Feat: add model quality-control checks workflow#1046
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…ounds, MEMOTE) Adds a "Model QC checks" GitHub Actions workflow with two jobs: - checks (every PR, fast): metabolite formula/charge completeness, reaction bound and GPR sanity, a growth sanity gate, and annotation cross-reference validation across namespaces. Posts a compact status table as a PR comment with the change versus the target branch and an icon per check. - memote (separate job): runs MEMOTE in-process and builds the snapshot report to obtain the total score (memote run alone does not compute one). A fast core subset (skipping the three FVA/loopless tests) runs on every PR; the full suite runs only on PRs to main. It updates the same PR comment when it finishes. Detailed per-finding output is written to diff-friendly CSVs in data/testResults; the compact comment is for a quick visual check.
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Adds buildReport.py, which builds one consolidated model-quality comment from the committed result files: a compact Model QC status table, the MACAW and mass/charge balance summary, and the Hart 2015 gene-essentiality metrics. Any result set not yet committed for the pull request shows as pending. The Model QC and QC-tests workflows both build and post this comment to a single shared identifier (GITHUB_COMMENT_QC), each rebuilding it from the committed files so the last to finish shows the complete picture. Replaces the separate buildQcComment.py / commentModelQC.md / commentQC.md.
The core subset still ran the stoichiometric-consistency / energy-cycle MILPs and the per-metabolite open-bound checks (~32 min) and the O(n^3) matrix rank / null- space tests, so it exceeded the per-PR budget. Skip those twelve tests in the subset; the full suite (PRs to main) still runs them.
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checkout v4->v7, setup-python v5->v6, upload-artifact v4->v7, git-auto-commit-action v5->v7.
Model quality report✅ Model QC checks fine, no changes compared to Model QC checks
MACAW and mass/charge balanceMACAW: dead-end and duplicate testsMass and charge balanceGene essentiality (Hart 2015)
Per-finding detail is committed to Results for commit 4ca5e17. Full workflow run · this comment is edited on subsequent runs |
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Merge to develop for now, further troubleshooting once combined with #1027 |
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Main improvements in this PR:
Addresses #732 (more diverse workflows around simulation and functional behaviour, beyond the existing structure/format checks).
Adds a
Model QC checksworkflow with lightweight, diff-friendly checks that complement the existing MACAW, mass/charge balance and gene-essentiality tests:qc_metabolite_completeness.csv).qc_reaction_sanity.csv).qc_annotation_issues.csv).memote_score.md) — a fast core subset on every PR, the full suite on PRs tomain.The fast checks and MEMOTE run as separate jobs, so quick feedback is not blocked by the slow MEMOTE run. Per-finding detail is committed as CSVs under
data/testResults/. The MACAW/balance, gene-essentiality and QC results are combined into a single pull-request comment: a compact status table with each check's value, its change versus the target branch, and an icon for a quick visual check.I hereby confirm that I have:
data/deprecatedIdentifiers/. (No reactions or metabolites are removed in this PR.)developas target branch, and will be resolved with a squash-merge.mainas target branch, and will be resolved with a merge commit.