Accept the BMDB baseline after the SBML scope fixes

[jcschaff]

Accepts the BMDB baseline after the SBML scope fixes, so the nightly goes green again.

Nightly run 32094317081 reported FAIL: 28 changed — the first run after #1983 (reaction-rate references) and #1985 (UNRESOLVED.initConc / UNRESOLVED.Size) landed. Every shard passed. The gate was refusing a baseline those fixes had made stale, which is what it is for.

Eighteen archives improved outright

They now import and simulate:

256 457 499 589 599 628 632 705 710 739 764 804 832 867 872 908 969    FAIL → PASS
1065                                                                   SOLVER_FAILURE → PASS

Seven get further than before

Import now works; they fail later, at solve:

models
534, 535, 536, 537, 547, 1021	SBML_IMPORT_FAILURE → SOLVER_FAILURE
613	SBML_IMPORT_FAILURE → DIVIDE_BY_ZERO

Three look like a step backwards and are not

model	change
63	UNSUPPORTED_NON_INT_STOCH → SBML_IMPORT_FAILURE
245	UNSUPPORTED_NON_INT_STOCH → SBML_IMPORT_FAILURE
627	UNSUPPORTED_NON_CONSTANT_COMPARTMENTS → SBML_IMPORT_FAILURE

Each has two unsupported features, and the reaction-rate check from #1983 now reports first. Verified against the models rather than assumed:

• Vhk in 63 and r2 in 245 are both genuine <reaction> elements referenced from an assignmentRule, and neither is declared as a species, parameter or compartment — so these are not false positives.
• Both models also genuinely carry the non-integer stoichiometries their old entries named (0.5; 0.063, 0.127, …).
• 627 is the same shape, on reaction vSTIM alongside its non-constant compartment.

Both the old and new reasons are true; only which one is reached first has changed. The models fail either way.

No archive went from PASS to FAIL.

The diff

Taken verbatim from the run's test_cases.updated.ndjson artifact, not hand-edited:

1182 rows before, 1182 after
28 insertions(+), 28 deletions(-)

No rows added, removed or reordered; only the 28 known_status / known_failure_type values changed.

🤖 Generated with Claude Code