fix: install raven-toolbox for the full MEMOTE run, and stop hiding crashes

[edkerk]

The bug

The dispatched full-MEMOTE run (29537354961) reported success in 65 seconds and produced nothing. It died 1.4s in:

File "code/test/memoteSnapshot.py", line 49, in <module>
    from annotateGEM import annotate_gem
File "code/annotateGEM.py", line 28, in <module>
    from raven_toolbox.annotation import add_sbo_terms
ModuleNotFoundError: No module named 'raven_toolbox'

memoteSnapshot started importing annotateGEM, and therefore raven_toolbox, in #1062. model-qc.yml installs raven-toolbox in a step of its own before MEMOTE, but memote-full.yml installed only cobra memote gurobipy. The script and one of its two callers went out of sync. Regression from #1062.

Why it passed, which is the worse half

timeout 19800 python code/test/memoteSnapshot.py \
  || echo "::warning::MEMOTE did not finish within the time limit; score unavailable."

|| swallows every non-zero exit, so a 1.4-second crash was annotated as "did not finish within the time limit". With continue-on-error: true and an auto-commit that had nothing to commit and so succeeded, the whole run went green. A full MEMOTE suite "passing" in 65 seconds is not a thing, but nothing in the run said so.

Changes

Install raven-toolbox in memote-full.yml via requirements.txt, the same source model-qc.yml uses.

Branch on the exit code instead of || echo, in both workflows. 124 stays a tolerated timeout warning; anything else is an error annotation.

The two workflows then diverge deliberately:

• memote-full.yml: the score is the entire deliverable, so a crash now fails the run. continue-on-error dropped. The publish steps are !cancelled() (from ci: let results reach a protected branch, and never lose a long run #1065), so a failure still salvages whatever exists.
• model-qc.yml: MEMOTE is one report among many and must not block the other checks' results being committed, so it keeps continue-on-error but now annotates honestly. Previously a silent crash meant the comment kept showing the last committed score with no indication it was stale.

Verifying

Re-dispatch after merge; the run should take hours rather than a minute:

gh workflow run memote-full.yml --repo SysBioChalmers/Human-GEM --ref develop -f pr=1061

[github-actions]

Model quality report

⚠️ 6 pre-existing finding(s), no regressions vs main. Non-blocking.

Each check name links to its explanation in the testResults README.

Model checks

Duplicate keys (model unloadable) and no growth block the merge; every other row is a non-blocking report.

Check	Result	Δ vs main
Duplicate !!omap keys	0	new	✅
Growth (biomass producible)	125	new	✅
Reactions with no metabolites	0	new	✅
Model / annotation-table inconsistencies	0	new	✅
Removed reactions or metabolites not deprecated	0	new	✅
Metabolites missing formula	0	new	✅
Metabolites missing charge	0	new	✅
Reaction bound / GPR issues	0	new	✅
Exact-duplicate reaction groups	0	new	✅
Unused metabolites	0	new	✅
Unused genes	0	new	✅
Malformed cross-references	0	new	✅
Cross-refs inconsistent across compartments	3	new	⚠️

MACAW and mass/charge balance

Check	Result	Δ vs main
Reactions flagged by MACAW dead-end test	2510	-703	⚠️
Reactions flagged as MACAW duplicates	377	-2	⚠️
Mass-imbalanced reactions	87	new	⚠️
Charge-imbalanced reactions	234	new	⚠️
Structure vs formula/charge inconsistencies	397	new	⚠️

Model file and metabolic tasks

Check	Result
YAML round-trip (cobrapy)	pass	✅
YAML round-trip (RAVEN)	pass	✅
YAML lint	pass	✅
Essential metabolic tasks	57 passed	✅
Verification metabolic tasks	21 passed	✅

MEMOTE

Total score: 63.2% (core subset)  

Section	Score	Δ vs base
consistency	42.4%
annotation_met	73.0%
annotation_rxn	72.7%
annotation_gene	46.7%
annotation_sbo	81.7%

Per-test scores

Section	Test	Score
Consistency	Stoichiometric Consistency	100.0%
Consistency	Mass Balance	0.8%
Consistency	Charge Balance	2.1%
Consistency	Metabolite Connectivity	0.0%
Consistency	Unbounded Flux In Default Medium	100.0%
Annotation - Metabolites	Presence of Metabolite Annotation	0.0%
Annotation - Metabolites	Metabolite Annotations Per Database	62.3%
Annotation - Metabolites	Metabolite Annotation Conformity Per Database	45.8%
Annotation - Metabolites	Uniform Metabolite Identifier Namespace	0.0%
Annotation - Reactions	Presence of Reaction Annotation	0.0%
Annotation - Reactions	Reaction Annotations Per Database	75.9%
Annotation - Reactions	Reaction Annotation Conformity Per Database	33.3%
Annotation - Reactions	Uniform Reaction Identifier Namespace	0.0%
Annotation - Genes	Presence of Gene Annotation	0.0%
Annotation - Genes	Gene Annotations Per Database	80.0%
Annotation - Genes	Gene Annotation Conformity Per Database	80.0%
Annotation - SBO Terms	Metabolite General SBO Presence	0.0%
Annotation - SBO Terms	Metabolite SBO:0000247 Presence	0.1%
Annotation - SBO Terms	Reaction General SBO Presence	0.0%
Annotation - SBO Terms	Metabolic Reaction SBO:0000176 Presence	0.0%
Annotation - SBO Terms	Transport Reaction SBO:0000185 Presence	0.7%
Annotation - SBO Terms	Exchange Reaction SBO:0000627 Presence	0.0%
Annotation - SBO Terms	Demand Reaction SBO:0000628 Presence	100.0%
Annotation - SBO Terms	Sink Reactions SBO:0000632 Presence	100.0%
Annotation - SBO Terms	Gene General SBO Presence	0.0%
Annotation - SBO Terms	Gene SBO:0000243 Presence	0.0%
Annotation - SBO Terms	Biomass Reactions SBO:0000629 Presence	0.0%

Full suite not run for this commit; comment /run memote to add it.

The score above is the fast core subset. Comment /run memote to run the full suite on this pull request; the score updates here when it finishes.

Gene essentiality (Hart 2015)

Not run automatically (it takes hours). Comment /run gene-essentiality to run it on this pull request; the result posts as its own comment.

❌ = a count rose vs the target branch (regression) · ⚠️ = a pre-existing non-zero finding (non-blocking) · ⏳ = still running. Counts link to the CSV listing the exact entries.

Full workflow run · this comment is edited as results come in