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RELEASENOTES.md

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release notes for version 2.31.0 (March 2021)

  • new requirement: pyeda
  • adds module generators for the generating Boolean networks
  • adds selvaggio_emt to repository, see http://ginsim.org/model/EMT_Selvaggio_etal
  • migrated unit tests to pytest framework
  • bugfix in STGs.successors_mixed (by @nanls)
  • adds parameter MaxOutput to Attractors.completeness (by @Lauracf) PR

release notes for version 2.3.0 (January 2021)

  • bugfix in find_attractor_state_by_randomwalk_and_ctl (by @etonello)
  • adds STGs.successors_mixed (by @nanls)
  • bugfix in random_successor_mixed (by @nanls)
  • added STGs.successors_mixed (by @nanls)
  • bugfix random_successor_mixed (by @nanls)
  • bugfix in input_combinations of PrimeImplicants, typo: primes -> Primes (by @leonardogian)
  • modified primes2stg to return empty stg if primes are empty (by @nanls)
  • support for drawing multi -digraphs in digraph2image(by @nanls)

release notes for version 2.2.9 (September 2020)

  • adds Conda recipe PR
  • support installation from github PR
  • support for CoLoMoTo image PR

release notes for version 2.2.8 (March 2020)

  • bugfix binaries of eqntott for windows
  • adds detection of os when calling eqntott

release notes for version 2.2.5 (June 2018)

  • bugfix in create_piechart, affects python3
  • bugfix in Commitment.create_diagram caused by moving to networkx2
  • bugifx in Basins.create_barplot caused by range, affects python3
  • bugfix in ModelChecking.primes2smv for van ham init constraints, caused by zip, affects python3
  • bugfix in StateTransitionGraphs.random_walk
  • bugfix in StateTransitionGraphs.create_image: adding styles anonymous and mintrapspaces
  • bugfix in InteractionGraphs: drawing subgraphs, caused by moving to networkx2

release notes for version 2.2.4 (February 2018)

  • started to refactor the unittests (split into several files)
  • PyBoolNet is now developed with Python3
  • PyBoolNet is now compatible with networkx2
  • continued work and tuning on Basins, Commitment and Phenotypes
  • fixed encoding of mutli -valued variables in remy_tumorigenesis.bnet of the Repository (using GINsim)

release notes for version 2.2.3 (February 2018)

  • bugfixes for Python3: encoding / decoding and long / int

release notes for version 2.2.2 (February 2018)

  • new Module Commitment for the computation of commitment diagrams
  • new Module Phenotypes for the computation of phenotype diagrams
  • bugfix of encoding of mutli -valued variables in remy_tumorigenesis.bnet of the Repository
  • added function Attractors.open_json(..) to module Attractors
  • added function Attractors.save_json(..) to module Attractors
  • added function Attractors.compute_json(..) to module Attractors
  • the PyBoolNet git repository is now in "hard tab" format (tab instead of whitespace)
  • refactored list_states_referenced_by_proposition(..) as enumerate_states(..) for simplicity
  • refactored the module AttractorDetection as Attractors for simplicity
  • refactored the module QueryPatterns as TemporalLogic for clarity
  • refactored the module BooleanExpressions as BooleanLogic for clarity
  • adapted modules Basins and ModelChecking to handle Boolean variables that represent multi -valued variables (see van Ham encoding)
  • added StateTransitionGraphs.size_state_space to determine size of state spaces, taking into account only the admissible states of Boolean variables that represent multi -valued variables (see van Ham encoding)
  • added StateTransitionGraphs.find_vanham_variables(..) to detect variables that represent ternary variables

release notes for hotfix version 2.2.1 (January 2018)

  • bugfix: removed slowdown that was introduced by unnecessarily computing counterexamples in AttractorDetection.completeness(..), AttractorDetection.univocality(..) and AttractorDetection.faithfulness(..)

release notes for version 2.2.0 (November 2017)

  • bugfix for linux dependencies, see Issue17
  • removed support for linux 32 bit
  • added module BooleanExpressions with minimize_espresso(..) (work by Sarah Nee)
  • bugfix for Utility.Diagraphs.subgraphs2tree(..) that affected StateTransitionGraphs.add_style_subspaces(..)
  • added functions weak_basins(..) strong_basins(..) with bar plot and pie chart visualizations to Basins. Plotting requires matplotlib.
  • added add_style_anonymous(..) to InteractionGraphs which hides node labels
  • added some toy networks to the Repository
  • renamed module TrapSpaces to AspSolver
  • renamed module AttractorBasins to Basins
  • added energy function energy(..) to StateTransitionGraphs
  • added pretty print function pprint(..) to PyBoolNet
  • bugfix in NuSMV -a for dynamic reordering (currently compiled only in 32bit)
  • bugfix in NuSMV -a for large numbers (currently compiled only in 32bit)
  • removed parameter Aggregate from TrapSpaces.trap_spaces(..) and similar functions as it is rarely useful
  • added warning for accepting states bug (see issue #14)
  • added T -Helper cell plasticity model of Wassim Abou -Jaoudé
  • improved formatting of primes2bnet(..) and primes2mindnf(..)
  • added parameter Representation and option percolated to parameter Type of trap_spaces(..)
  • implemented tempfile for functions check_primes(..), check_primes_with_counterexample(..) and check_primes_with_acceptingstates(..) (bugfix for windows)
  • bugfix in subspace2proposition
  • renamed subspace1_is_in_subspace2(..) to A_is_subspace_of_B(..) for clarity

release notes for version 2.1.1 (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 enumerate_states
  • 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](http://nvie.com/posts/a -successful -git -branching -model/)
  • 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](https://github.com/hklarner/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