Accept check_iso flag on generate_network action#77
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wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
Open
Accept check_iso flag on generate_network action#77wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
check_iso flag on generate_network action#77wshlavacek wants to merge 1 commit intoRuleWorld:mainfrom
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`check_iso` is a real BNG2.pl flag (`Perl2/SpeciesList.pm`,
`Perl2/RxnRule.pm`) that controls canonical-isomorphism checking when
adding species. The modelapi action allowlist in `ActionList.arg_dict`
was missing it, so any model that used
`generate_network({check_iso=>1, ...})` failed at parse time with:
Action argument check_iso not recognized for action generate_network!
before BNG2.pl was ever invoked.
One-line fix: add `"check_iso"` to `ActionList.arg_dict["generate_network"]`.
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Summary
`check_iso` is a real BNG2.pl flag (`Perl2/SpeciesList.pm`, `Perl2/RxnRule.pm`) that controls canonical-isomorphism checking when adding species. The modelapi action allowlist in `ActionList.arg_dict` is missing it, so any model that uses `generate_network({check_iso=>1, ...})` fails at parse time with:
```
Action argument check_iso not recognized for action generate_network!
```
before BNG2.pl is ever invoked.
Fix
One-line addition: `"check_iso"` joins the existing list of accepted args for `generate_network` in `bionetgen/core/utils/utils.py`.
Test plan