Collapse repeated commas in action normalization - #90
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jrfaeder merged 1 commit intoMay 12, 2026
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@wshlavacek : This branch has conflicts. Please resolve them and let me know when it's ready to go. |
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@jrfaeder conflicts resolved and the branch has been rebased onto current main. It should be ready for another look. |
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…er (#90) * Address FIXME for tracking boundary species Replaced an old FIXME in `bionetgen/atomizer/sbml2bngl.py` with the correct handling logic. Boundary species that are not natively constant are now explicitly flagged as `isConstant = True` to ensure they receive the `$` prefix in the generated BNGL, allowing downstream logic (like `getAssignmentRules`) to accurately track and substitute their references via `only_assignment_dict`. Added a comment to clarify the downstream tracking mechanism. Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com> * chore: PR #90 remove forbidden artifacts and run black * chore: remove generated artifact files from PR #90 --------- Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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Summary
_normalize_action_text()to collapse repeated commas that appear outside quoted stringstests/test_bng_parsing.pyWhy
BNG2.pl tolerates malformed action text like
n_steps=>20,,print_functions=>1, but the pyparsing action parser does not.Testing
uv run python -m pytest -q tests/test_bng_parsing.pyuvx black --check bionetgen/modelapi/bngparser.py tests/test_bng_parsing.py