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chore: remove legacy getINITModel2 gene-essentiality code #1068

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chore: remove legacy getINITModel2 gene-essentiality code #1068

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a357083
chore: remove legacy getINITModel2 gene-essentiality code
edkerk Jul 17, 2026
3c1a85e
chore: update model QC results [skip ci]
edkerk Jul 17, 2026
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464 changes: 0 additions & 464 deletions code/tINIT/getINITModel2.m
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41 changes: 0 additions & 41 deletions code/tINIT/restoreModelGrRules.m
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107 changes: 0 additions & 107 deletions code/test/estimateEssentialGenes.m
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156 changes: 0 additions & 156 deletions code/test/evaluateHart2015Essentiality.m
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10 changes: 5 additions & 5 deletions data/testResults/README.md
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Expand Up @@ -21,11 +21,11 @@ own files. The pull request in each row is the one whose run last wrote those fi

| Result file(s) | Produced by | Last updated by |
| --- | --- | --- |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) |
| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1068** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1068** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1068** (model QC checks) |
| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1068** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1068** (MEMOTE) |
| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) |

## 2. What each check means
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