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Use Github Action to detect file changes instead of custom Python code #1322

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merged 3 commits into from
Jun 19, 2024
Merged

Use Github Action to detect file changes instead of custom Python code #1322

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89722c8
Use Github Action to detect file changes instead of custom Python code
adamrtalbot Jun 19, 2024
b6a0720
Update CHANGELOG.md
adamrtalbot Jun 19, 2024
923ba72
Merge branch 'dev' into detect-changes-via-pre-built-gha
adamrtalbot Jun 19, 2024
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0 .github/python/include.yaml → .github/include.yaml
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317 changes: 0 additions & 317 deletions .github/python/find_changed_files.py
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33 changes: 11 additions & 22 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -18,34 +18,23 @@ jobs:
name: Check for changes
runs-on: ubuntu-latest
outputs:
nf_test_files: ${{ steps.list.outputs.nf_test_files }}
nf_test_files: ${{ steps.list.outputs.components }}
steps:
- uses: actions/setup-python@v4
with:
python-version: "3.11"
architecture: "x64"
- uses: actions/checkout@v4
- uses: actions/checkout@v3
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Reason for the reversion?

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Bugger: #1323

with:
fetch-depth: 0

- name: Install Python dependencies
run: |
python -m pip install --upgrade pip
pip install gitpython pyyaml

- name: list nf_test_files
- name: List nf-test files
id: list
uses: adamrtalbot/detect-nf-test-changes@v0.0.2
with:
head: ${{ github.sha }}
base: origin/${{ github.base_ref }}
include: .github/include.yaml

- name: print list of nf-test files
run: |
echo nf_test_files=$(python \
.github/python/find_changed_files.py \
-t pipeline workflow process \
--head_ref ${{ github.sha }} \
--base_ref origin/${{ github.base_ref }} \
) >> $GITHUB_OUTPUT

- name: debug
run: |
echo ${{ steps.list.outputs.nf_test_files }}
echo ${{ steps.list.outputs.components }}

test:
name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -77,6 +77,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1310](https://github.com/nf-core/rnaseq/pull/1310) - Reinstate pseudoalignment subworkflow config
- [PR #1309](https://github.com/nf-core/rnaseq/pull/1309) - Document FASTP sampling
- [PR #1312](https://github.com/nf-core/rnaseq/pull/1312) - Fix issues with unzipping of GTF/ GFF files without absolute paths
- [PR #1322](https://github.com/nf-core/rnaseq/pull/1322) - Use pre-built Github Action to detect nf-test changes

### Parameters

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