ci: let results reach a protected branch, and never lose a long run

.github/workflows/gene-essentiality.yml

@@ -24,8 +24,12 @@ jobs:
       PYTHONUNBUFFERED: "1"
 
     steps:
+      # CI_PUSH_TOKEN lets the results push reach a protected branch (e.g. a run
+      # dispatched against develop); GITHUB_TOKEN is the fallback. See model-qc.yml.
       - name: Checkout
         uses: actions/checkout@v7
+        with:
+          token: ${{ secrets.CI_PUSH_TOKEN || secrets.GITHUB_TOKEN }}
 
       - name: Set up Python 3
         uses: actions/setup-python@v6
@@ -110,8 +114,10 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PR_NUMBER: ${{ github.event.number }}
 
+      # !cancelled() rather than the implicit success(): this run takes hours, so its
+      # result must still be posted even if the results push above failed.
       - name: Post comment
-        if: inputs.pr != ''
+        if: ${{ !cancelled() && inputs.pr != '' }}
         uses: actions/github-script@v9
         env:
           TEST_RESULTS: ${{ steps.essentiality.outputs.results }}

.github/workflows/memote-full.yml

@@ -25,8 +25,12 @@ jobs:
     timeout-minutes: 350
 
     steps:
+      # CI_PUSH_TOKEN lets the results push reach a protected branch (e.g. a run
+      # dispatched against develop); GITHUB_TOKEN is the fallback. See model-qc.yml.
       - name: Checkout
         uses: actions/checkout@v7
+        with:
+          token: ${{ secrets.CI_PUSH_TOKEN || secrets.GITHUB_TOKEN }}
 
       - name: Set up Python 3
         uses: actions/setup-python@v6
@@ -91,14 +95,18 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
+      # !cancelled() rather than the implicit success(): the full suite runs for hours,
+      # so the artifact and the comment must survive a failed results push above.
       - name: Upload full MEMOTE result
+        if: ${{ !cancelled() }}
         uses: actions/upload-artifact@v7
         with:
           name: memote-result
           path: memote_result.json
           if-no-files-found: ignore
 
       - name: Update the Model QC comment
+        if: ${{ !cancelled() }}
         uses: ./.github/actions/post-qc-comment
         with:
           running-groups: ""

.github/workflows/model-qc.yml

@@ -35,8 +35,15 @@ jobs:
       RUN_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
 
     steps:
+      # actions/checkout persists these credentials for the results push below. The
+      # default GITHUB_TOKEN cannot push to a protected branch, which the release
+      # pull request needs (its head is develop), so use CI_PUSH_TOKEN when it is
+      # set and fall back to GITHUB_TOKEN otherwise (forks, or before the secret
+      # exists) - the fallback still works for every ordinary topic-branch head.
       - name: Checkout
         uses: actions/checkout@v7
+        with:
+          token: ${{ secrets.CI_PUSH_TOKEN || secrets.GITHUB_TOKEN }}
 
       - name: Configure
         run: |
@@ -206,9 +213,12 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       # Now that the results (including model_qc_summary.md) are committed, post the
-      # comment from the committed summary.
+      # comment from the committed summary. The steps from here on are guarded with
+      # !cancelled() rather than the implicit success(): if the results push fails
+      # (e.g. a protected head branch), the comment, the artifact and the gate verdict
+      # must still happen instead of being skipped, so a long run is never lost.
       - name: Post final comment
-        if: always()
+        if: ${{ !cancelled() }}
         uses: ./.github/actions/post-qc-comment
         with:
           mode: post
@@ -217,6 +227,7 @@ jobs:
           github-token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Upload full MEMOTE result
+        if: ${{ !cancelled() }}
         uses: actions/upload-artifact@v7
         with:
           name: memote-result
@@ -226,7 +237,10 @@ jobs:
       # Fail the build if a gate failed, but only after the detail is committed and
       # the comment updated, so the failure is visible in both. Gates: structural QC
       # (duplicate keys / no growth), YAML round-trip, YAML lint, metabolic tasks.
+      # Runs even when an earlier step failed, so a plumbing failure (a rejected
+      # results push, say) can never mask which gate actually went red.
       - name: Fail if a build gate failed
+        if: ${{ !cancelled() }}
         run: |
           fail=0
           [ "${{ steps.qc.outcome }}" = "failure" ] && fail=1

data/testResults/README.md

@@ -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 #1062** (model QC checks) |
-| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1062** (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 #1062** (model QC checks) |
-| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1062** (MACAW and balance) |
-| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1062** (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 #1065** (model QC checks) |
+| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1065** (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 #1065** (model QC checks) |
+| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1065** (MACAW and balance) |
+| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1065** (MEMOTE) |
 | `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) |
 
 ## 2. What each check means

data/testResults/model_qc_summary.md

@@ -2,58 +2,58 @@
 
 :warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking.
 
-_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md)._
+_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md)._
 
 ### 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](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: |
-| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#growth-biomass-producible) | 125 | new | :white_check_mark: |
-| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: |
-| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: |
-| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | new | :white_check_mark: |
-| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: |
-| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: |
-| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: |
-| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: |
-| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: |
-| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: |
-| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: |
-| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |
+| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: |
+| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: |
+| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: |
+| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: |
+| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: |
+| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: |
+| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: |
+| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: |
+| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: |
+| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: |
+| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: |
+| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: |
+| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |
 
 ### MACAW and mass/charge balance
 
 | Check | Result | Δ vs `develop` | |
 | --- | ---: | ---: | :---: |
-| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/macaw_results.csv) | 0 | :warning: |
-| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/macaw_results.csv) | 0 | :warning: |
-| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/balance_results.csv) | 0 | :warning: |
-| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/balance_results.csv) | 0 | :warning: |
-| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |
+| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/macaw_results.csv) | 0 | :warning: |
+| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/macaw_results.csv) | 0 | :warning: |
+| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/balance_results.csv) | 0 | :warning: |
+| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/balance_results.csv) | 0 | :warning: |
+| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |
 
 ### Model file and metabolic tasks
 
 | Check | Result | |
 | --- | ---: | :---: |
-| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
-| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
-| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
-| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
-| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |
+| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
+| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
+| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
+| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
+| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |
 
-### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#memote)
+### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#memote)
 
-**Total score: 63.2%** (core subset)   +43.0 :white_check_mark:
+**Total score: 63.2%** (core subset)   0
 
 | Section | Score | Δ vs base |
 | --- | ---: | ---: |
 | consistency | 42.4% | 0 |
-| annotation_met | 73.0% | +48.0 :white_check_mark: |
-| annotation_rxn | 72.7% | +47.7 :white_check_mark: |
-| annotation_gene | 46.7% | +46.7 :white_check_mark: |
-| annotation_sbo | 81.7% | +81.7 :white_check_mark: |
+| annotation_met | 73.0% | 0 |
+| annotation_rxn | 72.7% | 0 |
+| annotation_gene | 46.7% | 0 |
+| annotation_sbo | 81.7% | 0 |
 
 <details><summary>Per-test scores</summary>
 
@@ -93,7 +93,7 @@ _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)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/qc-comment-running-state/data/testResults/README.md#gene-essentiality-hart-2015)
+### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/ci/results-push-and-salvage/data/testResults/README.md#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._