chore: Human2 repository and code cleanup

[edkerk]

Main improvements in this PR:

Repository and code/ cleanup for the Human2 (v2.0.0) era, plus one model data-integrity fix.

Model fix

• Remove a duplicate empty name: "" field from reaction MAR01801 (it carried both a descriptive name and a leftover empty one). The duplicate made cobra.io.load_yaml_model raise a duplicate-key error, which was failing qcModelChecks.py (checks) and memoteTest.py (yaml-validation) on develop, independent of this PR. The descriptive name thioredoxin-disulfide reductase (NADPH) (ubiquinone) (EC 1.8.1.9) is kept; both scripts pass locally after the fix. No reactions or metabolites are added or removed.

Repository pruning

• Prune .deprecated/ (136 archived Human1-era files) to a single README.md that points to where they remain available: the git history and the last Human1 release, v1.19.0.
• Remove the completed one-off curation scripts (code/modelCuration/* and code/curateReactionNames.py) together with their input data.
• Remove stale external dumps in data/modelCuration/ (SwissProt / Cell Atlas / DeepLoc2 subcellular locations, Rhea reaction associations, metabolite SMILES/InChI); these are better queried fresh from the source when needed.

code/ function cleanup

• Remove 15 functions that have no remaining callers or are superseded by RAVEN (e.g. removeReactionsFull, standardizeMetFormulas, orphaned misc/ and qc/ utilities, GPRs/updateGrRules, GPRs/fetch_ensembl_gene_annotations.py).
• Merge getCompNetwork into its only caller getSubNetworksInComp (as a local function).
• Group the animal-GEM derivation and its helpers under a new code/animalGEM/ subfolder (10 functions).
• Replace the local addBoundaryMets with RAVEN's closeModel, verified functionally equivalent on Human-GEM (identical checkTasks outcomes: essential 57/57, verification 21/21).

Validated locally in MATLAB R2024b (the merged getSubNetworksInComp runs on the model; testMetabolicTasks passes with closeModel) and in Python (qcModelChecks.py and memoteTest.py pass after the model fix).

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.

[github-actions]

Model quality report

✅ Model QC checks fine, no changes compared to develop.

Model QC checks

Check	Result	Δ vs develop
Growth (biomass producible)	125	0	✅
Metabolites missing formula	7	0	✅
Metabolites missing charge	0	0	✅
Reaction bound / GPR issues	0	0	✅
Malformed cross-references	59	0	✅
Cross-refs inconsistent across compartments	59	0	✅
MEMOTE score (%)	20.2	new	🆕

MACAW and mass/charge balance

MACAW: dead-end and duplicate tests

Starting dead-end test...
 - Found 1384 dead-end metabolites.
 - Found 1141 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
 - Found 1369 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
 - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
 - Found 377 reactions that were some type of duplicate:
   - 0 were completely identical to at least one other reaction.
   - 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
   - 377 involve the same metabolites but with different coefficients as at least one other reaction.

Mass and charge balance

Unbalanced reactions (excluding boundary and biomass): 277 (87 mass, 240 charge)

Gene essentiality (Hart 2015)

cellLine	TP	TN	FP	FN	accuracy	sensitivity	specificity	F1	MCC
DLD1	38	2158	60	280	0.8659	0.1195	0.9729	0.1827	0.1588
GBM	34	2137	64	300	0.8564	0.1018	0.9709	0.1574	0.1276
HCT116	47	2181	55	308	0.8599	0.1324	0.9754	0.2057	0.1906
HELA	32	2241	70	250	0.8766	0.1135	0.9697	0.1667	0.1332
RPE1	15	2179	83	258	0.8655	0.05495	0.9633	0.08086	0.02935
all	7	2379	95	112	0.9202	0.05882	0.9616	0.06335	0.02199

Per-finding detail is committed to data/testResults/ (qc_metabolite_completeness.csv, qc_reaction_sanity.csv, qc_annotation_issues.csv, macaw_results.csv, balance_results.csv, gene-essential.csv); the full MEMOTE result is uploaded as a build artifact.

Results for commit 01ee965.

Full workflow run · this comment is edited on subsequent runs

[edkerk]

No structural model changes (except a small fix of duplicate name entry)