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Unify modelapi export and XML error handling - #94

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jrfaeder merged 1 commit into
RuleWorld:mainfrom
wshlavacek:modelapi-export-xml-errors
May 12, 2026
Merged

Unify modelapi export and XML error handling#94
jrfaeder merged 1 commit into
RuleWorld:mainfrom
wshlavacek:modelapi-export-xml-errors

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Summary

Testing

  • uv run python -m pytest -q tests/test_modelapi_export_errors.py tests/test_xmlparsers_errors.py tests/test_get_rule_mod.py tests/test_bng_parsing.py
  • uvx black --check bionetgen/modelapi/bngfile.py bionetgen/modelapi/bngparser.py bionetgen/modelapi/model.py bionetgen/modelapi/xmlparsers.py tests/test_modelapi_export_errors.py tests/test_xmlparsers_errors.py

@jrfaeder
jrfaeder merged commit 43b44ed into RuleWorld:main May 12, 2026
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@wshlavacek
wshlavacek deleted the modelapi-export-xml-errors branch May 15, 2026 15:14
jrfaeder pushed a commit that referenced this pull request Jul 20, 2026
Replaced plain `assert` statements used during species and parameter initialization in `csimulator.py` with proper error handling.
The code now explicitly checks lengths, logs detailed mismatch info using `BNGLogger`, and raises a newly introduced `BNGSimulatorError`.

Co-authored-by: google-labs-jules[bot] <161369871+google-labs-jules[bot]@users.noreply.github.com>
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2 participants