fix: retry transient GitHub API errors when posting the QC comment

[edkerk]

Main improvements in this PR:

The full MEMOTE run does all of its real work — running the suite and committing the scores — hours before it posts the Model QC comment. The final github-script step in the post-qc-comment composite action made unguarded listComments/updateComment/createComment calls, so a transient 503 from the GitHub API on that last call raised an unhandled HttpError and failed the whole run even though the results were already produced and committed (this is what sank run 29538381748).

This PR wraps those three API calls in an exponential-backoff withRetry helper that retries only transient errors (429 and 5xx), backing off 2s → 4s → 8s → 16s (capped at 30s, up to 5 attempts) and logging a core.warning on each retry. Genuine errors (auth, 404, etc.) still fail fast. Because the action is shared, this also protects the incremental model-qc workflow's comment updates.

No model content, tests, or MEMOTE behaviour is changed — only the resilience of the cosmetic comment-posting step.

I hereby confirm that I have:

• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists in data/deprecatedIdentifiers/.
• This PR has develop as target branch, and will be resolved with a squash-merge.
• This PR has main as target branch, and will be resolved with a merge commit.

---

_{Maintainers: after merge, credit new contributors by commenting @all-contributors please add @username for <type> on this PR or the linked issue (see CONTRIBUTING).}

[github-actions]

Model quality report

⚠️ 6 pre-existing finding(s), no regressions vs develop. 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 develop
Duplicate !!omap keys	0	0	✅
Growth (biomass producible)	125	0	✅
Reactions with no metabolites	0	0	✅
Model / annotation-table inconsistencies	0	0	✅
Removed reactions or metabolites not deprecated	0	0	✅
Metabolites missing formula	0	0	✅
Metabolites missing charge	0	0	✅
Reaction bound / GPR issues	0	0	✅
Exact-duplicate reaction groups	0	0	✅
Unused metabolites	0	0	✅
Unused genes	0	0	✅
Malformed cross-references	0	0	✅
Cross-refs inconsistent across compartments	3	0	⚠️

MACAW and mass/charge balance

Check	Result	Δ vs develop
Reactions flagged by MACAW dead-end test	2510	0	⚠️
Reactions flagged as MACAW duplicates	377	0	⚠️
Mass-imbalanced reactions	87	0	⚠️
Charge-imbalanced reactions	234	0	⚠️
Structure vs formula/charge inconsistencies	397	0	⚠️

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)   0

Section	Score	Δ vs base
consistency	42.4%	0
annotation_met	73.0%	0
annotation_rxn	72.7%	0
annotation_gene	46.7%	0
annotation_sbo	81.7%	0

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: 64.2%   0 · from the last /run memote.

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