Add Vignette and functions for Chembl #107
Workflow file for this run
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| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main, development] | |
| name: CI/CD | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - {os: macos-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'oldrel-1'} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.config.r }} | |
| http-user-agent: ${{ matrix.config.http-user-agent }} | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck | |
| needs: check | |
| - uses: r-lib/actions/check-r-package@v2 | |
| with: | |
| upload-snapshots: true | |
| Test-Docker-Build: | |
| # needs: R-CMD-check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Get TAG from DESCRIPTION | |
| run: | | |
| TAG=$(grep 'Version:' DESCRIPTION | grep -oE '[0-9]+(\.[0-9]+)*') | |
| echo "TAG=$TAG" >> $GITHUB_ENV | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Test Docker Build | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| platforms: linux/amd64 | |
| file: ./Dockerfile | |
| push: false | |
| Code-Coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr | |
| needs: coverage | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package"), | |
| token = "${{ secrets.CODECOV_TOKEN }}" | |
| ) | |
| shell: Rscript {0} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package | |
| Upload-Docker: | |
| if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/newAnnotationGx' | |
| # needs: R-CMD-check | |
| needs: R-CMD-check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Get TAG from DESCRIPTION | |
| run: | | |
| TAG=$(grep 'Version:' DESCRIPTION | grep -oE '[0-9]+(\.[0-9]+)*') | |
| echo "TAG=$TAG" >> $GITHUB_ENV | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.BHKLAB_DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.BHKLAB_DOCKERHUB_ACCESS_KEY }} | |
| - name: Login to the GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v3 | |
| with: | |
| images: | | |
| bhklab/annotationgx-r:${{ env.TAG }} | |
| bhklab/annotationgx-r:latest | |
| - name: Build | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| platforms: linux/amd64,linux/arm64 | |
| file: ./Dockerfile | |
| push: true | |
| tags: | | |
| bhklab/annotationgx-r:${{ env.TAG }} | |
| bhklab/annotationgx-r:latest |