CMakeLists.txt
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
pybind11/CMakeLists.txt
pybind11/include/pybind11/attr.h
pybind11/include/pybind11/buffer_info.h
pybind11/include/pybind11/cast.h
pybind11/include/pybind11/chrono.h
pybind11/include/pybind11/common.h
pybind11/include/pybind11/complex.h
pybind11/include/pybind11/eigen.h
pybind11/include/pybind11/embed.h
pybind11/include/pybind11/eval.h
pybind11/include/pybind11/functional.h
pybind11/include/pybind11/iostream.h
pybind11/include/pybind11/numpy.h
pybind11/include/pybind11/operators.h
pybind11/include/pybind11/options.h
pybind11/include/pybind11/pybind11.h
pybind11/include/pybind11/pytypes.h
pybind11/include/pybind11/stl.h
pybind11/include/pybind11/stl_bind.h
pybind11/include/pybind11/detail/class.h
pybind11/include/pybind11/detail/common.h
pybind11/include/pybind11/detail/descr.h
pybind11/include/pybind11/detail/init.h
pybind11/include/pybind11/detail/internals.h
pybind11/include/pybind11/detail/typeid.h
pybind11/tests/CMakeLists.txt
pybind11/tests/test_cmake_build/CMakeLists.txt
pybind11/tests/test_cmake_build/installed_embed/CMakeLists.txt
pybind11/tests/test_cmake_build/installed_function/CMakeLists.txt
pybind11/tests/test_cmake_build/installed_target/CMakeLists.txt
pybind11/tests/test_cmake_build/subdirectory_embed/CMakeLists.txt
pybind11/tests/test_cmake_build/subdirectory_function/CMakeLists.txt
pybind11/tests/test_cmake_build/subdirectory_target/CMakeLists.txt
pybind11/tests/test_embed/CMakeLists.txt
pybind11/tools/FindCatch.cmake
pybind11/tools/FindEigen3.cmake
pybind11/tools/FindPythonLibsNew.cmake
pybind11/tools/pybind11Tools.cmake
software/DSGRN-Database/CMakeLists.txt
software/DSGRN-Database/source/CMakeLists.txt
software/NetworkLogic/CMakeLists.txt
software/NetworkLogic/source/CMakeLists.txt
software/PatternMatch/CMakeLists.txt
software/PatternMatch/source/CMakeLists.txt
src/DSGRN/BlowupGraph.py
src/DSGRN/EquilibriumCells.py
src/DSGRN/EssentialParameterNeighbors.py
src/DSGRN/Graphics.py
src/DSGRN/ParameterFromSample.py
src/DSGRN/ParameterPartialOrders.py
src/DSGRN/SaveDatabaseJSON.py
src/DSGRN/Signatures.py
src/DSGRN/SubdomainGraph.py
src/DSGRN/__init__.py
src/DSGRN.egg-info/PKG-INFO
src/DSGRN.egg-info/SOURCES.txt
src/DSGRN.egg-info/dependency_links.txt
src/DSGRN.egg-info/entry_points.txt
src/DSGRN.egg-info/not-zip-safe
src/DSGRN.egg-info/requires.txt
src/DSGRN.egg-info/top_level.txt
src/DSGRN/Query/AlignmentGraph.py
src/DSGRN/Query/BistableQuery.py
src/DSGRN/Query/ComputeSingleGeneQuery.py
src/DSGRN/Query/Database.py
src/DSGRN/Query/DoubleFixedPointQuery.py
src/DSGRN/Query/FixedPointTables.py
src/DSGRN/Query/Graph.py
src/DSGRN/Query/Hexcodes.py
src/DSGRN/Query/HysteresisQuery.py
src/DSGRN/Query/InducibilityQuery.py
src/DSGRN/Query/Logging.py
src/DSGRN/Query/MonostableFixedPointQuery.py
src/DSGRN/Query/MonostableQuery.py
src/DSGRN/Query/MultistableQuery.py
src/DSGRN/Query/NstableQuery.py
src/DSGRN/Query/PhenotypeQuery.py
src/DSGRN/Query/PosetOfExtrema.py
src/DSGRN/Query/SingleFixedPointQuery.py
src/DSGRN/Query/SingleGeneQuery.py
src/DSGRN/Query/StableFCQuery.py
src/DSGRN/Query/__init__.py
src/DSGRN/Resources/CAD/1_1_1.json
src/DSGRN/Resources/CAD/1_2_1.json
src/DSGRN/Resources/CAD/1_3_1.json
src/DSGRN/Resources/CAD/1_4_1.json
src/DSGRN/Resources/CAD/1_5_1.json
src/DSGRN/Resources/CAD/1_6_1.json
src/DSGRN/Resources/CAD/1_7_1.json
src/DSGRN/Resources/CAD/2_1_1_1.json
src/DSGRN/Resources/CAD/2_1_2.json
src/DSGRN/Resources/CAD/2_2_1_1.json
src/DSGRN/Resources/CAD/2_2_2.json
src/DSGRN/Resources/CAD/2_3_1_1.json
src/DSGRN/Resources/CAD/2_3_2.json
src/DSGRN/Resources/CAD/2_4_1_1.json
src/DSGRN/Resources/CAD/2_4_2.json
src/DSGRN/Resources/CAD/2_5_1_1.json
src/DSGRN/Resources/CAD/2_5_2.json
src/DSGRN/Resources/CAD/2_6_1_1.json
src/DSGRN/Resources/CAD/2_6_2.json
src/DSGRN/Resources/CAD/2_7_1_1.json
src/DSGRN/Resources/CAD/2_7_2.json
src/DSGRN/Resources/CAD/3_1_1_1_1.json
src/DSGRN/Resources/CAD/3_1_1_2.json
src/DSGRN/Resources/CAD/3_1_3.json
src/DSGRN/Resources/CAD/3_2_1_1_1.json
src/DSGRN/Resources/CAD/3_2_1_2.json
src/DSGRN/Resources/CAD/3_2_3.json
src/DSGRN/Resources/CAD/3_3_1_1_1.json
src/DSGRN/Resources/CAD/3_3_1_2.json
src/DSGRN/Resources/CAD/5_1_5.json
src/DSGRN/Resources/logic/0_1.dat
src/DSGRN/Resources/logic/0_1_E.dat
src/DSGRN/Resources/logic/0_2.dat
src/DSGRN/Resources/logic/0_2_E.dat
src/DSGRN/Resources/logic/0_3.dat
src/DSGRN/Resources/logic/0_3_E.dat
src/DSGRN/Resources/logic/0_4.dat
src/DSGRN/Resources/logic/0_4_E.dat
src/DSGRN/Resources/logic/0_5.dat
src/DSGRN/Resources/logic/0_5_E.dat
src/DSGRN/Resources/logic/0_6.dat
src/DSGRN/Resources/logic/0_6_E.dat
src/DSGRN/Resources/logic/0_7.dat
src/DSGRN/Resources/logic/0_7_E.dat
src/DSGRN/Resources/logic/1_1_1.dat
src/DSGRN/Resources/logic/1_1_1_E.dat
src/DSGRN/Resources/logic/1_2_1.dat
src/DSGRN/Resources/logic/1_2_1_E.dat
src/DSGRN/Resources/logic/1_3_1.dat
src/DSGRN/Resources/logic/1_3_1_E.dat
src/DSGRN/Resources/logic/1_4_1.dat
src/DSGRN/Resources/logic/1_4_1_E.dat
src/DSGRN/Resources/logic/1_5_1.dat
src/DSGRN/Resources/logic/1_5_1_E.dat
src/DSGRN/Resources/logic/1_6_1.dat
src/DSGRN/Resources/logic/1_6_1_E.dat
src/DSGRN/Resources/logic/1_7_1.dat
src/DSGRN/Resources/logic/1_7_1_E.dat
src/DSGRN/Resources/logic/2_1_1_1.dat
src/DSGRN/Resources/logic/2_1_1_1_E.dat
src/DSGRN/Resources/logic/2_1_2.dat
src/DSGRN/Resources/logic/2_1_2_E.dat
src/DSGRN/Resources/logic/2_2_1_1.dat
src/DSGRN/Resources/logic/2_2_1_1_E.dat
src/DSGRN/Resources/logic/2_2_2.dat
src/DSGRN/Resources/logic/2_2_2_E.dat
src/DSGRN/Resources/logic/2_3_1_1.dat
src/DSGRN/Resources/logic/2_3_1_1_E.dat
src/DSGRN/Resources/logic/2_3_2.dat
src/DSGRN/Resources/logic/2_3_2_E.dat
src/DSGRN/Resources/logic/2_4_1_1.dat
src/DSGRN/Resources/logic/2_4_1_1_E.dat
src/DSGRN/Resources/logic/2_4_2.dat
src/DSGRN/Resources/logic/2_4_2_E.dat
src/DSGRN/Resources/logic/2_5_1_1.dat
src/DSGRN/Resources/logic/2_5_1_1_E.dat
src/DSGRN/Resources/logic/2_5_2.dat
src/DSGRN/Resources/logic/2_5_2_E.dat
src/DSGRN/Resources/logic/2_6_1_1.dat
src/DSGRN/Resources/logic/2_6_1_1_E.dat
src/DSGRN/Resources/logic/2_6_2.dat
src/DSGRN/Resources/logic/2_6_2_E.dat
src/DSGRN/Resources/logic/2_7_1_1.dat
src/DSGRN/Resources/logic/2_7_1_1_E.dat
src/DSGRN/Resources/logic/2_7_2.dat
src/DSGRN/Resources/logic/2_7_2_E.dat
src/DSGRN/Resources/logic/3_1_1_1_1.dat
src/DSGRN/Resources/logic/3_1_1_1_1_E.dat
src/DSGRN/Resources/logic/3_1_1_2.dat
src/DSGRN/Resources/logic/3_1_1_2_E.dat
src/DSGRN/Resources/logic/3_1_3.dat
src/DSGRN/Resources/logic/3_1_3_E.dat
src/DSGRN/Resources/logic/3_2_1_1_1.dat
src/DSGRN/Resources/logic/3_2_1_1_1_E.dat
src/DSGRN/Resources/logic/3_2_1_2.dat
src/DSGRN/Resources/logic/3_2_1_2_E.dat
src/DSGRN/Resources/logic/3_2_3.dat
src/DSGRN/Resources/logic/3_2_3_E.dat
src/DSGRN/Resources/logic/3_3_1_1_1.dat
src/DSGRN/Resources/logic/3_3_1_1_1_E.dat
src/DSGRN/Resources/logic/3_3_1_2.dat
src/DSGRN/Resources/logic/3_3_1_2_E.dat
src/DSGRN/Resources/logic/3_3_3.dat
src/DSGRN/Resources/logic/3_3_3_E.dat
src/DSGRN/Resources/logic/3_4_1_1_1.dat
src/DSGRN/Resources/logic/3_4_1_1_1_E.dat
src/DSGRN/Resources/logic/3_4_1_2.dat
src/DSGRN/Resources/logic/3_4_1_2_E.dat
src/DSGRN/Resources/logic/3_4_3.dat
src/DSGRN/Resources/logic/3_4_3_E.dat
src/DSGRN/Resources/logic/3_5_1_1_1.dat
src/DSGRN/Resources/logic/3_5_1_1_1_E.dat
src/DSGRN/Resources/logic/3_5_1_2.dat
src/DSGRN/Resources/logic/3_5_1_2_E.dat
src/DSGRN/Resources/logic/3_5_3.dat
src/DSGRN/Resources/logic/3_5_3_E.dat
src/DSGRN/Resources/logic/3_6_1_1_1.dat
src/DSGRN/Resources/logic/3_6_1_1_1_E.dat
src/DSGRN/Resources/logic/3_6_1_2.dat
src/DSGRN/Resources/logic/3_6_1_2_E.dat
src/DSGRN/Resources/logic/3_6_3.dat
src/DSGRN/Resources/logic/3_6_3_E.dat
src/DSGRN/Resources/logic/3_7_1_1_1.dat
src/DSGRN/Resources/logic/3_7_1_1_1_E.dat
src/DSGRN/Resources/logic/3_7_1_2.dat
src/DSGRN/Resources/logic/3_7_1_2_E.dat
src/DSGRN/Resources/logic/3_7_3.dat
src/DSGRN/Resources/logic/3_7_3_E.dat
src/DSGRN/Resources/logic/4_1_1_1_1_1.dat
src/DSGRN/Resources/logic/4_1_1_1_1_1_E.dat
src/DSGRN/Resources/logic/4_1_1_1_2.dat
src/DSGRN/Resources/logic/4_1_1_1_2_E.dat
src/DSGRN/Resources/logic/4_1_1_3.dat
src/DSGRN/Resources/logic/4_1_1_3_E.dat
src/DSGRN/Resources/logic/4_1_2_2.dat
src/DSGRN/Resources/logic/4_1_2_2_E.dat
src/DSGRN/Resources/logic/4_1_4.dat
src/DSGRN/Resources/logic/4_1_4_E.dat
src/DSGRN/Resources/logic/4_2_1_1_1_1.dat
src/DSGRN/Resources/logic/4_2_1_1_1_1_E.dat
src/DSGRN/Resources/logic/4_2_1_1_2.dat
src/DSGRN/Resources/logic/4_2_1_1_2_E.dat
src/DSGRN/Resources/logic/4_2_1_3.dat
src/DSGRN/Resources/logic/4_2_1_3_E.dat
src/DSGRN/Resources/logic/4_2_2_2.dat
src/DSGRN/Resources/logic/4_2_2_2_E.dat
src/DSGRN/Resources/logic/4_2_4.dat
src/DSGRN/Resources/logic/4_2_4_E.dat
src/DSGRN/Resources/logic/4_3_1_1_1_1.dat
src/DSGRN/Resources/logic/4_3_1_1_1_1_E.dat
src/DSGRN/Resources/logic/4_3_1_1_2.dat
src/DSGRN/Resources/logic/4_3_1_1_2_E.dat
src/DSGRN/Resources/logic/4_3_1_3.dat
src/DSGRN/Resources/logic/4_3_1_3_E.dat
src/DSGRN/Resources/logic/4_3_2_2.dat
src/DSGRN/Resources/logic/4_3_2_2_E.dat
src/DSGRN/Resources/logic/4_3_4.dat
src/DSGRN/Resources/logic/4_3_4_E.dat
src/DSGRN/Resources/logic/4_4_1_1_1_1.dat
src/DSGRN/Resources/logic/4_4_1_1_1_1_E.dat
src/DSGRN/Resources/logic/4_4_1_1_2.dat
src/DSGRN/Resources/logic/4_4_1_1_2_E.dat
src/DSGRN/Resources/logic/4_4_1_3.dat
src/DSGRN/Resources/logic/4_4_1_3_E.dat
src/DSGRN/Resources/logic/4_4_2_2.dat
src/DSGRN/Resources/logic/4_4_2_2_E.dat
src/DSGRN/Resources/logic/4_4_4.dat
src/DSGRN/Resources/logic/4_4_4_E.dat
src/DSGRN/Resources/logic/5_1_1_1_1_1_1.dat
src/DSGRN/Resources/logic/5_1_1_1_1_1_1_E.dat
src/DSGRN/Resources/logic/5_1_1_1_1_2.dat
src/DSGRN/Resources/logic/5_1_1_1_1_2_E.dat
src/DSGRN/Resources/logic/5_1_5.dat
src/DSGRN/Resources/logic/5_1_5_E.dat
src/DSGRN/Resources/logic/5_2_1_1_1_1_1.dat
src/DSGRN/Resources/logic/5_2_1_1_1_1_1_E.dat
src/DSGRN/Resources/logic/5_2_1_1_1_2.dat
src/DSGRN/Resources/logic/5_2_1_1_1_2_E.dat
src/DSGRN/Resources/logic/5_2_5.dat
src/DSGRN/Resources/logic/5_2_5_E.dat
src/DSGRN/_dsgrn/DSGRN.cpp
src/DSGRN/_dsgrn/include/DSGRN.h
src/DSGRN/_dsgrn/include/DSGRN.hpp
src/DSGRN/_dsgrn/include/common.h
src/DSGRN/_dsgrn/include/Dynamics/Annotation.h
src/DSGRN/_dsgrn/include/Dynamics/Annotation.hpp
src/DSGRN/_dsgrn/include/Dynamics/MorseDecomposition.h
src/DSGRN/_dsgrn/include/Dynamics/MorseDecomposition.hpp
src/DSGRN/_dsgrn/include/Dynamics/MorseGraph.h
src/DSGRN/_dsgrn/include/Dynamics/MorseGraph.hpp
src/DSGRN/_dsgrn/include/Graph/Components.h
src/DSGRN/_dsgrn/include/Graph/Components.hpp
src/DSGRN/_dsgrn/include/Graph/Digraph.h
src/DSGRN/_dsgrn/include/Graph/Digraph.hpp
src/DSGRN/_dsgrn/include/Graph/LabelledMultidigraph.h
src/DSGRN/_dsgrn/include/Graph/LabelledMultidigraph.hpp
src/DSGRN/_dsgrn/include/Graph/Poset.h
src/DSGRN/_dsgrn/include/Graph/Poset.hpp
src/DSGRN/_dsgrn/include/Graph/StrongComponents.h
src/DSGRN/_dsgrn/include/Graph/StrongComponents.hpp
src/DSGRN/_dsgrn/include/Parameter/Configuration.h
src/DSGRN/_dsgrn/include/Parameter/LogicParameter.h
src/DSGRN/_dsgrn/include/Parameter/LogicParameter.hpp
src/DSGRN/_dsgrn/include/Parameter/Network.h
src/DSGRN/_dsgrn/include/Parameter/Network.hpp
src/DSGRN/_dsgrn/include/Parameter/OrderParameter.h
src/DSGRN/_dsgrn/include/Parameter/OrderParameter.hpp
src/DSGRN/_dsgrn/include/Parameter/Parameter.h
src/DSGRN/_dsgrn/include/Parameter/Parameter.hpp
src/DSGRN/_dsgrn/include/Parameter/ParameterGraph.h
src/DSGRN/_dsgrn/include/Parameter/ParameterGraph.hpp
src/DSGRN/_dsgrn/include/Parameter/ParameterSampler.h
src/DSGRN/_dsgrn/include/Parameter/ParameterSampler.hpp
src/DSGRN/_dsgrn/include/Pattern/MatchingGraph.h
src/DSGRN/_dsgrn/include/Pattern/MatchingGraph.hpp
src/DSGRN/_dsgrn/include/Pattern/MatchingRelation.h
src/DSGRN/_dsgrn/include/Pattern/MatchingRelation.hpp
src/DSGRN/_dsgrn/include/Pattern/Pattern.h
src/DSGRN/_dsgrn/include/Pattern/Pattern.hpp
src/DSGRN/_dsgrn/include/Pattern/PatternGraph.h
src/DSGRN/_dsgrn/include/Pattern/PatternGraph.hpp
src/DSGRN/_dsgrn/include/Pattern/PatternMatch.h
src/DSGRN/_dsgrn/include/Pattern/PatternMatch.hpp
src/DSGRN/_dsgrn/include/Pattern/SearchGraph.h
src/DSGRN/_dsgrn/include/Pattern/SearchGraph.hpp
src/DSGRN/_dsgrn/include/Phase/Domain.h
src/DSGRN/_dsgrn/include/Phase/Domain.hpp
src/DSGRN/_dsgrn/include/Phase/DomainGraph.h
src/DSGRN/_dsgrn/include/Phase/DomainGraph.hpp
src/DSGRN/_dsgrn/include/Phase/Wall.h
src/DSGRN/_dsgrn/include/Phase/Wall.hpp
src/DSGRN/_dsgrn/include/Phase/WallGraph.h
src/DSGRN/_dsgrn/include/Phase/WallGraph.hpp
src/DSGRN/_dsgrn/include/Query/ComputeSingleGeneQuery.h
src/DSGRN/_dsgrn/include/Query/ComputeSingleGeneQuery.hpp
src/DSGRN/_dsgrn/include/Query/NFA.h
src/DSGRN/_dsgrn/include/Query/NFA.hpp
src/DSGRN/_dsgrn/include/Query/ThompsonsConstruction.h
src/DSGRN/_dsgrn/include/Query/ThompsonsConstruction.hpp
src/DSGRN/_dsgrn/include/Tools/SHA256.h
src/DSGRN/_dsgrn/include/Tools/hash.hpp
src/DSGRN/_dsgrn/include/Tools/json.hpp
src/DSGRN/_dsgrn/include/Tools/sqlambda.h
tests/CMakeLists.txt