biocondcutor-variantannotation: zlib as host dep #1681
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| name: Bulk branch | |
| on: | |
| push: | |
| branches: | |
| - bulk | |
| jobs: | |
| build-linux: | |
| name: Bulk Linux Builds | |
| if: "contains(github.event.head_commit.message, '[ci run]')" | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 6 | |
| matrix: | |
| # runner: [0, 1, 2] # 3, 4, 5] | |
| runner: [0] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # checkout as BiocondaBot in order to have the permission to push fail logs | |
| token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} | |
| - name: set git user | |
| run: | | |
| git config user.name BiocondaBot | |
| git config user.email [email protected] | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and upload | |
| env: | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| echo '============' | |
| conda info --all | |
| conda config --show-sources | |
| python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | |
| echo '============' | |
| bioconda-utils build recipes config.yml \ | |
| --worker-offset ${{ matrix.runner }} --n-workers 1 \ | |
| --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ | |
| --lint --record-build-failures --skiplist-leafs \ | |
| --packages bioconductor-ensembldb bioconductor-bsgenome bioconductor-biovizbase bioconductor-gviz bioconductor-variantannotation bioconductor-ggbio bioconductor-geneplotter | |
| # --exclude bioconda-repodata-patches # --subdag-depth 5 | |
| conda clean -y --all | |
| build-osx: | |
| name: Bulk OSX-64 Builds | |
| if: "contains(github.event.head_commit.message, '[ci run]')" | |
| runs-on: macos-13 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 3 | |
| matrix: | |
| runner: [0] # 1, 2] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # checkout as BiocondaBot in order to have the permission to push fail logs | |
| token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} | |
| - name: set git user | |
| run: | | |
| git config user.name BiocondaBot | |
| git config user.email [email protected] | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and upload | |
| env: | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| run_conda_forge_build_setup | |
| echo '============' | |
| conda info --all | |
| conda config --show-sources | |
| conda activate bioconda | |
| python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | |
| echo '============' | |
| bioconda-utils build recipes config.yml \ | |
| --worker-offset ${{ matrix.runner }} --n-workers 1 \ | |
| --lint --anaconda-upload --record-build-failures --skiplist-leafs \ | |
| --exclude bioconda-repodata-patches # --subdag-depth 5 | |
| conda clean -y --all | |
| build-osx-arm: | |
| name: Bulk OSX-ARM64 Builds | |
| if: "contains(github.event.head_commit.message, '[ci run DISABLE ARM]')" | |
| runs-on: macOS-14 # M1 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 1 # GHA free plan allows 5 concurrent Mac runners total, we still need most on osx-64. | |
| matrix: | |
| runner: [0] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| # checkout as BiocondaBot in order to have the permission to push fail logs | |
| token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} | |
| - name: set git user | |
| run: | | |
| git config user.name BiocondaBot | |
| git config user.email [email protected] | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh | |
| - name: Set up bioconda-utils | |
| run: bash install-and-set-up-conda.sh | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Build and upload | |
| env: | |
| ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} | |
| INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} | |
| QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -xe | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| source common.sh | |
| # Sets up OSX SDK | |
| run_conda_forge_build_setup | |
| echo '============' | |
| conda info --all | |
| conda config --show-sources | |
| conda activate bioconda | |
| python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | |
| echo '============' | |
| bioconda-utils build recipes config.yml \ | |
| --worker-offset ${{ matrix.runner }} --n-workers 1 \ | |
| --lint --anaconda-upload --record-build-failures --skiplist-leafs \ | |
| --exclude bioconda-repodata-patches | |
| conda clean -y --all |