Sk/test rate rule converter rigorously#450
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skeating merged 135 commits intodevelopmentfrom Oct 18, 2025
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there are some untested things in here
…rously' into sk/test-rate-rule-converter-rigorously
- only run build if repo is ours
…ter it is impossible to roundtrip
The ODEs were being copied by reference, leading to issues where modifications to the ODEs in the ExpressionAnalyser were affecting the original ODEs. To resolve this, a deep copy of the ODEs is now created when the ExpressionAnalyser is initialized. In addition, the ASTNodes returned by getODEFor() are now deep copied. This ensures that the ExpressionAnalyser operates on its own independent copy of the ODEs and ASTNodes, preventing unintended side effects.
Addresses an issue where assignment rules were not properly integrated into rate rule conversion. This change introduces a new method to replace assigned variables with their corresponding math expressions within rate rules. This ensures that the conversion process accurately reflects the underlying model dynamics. Also, adds an option to use stoichiometry from math in rate rule conversion.
Addresses issues in SBML rate rule conversion by refining stoichiometry handling and variable replacement. The changes ensure correct reaction stoichiometry by considering the `useStoichiometryFromMath` option. It also prevents replacement of CSymbolFunction to avoid unexpected behavior.
Makes replaceMathWithAssignedVariables, getListAssignmentRuleVariables, and replaceAssignedVariablesWithMath virtual methods in SBMLConverter to allow for overriding in derived classes.
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@skeating or at least i would have but it is failing to merge automatically |
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Testing