forgot to add this to prev commit #61
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| name: Docker Image CI | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: rocker/verse:latest | |
| strategy: | |
| matrix: | |
| TEST_DATA: [ | |
| "inst/extdata/ExampleDb.tsv", | |
| "test_repertoires/airr-covid-19.tsv", | |
| "test_repertoires/PRJNA381394_12.tsv" | |
| ] | |
| FORMAT: [ | |
| "html", | |
| "pdf" | |
| ] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") | |
| BiocManager::install(c("Biostrings", "GenomicAlignments", "IRanges")) | |
| install.packages(c("airr", "alakazam", "ape", "ggpubr", "kableExtra", "optparse")) | |
| shell: Rscript {0} | |
| - name: Document | |
| run: | | |
| devtools::document() | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_: false | |
| run: | | |
| options(crayon.enabled=TRUE) | |
| rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran", "--run-donttest"), error_on="warning", check_dir="check") | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Install repcred | |
| run: | | |
| devtools::install(".") | |
| shell: Rscript {0} | |
| - name: Run tests matrix | |
| run: | | |
| inst/repcred.R -r ${{ matrix.TEST_DATA }} -o outdir -d TRUE -f ${{ matrix.FORMAT }} | |
| - name: Create artifact name | |
| run: | | |
| test_name="${{ matrix.FORMAT }}_${{ matrix.TEST_DATA }}" | |
| artifact_name=$(echo -n "$test_name" | sed -e 's/\//_/g' | sed -e 's/.tsv$//g' ) | |
| echo "ARTIFACT_NAME=$artifact_name" >> $GITHUB_ENV | |
| - name: Archive results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: "repcred-report_${{ env.ARTIFACT_NAME }}" | |
| path: | | |
| outdir/results | |
| build-container: | |
| runs-on: ubuntu-latest | |
| needs: R-CMD-check | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | |
| - name: Build and push to Docker | |
| uses: docker/build-push-action@v4 | |
| with: | |
| context: ./docker | |
| file: ./docker/Dockerfile | |
| push: true | |
| no-cache: true | |
| tags: airrc/rep-cred:latest | |
| test-container: | |
| runs-on: ubuntu-latest | |
| needs: build-container | |
| container: | |
| image: airrc/rep-cred:latest | |
| strategy: | |
| matrix: | |
| TEST_DATA: [ | |
| "test_repertoires/airr-covid-19.tsv" | |
| ] | |
| FORMAT: [ | |
| "html", | |
| "pdf" | |
| ] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Run repcred command | |
| run: | | |
| repcred -r ${{ matrix.TEST_DATA }} -o outdir -d TRUE -f ${{ matrix.FORMAT }} |