Fix two stale SEDML export test expectations - #1835
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Two of the five failures in the nightly SEDML_SBML_IT regression are test bookkeeping rather than product defects. Both are in the slow set, so they only run on the nightly and never in the merge gate. biomodel_188880263.vcml declared no unsupported applications, but the exporter correctly reports eight: every application in that model is rule-based, and SBML export does not support reaction rules. The assertion message has been printing the exact lines to add. Added them. biomodel_34826524.vcml had SEDML_FAULT.MATH_OVERRIDE_NOT_EQUIVALENT registered for a fault that no longer occurs, so it failed for *passing*: "file SBML.biomodel_34826524.vcml passed SEDML Round trip, but knownSEDMLFault was set". Removed the entry. Verified by running each model, which needs -Dtest.include.slow=true since both are slow-gated. Both now pass: 188880263 in 51s, 34826524 in 346s. This does not touch the remaining three failures, which are genuine SED-ML export defects (exported SED-ML referencing entities by XPath that are absent from the exported SBML, plus a duplicate SED-ML id) and want a real fix rather than a knownSEDMLFault entry. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01SvqmME7MkRUNEYje5HpiLt
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Two of the five failures in the nightly
SEDML_SBML_ITregression are testbookkeeping, not product defects. Both models are in the slow set, so they run
only on the nightly and never in the merge gate.
biomodel_188880263.vcml — undeclared unsupported applications
The test declared no unsupported applications; the exporter reports eight. Every
application in that model is rule-based, and SBML export does not support
reaction rules, so the exporter is right and the declaration was simply never
filled in. The assertion has been printing the exact lines to add:
Added all eight, in the file-ordered position the list already uses.
biomodel_34826524.vcml — a known fault that no longer happens
It had
SEDML_FAULT.MATH_OVERRIDE_NOT_EQUIVALENTregistered, so it failed forpassing:
Removed the entry.
Verification
Run individually — these need
-Dtest.include.slow=true, since both areslow-gated and are otherwise skipped:
biomodel_188880263.vcmlbiomodel_34826524.vcmlNote this repo's PR CI cannot exercise either:
SEDML_SBML_ITruns only inregression.yml, and these two are additionally behindtest.include.slow. Thechecks on this PR say nothing about the change; the runs above are the evidence.
Incidentally
biomodel_34826524took 346s locally against the 129s recorded nextto it in
slowModels, so that annotation is optimistic.Not included
The other three nightly failures are genuine export defects — exported SED-ML
referencing species and parameters by XPath that are absent from the exported
SBML, plus one duplicate SED-ML id. Those deserve a real fix rather than a
knownSEDMLFaultentry, which would make a live bug permanently invisible. Seealso #1827, which makes those failures legible in CI output (they currently
report as a bare
» OmexValidation).🤖 Generated with Claude Code
https://claude.ai/code/session_01SvqmME7MkRUNEYje5HpiLt