├── pygmodels ├── __init__.py ├── graph │ ├── gtype │ │ ├── __init__.py │ │ ├── typeutils.py │ │ └── graphobj.py │ ├── gmodel │ │ └── __init__.py │ └── graphops │ │ └── __init__.py ├── pgm │ ├── pgmf │ │ └── __init__.py │ ├── pgmodel │ │ └── __init__.py │ └── pgmtype │ │ ├── __init__.py │ │ └── abstractpgm.py ├── factor │ ├── __init__.py │ ├── factorf │ │ └── __init__.py │ └── ftype │ │ └── abstractfactor.py ├── randvar │ ├── __init__.py │ └── rtype │ │ ├── __init__.py │ │ └── abstractrandvar.py └── value │ ├── abstractvalue.py │ ├── domain.py │ ├── codomain.py │ └── value.py ├── test ├── __init__.py ├── test_node.py └── test_edge.py ├── docs ├── _config.yml ├── html │ ├── bc_s.png │ ├── bdwn.png │ ├── doc.png │ ├── nav_f.png │ ├── nav_g.png │ ├── nav_h.png │ ├── open.png │ ├── tab_a.png │ ├── tab_b.png │ ├── tab_h.png │ ├── tab_s.png │ ├── closed.png │ ├── doxygen.png │ ├── sync_on.png │ ├── arrowdown.png │ ├── arrowright.png │ ├── folderopen.png │ ├── splitbar.png │ ├── sync_off.png │ ├── folderclosed.png │ ├── search │ │ ├── close.png │ │ ├── mag_sel.png │ │ ├── search_l.png │ │ ├── search_m.png │ │ ├── search_r.png │ │ ├── files_2.js │ │ ├── files_4.js │ │ ├── files_5.js │ │ ├── files_1.js │ │ ├── files_3.js │ │ ├── files_6.js │ │ ├── files_0.js │ │ ├── files_7.js │ │ ├── classes_5.js │ │ ├── all_1.js │ │ ├── pages_1.js │ │ ├── pages_2.js │ │ ├── classes_a.js │ │ ├── classes_d.js │ │ ├── groups_0.js │ │ ├── classes_8.js │ │ ├── classes_3.js │ │ ├── classes_7.js │ │ ├── classes_1.js │ │ ├── classes_e.js │ │ ├── classes_f.js │ │ ├── variables_2.js │ │ ├── classes_c.js │ │ ├── functions_18.js │ │ ├── variables_1.js │ │ ├── all_b.js │ │ ├── functions_b.js │ │ ├── all_16.js │ │ ├── all_17.js │ │ ├── variables_0.js │ │ ├── functions_16.js │ │ ├── functions_17.js │ │ ├── all_a.js │ │ ├── functions_a.js │ │ ├── functions_2.js │ │ ├── functions_c.js │ │ ├── searchdata.js │ │ ├── classes_4.js │ │ ├── all_0.js │ │ ├── pages_0.js │ │ ├── all_18.js │ │ ├── all_2.js │ │ ├── all_c.js │ │ ├── classes_6.js │ │ ├── classes_9.js │ │ ├── classes_2.js │ │ ├── functions_14.js │ │ ├── classes_b.js │ │ ├── nomatches.html │ │ ├── classes_0.js │ │ ├── functions_4.js │ │ ├── all_14.js │ │ ├── all_8.js │ │ ├── functions_11.js │ │ ├── functions_8.js │ │ ├── functions_f.js │ │ ├── namespaces_0.js │ │ ├── functions_1.js │ │ ├── all_4.js │ │ ├── all_11.js │ │ ├── all_f.js │ │ ├── functions_13.js │ │ ├── all_13.js │ │ ├── functions_e.js │ │ ├── close.svg │ │ ├── all_10.html │ │ ├── all_11.html │ │ ├── all_12.html │ │ ├── all_13.html │ │ ├── all_14.html │ │ ├── all_15.html │ │ ├── all_16.html │ │ ├── all_17.html │ │ ├── all_18.html │ │ ├── all_2.html │ │ ├── all_3.html │ │ ├── all_4.html │ │ ├── all_5.html │ │ ├── all_6.html │ │ ├── all_7.html │ │ ├── all_8.html │ │ ├── all_9.html │ │ ├── all_a.html │ │ ├── all_b.html │ │ ├── all_c.html │ │ ├── all_d.html │ │ ├── all_e.html │ │ ├── all_f.html │ │ ├── classes_0.html │ │ ├── classes_1.html │ │ ├── classes_2.html │ │ ├── classes_3.html │ │ ├── classes_4.html │ │ ├── classes_5.html │ │ ├── classes_6.html │ │ ├── classes_7.html │ │ ├── classes_8.html │ │ ├── classes_9.html │ │ ├── classes_a.html │ │ ├── classes_b.html │ │ ├── classes_c.html │ │ ├── classes_d.html │ │ ├── classes_e.html │ │ ├── classes_f.html │ │ ├── files_0.html │ │ ├── files_1.html │ │ ├── files_2.html │ │ ├── files_3.html │ │ ├── files_4.html │ │ ├── files_5.html │ │ ├── files_6.html │ │ ├── files_7.html │ │ ├── groups_0.html │ │ ├── pages_2.html │ │ ├── all_15.js │ │ ├── functions_0.html │ │ ├── functions_1.html │ │ ├── functions_2.html │ │ ├── functions_3.html │ │ ├── functions_4.html │ │ ├── functions_5.html │ │ ├── functions_6.html │ │ ├── functions_7.html │ │ ├── functions_8.html │ │ ├── functions_9.html │ │ ├── functions_a.html │ │ ├── functions_b.html │ │ ├── functions_c.html │ │ ├── functions_d.html │ │ ├── functions_e.html │ │ ├── functions_f.html │ │ ├── variables_0.html │ │ ├── variables_1.html │ │ ├── variables_2.html │ │ ├── functions_10.html │ │ ├── functions_11.html │ │ ├── functions_12.html │ │ ├── functions_13.html │ │ ├── functions_14.html │ │ ├── functions_15.html │ │ ├── functions_15.js │ │ ├── functions_16.html │ │ ├── functions_17.html │ │ ├── functions_18.html │ │ ├── namespaces_0.html │ │ ├── all_0.html │ │ ├── all_1.html │ │ ├── pages_0.html │ │ ├── pages_1.html │ │ ├── all_e.js │ │ ├── functions_3.js │ │ ├── functions_10.js │ │ ├── all_3.js │ │ ├── functions_5.js │ │ └── functions_7.js │ ├── de │ │ ├── d55 │ │ │ └── classgmodels_1_1factor_1_1Factor.png │ │ └── dfe │ │ │ └── classgmodels_1_1randomvariable_1_1RandomVariable.png │ ├── df │ │ ├── da1 │ │ │ └── classgmodels_1_1pgmodel_1_1PGModel.png │ │ ├── dd7 │ │ │ └── classgmodels_1_1markov_1_1MarkovNetwork.png │ │ └── d34 │ │ │ └── classgmodels_1_1randomvariable_1_1NumCatRVariable.png │ ├── d0 │ │ ├── d1c │ │ │ └── classgmodels_1_1gtypes_1_1path_1_1Path.png │ │ ├── d93 │ │ │ └── classgmodels_1_1gtypes_1_1edge_1_1Edge.png │ │ └── de3 │ │ │ └── classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractInfo.png │ ├── d7 │ │ └── db3 │ │ │ └── classgmodels_1_1gtypes_1_1tree_1_1Tree.png │ ├── d9 │ │ ├── d6b │ │ │ └── classgmodels_1_1searchtree_1_1OrTree.png │ │ └── d4b │ │ │ └── classgmodels_1_1legacy_1_1NaiveBayes_1_1BasicNaiveBayesMLE.png │ ├── db │ │ └── d8b │ │ │ └── classgmodels_1_1gtypes_1_1node_1_1Node.png │ ├── d2 │ │ ├── dfc │ │ │ └── classgmodels_1_1gtypes_1_1graph_1_1Graph.png │ │ ├── d4f │ │ │ └── classgmodels_1_1bayesian_1_1BayesianNetwork.png │ │ └── dfb │ │ │ └── classgmodels_1_1legacy_1_1NaiveBayes_1_1SingleNaiveBayesMLE.png │ ├── d8 │ │ ├── d43 │ │ │ └── classgmodels_1_1searchtree_1_1AndOrTree.png │ │ ├── d73 │ │ │ └── classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.png │ │ ├── d7c │ │ │ └── classgmodels_1_1legacy_1_1bayesutils_1_1Distribution.png │ │ └── d99 │ │ │ └── classgmodels_1_1randomvariable_1_1CatRandomVariable.png │ ├── da │ │ └── d1f │ │ │ └── classgmodels_1_1gtypes_1_1path_1_1Cycle.png │ ├── d1 │ │ └── da6 │ │ │ └── classgmodels_1_1lwfchain_1_1LWFChainGraph.png │ ├── dd │ │ ├── d00 │ │ │ └── classgmodels_1_1gtypes_1_1digraph_1_1DiGraph.png │ │ ├── d8d │ │ │ └── classgmodels_1_1gtypes_1_1abstractobj_1_1NodePosition.png │ │ └── dda │ │ │ └── classgmodels_1_1legacy_1_1NaiveBayes_1_1MultiNaiveBayesMLE.png │ ├── d6 │ │ └── d49 │ │ │ └── classgmodels_1_1markov_1_1ConditionalRandomField.png │ ├── dc │ │ ├── d16 │ │ │ └── classgmodels_1_1gtypes_1_1abstractobj_1_1EdgeType.png │ │ └── de3 │ │ │ └── classgmodels_1_1gtypes_1_1graphobj_1_1GraphObject.png │ ├── d5 │ │ └── d46 │ │ │ └── classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractEdge.png │ ├── d3 │ │ └── dc4 │ │ │ └── classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractGraphObj.png │ └── menudata.js ├── doxygen_sqlite3.db └── index.html ├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ └── python-package.yml ├── setup.py └── .pre-commit-config.yaml /pygmodels/__init__.py: 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['bayesiannetwork_272',['BayesianNetwork',['../d2/d4f/classgmodels_1_1bayesian_1_1BayesianNetwork.html',1,'gmodels::bayesian']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/dc/d16/classgmodels_1_1gtypes_1_1abstractobj_1_1EdgeType.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/dc/d16/classgmodels_1_1gtypes_1_1abstractobj_1_1EdgeType.png -------------------------------------------------------------------------------- /docs/html/dc/de3/classgmodels_1_1gtypes_1_1graphobj_1_1GraphObject.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/dc/de3/classgmodels_1_1gtypes_1_1graphobj_1_1GraphObject.png -------------------------------------------------------------------------------- /docs/html/df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.png -------------------------------------------------------------------------------- /docs/html/search/classes_e.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['undigraph_295',['UndiGraph',['../d8/d73/classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.html',1,'gmodels::gtypes::undigraph']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/classes_f.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['undigraph_310',['UndiGraph',['../d8/d73/classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.html',1,'gmodels::gtypes::undigraph']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/variables_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['z_531',['Z',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a6e5496bfa7e744735901ee4cdee8b7b8',1,'gmodels::factor::Factor']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/d0/de3/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractInfo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/d0/de3/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractInfo.png -------------------------------------------------------------------------------- /docs/html/d5/d46/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractEdge.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/d5/d46/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractEdge.png -------------------------------------------------------------------------------- /docs/html/d8/d7c/classgmodels_1_1legacy_1_1bayesutils_1_1Distribution.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/d8/d7c/classgmodels_1_1legacy_1_1bayesutils_1_1Distribution.png -------------------------------------------------------------------------------- /docs/html/d8/d99/classgmodels_1_1randomvariable_1_1CatRandomVariable.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/d8/d99/classgmodels_1_1randomvariable_1_1CatRandomVariable.png -------------------------------------------------------------------------------- /docs/html/dd/d8d/classgmodels_1_1gtypes_1_1abstractobj_1_1NodePosition.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/dd/d8d/classgmodels_1_1gtypes_1_1abstractobj_1_1NodePosition.png -------------------------------------------------------------------------------- /docs/html/search/classes_c.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['randomvariable_293',['RandomVariable',['../de/dfe/classgmodels_1_1randomvariable_1_1RandomVariable.html',1,'gmodels::randomvariable']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/functions_18.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['zval_528',['zval',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a487a5dff817c4afa4d2e59ff908b8d58',1,'gmodels::factor::Factor']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/variables_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['svars_530',['svars',['../de/d55/classgmodels_1_1factor_1_1Factor.html#ace5bbf86fb98712a090502764a2bb5d6',1,'gmodels::factor::Factor']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/all_b.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['k_141',['K',['../d1/da6/classgmodels_1_1lwfchain_1_1LWFChainGraph.html#a7e25c53250c208a8039c39679601fecb',1,'gmodels::lwfchain::LWFChainGraph']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/d3/dc4/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractGraphObj.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/d3/dc4/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractGraphObj.png -------------------------------------------------------------------------------- /docs/html/d9/d4b/classgmodels_1_1legacy_1_1NaiveBayes_1_1BasicNaiveBayesMLE.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/D-K-E/graphical-models/master/docs/html/d9/d4b/classgmodels_1_1legacy_1_1NaiveBayes_1_1BasicNaiveBayesMLE.png 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['y_265',['Y',['../d6/d49/classgmodels_1_1markov_1_1ConditionalRandomField.html#af06dc902499025dd717641d56928fef6',1,'gmodels::markov::ConditionalRandomField']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/variables_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['domain_5ftable_529',['domain_table',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a8f8cd3febd40d6f239304fe140f2236f',1,'gmodels::factor::Factor']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/functions_16.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['x_526',['X',['../d6/d49/classgmodels_1_1markov_1_1ConditionalRandomField.html#a43e24e9c9b09a3a2ce1924167d79c865',1,'gmodels::markov::ConditionalRandomField']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/functions_17.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['y_527',['Y',['../d6/d49/classgmodels_1_1markov_1_1ConditionalRandomField.html#af06dc902499025dd717641d56928fef6',1,'gmodels::markov::ConditionalRandomField']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/all_a.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['joint_140',['joint',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html#a3356eda74cabd51b72c73c7603d9ae44',1,'gmodels::randomvariable::NumCatRVariable']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/functions_a.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['joint_421',['joint',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html#a3356eda74cabd51b72c73c7603d9ae44',1,'gmodels::randomvariable::NumCatRVariable']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /pygmodels/graph/gtype/typeutils.py: -------------------------------------------------------------------------------- 1 | # type related utility functions 2 | from pygmodels.gtypes.abstractobj import AbstractGraph 3 | from pygmodels.gtypes.basegraph import BaseGraph 4 | from pygmodels.gtypes.finitegraph import FiniteGraph 5 | -------------------------------------------------------------------------------- /docs/html/search/functions_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['bron_5fkerbosch_325',['bron_kerbosch',['../d8/d73/classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.html#a9554d5f8e229e8504b7367fea8d0a7fa',1,'gmodels::gtypes::undigraph::UndiGraph']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/functions_c.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['lower_5fbound_5ffor_5fpath_5flength_423',['lower_bound_for_path_length',['../d8/d73/classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.html#a5e098d9465eb775331376bbadb4a335e',1,'gmodels::gtypes::undigraph::UndiGraph']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /docs/html/search/searchdata.js: -------------------------------------------------------------------------------- 1 | var indexSectionsWithContent = 2 | { 3 | 0: "gu", 4 | 1: "gu" 5 | }; 6 | 7 | var indexSectionNames = 8 | { 9 | 0: "all", 10 | 1: "pages" 11 | }; 12 | 13 | var indexSectionLabels = 14 | { 15 | 0: "All", 16 | 1: "Pages" 17 | }; 18 | 19 | -------------------------------------------------------------------------------- /docs/html/search/classes_4.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['edge_277',['Edge',['../d0/d93/classgmodels_1_1gtypes_1_1edge_1_1Edge.html',1,'gmodels::gtypes::edge']]], 4 | ['edgetype_278',['EdgeType',['../dc/d16/classgmodels_1_1gtypes_1_1abstractobj_1_1EdgeType.html',1,'gmodels::gtypes::abstractobj']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /docs/html/search/all_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['general_20remarks_20about_20the_20design_20of_20pygmodels_0',['General Remarks about the Design of PyGModels',['../db/d09/md_graphical_models_docs_mdpages_design.html',1,'']]], 4 | ['graphical_20models_1',['Graphical Models',['../index.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /docs/html/search/pages_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['general_20remarks_20about_20the_20design_20of_20pygmodels_3',['General Remarks about the Design of PyGModels',['../db/d09/md_graphical_models_docs_mdpages_design.html',1,'']]], 4 | ['graphical_20models_4',['Graphical Models',['../index.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /docs/html/search/all_18.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['z_266',['Z',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a6e5496bfa7e744735901ee4cdee8b7b8',1,'gmodels::factor::Factor']]], 4 | ['zval_267',['zval',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a487a5dff817c4afa4d2e59ff908b8d58',1,'gmodels::factor::Factor']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /docs/html/search/all_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['bayesiannetwork_17',['BayesianNetwork',['../d2/d4f/classgmodels_1_1bayesian_1_1BayesianNetwork.html',1,'gmodels::bayesian']]], 4 | ['bron_5fkerbosch_18',['bron_kerbosch',['../d8/d73/classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.html#a9554d5f8e229e8504b7367fea8d0a7fa',1,'gmodels::gtypes::undigraph::UndiGraph']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /docs/html/search/all_c.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['lower_5fbound_5ffor_5fpath_5flength_142',['lower_bound_for_path_length',['../d8/d73/classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.html#a5e098d9465eb775331376bbadb4a335e',1,'gmodels::gtypes::undigraph::UndiGraph']]], 4 | ['lwfchaingraph_143',['LWFChainGraph',['../d1/da6/classgmodels_1_1lwfchain_1_1LWFChainGraph.html',1,'gmodels::lwfchain']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /docs/html/search/classes_6.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['graph_280',['Graph',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html',1,'gmodels::gtypes::graph']]], 4 | ['graphanalyzer_281',['GraphAnalyzer',['../dc/dfb/classgmodels_1_1gtypes_1_1analyzer_1_1GraphAnalyzer.html',1,'gmodels::gtypes::analyzer']]], 5 | ['graphobject_282',['GraphObject',['../dc/de3/classgmodels_1_1gtypes_1_1graphobj_1_1GraphObject.html',1,'gmodels::gtypes::graphobj']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /docs/html/search/classes_9.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['node_285',['Node',['../db/d8b/classgmodels_1_1gtypes_1_1node_1_1Node.html',1,'gmodels::gtypes::node']]], 4 | ['nodeposition_286',['NodePosition',['../dd/d8d/classgmodels_1_1gtypes_1_1abstractobj_1_1NodePosition.html',1,'gmodels::gtypes::abstractobj']]], 5 | ['numcatrvariable_287',['NumCatRVariable',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html',1,'gmodels::randomvariable']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /docs/html/search/classes_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['catrandomvariable_273',['CatRandomVariable',['../d8/d99/classgmodels_1_1randomvariable_1_1CatRandomVariable.html',1,'gmodels::randomvariable']]], 4 | ['conditionalrandomfield_274',['ConditionalRandomField',['../d6/d49/classgmodels_1_1markov_1_1ConditionalRandomField.html',1,'gmodels::markov']]], 5 | ['cycle_275',['Cycle',['../da/d1f/classgmodels_1_1gtypes_1_1path_1_1Cycle.html',1,'gmodels::gtypes::path']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /pygmodels/value/abstractvalue.py: -------------------------------------------------------------------------------- 1 | """! 2 | \file abstractvalue.py Value of a set 3 | """ 4 | 5 | from abc import ABC, abstractmethod 6 | from typing import Any 7 | 8 | 9 | class AbstractSetValue: 10 | @abstractmethod 11 | def belongs_to(self) -> str: 12 | "The name of the set that contains the value" 13 | raise NotImplementedError 14 | 15 | @abstractmethod 16 | def value(self) -> Any: 17 | "Returns the value associated with the set value" 18 | raise NotImplementedError 19 | -------------------------------------------------------------------------------- /docs/html/search/functions_14.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['uniform_5fcost_5fsearch_514',['uniform_cost_search',['../d0/d1c/classgmodels_1_1gtypes_1_1path_1_1Path.html#a77a304703d7b511f6245fa2554ccc273',1,'gmodels::gtypes::path::Path']]], 4 | ['union_515',['union',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a2ee3e394b96067bec663d665f7438ae8',1,'gmodels::gtypes::graph::Graph']]], 5 | ['upset_5fof_516',['upset_of',['../d7/db3/classgmodels_1_1gtypes_1_1tree_1_1Tree.html#ac51409a988123ac84c6d210fa48d4d9e',1,'gmodels::gtypes::tree::Tree']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /docs/html/search/classes_b.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['path_289',['Path',['../d0/d1c/classgmodels_1_1gtypes_1_1path_1_1Path.html',1,'gmodels::gtypes::path']]], 4 | ['pgmodel_290',['PGModel',['../df/da1/classgmodels_1_1pgmodel_1_1PGModel.html',1,'gmodels::pgmodel']]], 5 | ['possibleoutcomes_291',['PossibleOutcomes',['../d8/dbf/classgmodels_1_1randomvariable_1_1PossibleOutcomes.html',1,'gmodels::randomvariable']]], 6 | ['priorityqueue_292',['PriorityQueue',['../d7/d6e/classgmodels_1_1gtypes_1_1queue_1_1PriorityQueue.html',1,'gmodels::gtypes::queue']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /docs/html/search/nomatches.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
10 |
No Matches
11 |
12 | 13 | 14 | -------------------------------------------------------------------------------- /docs/html/search/classes_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['abstractedge_268',['AbstractEdge',['../d5/d46/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractEdge.html',1,'gmodels::gtypes::abstractobj']]], 4 | ['abstractgraphobj_269',['AbstractGraphObj',['../d3/dc4/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractGraphObj.html',1,'gmodels::gtypes::abstractobj']]], 5 | ['abstractinfo_270',['AbstractInfo',['../d0/de3/classgmodels_1_1gtypes_1_1abstractobj_1_1AbstractInfo.html',1,'gmodels::gtypes::abstractobj']]], 6 | ['andortree_271',['AndOrTree',['../d8/d43/classgmodels_1_1searchtree_1_1AndOrTree.html',1,'gmodels::searchtree']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /pygmodels/randvar/rtype/abstractrandvar.py: -------------------------------------------------------------------------------- 1 | """! 2 | \file abstractrandvar.py Represents an abstract random variable 3 | """ 4 | from abc import ABC, abstractmethod 5 | 6 | from pygmodels.graph.gtype.abstractobj import AbstractNode 7 | from pygmodels.value.codomain import Outcome 8 | from pygmodels.value.value import NumericValue 9 | 10 | 11 | class AbstractRandomVariable(AbstractNode): 12 | """! 13 | Abstract random variable 14 | """ 15 | 16 | @abstractmethod 17 | def p(self, out: Outcome) -> NumericValue: 18 | """! 19 | Measure the probability of the given outcome 20 | """ 21 | raise NotImplementedError 22 | -------------------------------------------------------------------------------- /docs/html/search/functions_4.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['dfs_5fforest_336',['dfs_forest',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a0d0e8d39b5c3e805ff0a8f935963c95a',1,'gmodels::gtypes::graph::Graph']]], 4 | ['difference_337',['difference',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a51f4cb4857bd981019d5d1cea3c9b037',1,'gmodels::gtypes::graph::Graph']]], 5 | ['domain_5fscope_338',['domain_scope',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a8e52bcb35f56e45cd64056ddd1bcdaa2',1,'gmodels::factor::Factor']]], 6 | ['downset_5fof_339',['downset_of',['../d7/db3/classgmodels_1_1gtypes_1_1tree_1_1Tree.html#ad559cef4b6b88554bb036ba415903c8a',1,'gmodels::gtypes::tree::Tree']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.md: -------------------------------------------------------------------------------- 1 | --- 2 | name: Bug report 3 | about: Create a report to help us improve 4 | title: "[BUG]: XXX problem during the evaluation of YYY" 5 | labels: bug 6 | assignees: '' 7 | 8 | --- 9 | 10 | **Describe the bug** 11 | A clear and concise description of what the bug is. 12 | 13 | **To Reproduce** 14 | Steps to reproduce the behavior: 15 | 1. Go to '...' 16 | 2. Click on '....' 17 | 3. Scroll down to '....' 18 | 4. See error 19 | 20 | **Expected behavior** 21 | A clear and concise description of what you expected to happen. 22 | 23 | 24 | **Python version** 25 | Python language version, 3.6, 3.7, ... etc 26 | 27 | **Additional context** 28 | Add any other context about the problem here. 29 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | import setuptools 2 | 3 | with open("README.md", "r", encoding="utf-8") as fh: 4 | long_description = fh.read() 5 | 6 | setuptools.setup( 7 | name="pygmodels", 8 | version="0.0.1", 9 | author="D-K-E", 10 | author_email="D-K-E@users.noreply.github.com", 11 | description="Probabilistic Graphical Models in Standard Python", 12 | long_description=long_description, 13 | long_description_content_type="text/markdown", 14 | url="https://github.com/D-K-E/graphical-models", 15 | packages=setuptools.find_packages(), 16 | classifiers=[ 17 | "Programming Language :: Python :: 3", 18 | "License :: OSI Approved :: GNU GPL License", 19 | "Operating System :: OS Independent", 20 | ], 21 | python_requires=">=3.6", 22 | ) 23 | -------------------------------------------------------------------------------- /pygmodels/graph/gtype/graphobj.py: -------------------------------------------------------------------------------- 1 | """ 2 | object contained in a graph 3 | """ 4 | from copy import deepcopy 5 | 6 | from pygmodels.graph.gtype.abstractobj import AbstractGraphObj 7 | 8 | 9 | class GraphObject(AbstractGraphObj): 10 | """!object contained in a graph""" 11 | 12 | def __init__(self, oid: str, odata={}): 13 | """!""" 14 | self.object_id = oid 15 | self.object_data = odata 16 | 17 | def data(self): 18 | """!""" 19 | return self.object_data 20 | 21 | def id(self): 22 | """!""" 23 | return self.object_id 24 | 25 | def copy(self): 26 | return deepcopy(self) 27 | 28 | def clear_data(self): 29 | """!""" 30 | self.object_data.clear() 31 | 32 | def update_data(self, ndata: dict): 33 | """!""" 34 | self.object_data.update(ndata) 35 | -------------------------------------------------------------------------------- /pygmodels/value/domain.py: -------------------------------------------------------------------------------- 1 | """! 2 | \file domain.py Represents the domain of a function. It can be anything. 3 | """ 4 | 5 | from typing import Any, FrozenSet, List, Optional, Set, Tuple 6 | 7 | from pygmodels.value.abstractvalue import AbstractSetValue 8 | 9 | 10 | class DomainValue(AbstractSetValue): 11 | def __init__(self, v: Any, dom_id: Optional[str]): 12 | self.v = v 13 | self._domain = dom_id 14 | 15 | @property 16 | def belongs_to(self): 17 | if self._domain is None: 18 | raise ValueError("Value is not associated to a domain") 19 | return self._domain 20 | 21 | @property 22 | def value(self): 23 | return self.v 24 | 25 | 26 | Domain = Set[DomainValue] 27 | OrderedCodomain = List[DomainValue] 28 | 29 | FiniteDomain = FrozenSet[DomainValue] 30 | OrderedFiniteDomain = Tuple[DomainValue] 31 | -------------------------------------------------------------------------------- /docs/html/search/all_14.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['usage_20examples_249',['Usage Examples',['../d3/db0/md_graphical-models_docs_mdpages_usage.html',1,'']]], 4 | ['undigraph_250',['UndiGraph',['../d8/d73/classgmodels_1_1gtypes_1_1undigraph_1_1UndiGraph.html',1,'gmodels::gtypes::undigraph']]], 5 | ['undigraph_2epy_251',['undigraph.py',['../d7/daa/undigraph_8py.html',1,'']]], 6 | ['uniform_5fcost_5fsearch_252',['uniform_cost_search',['../d0/d1c/classgmodels_1_1gtypes_1_1path_1_1Path.html#a77a304703d7b511f6245fa2554ccc273',1,'gmodels::gtypes::path::Path']]], 7 | ['union_253',['union',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a2ee3e394b96067bec663d665f7438ae8',1,'gmodels::gtypes::graph::Graph']]], 8 | ['upset_5fof_254',['upset_of',['../d7/db3/classgmodels_1_1gtypes_1_1tree_1_1Tree.html#ac51409a988123ac84c6d210fa48d4d9e',1,'gmodels::gtypes::tree::Tree']]] 9 | ]; 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9 | -------------------------------------------------------------------------------- /docs/html/search/namespaces_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['abstractobj_296',['abstractobj',['../d0/dab/namespacegmodels_1_1gtypes_1_1abstractobj.html',1,'gmodels::gtypes']]], 4 | ['bayesian_297',['bayesian',['../d6/dad/namespacegmodels_1_1bayesian.html',1,'gmodels']]], 5 | ['graphobj_298',['graphobj',['../de/df5/namespacegmodels_1_1gtypes_1_1graphobj.html',1,'gmodels::gtypes']]], 6 | ['lwfchain_299',['lwfchain',['../de/d41/namespacegmodels_1_1lwfchain.html',1,'gmodels']]], 7 | ['markov_300',['markov',['../da/d54/namespacegmodels_1_1markov.html',1,'gmodels']]], 8 | ['path_301',['path',['../db/d71/namespacegmodels_1_1gtypes_1_1path.html',1,'gmodels::gtypes']]], 9 | ['randomvariable_302',['randomvariable',['../da/d3d/namespacegmodels_1_1randomvariable.html',1,'gmodels']]], 10 | ['searchtree_303',['searchtree',['../d6/d6e/namespacegmodels_1_1searchtree.html',1,'gmodels']]], 11 | ['tree_304',['tree',['../d4/d53/namespacegmodels_1_1gtypes_1_1tree.html',1,'gmodels::gtypes']]] 12 | ]; 13 | -------------------------------------------------------------------------------- /pygmodels/value/codomain.py: -------------------------------------------------------------------------------- 1 | """! 2 | \file codomain.py Represents a codomain of a function. Since we are dealing 3 | with probabilities and related concepts the codomain should be a measurable 4 | value 5 | """ 6 | 7 | from typing import Any, Callable, Dict, FrozenSet, List, Set, Tuple 8 | 9 | from pygmodels.value.value import SetValue 10 | 11 | 12 | class Outcome: 13 | def __init__(self, v): 14 | self.data = v 15 | 16 | 17 | CodomainValue = SetValue 18 | Codomain = Set[CodomainValue] 19 | OrderedCodomain = List[CodomainValue] 20 | 21 | FiniteCodomain = FrozenSet[CodomainValue] 22 | OrderedFiniteCodomain = Tuple[CodomainValue] 23 | 24 | 25 | class PossibleOutcomes: 26 | """! 27 | \brief set of possible outcomes from Koller, Friedman 2009, p. 15, 20 28 | 29 | This is simply a frozenset. We assume that possible outcomes contained in 30 | this object are measurable. 31 | """ 32 | 33 | def __init__(self, omega: FrozenSet[Outcome]): 34 | self.data = omega 35 | -------------------------------------------------------------------------------- /docs/html/search/functions_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['add_5fevidence_320',['add_evidence',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html#a8ec238547d40e25aa76a60211e67e478',1,'gmodels::randomvariable::NumCatRVariable']]], 4 | ['added_5fedge_5fbetween_5fif_5fnone_321',['added_edge_between_if_none',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a2f3fdc737d911d95ea44d266e4af67d1',1,'gmodels::gtypes::graph::Graph']]], 5 | ['apply_322',['apply',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html#a58b988be86815869cca5adebc6f90043',1,'gmodels::randomvariable::NumCatRVariable']]], 6 | 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['digraph_34',['DiGraph',['../dd/d00/classgmodels_1_1gtypes_1_1digraph_1_1DiGraph.html',1,'gmodels::gtypes::digraph']]], 6 | ['digraph_2epy_35',['digraph.py',['../dd/d89/digraph_8py.html',1,'']]], 7 | ['domain_5fscope_36',['domain_scope',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a8e52bcb35f56e45cd64056ddd1bcdaa2',1,'gmodels::factor::Factor']]], 8 | ['domain_5ftable_37',['domain_table',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a8f8cd3febd40d6f239304fe140f2236f',1,'gmodels::factor::Factor']]], 9 | ['downset_5fof_38',['downset_of',['../d7/db3/classgmodels_1_1gtypes_1_1tree_1_1Tree.html#ad559cef4b6b88554bb036ba415903c8a',1,'gmodels::gtypes::tree::Tree']]] 10 | ]; 11 | -------------------------------------------------------------------------------- /test/test_node.py: -------------------------------------------------------------------------------- 1 | """ 2 | Node unit tests 3 | """ 4 | import unittest 5 | 6 | from pygmodels.graph.gtype.node import Node 7 | 8 | 9 | class NodeTest(unittest.TestCase): 10 | def setUp(self): 11 | """""" 12 | self.node = Node(node_id="mnode", data={"my": "data"}) 13 | 14 | def test_id(self): 15 | """""" 16 | self.assertEqual(self.node.id(), "mnode") 17 | 18 | def test_data(self): 19 | """""" 20 | self.assertEqual(self.node.data(), {"my": "data"}) 21 | 22 | def test_equal(self): 23 | self.assertEqual(self.node, Node("mnode", {"my": "data"})) 24 | 25 | def test_str(self): 26 | n1 = Node("mnode", {"my": "data", "is": "awesome"}) 27 | mstr = "mnode--my-data::is-awesome" 28 | self.assertEqual(str(n1), mstr) 29 | 30 | def test_hash(self): 31 | mstr = "mnode--my-data::is-awesome" 32 | n1 = Node("mnode", {"my": "data", "is": "awesome"}) 33 | self.assertEqual(hash(n1), hash(mstr)) 34 | 35 | 36 | if __name__ == "__main__": 37 | unittest.main() 38 | -------------------------------------------------------------------------------- /docs/html/search/all_11.js: 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/pygmodels/factor/ftype/abstractfactor.py: -------------------------------------------------------------------------------- 1 | # abstract factor type 2 | """! 3 | \file abstractfactor.py Contains abstract class for the factor 4 | """ 5 | from abc import ABC, abstractmethod 6 | from typing import Callable, FrozenSet, List, Set, Tuple 7 | 8 | from pygmodels.graph.gtype.abstractobj import AbstractGraphObj 9 | from pygmodels.randvar.rtype.abstractrandvar import AbstractRandomVariable 10 | from pygmodels.value.value import NumericValue, OrderedFiniteVSet 11 | 12 | FactorScope = Set[AbstractRandomVariable] 13 | OrderedSubset = OrderedFiniteVSet 14 | DomainSliceSet = FrozenSet[OrderedSubset] 15 | DomainSubset = DomainSliceSet 16 | FactorDomain = List[DomainSubset] 17 | FactorCartesianProduct = FactorDomain 18 | 19 | 20 | class AbstractFactor(AbstractGraphObj): 21 | """""" 22 | 23 | @abstractmethod 24 | def scope_vars(self, filter_fn: Callable[[FactorScope], Set[FactorScope]]): 25 | """""" 26 | raise NotImplementedError 27 | 28 | @abstractmethod 29 | def partition_value(self, vd: FactorDomain): 30 | """""" 31 | raise NotImplementedError 32 | 33 | @abstractmethod 34 | def phi(self, scope_product: DomainSliceSet): 35 | """""" 36 | raise NotImplementedError 37 | -------------------------------------------------------------------------------- /docs/html/search/all_13.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['target_5fvariables_241',['target_variables',['../d6/d49/classgmodels_1_1markov_1_1ConditionalRandomField.html#a5caddb739e87136d38bf104d1a7e5f48',1,'gmodels::markov::ConditionalRandomField']]], 4 | ['to_5fadjmat_242',['to_adjmat',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a995842afcea5e62b7fb96394a4b4c606',1,'gmodels::gtypes::graph::Graph']]], 5 | 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| from typing import Callable, Dict, FrozenSet, List, Set, Tuple 8 | 9 | from pygmodels.factor.ftype.abstractfactor import AbstractFactor 10 | from pygmodels.gtype.abstractobj import ( 11 | AbstractEdge, 12 | AbstractGraph, 13 | AbstractGraphObj, 14 | AbstractNode, 15 | ) 16 | from pygmodels.randvar.rtype.abstractrandvar import AbstractRandomVariable 17 | from pygmodels.value.codomain import Outcome 18 | from pygmodels.value.value import NumericValue 19 | 20 | 21 | class AbstractPGM(AbstractGraph): 22 | """! 23 | Abstract probabilistic graphical models 24 | """ 25 | 26 | @property 27 | @abstractmethod 28 | def V(self) -> Dict[str, AbstractRandomVariable]: 29 | """! 30 | Acces to node set of PGM 31 | """ 32 | raise NotImplementedError 33 | 34 | @property 35 | @abstractmethod 36 | def E(self) -> Dict[str, AbstractEdge]: 37 | """! 38 | Acces to edge set set of PGM 39 | """ 40 | raise NotImplementedError 41 | 42 | @property 43 | @abstractmethod 44 | def F(self) -> Dict[str, AbstractFactor]: 45 | """! 46 | Acces to factor set of PGM 47 | """ 48 | raise NotImplementedError 49 | -------------------------------------------------------------------------------- /pygmodels/value/value.py: -------------------------------------------------------------------------------- 1 | """! 2 | \file value.py Represents the value of functions in the case of PGMs 3 | """ 4 | 5 | from typing import Callable, FrozenSet, List, Optional, Set, Tuple, Union 6 | 7 | from pygmodels.value.abstractvalue import AbstractSetValue 8 | 9 | NumericValue = float 10 | DiscreteValue = str 11 | BinaryValue = bool 12 | 13 | Value = Union[ 14 | NumericValue, DiscreteValue, BinaryValue, set, list, dict, tuple, Callable 15 | ] 16 | 17 | 18 | class SetValue(AbstractSetValue): 19 | "Value contained by a set" 20 | 21 | def __init__(self, v: Optional[Value], set_id: Optional[str] = None): 22 | if v is None: 23 | val = None 24 | elif isinstance(v, Value): 25 | val = v 26 | else: 27 | raise TypeError("the associated value must have type Value") 28 | self.v = val 29 | self._set = set_id 30 | 31 | def belongs_to(self) -> str: 32 | """""" 33 | if self._set is None: 34 | raise ValueError("Value not associated to any set") 35 | return self._set 36 | 37 | def value(self) -> Value: 38 | if self.v is None: 39 | raise ValueError("Value is not associated to any data") 40 | return self.v 41 | 42 | 43 | VSet = Set[SetValue] 44 | OrderedVSet = List[SetValue] 45 | 46 | FiniteVSet = FrozenSet[SetValue] 47 | OrderedFiniteVSet = Tuple[SetValue] 48 | -------------------------------------------------------------------------------- /docs/html/search/close.svg: -------------------------------------------------------------------------------- 1 | 2 | 13 | 15 | 16 | 18 | image/svg+xml 19 | 21 | 22 | 23 | 24 | 25 | 27 | 31 | 32 | -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | # isort 2 | - repo: https://github.com/asottile/seed-isort-config 3 | rev: v1.9.3 4 | hooks: 5 | - id: seed-isort-config 6 | - repo: https://github.com/pre-commit/mirrors-isort 7 | rev: v4.3.21 8 | hooks: 9 | - id: isort 10 | 11 | # black 12 | - repo: https://github.com/ambv/black 13 | rev: stable 14 | hooks: 15 | - id: black 16 | args: # arguments to configure black 17 | - --line-length=79 18 | - --include='\.pyi?$' 19 | 20 | # these folders wont be formatted by black 21 | - --exclude="""\.git | 22 | \.__pycache__| 23 | \.hg| 24 | \.mypy_cache| 25 | \.tox| 26 | \.venv| 27 | _build| 28 | buck-out| 29 | build| 30 | dist""" 31 | 32 | language_version: python3 33 | 34 | 35 | # flake8 36 | - repo: https://github.com/pre-commit/pre-commit-hooks 37 | rev: v2.3.0 38 | hooks: 39 | - id: flake8 40 | args: # arguments to configure flake8 41 | # making isort line length compatible with black 42 | - "--max-line-length=79" 43 | - "--max-complexity=18" 44 | - "--select=B,C,E,F,W,T4,B9" 45 | 46 | # these are errors that will be ignored by flake8 47 | # check out their meaning here 48 | # https://flake8.pycqa.org/en/latest/user/error-codes.html 49 | - "--ignore=E203,E266,E501,W503,F403,F401,E402,W605" 50 | #- "--ignore=F403,F401,E402" 51 | -------------------------------------------------------------------------------- /.github/workflows/python-package.yml: -------------------------------------------------------------------------------- 1 | # This workflow will install Python dependencies, run tests and lint with a variety of Python versions 2 | # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions 3 | 4 | name: Python package 5 | 6 | on: 7 | push: 8 | branches: [ master ] 9 | pull_request: 10 | branches: [ master ] 11 | 12 | jobs: 13 | build: 14 | 15 | runs-on: ubuntu-latest 16 | strategy: 17 | matrix: 18 | python-version: ["3.7", "3.8", "3.9", "3.10"] 19 | 20 | steps: 21 | - uses: actions/checkout@v2 22 | - name: Set up Python ${{ matrix.python-version }} 23 | uses: actions/setup-python@v2 24 | with: 25 | python-version: ${{ matrix.python-version }} 26 | - name: Install dependencies 27 | run: | 28 | python -m pip install --upgrade pip 29 | python -m pip install flake8 pytest 30 | if [ -f requirements.txt ]; then pip install -r requirements.txt; fi 31 | - name: Lint with flake8 32 | run: | 33 | # stop the build if there are Python syntax errors or undefined names 34 | flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics 35 | # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide 36 | flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics 37 | - name: Test with pytest 38 | run: | 39 | pytest 40 | -------------------------------------------------------------------------------- /docs/html/menudata.js: -------------------------------------------------------------------------------- 1 | /* 2 | @licstart The following is the entire license notice for the JavaScript code in this file. 3 | 4 | The MIT License (MIT) 5 | 6 | Copyright (C) 1997-2020 by Dimitri van Heesch 7 | 8 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software 9 | and associated documentation files (the "Software"), to deal in the Software without restriction, 10 | including without limitation the rights to use, copy, modify, merge, publish, distribute, 11 | sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is 12 | furnished to do so, subject to the following conditions: 13 | 14 | The above copyright notice and this permission notice shall be included in all copies or 15 | substantial portions of the Software. 16 | 17 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING 18 | BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND 19 | NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, 20 | DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 21 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 22 | 23 | @licend The above is the entire license notice for the JavaScript code in this file 24 | */ 25 | var menudata={children:[ 26 | {text:"Main Page",url:"index.html"}, 27 | {text:"Related Pages",url:"pages.html"}]} 28 | -------------------------------------------------------------------------------- /docs/html/search/all_10.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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35 | 36 | 37 | -------------------------------------------------------------------------------- /docs/html/search/all_15.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['v_255',['V',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#aa3a7bfb128185fbd175af7b2b96ca1dc',1,'gmodels::gtypes::graph::Graph']]], 4 | ['value_5fset_256',['value_set',['../d8/d99/classgmodels_1_1randomvariable_1_1CatRandomVariable.html#a295634090cb501412759cbc36f6ae1f2',1,'gmodels::randomvariable::CatRandomVariable']]], 5 | ['values_257',['values',['../d8/d99/classgmodels_1_1randomvariable_1_1CatRandomVariable.html#a70c6a29e38438ff662b8f31190dc5ee2',1,'gmodels::randomvariable::CatRandomVariable']]], 6 | ['variance_258',['variance',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html#adb0658c1d31b4ef57eb5c493c698f2bd',1,'gmodels::randomvariable::NumCatRVariable']]], 7 | ['vars_5fdomain_259',['vars_domain',['../de/d55/classgmodels_1_1factor_1_1Factor.html#ac326cb87a196bcc5db3ce3ff56882317',1,'gmodels::factor::Factor']]], 8 | ['vertex_5fby_5fid_260',['vertex_by_id',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a28faa97a14c1b297054dff59aea4be03',1,'gmodels::gtypes::graph::Graph']]], 9 | ['vertices_261',['vertices',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a8604d28b17fa7c13acfce7a672cd7e94',1,'gmodels::gtypes::graph::Graph']]], 10 | ['vertices_5fof_262',['vertices_of',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#ae6626c5feebb7366b90776e47effef10',1,'gmodels::gtypes::graph::Graph']]], 11 | ['visit_5fgraph_5fdfs_263',['visit_graph_dfs',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#aa8ce9cb8cf0951f366f6a012c8c859a0',1,'gmodels::gtypes::graph::Graph']]] 12 | ]; 13 | -------------------------------------------------------------------------------- /docs/html/search/functions_0.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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35 | 36 | 37 | -------------------------------------------------------------------------------- /docs/html/search/functions_15.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['v_517',['V',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#aa3a7bfb128185fbd175af7b2b96ca1dc',1,'gmodels::gtypes::graph::Graph']]], 4 | ['value_5fset_518',['value_set',['../d8/d99/classgmodels_1_1randomvariable_1_1CatRandomVariable.html#a295634090cb501412759cbc36f6ae1f2',1,'gmodels::randomvariable::CatRandomVariable']]], 5 | ['values_519',['values',['../d8/d99/classgmodels_1_1randomvariable_1_1CatRandomVariable.html#a70c6a29e38438ff662b8f31190dc5ee2',1,'gmodels::randomvariable::CatRandomVariable']]], 6 | ['variance_520',['variance',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html#adb0658c1d31b4ef57eb5c493c698f2bd',1,'gmodels::randomvariable::NumCatRVariable']]], 7 | ['vars_5fdomain_521',['vars_domain',['../de/d55/classgmodels_1_1factor_1_1Factor.html#ac326cb87a196bcc5db3ce3ff56882317',1,'gmodels::factor::Factor']]], 8 | ['vertex_5fby_5fid_522',['vertex_by_id',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a28faa97a14c1b297054dff59aea4be03',1,'gmodels::gtypes::graph::Graph']]], 9 | ['vertices_523',['vertices',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a8604d28b17fa7c13acfce7a672cd7e94',1,'gmodels::gtypes::graph::Graph']]], 10 | ['vertices_5fof_524',['vertices_of',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#ae6626c5feebb7366b90776e47effef10',1,'gmodels::gtypes::graph::Graph']]], 11 | ['visit_5fgraph_5fdfs_525',['visit_graph_dfs',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#aa8ce9cb8cf0951f366f6a012c8c859a0',1,'gmodels::gtypes::graph::Graph']]] 12 | ]; 13 | -------------------------------------------------------------------------------- /docs/html/search/functions_16.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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36 | 37 | 38 | -------------------------------------------------------------------------------- /test/test_edge.py: -------------------------------------------------------------------------------- 1 | """! 2 | Edge unit tests 3 | """ 4 | import unittest 5 | 6 | from pygmodels.graph.gtype.edge import Edge, EdgeType 7 | from pygmodels.graph.gtype.node import Node 8 | 9 | 10 | class EdgeTest(unittest.TestCase): 11 | """""" 12 | 13 | def setUp(self): 14 | """""" 15 | n1 = Node("m1", {}) 16 | n2 = Node("m2", {}) 17 | self.dedge = Edge( 18 | edge_id="medge", 19 | start_node=n1, 20 | end_node=n2, 21 | edge_type=EdgeType.DIRECTED, 22 | data={"my": "data"}, 23 | ) 24 | self.uedge = Edge( 25 | edge_id="uedge", 26 | start_node=n1, 27 | end_node=n2, 28 | edge_type=EdgeType.UNDIRECTED, 29 | data={"my": "data"}, 30 | ) 31 | 32 | def test_id(self): 33 | """""" 34 | self.assertEqual(self.uedge.id(), "uedge") 35 | 36 | def test_type(self): 37 | """""" 38 | self.assertEqual(self.uedge.type(), EdgeType.UNDIRECTED) 39 | 40 | def test_start(self): 41 | self.assertEqual(self.uedge.start(), Node("m1", {})) 42 | 43 | def test_end(self): 44 | self.assertEqual(self.uedge.end(), Node("m2", {})) 45 | 46 | def test_node_ids(self): 47 | self.assertEqual(self.uedge.node_ids(), set(["m1", "m2"])) 48 | 49 | def test_is_endvertice_true(self): 50 | """""" 51 | positive = self.uedge.is_endvertice(Node("m1", {})) 52 | self.assertEqual(positive, True) 53 | 54 | def test_is_endvertice_false(self): 55 | """""" 56 | negative = self.uedge.is_endvertice(Node("m3", {})) 57 | self.assertEqual(negative, False) 58 | -------------------------------------------------------------------------------- /docs/html/search/all_e.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['nb_5fcomponents_176',['nb_components',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a4b90352b4987f8f5dd60185eae65be35',1,'gmodels::gtypes::graph::Graph']]], 4 | ['nb_5fedges_177',['nb_edges',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#ab8ad6e200e8efac7a5d420e14b6952a9',1,'gmodels::gtypes::graph::Graph']]], 5 | ['nb_5fneighbours_5fof_178',['nb_neighbours_of',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#afd022b8f1fb077dbc7b7dc9dc6974162',1,'gmodels::gtypes::graph::Graph']]], 6 | ['neighbours_5fof_179',['neighbours_of',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#aa7931cbb1cd0bc28a03ef114c3efbc9d',1,'gmodels::gtypes::graph::Graph']]], 7 | ['node_180',['Node',['../db/d8b/classgmodels_1_1gtypes_1_1node_1_1Node.html',1,'gmodels::gtypes::node']]], 8 | ['node_2epy_181',['node.py',['../d1/dfb/node_8py.html',1,'']]], 9 | ['node_5fids_182',['node_ids',['../d0/d93/classgmodels_1_1gtypes_1_1edge_1_1Edge.html#a2d6f5a1161e6a3980528ff698c71a06d',1,'gmodels::gtypes::edge::Edge']]], 10 | ['nodeposition_183',['NodePosition',['../dd/d8d/classgmodels_1_1gtypes_1_1abstractobj_1_1NodePosition.html',1,'gmodels::gtypes::abstractobj']]], 11 | ['nodes_184',['nodes',['../d2/dfc/classgmodels_1_1gtypes_1_1graph_1_1Graph.html#a14ea9c8ea2ee1f0dd204b21d42308783',1,'gmodels::gtypes::graph::Graph']]], 12 | ['nodes_5fper_5flevel_185',['nodes_per_level',['../d7/db3/classgmodels_1_1gtypes_1_1tree_1_1Tree.html#a484de105cc940f25f197e7ce8b8849d1',1,'gmodels::gtypes::tree::Tree']]], 13 | ['normalize_186',['normalize',['../de/d55/classgmodels_1_1factor_1_1Factor.html#a551761e6454d7b072284ec34c630677f',1,'gmodels::factor::Factor']]], 14 | ['numcatrvariable_187',['NumCatRVariable',['../df/d34/classgmodels_1_1randomvariable_1_1NumCatRVariable.html',1,'gmodels::randomvariable']]] 15 | ]; 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