+<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>Abstract method to estimate the structure</p>
+<dd><p>Compute the constraint-based algorithm to find the optimal structure</p>
 <dl class="field-list simple">
-<dt class="field-odd">Returns</dt>
+<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p>List of estimated edges</p>
+<dd class="field-odd"><ul class="simple">
-</dd>
+<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>
-<dt class="field-even">Return type</dt>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
-<dd class="field-even"><p>Typing.List</p>
+</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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_estimator">
+<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">
@@ -636,8 +648,7 @@ 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.
+<dd><p>Plot the estimated structure in a graphical model style, use .png extension.</p>
-Spurious edges are colored in red if a prior structure is present.</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>
@@ -678,8 +689,8 @@ Spurious edges are colored in red if a prior structure is present.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator">
+<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">
@@ -724,7 +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>
@@ -736,9 +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">
@@ -763,11 +777,11 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.hill_climbing_search">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.optimizer">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.tabu_search">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.network_graph">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.sample_path">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.set_of_cims">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.structure">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.trajectory">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.abstract_importer">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.cache">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.json_importer">
+<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">
@@ -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>
@@ -531,8 +531,8 @@ as keys for the set of CIMS of a particular node.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.sample_importer">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="submodules">
+<section id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
-</div>
+</section>
-<div class="section" id="module-PyCTBN">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.tests.estimators.test_parameters_estimator">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_estimator">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_score_based_estimator">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.estimators">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.tests">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.tests.optimizers.test_hill_climbing_search">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.optimizers.test_tabu_search">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.optimizers">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_cim">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_networkgraph">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_sample_path">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_setofcims">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_structure">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.structure_graph.test_trajectory">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.structure_graph">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>
+</section>
-<div class="section" id="module-PyCTBN.tests.utility.test_cache">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.utility.test_json_importer">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.utility.test_sample_importer">
+<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>
+</section>
-<div class="section" id="module-PyCTBN.tests.utility">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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

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>

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>
+<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>$pip install PyCTBN-1.0.tar.gz
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$pip install PyCTBN-2.2.tar.gz
 </pre></div>
 </div>
-</div>
+</section>
-<div class="section" id="implementing-your-own-data-importer">
+<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>
+</section>
-<div class="section" id="parameters-estimation-example">
+<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>
+</section>
-<div class="section" id="structure-estimation-example">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

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>

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>
+</section>
-<div class="section" id="indices-and-tables">
+<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>

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>

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>

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>

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>

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

docs/PyCTBN.PyCTBN.estimators.html

@@ -65,7 +65,7 @@
 	
           
           
-              <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>
@@ -119,12 +119,12 @@
           <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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.fam_score_calculator">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.fam_score_calculator.FamScoreCalculator">
@@ -304,8 +304,8 @@ and a specif parents’s assignment</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.parameters_estimator">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.parameters_estimator.ParametersEstimator">
@@ -389,8 +389,8 @@ in the graph <code class="docutils literal notranslate"><span class="pre">_net_g
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator">
@@ -470,23 +470,39 @@ Generates all the necessary structures and datas to perform the tests.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.ctpc_algorithm">
+
-<span class="sig-name descname"><span class="pre">ctpc_algorithm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">disable_multiprocessing</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></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>
+<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>, <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 class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure">
+
-<span class="sig-name descname"><span class="pre">estimate_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">disable_multiprocessing</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></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>
+<dt id="PyCTBN.PyCTBN.estimators.structure_constraint_based_estimator.StructureConstraintBasedEstimator.estimate_structure">
-<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>
+<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p>List of estimated edges</p>
+<dd class="field-odd"><ul class="simple">
-</dd>
+<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>
-<dt class="field-even">Return type</dt>
+<li><p><strong>processes_number</strong> – if disable_multiprocessing is false indicates</p></li>
-<dd class="field-even"><p>Typing.List</p>
+</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">
@@ -525,8 +541,8 @@ it is performed also the chi_test.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_estimator">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator">
@@ -638,10 +654,11 @@ that do not contains a the node identified by <code class="docutils literal notr
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph">
+
-<span class="sig-name descname"><span class="pre">save_plot_estimated_structure_graph</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">file_path</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span></em><span class="sig-paren">)</span> &#x2192; <span class="pre">None</span><a class="headerlink" href="#PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph" title="Permalink to this definition">¶</a></dt>
+<dt id="PyCTBN.PyCTBN.estimators.structure_estimator.StructureEstimator.save_plot_estimated_structure_graph">
-<dd><p>Plot the estimated structure in a graphical model style, use .png extension.
+<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>
-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>
@@ -682,8 +699,8 @@ Spurious edges are colored in red if a prior structure is present.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators.structure_score_based_estimator">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator">
@@ -727,8 +744,10 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.estimators.structure_score_based_estimator.StructureScoreBasedEstimator.estimate_structure">
+
-<span class="sig-name descname"><span class="pre">estimate_structure</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">max_parents</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">iterations_number</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">40</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">patience</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tabu_length</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tabu_rules_duration</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">optimizer</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">'tabu'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">disable_multiprocessing</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></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>
+<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>, <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>
@@ -740,9 +759,12 @@ 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">
@@ -767,11 +789,11 @@ using a score based approach and differt kinds of optimization algorithms.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.estimators">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

docs/PyCTBN.PyCTBN.html

@@ -64,7 +64,7 @@
 	
           
           
-              <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>
@@ -118,9 +118,9 @@
           <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>
@@ -169,11 +169,11 @@
 </li>
 </ul>
 </div>
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

docs/PyCTBN.PyCTBN.optimizers.html

@@ -65,7 +65,7 @@
 	
           
           
-              <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>
@@ -119,12 +119,12 @@
           <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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.constraint_based_optimizer">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.optimizers.constraint_based_optimizer.ConstraintBasedOptimizer">
@@ -156,8 +156,8 @@
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.hill_climbing_search">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.optimizers.hill_climbing_search.HillClimbing">
@@ -191,8 +191,8 @@
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.optimizer">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.optimizers.optimizer.Optimizer">
@@ -223,8 +223,8 @@
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers.tabu_search">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.optimizers.tabu_search.TabuSearch">
@@ -260,11 +260,11 @@
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.optimizers">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

docs/PyCTBN.PyCTBN.structure_graph.html

@@ -65,7 +65,7 @@
 	
           
           
-              <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>
@@ -119,12 +119,12 @@
           <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>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.conditional_intensity_matrix.ConditionalIntensityMatrix">
@@ -244,8 +244,8 @@ This method must obviously be executed after the graph has been generated.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.network_graph">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.network_graph.NetworkGraph">
@@ -537,8 +537,8 @@ Initialize all the filtering/indexing structures.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.sample_path">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.sample_path.SamplePath">
@@ -601,8 +601,8 @@ Clears all the unused dataframes in <code class="docutils literal notranslate"><
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.set_of_cims">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.set_of_cims.SetOfCims">
@@ -687,8 +687,8 @@ Compute the cim coefficients.The class member <code class="docutils literal notr
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.structure">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.structure.Structure">
@@ -816,8 +816,8 @@ The class member <code class="docutils literal notranslate"><span class="pre">_t
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.structure_graph.trajectory">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.trajectory.Trajectory">
@@ -861,82 +861,13 @@ 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_generator">
-<span id="pyctbn-pyctbn-structure-graph-trajectory-generator-module"></span><h2>PyCTBN.PyCTBN.structure_graph.trajectory_generator module<a class="headerlink" href="#module-PyCTBN.PyCTBN.structure_graph.trajectory_generator" title="Permalink to this headline">¶</a></h2>
-<dl class="py class">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">PyCTBN.PyCTBN.structure_graph.trajectory_generator.</span></span><span class="sig-name descname"><span class="pre">TrajectoryGenerator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">importer</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="PyCTBN.PyCTBN.utility.html#PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter" title="PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter"><span class="pre">PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter</span></a><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">pandas.core.frame.DataFrame</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dyn_str</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">pandas.core.frame.DataFrame</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dyn_cims</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
-<p>Provides the methods to generate a trajectory basing on the network defined
-in the importer.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>_importer</strong> (<a class="reference internal" href="PyCTBN.PyCTBN.utility.html#PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter" title="PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter"><em>AbstractImporter</em></a>) – the Importer object which contains the imported and processed data</p></li>
-<li><p><strong>_vnames</strong> (<em>List</em>) – List of the variables labels that belong to the network</p></li>
-<li><p><strong>_parents</strong> (<em>Dict</em>) – It contains, for each variable label (the key), the list of related parents labels</p></li>
-<li><p><strong>_cims</strong> (<em>Dict</em>) – It contains, for each variable label (the key), the SetOfCims object related to it</p></li>
-<li><p><strong>_generated_trajectory</strong> (<em>pandas.DataFrame</em>) – Result of the execution of CTBN_Sample, contains the output trajectory</p></li>
-</ul>
-</dd>
-</dl>
-<dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator.CTBN_Sample">
-<span class="sig-name descname"><span class="pre">CTBN_Sample</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">t_end</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_tr</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">-</span> <span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator.CTBN_Sample" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="simple">
-<dt>This method implements the generation of a trajectory, basing on the network structure and</dt><dd><p>on the coefficients defined in the CIMs.
-The variables are initialized with value 0, and the method takes care of adding the
-conventional last row made up of -1.</p>
-</dd>
-</dl>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>t_end</strong> (<em>float</em>) – If defined, the sampling ends when end time is reached</p></li>
-<li><p><strong>max_tr</strong> (<em>int</em>) – Parameter taken in consideration in case that t_end isn’t defined. It specifies the number of transitions to execute</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator.multi_trajectory">
-<span class="sig-name descname"><span class="pre">multi_trajectory</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">t_ends</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_trs</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">list</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator.multi_trajectory" title="Permalink to this definition">¶</a></dt>
-<dd><p>Generate n trajectories in parallel, where n is the number of items in 
-t_ends, if defined, or the number of items in max_trs otherwise</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>t_ends</strong> (<em>list</em>) – List of t_end values for the trajectories that will be generated</p></li>
-<li><p><strong>max_trs</strong> (<em>list</em>) – List of max_tr values for the trajectories that will be generated</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
-
-<dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator.worker">
-<span class="sig-name descname"><span class="pre">worker</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">t_end</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_tr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trajectories</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.structure_graph.trajectory_generator.TrajectoryGenerator.worker" title="Permalink to this definition">¶</a></dt>
-<dd><p>Single process that will be executed in parallel in order to generate one trajectory.</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>t_end</strong> (<em>float</em>) – If defined, the sampling ends when end time is reached</p></li>
-<li><p><strong>max_tr</strong> (<em>int</em>) – Parameter taken in consideration in case that t_end isn’t defined. It specifies the number of transitions to execute</p></li>
-<li><p><strong>trajectories</strong> (<em>list</em>) – Shared list that contains to which the generated trajectory is added</p></li>
-</ul>
-</dd>
-</dl>
-</dd></dl>
 
-</dd></dl>
+</section>
+<section id="module-PyCTBN.PyCTBN.structure_graph">
 
-</div>
-<div class="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>
+</section>
-</div>
+</section>
 
 
 	    </div>

docs/PyCTBN.PyCTBN.utility.html

@@ -65,7 +65,7 @@
 	
           
           
-              <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>
@@ -119,58 +119,14 @@
           <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_exporter">
-<span id="pyctbn-pyctbn-utility-abstract-exporter-module"></span><h2>PyCTBN.PyCTBN.utility.abstract_exporter module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.abstract_exporter" title="Permalink to this headline">¶</a></h2>
-<dl class="py class">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">PyCTBN.PyCTBN.utility.abstract_exporter.</span></span><span class="sig-name descname"><span class="pre">AbstractExporter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variables</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">pandas.core.frame.DataFrame</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dyn_str</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">pandas.core.frame.DataFrame</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dyn_cims</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">abc.ABC</span></code></p>
-<p>Abstract class that exposes the methods to save in json format a network information
-along with one or more trajectories generated basing on it</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>_variables</strong> (<em>pandas.DataFrame</em>) – Dataframe containing the nodes labels and cardinalities</p></li>
-<li><p><strong>_dyn_str</strong> (<em>pandas.DataFrame</em>) – Dataframe containing the structure of the network (edges)</p></li>
-<li><p><strong>_dyn_cims</strong> (<em>dict</em>) – It contains, for every variable (label is the key), the SetOfCims object related to it</p></li>
-<li><p><strong>_trajectories</strong> (<em>List</em>) – List of trajectories, that can be added subsequently</p></li>
-</ul>
-</dd>
-</dl>
-<dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter.add_trajectory">
-<span class="sig-name descname"><span class="pre">add_trajectory</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">trajectory</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">list</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter.add_trajectory" title="Permalink to this definition">¶</a></dt>
-<dd><p>Add a new trajectory to the current list</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>trajectory</strong> (<em>pandas.DataFrame</em>) – The trajectory to add</p>
-</dd>
-</dl>
-</dd></dl>
 
-<dl class="py method">
+</section>
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter.out_file">
+<section id="module-PyCTBN.PyCTBN.utility.abstract_importer">
-<em class="property"><span class="pre">abstract</span> </em><span class="sig-name descname"><span class="pre">out_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter.out_file" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="simple">
-<dt>Create a file in current directory and write on it the previously added data </dt><dd><p>(variables, dyn_str, dyn_cims and trajectories)</p>
-</dd>
-</dl>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<em>string</em>) – Name of the output file (it must include json extension)</p>
-</dd>
-</dl>
-</dd></dl>
-
-</dd></dl>
 
-</div>
-<div class="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 class="sig sig-object py" id="PyCTBN.PyCTBN.utility.abstract_importer.AbstractImporter">
@@ -331,8 +287,8 @@ dataset</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.cache">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.utility.cache.Cache">
@@ -390,48 +346,10 @@ None otherwise.</p>
 
 </dd></dl>
 
-</div>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.json_exporter">
-<span id="pyctbn-pyctbn-utility-json-exporter-module"></span><h2>PyCTBN.PyCTBN.utility.json_exporter module<a class="headerlink" href="#module-PyCTBN.PyCTBN.utility.json_exporter" title="Permalink to this headline">¶</a></h2>
-<dl class="py class">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.utility.json_exporter.JsonExporter">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">PyCTBN.PyCTBN.utility.json_exporter.</span></span><span class="sig-name descname"><span class="pre">JsonExporter</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">variables</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">pandas.core.frame.DataFrame</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dyn_str</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">pandas.core.frame.DataFrame</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dyn_cims</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">dict</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_exporter.JsonExporter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference internal" href="#PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter" title="PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter"><code class="xref py py-class docutils literal notranslate"><span class="pre">PyCTBN.PyCTBN.utility.abstract_exporter.AbstractExporter</span></code></a></p>
-<p>Provides the methods to save in json format a network information
-along with one or more trajectories generated basing on it</p>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><ul class="simple">
-<li><p><strong>_variables</strong> (<em>pandas.DataFrame</em>) – Dataframe containing the nodes labels and cardinalities</p></li>
-<li><p><strong>_dyn_str</strong> (<em>pandas.DataFrame</em>) – Dataframe containing the structure of the network (edges)</p></li>
-<li><p><strong>_dyn_cims</strong> (<em>dict</em>) – It contains, for every variable (label is the key), the SetOfCims object related to it</p></li>
-<li><p><strong>_trajectories</strong> (<em>List</em>) – List of trajectories, that can be added subsequently</p></li>
-</ul>
-</dd>
-</dl>
-<dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.utility.json_exporter.JsonExporter.cims_to_json">
-<span class="sig-name descname"><span class="pre">cims_to_json</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span> &#x2192; <span class="pre">dict</span><a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_exporter.JsonExporter.cims_to_json" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
 
-<dl class="py method">
+</section>
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.utility.json_exporter.JsonExporter.out_file">
+<section id="module-PyCTBN.PyCTBN.utility.json_importer">
-<span class="sig-name descname"><span class="pre">out_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_exporter.JsonExporter.out_file" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="simple">
-<dt>Create a file in current directory and write on it the previously added data </dt><dd><p>(variables, dyn_str, dyn_cims and trajectories)</p>
-</dd>
-</dl>
-<dl class="field-list simple">
-<dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>filename</strong> (<em>string</em>) – Name of the output file (it must include json extension)</p>
-</dd>
-</dl>
-</dd></dl>
 
-</dd></dl>
-
-</div>
-<div class="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 class="sig sig-object py" id="PyCTBN.PyCTBN.utility.json_importer.JsonImporter">
@@ -480,12 +398,14 @@ dataset</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data">
+
-<span class="sig-name descname"><span class="pre">import_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">indx</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span></em><span class="sig-paren">)</span> &#x2192; <span class="pre">None</span><a class="headerlink" href="#PyCTBN.PyCTBN.utility.json_importer.JsonImporter.import_data" title="Permalink to this definition">¶</a></dt>
+<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> <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>
@@ -621,8 +541,8 @@ as keys for the set of CIMS of a particular node.</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility.sample_importer">
+<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 class="sig sig-object py" id="PyCTBN.PyCTBN.utility.sample_importer.SampleImporter">
@@ -665,11 +585,11 @@ dataset</p>
 
 </dd></dl>
 
-</div>
+</section>
-<div class="section" id="module-PyCTBN.PyCTBN.utility">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>

docs/PyCTBN.html

@@ -62,7 +62,7 @@
 	
           
           
-              <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>
@@ -116,9 +116,9 @@
           <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>
@@ -218,20 +218,16 @@
 </li>
 </ul>
 </div>
-</div>
+</section>
-<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="pyctbn-basic-main-module">
+</section>
-<h2>PyCTBN.basic_main module<a class="headerlink" href="#pyctbn-basic-main-module" title="Permalink to this headline">¶</a></h2>
+<section id="module-PyCTBN">
-</div>
+
-<div class="section" id="pyctbn-setup-module">
-<h2>PyCTBN.setup module<a class="headerlink" href="#pyctbn-setup-module" title="Permalink to this headline">¶</a></h2>
-</div>
-<div class="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>
+</section>
-</div>
+</section>
 
 
 	    </div>

docs/PyCTBN.tests.estimators.html

@@ -62,7 +62,7 @@
 	
           
           
-              <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>
@@ -116,12 +116,12 @@
           <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>
+</section>
-<div class="section" id="module-PyCTBN.tests.estimators.test_parameters_estimator">
+<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 class="sig sig-object py" id="PyCTBN.tests.estimators.test_parameters_estimator.TestParametersEstimatior">
@@ -160,11 +160,40 @@
 
 </dd></dl>
 
-</div>
+
-<div class="section" id="pyctbn-tests-estimators-test-structure-constraint-based-estimator-module">
+</section>
-<h2>PyCTBN.tests.estimators.test_structure_constraint_based_estimator module<a class="headerlink" href="#pyctbn-tests-estimators-test-structure-constraint-based-estimator-module" title="Permalink to this headline">¶</a></h2>
+<section id="module-PyCTBN.tests.estimators.test_structure_constraint_based_estimator">
-</div>
+<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>
-<div class="section" id="module-PyCTBN.tests.estimators.test_structure_estimator">
+<dl class="py class">
+<dt id="PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator">
+<em class="property">class </em><code class="sig-prename descclassname">PyCTBN.tests.estimators.test_structure_constraint_based_estimator.</code><code class="sig-name descname">TestStructureConstraintBasedEstimator</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">methodName</span><span class="o">=</span><span class="default_value">'runTest'</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.case.TestCase</span></code></p>
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.setUpClass">
+<em class="property">classmethod </em><code class="sig-name descname">setUpClass</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.setUpClass" title="Permalink to this definition">¶</a></dt>
+<dd><p>Hook method for setting up class fixture before running tests in the class.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.test_structure_1">
+<code class="sig-name descname">test_structure_1</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.test_structure_1" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.test_structure_2">
+<code class="sig-name descname">test_structure_2</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.test_structure_2" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.test_structure_3">
+<code class="sig-name descname">test_structure_3</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_constraint_based_estimator.TestStructureConstraintBasedEstimator.test_structure_3" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+</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 class="sig sig-object py" id="PyCTBN.tests.estimators.test_structure_estimator.TestStructureEstimator">
@@ -218,14 +247,47 @@
 
 </dd></dl>
 
-</div>
+
-<div class="section" id="pyctbn-tests-estimators-test-structure-score-based-estimator-module">
+</section>
-<h2>PyCTBN.tests.estimators.test_structure_score_based_estimator module<a class="headerlink" href="#pyctbn-tests-estimators-test-structure-score-based-estimator-module" title="Permalink to this headline">¶</a></h2>
+<section id="module-PyCTBN.tests.estimators.test_structure_score_based_estimator">
-</div>
+<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>
-<div class="section" id="module-PyCTBN.tests.estimators">
+<dl class="py class">
+<dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator">
+<em class="property">class </em><code class="sig-prename descclassname">PyCTBN.tests.estimators.test_structure_score_based_estimator.</code><code class="sig-name descname">TestStructureScoreBasedEstimator</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">methodName</span><span class="o">=</span><span class="default_value">'runTest'</span></em><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">unittest.case.TestCase</span></code></p>
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.setUpClass">
+<em class="property">classmethod </em><code class="sig-name descname">setUpClass</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.setUpClass" title="Permalink to this definition">¶</a></dt>
+<dd><p>Hook method for setting up class fixture before running tests in the class.</p>
+</dd></dl>
+
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_1">
+<code class="sig-name descname">test_structure_1</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_1" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_2">
+<code class="sig-name descname">test_structure_2</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_2" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_3">
+<code class="sig-name descname">test_structure_3</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_3" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="py method">
+<dt id="PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_monoprocesso">
+<code class="sig-name descname">test_structure_monoprocesso</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#PyCTBN.tests.estimators.test_structure_score_based_estimator.TestStructureScoreBasedEstimator.test_structure_monoprocesso" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+</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>
+</section>
-</div>
+</section>
 
 
 	    </div>

docs/PyCTBN.tests.html

@@ -62,7 +62,7 @@
 	
           
           
-              <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>
@@ -116,9 +116,9 @@
           <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>
@@ -161,11 +161,11 @@
 </li>
 </ul>
 </div>
-</div>
+</section>
-<div class="section" id="module-PyCTBN.tests">
+<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>
+</section>
-</div>
+</section>
 
 
 	    </div>