ci(petab): dogfood upstream libpetab-python main for native BNGL (merged #508) - #590
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…ged #508) The BnglModel loader PyBNF has been validating through a personal fork branch is now merged upstream (PEtab-dev/libpetab-python#508). Repoint the pytest-native-bngl leg's petab-spec from that fork branch to PEtab-dev/libpetab-python@main so the leg dogfoods the actual merged code (and survives the fork branch being deleted), and refresh the now-stale "Step B fork" wording across the workflow, the composite action, the _bngl drift note, and the pyproject comments. Runtime is unchanged. register_bngl() already collapses to a no-op against native support -- verified locally against upstream main: 'bngl' is a known model type, petab.v2.core imports, the no-op path triggers, and the native BnglModel parses parameters/observables. The latest PyPI petab (0.8.2) does not yet carry BNGL, so the petab>=0.8,<1 pin and the monkeypatch fallback both stay. Retiring them is a follow-up gated on the first PyPI release that ships BNGL.
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What & why
The native
BnglModelloader PyBNF has been validating through a personal fork branch is now merged upstream: PEtab-dev/libpetab-python#508. This repoints thepytest-native-bnglCI leg from that fork branch toPEtab-dev/libpetab-python@main, so the leg dogfoods the actual merged code (and survives the fork branch being deleted), and refreshes the now-stale "Step B fork" wording.Changes
.github/workflows/tests.yml—petab-specfor thepytest-native-bnglleg:wshlavacek/libpetab-python@bngl_model_support→PEtab-dev/libpetab-python@main; updated the assertion message and surrounding comments..github/actions/setup-pybnf/action.yml— refreshed thepetab-specinput description and the install comment.pybnf/petab/_bngl.py— drift note now points at the merged upstream twin instead of the fork branch.pyproject.toml— comments in thepetab/testsextras updated to reflect the merge.Runtime is unchanged
register_bngl()already collapses to a no-op against native support. Verified locally against upstreammain:bnglis inpetab.v1.models.known_model_typespetab.v2.coreimports cleanly (the no-op path doesn't raise)BnglModelparses parameters/observablesThe latest PyPI
petab(0.8.2) does not yet carry BNGL, so thepetab>=0.8,<1pin and theregister_bngl()monkeypatch fallback both stay in place.Follow-up (not in this PR)
When a PyPI
petabrelease after 0.8.2 ships native BNGL, bump the pin and retireregister_bngl().