.github/workflows/bioconda_pr.yaml #4
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| name: Auto Bioconda PR with Test (Manual Only) | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| bioconda_pr: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout this repo | |
| uses: actions/checkout@v3 | |
| - name: Extract version and package name using ast | |
| id: vars | |
| run: | | |
| set -e | |
| INIT_PATH=$(find . -type f -name '__init__.py' | head -n1) | |
| echo "📄 Found __init__.py at: $INIT_PATH" | |
| echo 'import ast' > get_version.py | |
| echo 'with open("'"$INIT_PATH"'") as f:' >> get_version.py | |
| echo ' tree = ast.parse(f.read())' >> get_version.py | |
| echo 'for node in ast.walk(tree):' >> get_version.py | |
| echo ' if isinstance(node, ast.Assign):' >> get_version.py | |
| echo ' if getattr(node.targets[0], "id", None) == "__version__":' >> get_version.py | |
| echo ' print(node.value.s)' >> get_version.py | |
| echo ' break' >> get_version.py | |
| VERSION=$(python3 get_version.py) | |
| PACKAGE=$(basename $(dirname "$INIT_PATH")) | |
| if [ -z "$VERSION" ]; then | |
| echo "❌ __version__ not found in $INIT_PATH" | |
| cat "$INIT_PATH" | |
| exit 1 | |
| fi | |
| echo "📦 PACKAGE: $PACKAGE" | |
| echo "📌 VERSION: $VERSION" | |
| echo "VERSION=$VERSION" >> $GITHUB_ENV | |
| echo "PACKAGE=$PACKAGE" >> $GITHUB_ENV | |
| - name: Download source archive and compute SHA256 | |
| run: | | |
| url="https://github.com/kamome1201/${PACKAGE}/archive/refs/tags/v${VERSION}.tar.gz" | |
| wget -O source.tar.gz "$url" | |
| sha256=$(sha256sum source.tar.gz | awk '{print $1}') | |
| echo "SHA256=$sha256" >> $GITHUB_ENV | |
| - name: Clone your fork of bioconda-recipes | |
| run: | | |
| git clone https://github.com/kamome1201/bioconda-recipes.git | |
| cd bioconda-recipes | |
| git remote add upstream https://github.com/bioconda/bioconda-recipes.git | |
| git fetch upstream | |
| - name: Create new branch | |
| run: | | |
| cd bioconda-recipes | |
| git checkout -b add-${PACKAGE}-${VERSION} | |
| - name: Copy recipe into bioconda-recipes | |
| run: | | |
| cp -r ${PACKAGE} bioconda-recipes/recipes/ | |
| if [ ! -f bioconda-recipes/recipes/${PACKAGE}/meta.yaml ]; then | |
| echo "❌ meta.yaml not found in expected location" | |
| exit 1 | |
| fi | |
| - name: Update meta.yaml version and sha256 | |
| run: | | |
| sed -i "s/{% set version = \".*\" %}/{% set version = \"$VERSION\" %}/" ${PACKAGE}/meta.yaml | |
| sed -i "s/sha256: .*/sha256: \"${SHA256}\"/" ${PACKAGE}/meta.yaml | |
| - name: Create config.yml for bioconda-utils | |
| run: | | |
| echo "channels:" > bioconda-recipes/config.yml | |
| echo " - bioconda" >> bioconda-recipes/config.yml | |
| echo " - conda-forge" >> bioconda-recipes/config.yml | |
| echo " - defaults" >> bioconda-recipes/config.yml | |
| - name: Run lint + build + test with bioconda-utils (Docker) | |
| run: | | |
| docker run --rm -v $PWD/bioconda-recipes:/bioconda-recipes \ | |
| quay.io/bioconda/bioconda-utils-build-env \ | |
| bioconda-utils build recipes config.yml --packages ${PACKAGE} --loglevel info --docker --git-range master | |
| # - name: Commit and push | |
| # run: | | |
| # cd bioconda-recipes | |
| # git add recipes/${PACKAGE} | |
| # git commit -m "Update ${PACKAGE} recipe to v$VERSION" | |
| # git push origin add-${PACKAGE}-${VERSION} | |
| # - name: Create Pull Request | |
| # uses: peter-evans/create-pull-request@v5 | |
| # with: | |
| # token: ${{ secrets.GH_PAT }} | |
| # title: "Update ${PACKAGE} recipe to v${{ env.VERSION }}" | |
| # commit-message: "Auto PR for Bioconda: ${PACKAGE} v${{ env.VERSION }}" | |
| # base: master | |
| # branch: add-${PACKAGE}-${{ env.VERSION }} | |
| # body: | | |
| # This PR was automatically generated by GitHub Actions. | |
| # - Package: ${{ env.PACKAGE }} | |
| # - Version: v${{ env.VERSION }} | |
| # - sha256: ${{ env.SHA256 }} |