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Add support for BNGL models (cont.) #508

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08979b0
Add support for BNGL models as a PEtab model language
wshlavacek Jun 15, 2026
6d959bd
Harden the BNGL block reader: block aliases + seed-species $ clamp
wshlavacek Jul 2, 2026
9251e77
Harden the BNGL block reader: join line continuations
wshlavacek Jul 2, 2026
a1ad576
Harden the BNGL block reader: strip line labels (index + named)
wshlavacek Jul 2, 2026
6f9ee76
Add a corpus regression gate: parse_bngl vs a cached BNG2.pl golden
wshlavacek Jul 3, 2026
31c5c9f
Match BNG2.pl: drop the `molecules`/`rules` block aliases (keep `spec…
wshlavacek Jul 3, 2026
e665cc6
Make None defaults Optional and pin utf-8 in to_file
wshlavacek Jul 5, 2026
95f75a2
Remove vendored BNGL corpus fixtures; fetch on demand instead
dweindl Aug 11, 2026
84102cd
Fetch the BNGL test corpus on demand instead of vendoring it
dweindl Aug 12, 2026
d1124cf
doc
dweindl Aug 12, 2026
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3 changes: 3 additions & 0 deletions .github/workflows/ci_tests.yml
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Expand Up @@ -29,6 +29,9 @@ jobs:
run: uvx pre-commit run --all-files
if: matrix.platform == 'ubuntu-latest'

- name: Fetch BNGL test corpus
run: uv run python tests/v1/fetch_bngl_corpus.py

- name: Unit tests
run: |
uv sync --group ci
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -114,3 +114,6 @@ venv.bak/

_untracked
doc/_static/README.rst

# BNGL corpus fixtures are fetched on demand (tests/v1/fetch_bngl_corpus.py)
tests/v1/bngl_corpus/*.bngl
11 changes: 10 additions & 1 deletion petab/v1/models/__init__.py
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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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