diff --git a/.gitignore b/.gitignore index 01cdb07..5b20a7b 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ __pycache__ ./data/ ./venv/ ./PyCTBN/.scannerwork +./results/ diff --git a/PyCTBN.egg-info/PKG-INFO b/PyCTBN.egg-info/PKG-INFO deleted file mode 100644 index 53ed588..0000000 --- a/PyCTBN.egg-info/PKG-INFO +++ /dev/null @@ -1,10 +0,0 @@ -Metadata-Version: 1.0 -Name: PyCTBN -Version: 1.0 -Summary: A Continuous Time Bayesian Network Library -Home-page: https://github.com/philipMartini/CTBN_Project -Author: Filippo Martini -Author-email: f.martini@campus.unimib.it -License: MIT -Description: # CTBN_Project -Platform: UNKNOWN diff --git a/PyCTBN.egg-info/SOURCES.txt b/PyCTBN.egg-info/SOURCES.txt deleted file mode 100644 index 69228f4..0000000 --- a/PyCTBN.egg-info/SOURCES.txt +++ /dev/null @@ -1,22 +0,0 @@ -README.md -setup.py -PyCTBN.egg-info/PKG-INFO -PyCTBN.egg-info/SOURCES.txt -PyCTBN.egg-info/dependency_links.txt -PyCTBN.egg-info/not-zip-safe -PyCTBN.egg-info/requires.txt -PyCTBN.egg-info/top_level.txt -classes/__init__.py -classes/abstract_importer.py -classes/cache.py -classes/conditional_intensity_matrix.py -classes/json_importer.py -classes/json_importer_mod.py -classes/network_graph.py -classes/parameters_estimator.py -classes/sample_path.py -classes/set_of_cims.py -classes/simple_cvs_importer.py -classes/structure.py -classes/structure_estimator.py -classes/trajectory.py \ No newline at end of file diff --git a/PyCTBN.egg-info/dependency_links.txt b/PyCTBN.egg-info/dependency_links.txt deleted file mode 100644 index 3e47e43..0000000 --- a/PyCTBN.egg-info/dependency_links.txt +++ /dev/null @@ -1,3 +0,0 @@ -https://github.com/numpy/numpy -https://github.com/pandas-dev/pandas -https://github.com/networkx/networkx diff --git a/PyCTBN.egg-info/not-zip-safe b/PyCTBN.egg-info/not-zip-safe deleted file mode 100644 index 8b13789..0000000 --- a/PyCTBN.egg-info/not-zip-safe +++ /dev/null @@ -1 +0,0 @@ - diff --git a/PyCTBN.egg-info/requires.txt b/PyCTBN.egg-info/requires.txt deleted file mode 100644 index 46d8b85..0000000 --- a/PyCTBN.egg-info/requires.txt +++ /dev/null @@ -1,3 +0,0 @@ -numpy -pandas -networkx diff --git a/PyCTBN.egg-info/top_level.txt b/PyCTBN.egg-info/top_level.txt deleted file mode 100644 index 90b07e9..0000000 --- a/PyCTBN.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -classes diff --git a/PyCTBN/.scannerwork/.sonar_lock b/PyCTBN/.scannerwork/.sonar_lock deleted file mode 100644 index e69de29..0000000 diff --git a/PyCTBN/.scannerwork/report-task.txt b/PyCTBN/.scannerwork/report-task.txt deleted file mode 100644 index 5394593..0000000 --- a/PyCTBN/.scannerwork/report-task.txt +++ /dev/null @@ -1,6 +0,0 @@ -projectKey=Ctbn_Project -serverUrl=http://localhost:9000 -serverVersion=8.4.1.35646 -dashboardUrl=http://localhost:9000/dashboard?id=Ctbn_Project -ceTaskId=AXPs4gCNB9mzoAo2hiLI -ceTaskUrl=http://localhost:9000/api/ce/task?id=AXPs4gCNB9mzoAo2hiLI diff --git a/PyCTBN/PyCTBN/__init__.py b/PyCTBN/PyCTBN/__init__.py deleted file mode 100644 index e69de29..0000000 diff --git a/PyCTBN/__init__.py b/PyCTBN/__init__.py index e69de29..80a6111 100644 --- a/PyCTBN/__init__.py +++ b/PyCTBN/__init__.py @@ -0,0 +1,2 @@ +import PyCTBN.classes +from PyCTBN.classes import * diff --git a/PyCTBN/classes/__init__.py b/PyCTBN/classes/__init__.py new file mode 100644 index 0000000..b987b5b --- /dev/null +++ b/PyCTBN/classes/__init__.py @@ -0,0 +1,11 @@ +from .json_importer import JsonImporter +from .abstract_importer import AbstractImporter +from .network_graph import NetworkGraph +from .sample_path import SamplePath +from .parameters_estimator import ParametersEstimator +from .structure import Structure +from .structure_estimator import StructureEstimator +from .trajectory import Trajectory +from .conditional_intensity_matrix import ConditionalIntensityMatrix +from .cache import Cache +from .set_of_cims import SetOfCims \ No newline at end of file diff --git a/PyCTBN/PyCTBN/abstract_importer.py b/PyCTBN/classes/abstract_importer.py similarity index 100% rename from PyCTBN/PyCTBN/abstract_importer.py rename to PyCTBN/classes/abstract_importer.py diff --git a/PyCTBN/PyCTBN/cache.py b/PyCTBN/classes/cache.py similarity index 100% rename from PyCTBN/PyCTBN/cache.py rename to PyCTBN/classes/cache.py diff --git a/PyCTBN/PyCTBN/conditional_intensity_matrix.py b/PyCTBN/classes/conditional_intensity_matrix.py similarity index 100% rename from PyCTBN/PyCTBN/conditional_intensity_matrix.py rename to PyCTBN/classes/conditional_intensity_matrix.py diff --git a/PyCTBN/PyCTBN/json_importer.py b/PyCTBN/classes/json_importer.py similarity index 100% rename from PyCTBN/PyCTBN/json_importer.py rename to PyCTBN/classes/json_importer.py diff --git a/PyCTBN/PyCTBN/network_graph.py b/PyCTBN/classes/network_graph.py similarity index 100% rename from PyCTBN/PyCTBN/network_graph.py rename to PyCTBN/classes/network_graph.py diff --git a/PyCTBN/PyCTBN/parameters_estimator.py b/PyCTBN/classes/parameters_estimator.py similarity index 100% rename from PyCTBN/PyCTBN/parameters_estimator.py rename to PyCTBN/classes/parameters_estimator.py diff --git a/PyCTBN/PyCTBN/sample_path.py b/PyCTBN/classes/sample_path.py similarity index 91% rename from PyCTBN/PyCTBN/sample_path.py rename to PyCTBN/classes/sample_path.py index 2fc8c1f..2f7fe9b 100644 --- a/PyCTBN/PyCTBN/sample_path.py +++ b/PyCTBN/classes/sample_path.py @@ -19,11 +19,9 @@ class SamplePath(object): """Constructor Method """ self._importer = importer - if (self._importer._df_variables is None or self._importer._df_structure is None - or self._importer._concatenated_samples is None): + if (self._importer._df_variables is None or self._importer._concatenated_samples is None): raise RuntimeError('The importer object has to contain the all processed data!') - if(self._importer._df_variables.empty or self._importer._df_structure.empty - or self._importer._concatenated_samples.empty): + if(self._importer._df_variables.empty or self._importer._concatenated_samples.empty): raise RuntimeError('The importer object has to contain the all processed data!') self._trajectories = None self._structure = None @@ -49,7 +47,10 @@ class SamplePath(object): labels = self._importer.variables.iloc[:, 0].to_list() indxs = self._importer.variables.index.to_numpy() vals = self._importer.variables.iloc[:, 1].to_numpy() - edges = list(self._importer.structure.to_records(index=False)) + if self._importer.structure is None or self._importer.structure.empty: + edges = [] + else: + edges = list(self._importer.structure.to_records(index=False)) self._structure = Structure(labels, indxs, vals, edges, self._total_variables_count) diff --git a/PyCTBN/PyCTBN/set_of_cims.py b/PyCTBN/classes/set_of_cims.py similarity index 100% rename from PyCTBN/PyCTBN/set_of_cims.py rename to PyCTBN/classes/set_of_cims.py diff --git a/PyCTBN/PyCTBN/structure.py b/PyCTBN/classes/structure.py similarity index 100% rename from PyCTBN/PyCTBN/structure.py rename to PyCTBN/classes/structure.py diff --git a/PyCTBN/PyCTBN/structure_estimator.py b/PyCTBN/classes/structure_estimator.py similarity index 100% rename from PyCTBN/PyCTBN/structure_estimator.py rename to PyCTBN/classes/structure_estimator.py diff --git a/PyCTBN/PyCTBN/trajectory.py b/PyCTBN/classes/trajectory.py similarity index 100% rename from PyCTBN/PyCTBN/trajectory.py rename to PyCTBN/classes/trajectory.py diff --git a/PyCTBN/deprecated/simple_cvs_importer.py b/PyCTBN/deprecated/simple_cvs_importer.py index 1b63c17..e53f7ac 100644 --- a/PyCTBN/deprecated/simple_cvs_importer.py +++ b/PyCTBN/deprecated/simple_cvs_importer.py @@ -3,8 +3,8 @@ import glob import os import typing -from PyCTBN.PyCTBN.abstract_importer import AbstractImporter -from PyCTBN.PyCTBN.sample_path import SamplePath +from PyCTBN.classes.abstract_importer import AbstractImporter +from PyCTBN.classes.sample_path import SamplePath class CSVImporter(AbstractImporter): diff --git a/PyCTBN/tests/original_ctpc_algorithm.py b/PyCTBN/tests/original_ctpc_algorithm.py index 1a9456c..e63154b 100644 --- a/PyCTBN/tests/original_ctpc_algorithm.py +++ b/PyCTBN/tests/original_ctpc_algorithm.py @@ -9,7 +9,7 @@ from scipy.stats import chi2 as chi2_dist from scipy.stats import f as f_dist from tqdm import tqdm -from PyCTBN.PyCTBN.abstract_importer import AbstractImporter +from PyCTBN.classes.abstract_importer import AbstractImporter class OriginalCTPCAlgorithm(AbstractImporter): diff --git a/PyCTBN/tests/performance_comparisons.py b/PyCTBN/tests/performance_comparisons.py index cc93f1c..08b6d1f 100644 --- a/PyCTBN/tests/performance_comparisons.py +++ b/PyCTBN/tests/performance_comparisons.py @@ -7,9 +7,9 @@ import networkx as nx import timeit import psutil -from ..PyCTBN.sample_path import SamplePath -from ..PyCTBN.structure_estimator import StructureEstimator -from ..PyCTBN.json_importer import JsonImporter +from ..classes.sample_path import SamplePath +from ..classes.structure_estimator import StructureEstimator +from ..classes.json_importer import JsonImporter from .original_ctpc_algorithm import OriginalCTPCAlgorithm diff --git a/PyCTBN/tests/test_cache.py b/PyCTBN/tests/test_cache.py index 7cb6706..8aa6900 100644 --- a/PyCTBN/tests/test_cache.py +++ b/PyCTBN/tests/test_cache.py @@ -2,8 +2,8 @@ import unittest import numpy as np -from ..PyCTBN.cache import Cache -from ..PyCTBN.set_of_cims import SetOfCims +from ..classes.cache import Cache +from ..classes.set_of_cims import SetOfCims class TestCache(unittest.TestCase): diff --git a/PyCTBN/tests/test_cim.py b/PyCTBN/tests/test_cim.py index e3228db..f1c2447 100644 --- a/PyCTBN/tests/test_cim.py +++ b/PyCTBN/tests/test_cim.py @@ -2,7 +2,7 @@ import unittest import numpy as np -from ..PyCTBN.conditional_intensity_matrix import ConditionalIntensityMatrix +from ..classes.conditional_intensity_matrix import ConditionalIntensityMatrix class TestConditionalIntensityMatrix(unittest.TestCase): diff --git a/PyCTBN/tests/test_json_importer.py b/PyCTBN/tests/test_json_importer.py index 2ac1baa..fde0067 100644 --- a/PyCTBN/tests/test_json_importer.py +++ b/PyCTBN/tests/test_json_importer.py @@ -7,7 +7,7 @@ import pandas as pd import json -from ..PyCTBN.json_importer import JsonImporter +from ..classes.json_importer import JsonImporter class TestJsonImporter(unittest.TestCase): diff --git a/PyCTBN/tests/test_networkgraph.py b/PyCTBN/tests/test_networkgraph.py index f9794a4..2f2cc66 100644 --- a/PyCTBN/tests/test_networkgraph.py +++ b/PyCTBN/tests/test_networkgraph.py @@ -6,9 +6,9 @@ import networkx as nx import numpy as np import itertools -from ..PyCTBN.sample_path import SamplePath -from ..PyCTBN.network_graph import NetworkGraph -from ..PyCTBN.json_importer import JsonImporter +from ..classes.sample_path import SamplePath +from ..classes.network_graph import NetworkGraph +from ..classes.json_importer import JsonImporter class TestNetworkGraph(unittest.TestCase): diff --git a/PyCTBN/tests/test_parameters_estimator.py b/PyCTBN/tests/test_parameters_estimator.py index 38994b9..640ddd8 100644 --- a/PyCTBN/tests/test_parameters_estimator.py +++ b/PyCTBN/tests/test_parameters_estimator.py @@ -4,11 +4,11 @@ import numpy as np import glob import os -from ..PyCTBN.network_graph import NetworkGraph -from ..PyCTBN.sample_path import SamplePath -from ..PyCTBN.set_of_cims import SetOfCims -from ..PyCTBN.parameters_estimator import ParametersEstimator -from ..PyCTBN.json_importer import JsonImporter +from ..classes.network_graph import NetworkGraph +from ..classes.sample_path import SamplePath +from ..classes.set_of_cims import SetOfCims +from ..classes.parameters_estimator import ParametersEstimator +from ..classes.json_importer import JsonImporter class TestParametersEstimatior(unittest.TestCase): diff --git a/PyCTBN/tests/test_sample_path.py b/PyCTBN/tests/test_sample_path.py index 4286bac..f61fe72 100644 --- a/PyCTBN/tests/test_sample_path.py +++ b/PyCTBN/tests/test_sample_path.py @@ -4,10 +4,10 @@ import glob import os import random -from ..PyCTBN.json_importer import JsonImporter -from ..PyCTBN.sample_path import SamplePath -from ..PyCTBN.trajectory import Trajectory -from ..PyCTBN.structure import Structure +from ..classes.json_importer import JsonImporter +from ..classes.sample_path import SamplePath +from ..classes.trajectory import Trajectory +from ..classes.structure import Structure class TestSamplePath(unittest.TestCase): @@ -57,6 +57,16 @@ class TestSamplePath(unittest.TestCase): random.shuffle(importer._sorter) self.assertRaises(RuntimeError, s1.build_structure) + def test_build_saplepath_no_prior_net_structure(self): + importer = JsonImporter(self.read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name') + importer.import_data(0) + importer._df_structure = None + s1 = SamplePath(importer) + s1.build_trajectories() + s1.build_structure() + self.assertFalse(s1.structure.edges) + + if __name__ == '__main__': unittest.main() diff --git a/PyCTBN/tests/test_setofcims.py b/PyCTBN/tests/test_setofcims.py index daed9f0..abcd6a2 100644 --- a/PyCTBN/tests/test_setofcims.py +++ b/PyCTBN/tests/test_setofcims.py @@ -3,7 +3,7 @@ import unittest import numpy as np import itertools -from ..PyCTBN.set_of_cims import SetOfCims +from ..classes.set_of_cims import SetOfCims class TestSetOfCims(unittest.TestCase): diff --git a/PyCTBN/tests/test_structure.py b/PyCTBN/tests/test_structure.py index b6b4493..19f892e 100644 --- a/PyCTBN/tests/test_structure.py +++ b/PyCTBN/tests/test_structure.py @@ -1,7 +1,7 @@ import unittest import numpy as np -from ..PyCTBN.structure import Structure +from ..classes.structure import Structure class TestStructure(unittest.TestCase): diff --git a/PyCTBN/tests/test_structure_estimator.py b/PyCTBN/tests/test_structure_estimator.py index e3d63d7..5e98fa0 100644 --- a/PyCTBN/tests/test_structure_estimator.py +++ b/PyCTBN/tests/test_structure_estimator.py @@ -8,10 +8,10 @@ import networkx as nx import numpy as np import timeit -from ..PyCTBN.cache import Cache -from ..PyCTBN.sample_path import SamplePath -from ..PyCTBN.structure_estimator import StructureEstimator -from ..PyCTBN.json_importer import JsonImporter +from ..classes.cache import Cache +from ..classes.sample_path import SamplePath +from ..classes.structure_estimator import StructureEstimator +from ..classes.json_importer import JsonImporter class TestStructureEstimator(unittest.TestCase): diff --git a/PyCTBN/tests/test_trajectory.py b/PyCTBN/tests/test_trajectory.py index f826632..6c3d808 100644 --- a/PyCTBN/tests/test_trajectory.py +++ b/PyCTBN/tests/test_trajectory.py @@ -2,7 +2,7 @@ import unittest import numpy as np -from ..PyCTBN.trajectory import Trajectory +from ..classes.trajectory import Trajectory class TestTrajectory(unittest.TestCase): diff --git a/dist/PyCTBN-1.0.tar.gz b/dist/PyCTBN-1.0.tar.gz deleted file mode 100644 index 439cde6..0000000 Binary files a/dist/PyCTBN-1.0.tar.gz and /dev/null differ diff --git a/documentation/PyCTBN.rst b/documentation/PyCTBN.rst deleted file mode 100644 index a41536a..0000000 --- a/documentation/PyCTBN.rst +++ /dev/null @@ -1,101 +0,0 @@ -PyCTBN package -============== - -Submodules ----------- - -PyCTBN.abstract\_importer module --------------------------------- - -.. automodule:: PyCTBN.abstract_importer - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.cache module -------------------- - -.. automodule:: PyCTBN.cache - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.conditional\_intensity\_matrix module --------------------------------------------- - -.. automodule:: PyCTBN.conditional_intensity_matrix - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.json\_importer module ----------------------------- - -.. automodule:: PyCTBN.json_importer - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.network\_graph module ----------------------------- - -.. automodule:: PyCTBN.network_graph - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.parameters\_estimator module ------------------------------------ - -.. automodule:: PyCTBN.parameters_estimator - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.sample\_path module --------------------------- - -.. automodule:: PyCTBN.sample_path - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.set\_of\_cims module ---------------------------- - -.. automodule:: PyCTBN.set_of_cims - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.structure module ------------------------ - -.. automodule:: PyCTBN.structure - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.structure\_estimator module ----------------------------------- - -.. automodule:: PyCTBN.structure_estimator - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.trajectory module ------------------------- - -.. automodule:: PyCTBN.trajectory - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: PyCTBN - :members: - :undoc-members: - :show-inheritance: diff --git a/documentation/_build/doctrees/PyCTBN.doctree b/documentation/_build/doctrees/PyCTBN.doctree deleted file mode 100644 index 94c9ec4..0000000 Binary files a/documentation/_build/doctrees/PyCTBN.doctree and /dev/null differ diff --git a/documentation/_build/doctrees/environment.pickle b/documentation/_build/doctrees/environment.pickle deleted file mode 100644 index aea8734..0000000 Binary files a/documentation/_build/doctrees/environment.pickle and /dev/null differ diff --git a/documentation/_build/html/_sources/PyCTBN.rst.txt b/documentation/_build/html/_sources/PyCTBN.rst.txt deleted file mode 100644 index a41536a..0000000 --- a/documentation/_build/html/_sources/PyCTBN.rst.txt +++ /dev/null @@ -1,101 +0,0 @@ -PyCTBN package -============== - -Submodules ----------- - -PyCTBN.abstract\_importer module --------------------------------- - -.. automodule:: PyCTBN.abstract_importer - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.cache module -------------------- - -.. automodule:: PyCTBN.cache - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.conditional\_intensity\_matrix module --------------------------------------------- - -.. automodule:: PyCTBN.conditional_intensity_matrix - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.json\_importer module ----------------------------- - -.. automodule:: PyCTBN.json_importer - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.network\_graph module ----------------------------- - -.. automodule:: PyCTBN.network_graph - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.parameters\_estimator module ------------------------------------ - -.. automodule:: PyCTBN.parameters_estimator - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.sample\_path module --------------------------- - -.. automodule:: PyCTBN.sample_path - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.set\_of\_cims module ---------------------------- - -.. automodule:: PyCTBN.set_of_cims - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.structure module ------------------------ - -.. automodule:: PyCTBN.structure - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.structure\_estimator module ----------------------------------- - -.. automodule:: PyCTBN.structure_estimator - :members: - :undoc-members: - :show-inheritance: - -PyCTBN.trajectory module ------------------------- - -.. automodule:: PyCTBN.trajectory - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: PyCTBN - :members: - :undoc-members: - :show-inheritance: diff --git a/documentation/_build/html/genindex.html b/documentation/_build/html/genindex.html deleted file mode 100644 index 3ebecb1..0000000 --- a/documentation/_build/html/genindex.html +++ /dev/null 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- - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/documentation/_build/html/objects.inv b/documentation/_build/html/objects.inv deleted file mode 100644 index 46976fa..0000000 Binary files a/documentation/_build/html/objects.inv and /dev/null differ diff --git a/documentation/_build/html/searchindex.js b/documentation/_build/html/searchindex.js deleted file mode 100644 index 4b24da6..0000000 --- a/documentation/_build/html/searchindex.js +++ /dev/null @@ -1 +0,0 @@ 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package","Examples","Welcome to PyCTBN\u2019s documentation!","PyCTBN"],titleterms:{"import":1,abstract_import:0,cach:0,conditional_intensity_matrix:0,content:0,data:1,document:2,estim:1,exampl:1,implement:1,indic:2,instal:1,json_import:0,modul:0,network_graph:0,own:1,packag:0,paramet:1,parameters_estim:0,pyctbn:[0,2,3],sample_path:0,set_of_cim:0,structur:[0,1],structure_estim:0,submodul:0,tabl:2,trajectori:0,usag:1,welcom:2,your:1}}) \ No newline at end of file diff --git a/parameters_estimation_example.py b/examples/parameters_estimation_example.py similarity index 76% rename from parameters_estimation_example.py rename to examples/parameters_estimation_example.py index be97a28..f5aa3ce 100644 --- a/parameters_estimation_example.py +++ b/examples/parameters_estimation_example.py @@ -3,14 +3,14 @@ import os import glob -from PyCTBN.PyCTBN.json_importer import JsonImporter -from PyCTBN.PyCTBN.sample_path import SamplePath -from PyCTBN.PyCTBN.network_graph import NetworkGraph -from PyCTBN.PyCTBN.parameters_estimator import ParametersEstimator +from PyCTBN.classes.json_importer import JsonImporter +from PyCTBN.classes.sample_path import SamplePath +from PyCTBN.classes.network_graph import NetworkGraph +from PyCTBN.classes.parameters_estimator import ParametersEstimator def main(): - read_files = glob.glob(os.path.join('./data', "*.json")) #Take all json files in this dir + read_files = glob.glob(os.path.join('../data', "*.json")) #Take all json files in this dir #import data importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name') importer.import_data(0) diff --git a/structure_estimation_example.py b/examples/structure_estimation_example.py similarity index 78% rename from structure_estimation_example.py rename to examples/structure_estimation_example.py index cc8ce75..b1ef609 100644 --- a/structure_estimation_example.py +++ b/examples/structure_estimation_example.py @@ -1,15 +1,15 @@ import os import glob -from PyCTBN.PyCTBN.json_importer import JsonImporter -from PyCTBN.PyCTBN.sample_path import SamplePath -from PyCTBN.PyCTBN.structure_estimator import StructureEstimator +from PyCTBN.classes.json_importer import JsonImporter +from PyCTBN.classes.sample_path import SamplePath +from PyCTBN.classes.structure_estimator import StructureEstimator def structure_estimation_example(): # read the json files in ./data path - read_files = glob.glob(os.path.join('./data', "*.json")) + read_files = glob.glob(os.path.join('../data', "*.json")) # initialize a JsonImporter object for the first file importer = JsonImporter(read_files[0], 'samples', 'dyn.str', 'variables', 'Time', 'Name') # import the data at index 0 of the outer json array diff --git a/setup.py b/setup.py index d15d928..fbb2182 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,7 @@ from setuptools import setup, find_packages +print(find_packages('.', exclude=['PyCTBN.tests'])) + setup(name='PyCTBN', version='1.0', url='https://github.com/philipMartini/PyCTBN', @@ -7,11 +9,14 @@ setup(name='PyCTBN', author=['Alessandro Bregoli', 'Filippo Martini'], author_email=['a.bregoli1@campus.unimib.it', 'f.martini@campus.unimib.it'], description='A Continuous Time Bayesian Networks Library', - packages=find_packages(exclude=['tests', 'data']), + packages=find_packages('.', exclude=['PyCTBN.tests']), + #packages=['PyCTBN.classes'], install_requires=[ 'numpy', 'pandas', 'networkx', 'scipy', '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) + zip_safe=False, + python_requires='>=3.6') + diff --git a/documentation/Makefile b/sphinx_output/Makefile similarity index 100% rename from documentation/Makefile rename to sphinx_output/Makefile diff --git a/sphinx_output/_build/doctrees/classes.doctree 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to sphinx_output/_build/doctrees/index.doctree index 12971da..6d9f356 100644 Binary files a/documentation/_build/doctrees/index.doctree and b/sphinx_output/_build/doctrees/index.doctree differ diff --git a/documentation/_build/doctrees/modules.doctree b/sphinx_output/_build/doctrees/modules.doctree similarity index 85% rename from documentation/_build/doctrees/modules.doctree rename to sphinx_output/_build/doctrees/modules.doctree index 854d01e..32c63d2 100644 Binary files a/documentation/_build/doctrees/modules.doctree and b/sphinx_output/_build/doctrees/modules.doctree differ diff --git a/documentation/_build/html/.buildinfo b/sphinx_output/_build/html/.buildinfo similarity index 100% rename from documentation/_build/html/.buildinfo rename to sphinx_output/_build/html/.buildinfo diff --git a/sphinx_output/_build/html/_sources/classes.rst.txt b/sphinx_output/_build/html/_sources/classes.rst.txt new file mode 100644 index 0000000..ad26a8c --- /dev/null +++ b/sphinx_output/_build/html/_sources/classes.rst.txt @@ -0,0 +1,101 @@ +classes package +=============== + +Submodules +---------- + +classes.abstract\_importer module +--------------------------------- + +.. automodule:: classes.abstract_importer + :members: + :undoc-members: + :show-inheritance: + +classes.cache module +-------------------- + +.. automodule:: classes.cache + :members: + :undoc-members: + :show-inheritance: + +classes.conditional\_intensity\_matrix module +--------------------------------------------- + +.. automodule:: classes.conditional_intensity_matrix + :members: + :undoc-members: + :show-inheritance: + +classes.json\_importer module +----------------------------- + +.. automodule:: classes.json_importer + :members: + :undoc-members: + :show-inheritance: + +classes.network\_graph module +----------------------------- + +.. automodule:: classes.network_graph + :members: + :undoc-members: + :show-inheritance: + +classes.parameters\_estimator module +------------------------------------ + +.. automodule:: classes.parameters_estimator + :members: + :undoc-members: + :show-inheritance: + +classes.sample\_path module +--------------------------- + +.. automodule:: classes.sample_path + :members: + :undoc-members: + :show-inheritance: + +classes.set\_of\_cims module +---------------------------- + +.. automodule:: classes.set_of_cims + :members: + :undoc-members: + :show-inheritance: + +classes.structure module +------------------------ + +.. automodule:: classes.structure + :members: + :undoc-members: + :show-inheritance: + +classes.structure\_estimator module +----------------------------------- + +.. automodule:: classes.structure_estimator + :members: + :undoc-members: + :show-inheritance: + +classes.trajectory module +------------------------- + +.. automodule:: classes.trajectory + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: classes + :members: + :undoc-members: + :show-inheritance: diff --git a/documentation/_build/html/_sources/examples.rst.txt b/sphinx_output/_build/html/_sources/examples.rst.txt similarity index 94% rename from documentation/_build/html/_sources/examples.rst.txt rename to sphinx_output/_build/html/_sources/examples.rst.txt index a30e4c7..01c6630 100644 --- a/documentation/_build/html/_sources/examples.rst.txt +++ b/sphinx_output/_build/html/_sources/examples.rst.txt @@ -10,7 +10,7 @@ Implementing your own data importer .. code-block:: python """This example demonstrates the implementation of a simple data importer the extends the class abstract importer to import data in csv format. - The net in exam has three ternary nodes. + The net in exam has three ternary nodes and no prior net structure. """ from .abstract_importer import AbstractImporter @@ -25,7 +25,6 @@ Implementing your own data importer self.read_csv_file() self._sorter = self.build_sorter(self._df_samples_list[0]) self.import_variables() - self.import_structure() self.compute_row_delta_in_all_samples_frames(self._df_samples_list) def read_csv_file(self): @@ -43,10 +42,6 @@ Implementing your own data importer def build_sorter(self, sample_frame: pd.DataFrame) -> typing.List: return list(sample_frame.columns)[1:] - def import_structure(self): - data = {'From':['X','Y','Z'], 'To':['Z','Z','Y']} - self._df_structure = pd.DataFrame(data) - def dataset_id(self) -> object: pass diff --git a/documentation/_build/html/_sources/index.rst.txt b/sphinx_output/_build/html/_sources/index.rst.txt similarity index 86% rename from documentation/_build/html/_sources/index.rst.txt rename to sphinx_output/_build/html/_sources/index.rst.txt index fe88b2e..cc4dc2d 100644 --- a/documentation/_build/html/_sources/index.rst.txt +++ b/sphinx_output/_build/html/_sources/index.rst.txt @@ -1,5 +1,5 @@ .. PyCTBN documentation master file, created by - sphinx-quickstart on Mon Dec 7 15:11:12 2020. + sphinx-quickstart on Mon Dec 14 20:33:17 2020. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. @@ -10,7 +10,7 @@ Welcome to PyCTBN's documentation! :maxdepth: 2 :caption: Contents: - PyCTBN + classes examples Indices and tables diff --git a/documentation/_build/html/_sources/modules.rst.txt b/sphinx_output/_build/html/_sources/modules.rst.txt similarity index 53% rename from documentation/_build/html/_sources/modules.rst.txt rename to sphinx_output/_build/html/_sources/modules.rst.txt index 447544d..6af3efe 100644 --- a/documentation/_build/html/_sources/modules.rst.txt +++ b/sphinx_output/_build/html/_sources/modules.rst.txt @@ -1,7 +1,7 @@ -PyCTBN -====== +classes +======= .. toctree:: :maxdepth: 4 - PyCTBN + classes diff --git a/sphinx_output/_build/html/_static/alabaster.css b/sphinx_output/_build/html/_static/alabaster.css new file mode 100644 index 0000000..0eddaeb --- /dev/null +++ b/sphinx_output/_build/html/_static/alabaster.css @@ -0,0 +1,701 @@ +@import url("basic.css"); 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+} + +div.topic { + background-color: #EEE; +} + +p.admonition-title { + display: inline; +} + +p.admonition-title:after { + content: ":"; +} + +pre, tt, code { + font-family: 'Consolas', 'Menlo', 'DejaVu Sans Mono', 'Bitstream Vera Sans Mono', monospace; + font-size: 0.9em; +} + +.hll { + background-color: #FFC; + margin: 0 -12px; + padding: 0 12px; + display: block; +} + +img.screenshot { +} + +tt.descname, tt.descclassname, code.descname, code.descclassname { + font-size: 0.95em; +} + +tt.descname, code.descname { + padding-right: 0.08em; +} + +img.screenshot { + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils { + border: 1px solid #888; + -moz-box-shadow: 2px 2px 4px #EEE; + -webkit-box-shadow: 2px 2px 4px #EEE; + box-shadow: 2px 2px 4px #EEE; +} + +table.docutils td, table.docutils th { + border: 1px solid #888; + padding: 0.25em 0.7em; +} + +table.field-list, table.footnote { + border: none; + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + +table.footnote { + margin: 15px 0; + width: 100%; + border: 1px solid #EEE; + background: #FDFDFD; + font-size: 0.9em; +} + +table.footnote + table.footnote { + margin-top: -15px; + border-top: none; +} + +table.field-list th { + padding: 0 0.8em 0 0; +} + +table.field-list td { + padding: 0; +} + +table.field-list p { + margin-bottom: 0.8em; +} + +/* Cloned from + * https://github.com/sphinx-doc/sphinx/commit/ef60dbfce09286b20b7385333d63a60321784e68 + */ +.field-name { + -moz-hyphens: manual; + -ms-hyphens: manual; + -webkit-hyphens: manual; + hyphens: manual; +} + +table.footnote td.label { + width: .1px; + padding: 0.3em 0 0.3em 0.5em; +} + +table.footnote td { + padding: 0.3em 0.5em; +} + +dl { + margin: 0; + padding: 0; +} + +dl dd { + margin-left: 30px; +} + +blockquote { + margin: 0 0 0 30px; + padding: 0; +} + +ul, ol { + /* Matches the 30px from the narrow-screen "li > ul" selector below */ + margin: 10px 0 10px 30px; + padding: 0; +} + +pre { + background: #EEE; + padding: 7px 30px; + margin: 15px 0px; + line-height: 1.3em; +} + +div.viewcode-block:target { + background: #ffd; +} + +dl pre, blockquote pre, li pre { + margin-left: 0; + padding-left: 30px; +} + +tt, code { + background-color: #ecf0f3; + color: #222; + /* padding: 1px 2px; */ +} + +tt.xref, code.xref, a tt { + background-color: #FBFBFB; + border-bottom: 1px solid #fff; +} + +a.reference { + text-decoration: none; + border-bottom: 1px dotted #004B6B; +} + +/* Don't put an underline on images */ +a.image-reference, a.image-reference:hover { + border-bottom: none; +} + +a.reference:hover { + border-bottom: 1px solid #6D4100; +} + +a.footnote-reference { + text-decoration: none; + font-size: 0.7em; + vertical-align: top; + border-bottom: 1px dotted #004B6B; +} + +a.footnote-reference:hover { + border-bottom: 1px solid #6D4100; +} + +a:hover tt, a:hover code { + background: #EEE; +} + + +@media screen and (max-width: 870px) { + + div.sphinxsidebar { + display: none; + } + + div.document { + width: 100%; + + } + + div.documentwrapper { + margin-left: 0; + margin-top: 0; + margin-right: 0; + margin-bottom: 0; + } + + div.bodywrapper { + margin-top: 0; + margin-right: 0; + margin-bottom: 0; + margin-left: 0; + } + + ul { + margin-left: 0; + } + + li > ul { + /* Matches the 30px from the "ul, ol" selector above */ + margin-left: 30px; + } + + .document { + width: auto; + } + + .footer { + width: auto; + } + + .bodywrapper { + margin: 0; + } + + .footer { + width: auto; + } + + .github { + display: none; + } + + + +} + + + +@media screen and (max-width: 875px) { + + body { + margin: 0; + padding: 20px 30px; + } + + div.documentwrapper { + float: none; + background: #fff; + } + + div.sphinxsidebar { + display: block; + float: none; + width: 102.5%; + margin: 50px -30px -20px -30px; + padding: 10px 20px; + background: #333; + color: #FFF; + } + + div.sphinxsidebar h3, div.sphinxsidebar h4, div.sphinxsidebar p, + div.sphinxsidebar h3 a { + color: #fff; + } + + div.sphinxsidebar a { + color: #AAA; + } + + div.sphinxsidebar p.logo { + display: none; + } + + div.document { + width: 100%; + margin: 0; + } + + div.footer { + display: none; + } + + div.bodywrapper { + margin: 0; + } + + div.body { + min-height: 0; + padding: 0; + } + + .rtd_doc_footer { + display: none; + } + + .document { + width: auto; + } + + .footer { + width: auto; + } + + .footer { + width: auto; + } + + .github { + display: none; + } +} + + +/* misc. */ + +.revsys-inline { + display: none!important; +} + +/* Make nested-list/multi-paragraph items look better in Releases changelog + * pages. Without this, docutils' magical list fuckery causes inconsistent + * formatting between different release sub-lists. + */ +div#changelog > div.section > ul > li > p:only-child { + margin-bottom: 0; +} + +/* Hide fugly table cell borders in ..bibliography:: directive output */ +table.docutils.citation, table.docutils.citation td, table.docutils.citation th { + border: none; + /* Below needed in some edge cases; if not applied, bottom shadows appear */ + -moz-box-shadow: none; + -webkit-box-shadow: none; + box-shadow: none; +} + + +/* relbar */ + +.related { + line-height: 30px; + width: 100%; + font-size: 0.9rem; +} + +.related.top { + border-bottom: 1px solid #EEE; + margin-bottom: 20px; +} + +.related.bottom { + border-top: 1px solid #EEE; +} + +.related ul { + padding: 0; + margin: 0; + list-style: none; +} + +.related li { + display: inline; +} + +nav#rellinks { + float: right; +} + +nav#rellinks li+li:before { + content: "|"; +} + +nav#breadcrumbs li+li:before { + content: "\00BB"; +} + +/* Hide certain items when printing */ +@media print { + div.related { + display: none; + } +} \ No newline at end of file diff --git a/documentation/_build/html/_static/basic.css b/sphinx_output/_build/html/_static/basic.css similarity index 100% rename from documentation/_build/html/_static/basic.css rename to sphinx_output/_build/html/_static/basic.css diff --git a/documentation/_build/html/_static/css/badge_only.css b/sphinx_output/_build/html/_static/css/badge_only.css similarity index 100% rename from documentation/_build/html/_static/css/badge_only.css rename to sphinx_output/_build/html/_static/css/badge_only.css diff --git a/documentation/_build/html/_static/css/darker.css b/sphinx_output/_build/html/_static/css/darker.css similarity index 100% rename from documentation/_build/html/_static/css/darker.css rename to sphinx_output/_build/html/_static/css/darker.css diff --git a/documentation/_build/html/_static/css/pdj.css b/sphinx_output/_build/html/_static/css/pdj.css similarity index 100% rename from documentation/_build/html/_static/css/pdj.css rename to sphinx_output/_build/html/_static/css/pdj.css diff --git a/documentation/_build/html/_static/css/theme.css b/sphinx_output/_build/html/_static/css/theme.css similarity index 100% rename from documentation/_build/html/_static/css/theme.css rename to sphinx_output/_build/html/_static/css/theme.css diff --git a/sphinx_output/_build/html/_static/custom.css b/sphinx_output/_build/html/_static/custom.css new file mode 100644 index 0000000..2a924f1 --- /dev/null +++ b/sphinx_output/_build/html/_static/custom.css @@ -0,0 +1 @@ +/* This file intentionally left blank. */ diff --git a/documentation/_build/html/_static/doctools.js b/sphinx_output/_build/html/_static/doctools.js similarity index 100% rename from documentation/_build/html/_static/doctools.js rename to sphinx_output/_build/html/_static/doctools.js diff --git a/documentation/_build/html/_static/documentation_options.js 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sphinx_output/_build/html/classes.html index ea85fb6..fe1061d 100644 --- a/documentation/_build/html/PyCTBN.html +++ b/sphinx_output/_build/html/classes.html @@ -8,7 +8,7 @@ - PyCTBN package — PyCTBN 1.0 documentation + classes package — PyCTBN 1.0 documentation @@ -62,20 +62,20 @@

Contents: