chore(petab): retire the BnglModel adapter and register_bngl() now that petab 0.9.0 ships the loader, and drop Python 3.11 (#591) - #682

Fixes #591.

The gate cleared on 2026-09-07: petab 0.9.0 is the first PyPI release whose known_model_types includes bngl, carrying the native BnglModel loader PyBNF contributed upstream in PEtab-dev/libpetab-python#508. On any 0.9.0 installation register_bngl() already saw bngl registered and returned without rebinding, so the local adapter was dead at runtime and only the tests that constructed it directly still exercised it.

Removed

• pybnf/petab/bngl_model.py: the BnglModel adapter, register_bngl(), and its _locate_bng2 helper, plus the automodule entry.
• The pytest-native-bngl CI leg that installed upstream libpetab-python main to reach the native loader ahead of a release, and the setup action's petab-spec input it used.
• Every register_bngl() call in the tests, tutorial lessons 12 and 13, the lint-clinic fixture generator, and the three real-world make_petab.py scripts. The docs section on the loader now shows the plain petab call.

Python 3.11 dropped

The petab and tests extras now floor at petab >= 0.9 (the action installs the same pin; test_packaging_metadata cross-checks the two). petab 0.9.0 requires Python 3.12, so the project floor moves with it: requires-python, the classifier, ruff's target-version, the CI matrix, the packaging test, and the install/cluster docs and batch scripts that named 3.11.

Kept, and one gap this exposes

_bngl.py stays: it is the reader the importer and exporter use, and its drift note now points at the shipped upstream module rather than a branch.

_bngl_expr.py (the #666 parameter-expression evaluator) also stays, with a caveat worth knowing. The adapter was its only consumer, and petab's native BnglModel does not evaluate an expression-valued parameter: get_parameter_value raises NotImplementedError and get_free_parameter_ids_with_values skips it. That is the pre-#666 behaviour on the petab-side validation path. It is not a regression of this PR, since the no-op already routed 0.9.0 users to the native class, but the #666 fix never reached the path it was written for. #681 tracks the upstream port; the evaluator stays as its staging copy and its unit tests now drive it directly.

Tests

• TestNativeBnglModel replaces the adapter unit tests: it pins the ABC seam the exporter relies on (parameter ids and values, entity namespace, formula symbols, state variables) against petab's class, and asserts the native loader is present, taking over the retired CI leg's assert step.
• The corpus validity test passes an explicit model_id: petab derives one from the file stem and requires a PEtab identifier, which the hyphenated corpus filenames are not.
• tests/_bngl_differential.py carries its own _locate_bng2; the tutorial tests import BnglModel / _locate_bng2 from petab where they still need them.

Locally under petab 0.9.0 on Python 3.12, every test_petab*.py file, the PEtab tutorial tests, the lint clinic, the priors lesson, new-era validation, and the packaging metadata tests pass (730 passed). The pinned ruff gate and the -W docs build are clean. ADR-0026 gains an addendum and the CHANGELOG records the floor change and the removal.