/PyBoolNet

PyBoolNet is a Python package for the generation, modification and analysis of Boolean networks.

Primary LanguagePython

About PyBoolNet

PyBoolNet is a Python package for the generation, modification and analysis of Boolean networks. The current version is available at PyBoolNet/releases.

For the manual, a reference and tutorials see the PyBoolNet manual. For bug reports and feedback do not hesitate to open issues at PyBoolNet issues or contact

release notes for version 2.2 (...)

release notes for version 2.11 (February 2017)

  • added section For Developers to manual
  • refactored git repository so that all necessary files for building PyBoolNet are available on github
  • added functions state_is_in_subspace and subspace1_is_in_subspace2 to StateTransitionGraphs
  • made the header targets, factors in FileExchange.primes2bnet(..) optional (default without header)
  • added argument Copy to create_blinkers(..), create_variables(..), create_disjoint_union(..), rename(..), remove_variables(..) and remove_all_variables_except(..) of module PrimeImplicants

release notes for version 2.1 (September 2016)

  • support for windows and macos
  • refactored subspace2states as list_states_in_subspace and proposition2states as list_states_referenced_by_proposition
  • refactored function for state and subspace conversions to state2str, state2dict, subspace2str, subspace2dict and added basic asserts
  • added functions univocality_with_counterexample, faithfulness_with_counterexample and completeness_with_counterexample
  • refactored the functions univocal, faithful and completeness_iterative to two univocality, faithfulness and completeness
  • removed function completeness_naive from AD since it is always less efficient than completeness_iterative
  • renamed module TemporalQueries to QueryPatterns for clarity
  • bugfix absolute import for Python 3.x

release notes for version 2.0 (August 2016)

  • added functions create_variables, create_disjoin_union to module PIs
  • split function percolate_constants from module PIs into percolate_and_keep_constants and percolate_and_remove_constants for clarity
  • bugfix in completeness_iterative of module AD
  • moved function compute_attractors_tarjan from module STGs to module AttractorDetection
  • split functions check_primes and check_smv from module MC into three functions each for counterexamples, acceptingstates and both of for clarity
  • removed feature add_style_condensationgraph from module STGs
  • bugfix for the computation of the condensation graph
  • added the parameter LayoutEngine for drawing graphs. Possible engines: dot,neato,fdp,sfdp,circo and twopi
  • added functions for the sccgraph, the condensationgraph and the HTG to module STGs
  • now following the git model described in nvie.com
  • refactored Utility.py in Utility\DiGraphs.py and Utility\Misc.py
  • added documentation source to Docs\Sphinx
  • added AttractorBasins.py, a library for visualizing basins of attraction
  • added support for model checking with accepting states via NuSMV-a
  • added Repository/, a folder with pre-defined networks
  • added support for Python 2.x and 3.x
  • added function input_combinations to module PrimeImplicants

release notes for version 1.0 (February 2016)

  • first official release