Merge pull request #179 from Reed-CompBio/contrib-2024 #658
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| name: Test SPRAS | |
| on: [push, pull_request] | |
| jobs: | |
| # Installs the conda environment but does not run tests because the tests require Linux Docker images | |
| conda-only: | |
| name: Test conda environment | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [macos-latest, windows-latest] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Install conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: spras | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| # Log conda environment contents | |
| - name: Log conda environment | |
| shell: bash --login {0} | |
| run: conda list | |
| # Runs the test code and Snakemake workflow in the conda environment | |
| test: | |
| name: Run test cases and workflow | |
| # The Docker images will be pulled in both the docker job and this test job | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Install conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: spras | |
| environment-file: environment.yml | |
| auto-activate-base: false | |
| miniconda-version: 'latest' | |
| # Log conda environment contents | |
| - name: Log conda environment | |
| shell: bash --login {0} | |
| run: conda list | |
| # Formerly used Singularity instead of Apptainer (see https://github.com/eWaterCycle/setup-singularity/issues/6) | |
| - name: Install Apptainer | |
| uses: eWaterCycle/setup-apptainer@v2 | |
| with: | |
| # Choose version from https://github.com/apptainer/apptainer/releases | |
| apptainer-version: 1.2.2 | |
| - name: Run tests | |
| shell: bash --login {0} | |
| # Verbose output and disable stdout and stderr capturing | |
| run: pytest -vs | |
| - name: Run Snakemake workflow | |
| shell: bash --login {0} | |
| run: snakemake --cores 2 --configfile config/config.yaml --show-failed-logs | |
| # Builds the Docker images | |
| docker: | |
| name: Build Docker images | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| # Pull from Docker Hub to use the cache | |
| # https://medium.com/mobileforgood/coding-tips-patterns-for-continuous-integration-with-docker-on-travis-ci-9cedb8348a62 | |
| # https://github.com/docker/build-push-action/issues/7 | |
| - name: Pull Docker images | |
| run: | | |
| docker pull reedcompbio/omics-integrator-1:latest | |
| docker pull reedcompbio/omics-integrator-2:v2 | |
| docker pull reedcompbio/pathlinker:v2 | |
| docker pull reedcompbio/meo:latest | |
| docker pull reedcompbio/mincostflow:latest | |
| docker pull reedcompbio/allpairs:v2 | |
| docker pull reedcompbio/domino:latest | |
| docker pull reedcompbio/py4cytoscape:v3 | |
| docker pull reedcompbio/spras:v0.1.0 | |
| - name: Build Omics Integrator 1 Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/OmicsIntegrator1/. | |
| dockerfile: docker-wrappers/OmicsIntegrator1/Dockerfile | |
| repository: reedcompbio/omics-integrator-1 | |
| tags: latest | |
| cache_froms: reedcompbio/omics-integrator-1:latest | |
| push: false | |
| - name: Remove Omics Integrator 1 Docker image | |
| # Remove the image to prevent the cache from being used. Here we use | |
| # `|| true` to prevent the job from failing if the image doesn't exist or | |
| # can't be removed for some reason | |
| run: docker rmi reedcompbio/omics-integrator-1:latest || true | |
| - name: Build Omics Integrator 2 Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/OmicsIntegrator2/. | |
| dockerfile: docker-wrappers/OmicsIntegrator2/Dockerfile | |
| repository: reedcompbio/omics-integrator-2 | |
| tags: v2 | |
| cache_froms: reedcompbio/omics-integrator-2:latest | |
| push: false | |
| - name: Remove Omics Integrator 2 Docker image | |
| run: docker rmi reedcompbio/omics-integrator-2:latest || true | |
| - name: Build PathLinker Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/PathLinker/. | |
| dockerfile: docker-wrappers/PathLinker/Dockerfile | |
| repository: reedcompbio/pathlinker | |
| tags: v2 | |
| cache_froms: reedcompbio/pathlinker:latest | |
| push: false | |
| - name: Remove PathLinker Docker image | |
| run: docker rmi reedcompbio/pathlinker:latest || true | |
| - name: Build Maximum Edge Orientation Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/MEO/. | |
| dockerfile: docker-wrappers/MEO/Dockerfile | |
| repository: reedcompbio/meo | |
| tags: latest | |
| cache_froms: reedcompbio/meo:latest | |
| push: false | |
| - name: Remove MEO Docker image | |
| run: docker rmi reedcompbio/meo:latest || true | |
| - name: Build MinCostFlow Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/MinCostFlow/. | |
| dockerfile: docker-wrappers/MinCostFlow/Dockerfile | |
| repository: reedcompbio/mincostflow | |
| tags: latest | |
| cache_froms: reedcompbio/mincostflow:latest | |
| push: false | |
| - name: Remove MinCostFlow Docker image | |
| run: docker rmi reedcompbio/mincostflow:latest || true | |
| - name: Build All Pairs Shortest Paths Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/AllPairs/. | |
| dockerfile: docker-wrappers/AllPairs/Dockerfile | |
| repository: reedcompbio/allpairs | |
| tags: v2 | |
| cache_froms: reedcompbio/allpairs:latest | |
| push: false | |
| - name: Remove All Pairs Shortest Paths Docker image | |
| run: docker rmi reedcompbio/allpairs:latest || true | |
| - name: Build DOMINO Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/DOMINO/. | |
| dockerfile: docker-wrappers/DOMINO/Dockerfile | |
| repository: reedcompbio/domino | |
| tags: latest | |
| cache_froms: reedcompbio/domino:latest | |
| push: false | |
| - name: Remove DOMINO Docker image | |
| run: docker rmi reedcompbio/domino:latest || true | |
| - name: Build Cytoscape Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: docker-wrappers/Cytoscape/. | |
| dockerfile: docker-wrappers/Cytoscape/Dockerfile | |
| repository: reedcompbio/py4cytoscape | |
| tags: v3 | |
| cache_froms: reedcompbio/py4cytoscape:v3 | |
| push: false | |
| - name: Remove Cytoscape Docker image | |
| run: docker rmi reedcompbio/py4cytoscape:v3 || true | |
| - name: Build SPRAS Docker image | |
| uses: docker/build-push-action@v1 | |
| with: | |
| path: . | |
| dockerfile: docker-wrappers/SPRAS/Dockerfile | |
| repository: reedcompbio/spras | |
| tags: v0.2.0 | |
| cache_froms: reedcompbio/spras:v0.2.0 | |
| push: false | |
| - name: Remove SPRAS Docker image | |
| run: docker rmi reedcompbio/spras:v0.2.0 || true | |
| # Run pre-commit checks on source files | |
| pre-commit: | |
| name: Run pre-commit checks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Setup Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' # Match this to the version specified in environment.yml | |
| - name: Run pre-commit checks | |
| uses: pre-commit/[email protected] |