Merge branch 'direction' of github.com:ntalluri/spras into direction #89
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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: 1.1.3 | |
| - 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:latest | |
| docker pull reedcompbio/meo:latest | |
| docker pull reedcompbio/mincostflow:latest | |
| docker pull reedcompbio/allpairs:latest | |
| docker pull reedcompbio/domino:latest | |
| - 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: 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:v2 | |
| push: false | |
| - 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: latest | |
| cache_froms: reedcompbio/pathlinker:latest | |
| push: false | |
| - 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: 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: 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: latest | |
| cache_froms: reedcompbio/allpairs:latest | |
| push: false | |
| - 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 | |
| # 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: '3.8' # Match this to the version specified in environment.yml | |
| - name: Run pre-commit checks | |
| uses: pre-commit/[email protected] |