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Add support for BNGL models #501

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Add support for BNGL models #501

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f23d71f
Add support for BNGL models as a PEtab model language
wshlavacek Jun 15, 2026
b1ab023
Harden the BNGL block reader: block aliases + seed-species $ clamp
wshlavacek Jul 2, 2026
b920d74
Harden the BNGL block reader: join line continuations
wshlavacek Jul 2, 2026
74ec6f2
Harden the BNGL block reader: strip line labels (index + named)
wshlavacek Jul 2, 2026
c2cf778
Add a corpus regression gate: parse_bngl vs a cached BNG2.pl golden
wshlavacek Jul 3, 2026
6276d1d
Match BNG2.pl: drop the `molecules`/`rules` block aliases (keep `spec…
wshlavacek Jul 3, 2026
a62b8a4
Make None defaults Optional and pin utf-8 in to_file
wshlavacek Jul 5, 2026
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11 changes: 10 additions & 1 deletion petab/v1/models/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,21 @@
MODEL_TYPE_SBML = "sbml"
#: PySB model type as used in a PEtab v2 yaml file as `language`.
MODEL_TYPE_PYSB = "pysb"
#: BNGL model type as used in a PEtab v2 yaml file as `language`.
MODEL_TYPE_BNGL = "bngl"

known_model_types = {
MODEL_TYPE_SBML,
MODEL_TYPE_PYSB,
MODEL_TYPE_BNGL,
}

from .model import Model # noqa F401

__all__ = ["MODEL_TYPE_SBML", "MODEL_TYPE_PYSB", "known_model_types", "Model"]
__all__ = [
"MODEL_TYPE_SBML",
"MODEL_TYPE_PYSB",
"MODEL_TYPE_BNGL",
"known_model_types",
"Model",
]
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