🧹 [Code Health] Refactor getAssignmentRules in libsbml2bngl#572
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- Extracted rate rule processing to `_process_rate_rule` - Extracted assignment rule processing to `_process_assignment_rule` - Extracted default/other rule processing to `_process_other_rule` - Preserved all existing behavior, including rule appending via early returns from helpers - Fixed SyntaxWarning with raw string literals Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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- Extracted rate rule processing to `_process_rate_rule` - Extracted assignment rule processing to `_process_assignment_rule` - Extracted default/other rule processing to `_process_other_rule` - Preserved all existing behavior, including rule appending via early returns from helpers - Fixed SyntaxWarning with raw string literals - Applied black formatting Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
- Fixed `NameError` by passing `zparams` to `_process_rate_rule` - Fixed broken logic control flow by replacing `return` with `return True` in helper function and executing `continue` in `getAssignmentRules` loop when returned True. - Cleaned up temp scripts and formatted code Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
🎯 What:
The incredibly large and complex
getAssignmentRulesmethod inbionetgen/atomizer/sbml2bngl.py(which had aFIXMEcalling it a mess) has been refactored. The giantfor arule in self.model.getListOfRules():loop body has been extracted into three separate, cleaner helper methods:_process_rate_rule,_process_assignment_rule, and_process_other_rule.💡 Why:
This refactoring directly addresses code health and maintainability concerns. The original method was hundreds of lines long, handling vastly different scenarios within deeply nested
if/elifblocks, making it error-prone to modify. Breaking it out separates concerns and allows developers to easily understand and update rule processing logic in isolation.✅ Verification:
I used a custom patch script to perform the exact text replacements accurately without breaking Python indentation. I verified the resulting code format using
blackand ran the full PyBioNetGen test suite usingpython -m pytest tests/which completed successfully with all tests passing, confirming that the change causes no regressions or runtime errors.✨ Result:
The method is now concise, delegating the heavy lifting to dedicated helper functions while retaining identical runtime behavior. Code readability is drastically improved.
PR created automatically by Jules for task 9533962785846725966 started by @akutuva21