RELEASENOTES.md

release 3.0.15: bugfix windows binaries

• bugfix: fix setup to copy windows binaries correctly #117
• setup.py: updates author email address
• compare: compare/3.0.14...3.0.15

release 3.0.14: fixes configparser

• helpers: fixes AttributeError: module 'configparser' has no attribute 'SafeConfigParser' #112
• github/test: only test Python version 3.8
• compare: compare/3.0.13...3.0.14

release 3.0.13: bugfix missing nusmvkeywords

• improves f-string variable substitution
• bugfix: typo in setup.py for macOS
• replaces file nusmvkeywords.json with hard-coded values
• bnet2primes: improves error message #111
• improves release announcement
• adds release notes and fixes wrong compare url in release script
• compare: compare/3.0.12...3.0.13

release 3.0.12: bugfix missing gringo clasp

• bugfix: missing gringo and clasp binaries in linux #107
• docs: updates installation instructions for MacOS
• compare: compare/3.0.11...3.0.12

release notes for version 3.0.0 (September 2021)

• adds pyboolnet command line tool
• adds logging for control of output
• conforms to PEP-8 coding style
• uses type hints
• renamed modules
• adds release script for faster releases

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