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feat: add DIA-NN 2.3.2 to CI/CD pipeline #7

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Merged
ypriverol merged 1 commit into from
Apr 3, 2026
Merged

feat: add DIA-NN 2.3.2 to CI/CD pipeline #7

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9 changes: 7 additions & 2 deletions .github/workflows/quantms-containers.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ on:
branches: ["main"]
paths:
- "diann-*/Dockerfile"
- "diann-*/**"
- "relink-*/Dockerfile"
- ".github/workflows/**"
release:
Expand Down Expand Up @@ -42,6 +43,7 @@ jobs:
if: github.event_name == 'push' || github.event_name == 'pull_request'
with:
filters: |
diann_2_3_2: [ 'diann-2.3.2/**', '.github/workflows/**' ]
diann_2_2_0: [ 'diann-2.2.0/**', '.github/workflows/**' ]
diann_2_1_0: [ 'diann-2.1.0/**', '.github/workflows/**' ]
diann_2_0: [ 'diann-2.0.2/**', '.github/workflows/**' ]
Expand All @@ -53,6 +55,7 @@ jobs:
id: set-matrix
env:
EVENT: ${{ github.event_name }}
CHG_232: ${{ steps.filter.outputs.diann_2_3_2 }}
CHG_220: ${{ steps.filter.outputs.diann_2_2_0 }}
CHG_210: ${{ steps.filter.outputs.diann_2_1_0 }}
CHG_20: ${{ steps.filter.outputs.diann_2_0 }}
Expand All @@ -61,7 +64,8 @@ jobs:
CHG_RLK: ${{ steps.filter.outputs.relink_1_0_0 }}
run: |
DIANN_ALL='[
{"context":"diann-2.2.0","tag":"ghcr.io/bigbio/diann:2.2.0","sif":"diann-sif:2.2.0","extra_tags":"ghcr.io/bigbio/diann:latest","chg":"CHG_220"},
{"context":"diann-2.3.2","tag":"ghcr.io/bigbio/diann:2.3.2","sif":"diann-sif:2.3.2","extra_tags":"ghcr.io/bigbio/diann:latest","chg":"CHG_232"},
{"context":"diann-2.2.0","tag":"ghcr.io/bigbio/diann:2.2.0","sif":"diann-sif:2.2.0","extra_tags":"","chg":"CHG_220"},
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@qodo-code-review qodo-code-review bot Apr 3, 2026

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Action required

1. Workflow repushes latest tag 🐞 Bug ☼ Reliability

Because .github/workflows/** is treated as a change for diann_2_3_2 and DIA-NN 2.3.2 is tagged
with ghcr.io/bigbio/diann:latest, a workflow-only change on main can rebuild and push :latest
even when the diann-2.3.2 build context did not change.
Agent Prompt 
### Issue description
Workflow-only changes (under `.github/workflows/**`) currently make `diann_2_3_2` appear “changed”, and since 2.3.2 carries the `ghcr.io/bigbio/diann:latest` extra tag, this can republish `:latest` even when the container context didn’t change.

### Issue Context
This makes `:latest` mutable due to CI config edits and can change image digests without any Dockerfile/context changes.

### Fix Focus Areas
- .github/workflows/quantms-containers.yml[41-52]
- .github/workflows/quantms-containers.yml[66-73]
- .github/workflows/quantms-containers.yml[82-94]

### Suggested change (one of)
1) Remove `.github/workflows/**` from the per-image `dorny/paths-filter` rules so only actual image-context changes trigger builds/pushes.
2) Add a separate `workflow_changed` filter and, when only workflow files changed, either:
   - build without pushing (`push: false`), or
   - exclude `extra_tags` (especially `:latest`) from the matrix for that run.
3) Gate publishing of `extra_tags` (e.g., `:latest`) to `release` events only.

ⓘ Copy this prompt and use it to remediate the issue with your preferred AI generation tools

{"context":"diann-2.1.0","tag":"ghcr.io/bigbio/diann:2.1.0","sif":"diann-sif:2.1.0","extra_tags":"","chg":"CHG_210"},
{"context":"diann-2.0.2","tag":"ghcr.io/bigbio/diann:2.0.2","sif":"diann-sif:2.0.2","extra_tags":"","chg":"CHG_20"},
{"context":"diann-1.9.2","tag":"ghcr.io/bigbio/diann:1.9.2","sif":"diann-sif:1.9.2","extra_tags":"","chg":"CHG_192"},
Expand All @@ -75,9 +79,10 @@ jobs:
DIANN=$(echo "$DIANN_ALL" | jq -c '[.[] | del(.chg)]')
RELINK=$(echo "$RELINK_ALL" | jq -c '[.[] | del(.chg)]')
else
DIANN=$(echo "$DIANN_ALL" | jq -c --arg c220 "${CHG_220:-false}" --arg c210 "${CHG_210:-false}" \
DIANN=$(echo "$DIANN_ALL" | jq -c --arg c232 "${CHG_232:-false}" --arg c220 "${CHG_220:-false}" --arg c210 "${CHG_210:-false}" \
--arg c20 "${CHG_20:-false}" --arg c192 "${CHG_192:-false}" --arg c181 "${CHG_181:-false}" \
'[.[] | select(
(.chg == "CHG_232" and $c232 == "true") or
(.chg == "CHG_220" and $c220 == "true") or
(.chg == "CHG_210" and $c210 == "true") or
(.chg == "CHG_20" and $c20 == "true") or
Expand Down
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