chore: merge main into develop to restore a shared ancestor

[edkerk]

⚠️ Merge this with a merge commit, not a squash

Squashing would discard the second parent and throw away the entire point of this PR. The repo's usual "squash for develop-targeted PRs" convention does not apply here.

What this is

main carried every release commit back to v1.1 that develop had never seen, so the merge base sat at a10375c4b and each release merge had to re-reconcile the same divergence. Merging develop into main today produces 9 conflicts.

This is an ancestry-only merge. The resulting tree is byte-identical to develop: no file changes at all. The only thing that changes is that main becomes an ancestor of develop again.

Payoff

After this lands, develop -> main (#1061) merges with zero conflicts instead of nine.

Conflict resolutions

All nine resolve in develop's favour, because develop is newer in every case. Each was checked rather than assumed:

file	resolution
data/deprecatedIdentifiers/deprecatedMetabolites.tsv	develop. Strict superset (2273 vs 2272 rows); zero retired identifiers exist only on main
.all-contributorsrc	develop. Has all 31 of main's logins plus 12 more. Main's extra badge types are the old 16-type scheme that PR #1049 deliberately replaced with six
README.md	develop. 43 contributors vs 32, published citation, and the {{nRXN}} placeholders the release fills
citation.cff	develop. Published PNAS DOI 10.1073/pnas.2516511123 vs main's empty doi / "In press"
.github/workflows/gene-essentiality.yml	develop. Python/raven-toolbox version vs main's MATLAB
code/test/testMetabolicTasks.m	develop
code/GPRs/updateGrRules.m	stays deleted (removed by the Human2 cleanup)
model/Human-GEM.yml, model/metabolites.tsv	develop. 2.0.1 curation

No deprecated identifiers and no contributors are lost.

Release artifacts are intentionally not brought over

main's Human-GEM.xml / .mat / .xlsx / .txt, dependencies.txt and version.txt are not merged into develop, which does not track them. increaseHumanGEMVersion regenerates the first five through export_for_git at release time.

Note the consequence for the next release: because main becomes an ancestor, develop -> main fast-forwards and removes those files from main until the release commit puts them back. version.txt is covered by the planned change to pass the version explicitly and create the file when it is absent.

[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	new	✅
Reactions with no metabolites	0	0	✅
Model / annotation-table inconsistencies	0	0	✅
Removed reactions or metabolites not deprecated	0	new	✅
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)   +43.0 ✅

Section	Score	Δ vs base
consistency	42.4%	0
annotation_met	73.0%	+48.0 ✅
annotation_rxn	72.7%	+47.7 ✅
annotation_gene	46.7%	+46.7 ✅
annotation_sbo	81.7%	+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