Issues

• Chemical reaction network theory analysis

  RuleWorld/PyBioNetGen#117 · Filter by author akutuva21 opened on Sep 7, 2026
  1

• Global sensitivity analysis

  RuleWorld/PyBioNetGen#116 · Filter by author akutuva21 opened on Sep 7, 2026
  1

• Structural identifiability analysis for BNGL models

  RuleWorld/PyBioNetGen#115 · Filter by author akutuva21 opened on Sep 7, 2026
  2

• BioNetGen.run() returns data arrays that share references and get overwritten

  RuleWorld/PyBioNetGen#113 · Filter by author jrfaeder opened on Jul 29, 2026

• Deduplicate block __setattr__ logging paths and add regression tests

  RuleWorld/PyBioNetGen#106 · Filter by author wshlavacek opened on Jun 10, 2026

• BNGResult loader crashes (np.loadtxt) on ragged .cdat files that BNG2.pl emits for SSA

  RuleWorld/PyBioNetGen#103 · Filter by author wshlavacek opened on May 28, 2026

• Make _recompile derived state computed from _changes

  RuleWorld/PyBioNetGen#74 · Filter by author wshlavacek opened on May 9, 2026

• Pattern equality should normalize bond labels (or document the limitation)

  RuleWorld/PyBioNetGen#73 · Filter by author wshlavacek opened on May 9, 2026

• Resolve BNG2.pl from $PATH via $BNGPATH env var

  RuleWorld/PyBioNetGen#72 · Filter by author wshlavacek opened on May 9, 2026

• Action argument grammar fails on empty [] or {} literals

  RuleWorld/PyBioNetGen#71 · Filter by author wshlavacek opened on May 9, 2026

• gdiff: copied subnodes aren't renamed/recolored after parent copy

  RuleWorld/PyBioNetGen#70 · Filter by author wshlavacek opened on May 9, 2026

• Atomizer tests assert list.sort() == list.sort() (compares None == None)

  RuleWorld/PyBioNetGen#69 · Filter by author wshlavacek opened on May 7, 2026

• PyBioNetGen fails with setuptools ≥81 (Python 3.12)

  RuleWorld/PyBioNetGen#61 · Filter by author wshlavacek opened on Mar 9, 2026
  1

• Automated testing of PyPI releases

  enhancement
  RuleWorld/PyBioNetGen#60 · Filter by author jrfaeder opened on Apr 24, 2025

• pkg_resources update breaks bngl

  RuleWorld/PyBioNetGen#59 · Filter by author luciansmith opened on Jul 15, 2024
  1

• NFsim version in bionetgen --version and info commands

  enhancement
  RuleWorld/PyBioNetGen#57 · Filter by author jrfaeder opened on Feb 28, 2024
  

• Model writing omits keywords in reaction rules

  bug
  RuleWorld/PyBioNetGen#55 · Filter by author jrfaeder opened on Feb 8, 2024
  3

  

• Add links in documentation to online validation, introspection, and execution of BNGL models through runBioSimulations

  RuleWorld/PyBioNetGen#33 · Filter by author jonrkarr opened on Oct 8, 2021

• Suggestion: use py-perl5 for more seamless bridge to BNGL2.pl

  enhancement
  RuleWorld/PyBioNetGen#22 · Filter by author jonrkarr opened on Sep 16, 2021
  2

• Raise exceptions on ill-formatted actions

  bug
  RuleWorld/PyBioNetGen#21 · Filter by author jonrkarr opened on Sep 10, 2021
  3

• Suggestion: remove requirement for specific file extensions

  enhancement
  RuleWorld/PyBioNetGen#6 · Filter by author jonrkarr opened on Jun 9, 2021

• Suggestion: different PyPI name or equate version number to the version of BNG2

  enhancement
  RuleWorld/PyBioNetGen#5 · Filter by author jonrkarr opened on Jun 8, 2021

• In some cases it would be helpful to parse comments from BNGL files

  enhancement
  RuleWorld/PyBioNetGen#2 · Filter by author jonrkarr opened on Jun 8, 2021
  1