Changes by Jules#104

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akutuva21 wants to merge 718 commits into

RuleWorld:mainfrom

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Commits on Jun 1, 2026

Merge ruleworld/main: protocol blocks, quote-aware actions, distutils compat, new tests
akutuva21
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Commits on Jun 2, 2026

Commits on Jun 4, 2026

PyBioNetGen: Refactor equivalent items grouping in ContextAnalyzer

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: Fix contactMap.py to only process the first cluster using slicing.

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: 🧪 Add unit test for printInfo in core/main.py

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: Fix string copying bug in `analyzeSBML.py`

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: Add verbosity option logging during XML parsing

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: Fix BNGL argument parsing to support 0 as a dictionary key

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: ⚡ Optimize Levenshtein distance calculations via memoization in analyzeSBML

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: 🧪 Add error test for shutil.rmtree in CSimulator

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: fix: Migrate BNGL function creation into bngModel class

akutuva21
and
google-labs-jules[bot]
authored
PyBioNetGen: 🔒 Fix Hardcoded BioGRID API Key

akutuva21
and
google-labs-jules[bot]
authored

Commits on Jun 9, 2026

Commits on Jun 10, 2026