Auto Bioconda PR with Test & meta.yaml generation (Manual Only) #16
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| name: Auto Bioconda PR with Test & meta.yaml generation (Manual Only) | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| bioconda_pr: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout this repo | |
| uses: actions/checkout@v3 | |
| - name: Set GH_PAT as env var | |
| run: echo "GH_PAT=${{ secrets.GH_PAT }}" >> $GITHUB_ENV | |
| - name: Extract version and package name using ast | |
| id: vars | |
| run: | | |
| set -e | |
| INIT_PATH=$(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" >> $GITHUB_ENV | |
| - name: Generate meta.yaml in recipes/${PACKAGE} | |
| run: | | |
| mkdir -p recipes/${PACKAGE} | |
| SUMMARY=$(awk ' | |
| found && NF { | |
| line = $0 | |
| gsub(/!\[[^]]*\]\([^)]*\)/, "", line) | |
| gsub(/\[[^]]+\]\([^)]*\)/, "", line) | |
| gsub(/\*\*/, "", line) | |
| gsub(/__/, "", line) | |
| gsub(/^[ \t*-]+/, "", line) | |
| gsub(/"/, "\\\"", line) | |
| print line; exit | |
| } | |
| /^##[ \t]+Overview/ { found = 1 } | |
| ' README.md) | |
| echo "{% set name = \"${PACKAGE}\" %}" > recipes/${PACKAGE}/meta.yaml | |
| echo "{% set version = \"${VERSION}\" %}" >> recipes/${PACKAGE}/meta.yaml | |
| echo "" >> recipes/${PACKAGE}/meta.yaml | |
| echo "package:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " name: \"{{ name|lower }}\"" >> recipes/${PACKAGE}/meta.yaml | |
| echo " version: \"{{ version }}\"" >> recipes/${PACKAGE}/meta.yaml | |
| echo "" >> recipes/${PACKAGE}/meta.yaml | |
| echo "source:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " url: https://github.com/kamome1201/${PACKAGE}/archive/refs/tags/v{{ version }}.tar.gz" >> recipes/${PACKAGE}/meta.yaml | |
| echo " sha256: \"TO_BE_REPLACED\"" >> recipes/${PACKAGE}/meta.yaml | |
| echo "" >> recipes/${PACKAGE}/meta.yaml | |
| echo "build:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " number: 0" >> recipes/${PACKAGE}/meta.yaml | |
| echo " noarch: python" >> recipes/${PACKAGE}/meta.yaml | |
| echo " script: \"{{ PYTHON }} -m pip install . -vv --ignore-installed --no-deps\"" >> recipes/${PACKAGE}/meta.yaml | |
| echo "" >> recipes/${PACKAGE}/meta.yaml | |
| echo "requirements:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " host:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " - python >=3.8" >> recipes/${PACKAGE}/meta.yaml | |
| echo " - pip" >> recipes/${PACKAGE}/meta.yaml | |
| echo " - setuptools" >> recipes/${PACKAGE}/meta.yaml | |
| echo " - wheel" >> recipes/${PACKAGE}/meta.yaml | |
| echo " run:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " - python >=3.8" >> recipes/${PACKAGE}/meta.yaml | |
| echo "" >> recipes/${PACKAGE}/meta.yaml | |
| echo "test:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " imports:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " - ${PACKAGE}" >> recipes/${PACKAGE}/meta.yaml | |
| echo "" >> recipes/${PACKAGE}/meta.yaml | |
| echo "about:" >> recipes/${PACKAGE}/meta.yaml | |
| echo " home: \"https://github.com/kfuku52/${PACKAGE}\"" >> recipes/${PACKAGE}/meta.yaml | |
| echo " license: \"BSD-3-Clause\"" >> recipes/${PACKAGE}/meta.yaml | |
| echo " license_file: \"LICENSE\"" >> recipes/${PACKAGE}/meta.yaml | |
| echo " summary: \"${SUMMARY}\"" >> recipes/${PACKAGE}/meta.yaml | |
| - 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" >> $GITHUB_ENV | |
| - name: Clone your fork of bioconda-recipes | |
| run: | | |
| git clone https://github.com/kamome1201/bioconda-recipes.git | |
| cd bioconda-recipes | |
| git remote add upstream https://github.com/bioconda/bioconda-recipes.git | |
| git fetch upstream | |
| git checkout -B add-${PACKAGE}-${VERSION} upstream/master | |
| - name: Copy recipe into bioconda-recipes | |
| run: | | |
| cp -r recipes/${PACKAGE} bioconda-recipes/recipes/ | |
| - name: Replace sha256 in meta.yaml | |
| run: | | |
| sed -i "s/sha256: .*/sha256: \"${SHA256}\"/" bioconda-recipes/recipes/${PACKAGE}/meta.yaml | |
| - name: Create config.yml and conda_build_config.yaml | |
| 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 | |
| echo "conda_build_config: conda_build_config.yaml" >> bioconda-recipes/config.yml | |
| touch bioconda-recipes/conda_build_config.yaml | |
| - name: Show config.yml and conda_build_config.yaml | |
| run: | | |
| cat bioconda-recipes/config.yml | |
| echo "---" | |
| cat bioconda-recipes/conda_build_config.yaml | |
| - name: Set authenticated remote URL | |
| run: | | |
| cd bioconda-recipes | |
| git remote set-url origin https://x-access-token:[email protected]/kamome1201/bioconda-recipes.git | |
| - name: Commit and push | |
| run: | | |
| cd bioconda-recipes | |
| git config user.name "github-actions" | |
| git config user.email "[email protected]" | |
| git add recipes/${PACKAGE} | |
| git commit -m "Add ${PACKAGE} v${VERSION} [auto-generated]" | |
| git push --force origin add-${PACKAGE}-${VERSION} | |
| - name: Create Pull Request | |
| uses: peter-evans/create-pull-request@v5 | |
| with: | |
| token: ${{ secrets.GH_PAT }} | |
| title: "Add ${{ env.PACKAGE }} recipe v${{ env.VERSION }}" | |
| commit-message: "Auto PR: ${PACKAGE} v${{ 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 }} |