From 9bf3d122da2bbeae9a4a8fbfd7d2a3c09b861505 Mon Sep 17 00:00:00 2001 From: Bill Hlavacek Date: Sun, 10 May 2026 15:41:53 -0600 Subject: [PATCH] Accept `check_iso` flag on `generate_network` in modelapi action allowlist `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"]`. --- bionetgen/core/utils/utils.py | 1 + 1 file changed, 1 insertion(+) diff --git a/bionetgen/core/utils/utils.py b/bionetgen/core/utils/utils.py index 7d19fd23..653bb124 100644 --- a/bionetgen/core/utils/utils.py +++ b/bionetgen/core/utils/utils.py @@ -104,6 +104,7 @@ def __init__(self): "max_agg", "max_iter", "max_stoich", + "check_iso", "TextReaction", "TextSpecies", ]