Add constava v1.0.0 #2
Workflow file for this run
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| name: PR Check | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| concurrency: | |
| group: build-${{ github.event.pull_request.number || github.head_ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 13 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-conda.sh') }} | |
| - name: Set up bioconda-utils | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| run: bash install-and-set-up-conda.sh | |
| - name: Configure conda | |
| run: bash configure-conda.sh | |
| - name: Perform lint | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| echo '============' | |
| conda info --all | |
| conda config --show-sources | |
| python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' | |
| echo '============' | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils lint --loglevel debug --full-report --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| conda clean -y --all | |
| build-linux: | |
| name: Linux Tests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 13 | |
| needs: lint | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-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 test | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "linux-gnu" | |
| CI: "true" | |
| run: | | |
| set -e | |
| # Clean up lingering build artifacts | |
| for n in linux-64 osx-64 noarch; do | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.conda | |
| done | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| docker pull quay.io/dpryan79/mulled_container:latest | |
| bioconda-utils build recipes config.yml \ | |
| --docker --mulled-test \ | |
| --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| docker rmi quay.io/dpryan79/mulled_container:latest | |
| - name: Prepare artifacts | |
| run: | | |
| ( | |
| rm -rf /tmp/artifacts | |
| mkdir -p /tmp/artifacts/packages | |
| cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| find -name .cache | xargs rm -rf || true | |
| for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
| cp -rv $n /tmp/artifacts/packages || true | |
| done | |
| if command -V docker >/dev/null; then | |
| mkdir -p /tmp/artifacts/images | |
| cd /tmp/artifacts/images | |
| docker image ls --format='{{.Repository}}:{{.Tag}}' | \ | |
| { grep biocontainers || true ; } | \ | |
| xargs -n1 -P4 bash -c ' | |
| test -n "${1+x}" || exit 0 | |
| echo "Start compressing docker image ${1} ..." | |
| docker save "${1}" | gzip -c > "${1##*/}.tar.gz" | |
| echo "Finished compressing docker image ${1} ." | |
| ' -- | |
| # There's no : allowed in artifact names, replace it with --- | |
| for f in /tmp/artifacts/images/*:* ; do mv -- "$f" "${f//:/---}"; done | |
| fi | |
| ) || true | |
| - name: Archive packages | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: linux-packages | |
| path: | | |
| /tmp/artifacts/packages | |
| - name: Archive images | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: docker-images | |
| path: | | |
| /tmp/artifacts/images | |
| build-osx: | |
| name: OSX Tests | |
| runs-on: macos-13 | |
| strategy: | |
| fail-fast: true | |
| max-parallel: 4 | |
| needs: build-linux | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: set path | |
| run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH | |
| - name: Fetch conda install script | |
| run: | | |
| wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh | |
| - name: Restore cache | |
| id: cache | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/mambaforge | |
| key: ${{ runner.os }}--bulk--${{ hashFiles('**/install-and-set-up-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 Test | |
| env: | |
| # Mimic circleci | |
| OSTYPE: "darwin" | |
| CI: "true" | |
| run: | | |
| set -e | |
| eval "$(conda shell.bash hook)" | |
| conda activate bioconda | |
| # Clean up lingering build artifacts | |
| for n in linux-64 osx-64 noarch; do | |
| rm -f /opt/mambaforge/envs/bioconda/conda-bld/$n/*.tar.bz2 | |
| done | |
| # The SDK isn't actually cached, so reinstall it | |
| run_conda_forge_build_setup | |
| if [ -z "$GITHUB_BASE_REF" ] ; then | |
| export GITHUB_BASE_REF="master" | |
| fi | |
| git fetch origin "$GITHUB_BASE_REF" | |
| bioconda-utils build recipes config.yml \ | |
| --git-range origin/"$GITHUB_BASE_REF" HEAD | |
| - name: Prepare artifacts | |
| run: | | |
| ( | |
| rm -rf /tmp/artifacts | |
| mkdir -p /tmp/artifacts/packages | |
| cd /opt/mambaforge/envs/bioconda/conda-bld || exit 0 | |
| find -name .cache | xargs rm -rf || true | |
| for n in index.html channeldata.json linux-64 osx-64 noarch; do | |
| cp -rv $n /tmp/artifacts/packages || true | |
| done | |
| ) || true | |
| - name: Archive packages | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: osx-packages | |
| path: | | |
| /tmp/artifacts/packages |