workflow for testing bulk failures #1319
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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-latest | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 6 | |
| matrix: | |
| runner: [0, 1, 2, 3, 4, 5] | |
| 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: Restore cache | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - 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 6 \ | |
| --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ | |
| --lint --record-build-failures --skiplist-leafs | |
| conda clean -y --all | |
| build-osx: | |
| name: Bulk OSX Builds | |
| if: "contains(github.event.head_commit.message, '[ci run]')" | |
| runs-on: macos-13 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| matrix: | |
| runner: [0, 1, 2, 3] | |
| 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: Restore cache | |
| id: cache | |
| uses: actions/cache@v4 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| # This script can be used to reconfigure conda to use the right channel setup. | |
| # This has to be done after the cache is restored, because | |
| # the channel setup is not cached as it resides in the home directory. | |
| # We could use a system-wide (and therefore cached) channel setup, | |
| # but mamba does not support that at the time of implementation | |
| # (it ignores settings made with --system). | |
| - 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 | |
| # The SDK isn't actually cached, so reinstall it | |
| 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 4 \ | |
| --lint --anaconda-upload --record-build-failures --skiplist-leafs | |
| conda clean -y --all |