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Action grammar rejects scientific-notation and trailing commas in list args (par_scan_vals) — stricter than BNG2.pl, causes silent legacy fallback under simulator='bngsim'

Status: Open.

#110 In RuleWorld/PyBioNetGen;

· wshlavacek opened on Jun 20, 2026

BNGsim bridge silently falls back to legacy subprocess when action inspection fails under simulator='bngsim' (should raise)

Status: Open.

#109 In RuleWorld/PyBioNetGen;

· wshlavacek opened on Jun 20, 2026

Deduplicate block __setattr__ logging paths and add regression tests

Status: Open.

#106 In RuleWorld/PyBioNetGen;

· wshlavacek opened on Jun 10, 2026

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

Status: Open.

#103 In RuleWorld/PyBioNetGen;

· wshlavacek opened on May 28, 2026

Make _recompile derived state computed from _changes

Status: Open.

#74 In RuleWorld/PyBioNetGen;

· wshlavacek opened on May 9, 2026

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

Status: Open.

#73 In RuleWorld/PyBioNetGen;

· wshlavacek opened on May 9, 2026

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

Status: Open.

#72 In RuleWorld/PyBioNetGen;

· wshlavacek opened on May 9, 2026

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

Status: Open.

#71 In RuleWorld/PyBioNetGen;

· wshlavacek opened on May 9, 2026

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

Status: Open.

#70 In RuleWorld/PyBioNetGen;

· wshlavacek opened on May 9, 2026

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

Status: Open.

#69 In RuleWorld/PyBioNetGen;

· wshlavacek opened on May 7, 2026

PyBioNetGen fails with setuptools ≥81 (Python 3.12)

Status: Open.

#61 In RuleWorld/PyBioNetGen;

· wshlavacek opened on Mar 9, 2026

Automated testing of PyPI releases

enhancementNew feature or requestNew feature or request

Status: Open.

#60 In RuleWorld/PyBioNetGen;

· jrfaeder opened on Apr 24, 2025