fix: Restore backward compatibility for Google Life Sciences executor… #17
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| name: CI | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches_ignore: [] | |
| jobs: | |
| cancel-previous: | |
| runs-on: ubuntu-latest | |
| if: github.ref != 'refs/heads/main' | |
| steps: | |
| - uses: khan/pull-request-workflow-cancel@1.0.1 | |
| with: | |
| workflows: main.yml | |
| env: | |
| GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}" | |
| formatting: | |
| permissions: | |
| contents: read # for actions/checkout to fetch code | |
| pull-requests: write # for marocchino/sticky-pull-request-comment to create or update PR comment | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Setup black environment | |
| run: | | |
| conda create -c conda-forge -y -q --name black black | |
| - name: Check formatting | |
| run: > | |
| export PATH="/usr/share/miniconda/bin:$PATH" | |
| source activate black | |
| black --check --diff . | |
| - name: Comment PR | |
| if: github.event_name == 'pull_request' && failure() | |
| uses: marocchino/sticky-pull-request-comment@v2.8.0 | |
| with: | |
| message: "Please format your code with [black](https://black.readthedocs.io): `black snakemake tests/*.py`." | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| testing: | |
| runs-on: ubuntu-latest | |
| needs: formatting | |
| services: | |
| mysql: | |
| image: mysql:8.0 | |
| env: | |
| MYSQL_ROOT_PASSWORD: root | |
| ports: | |
| - "8888:3306" | |
| options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3 | |
| env: | |
| AWS_AVAILABLE: "${{ secrets.AWS_ACCESS_KEY_ID }}" | |
| GCP_AVAILABLE: "${{ secrets.GCP_SA_KEY }}" | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup mamba | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: snakemake | |
| channels: "conda-forge, bioconda" | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| - name: Setup Snakemake environment | |
| shell: bash -el {0} | |
| run: | | |
| conda config --set channel_priority strict | |
| mamba env update -q -n snakemake --file test-environment.yml | |
| # TODO remove and add as regular dependency once released | |
| pip install git+https://github.com/snakemake/snakemake-interface-executor-plugins.git | |
| pip install git+https://github.com/snakemake/snakemake-executor-plugin-cluster-generic.git | |
| pip install -e . | |
| # additionally add singularity (not necessary anymore, included in the test env now) | |
| # TODO remove version constraint: needed because 3.8.7 fails with missing libz: | |
| # bin/unsquashfs: error while loading shared libraries: libz.so.1: | |
| # cannot open shared object file: No such file or directory | |
| # mamba install -n snakemake "singularity<=3.8.6" | |
| - name: Setup apt dependencies | |
| run: | | |
| sudo gem install apt-spy2 | |
| sudo apt-spy2 fix --commit --launchpad --country=US | |
| sudo apt-get update | |
| sudo apt install -y stress git wget openmpi-bin libopenmpi-dev mariadb-server | |
| - name: Setup iRODS | |
| run: | | |
| docker build -t irods-server tests/test_remote_irods | |
| docker run -d -p 1247:1247 --name provider irods-server -i run_irods | |
| sleep 10 | |
| docker exec -u irods provider iput /incoming/infile | |
| cp -r tests/test_remote_irods/setup-data ~/.irods | |
| - name: Test local | |
| env: | |
| CI: true | |
| ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}" | |
| shell: bash -el {0} | |
| run: | | |
| pytest --show-capture=stderr -v -x tests/test_expand.py tests/test_io.py tests/test_schema.py tests/test_linting.py tests/tests.py tests/test_schema.py tests/test_linting.py tests/test_executor_test_suite.py tests/tests.py | |
| - name: Build and publish docker image | |
| if: >- | |
| contains(github.event.pull_request.labels.*.name, | |
| 'update-container-image') | |
| uses: elgohr/Publish-Docker-Github-Action@v5 | |
| with: | |
| name: snakemake/snakemake | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_TOKEN }} | |
| tags: ${{ env.GITHUB_SHA }} | |
| - name: Set container image | |
| if: >- | |
| contains(github.event.pull_request.labels.*.name, | |
| 'update-container-image') | |
| run: | | |
| echo CONTAINER_IMAGE=snakemake/snakemake:$GITHUB_SHA >> $GITHUB_ENV | |
| - name: Delete container image | |
| if: >- | |
| contains(github.event.pull_request.labels.*.name, | |
| 'update-container-image') && always() | |
| run: | | |
| docker run --rm lumir/remove-dockerhub-tag \ | |
| --user ${{ secrets.DOCKER_USERNAME }} \ | |
| --password ${{ secrets.DOCKER_TOKEN }} \ | |
| snakemake/snakemake:${{ env.GITHUB_SHA }} | |
| - name: Build container image | |
| if: >- | |
| !contains(github.event.pull_request.labels.*.name, | |
| 'update-container-image') | |
| run: docker build . | |
| testing-windows: | |
| runs-on: windows-latest | |
| needs: formatting | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Remove unix-only dependencies | |
| shell: python | |
| run: | | |
| import fileinput | |
| excluded_on_win = ["environment-modules", "cwltool", "cwl-utils", "apptainer", "squashfuse"] | |
| for line in fileinput.input("test-environment.yml", inplace=True): | |
| if all(pkg not in line for pkg in excluded_on_win): | |
| print(line) | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: snakemake | |
| channels: "conda-forge, bioconda" | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| - name: Setup Snakemake environment | |
| run: | | |
| conda config --set channel_priority strict | |
| mamba env update -q --file test-environment.yml | |
| # TODO remove and add as regular dependency once released | |
| pip install git+https://github.com/snakemake/snakemake-interface-executor-plugins.git | |
| pip install -e . | |
| - name: Run tests | |
| env: | |
| CI: true | |
| ZENODO_SANDBOX_PAT: "${{ secrets.ZENODO_SANDBOX_PAT }}" | |
| run: | | |
| python -m pytest --show-capture=stderr -v -x tests/tests.py |