added segmentation #9
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| name: Check, build, and push image | |
| on: [push, pull_request] | |
| env: | |
| cache-version: v1 | |
| jobs: | |
| r-build-and-check: | |
| runs-on: ubuntu-latest | |
| container: bioconductor/bioconductor_docker:devel | |
| env: | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Query dependencies and update old packages | |
| run: | | |
| BiocManager::install(ask=FALSE) | |
| saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | |
| shell: Rscript {0} | |
| - name: Cache R packages | |
| if: runner.os != 'Windows' | |
| uses: actions/cache@v1 | |
| with: | |
| path: /usr/local/lib/R/site-library | |
| key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }} | |
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-r- | |
| # This lets us augment with additional dependencies | |
| - name: Install system dependencies | |
| if: runner.os == 'Linux' | |
| env: | |
| RHUB_PLATFORM: linux-x86_64-ubuntu-gcc | |
| run: | | |
| Rscript -e "remotes::install_github('r-hub/sysreqs')" | |
| sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") | |
| sudo -s eval "$sysreqs" | |
| - name: Install dependencies | |
| run: | | |
| BiocManager::repositories() | |
| remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories()) | |
| remotes::install_cran("rcmdcheck") | |
| shell: Rscript {0} | |
| - name: Check | |
| env: | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check") | |
| shell: Rscript {0} | |
| - name: Build pkgdown | |
| run: | | |
| PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")' | |
| # deploy needs rsync? Seems so. | |
| - name: Install deploy dependencies | |
| run: | | |
| apt-get update | |
| apt-get -y install rsync | |
| - name: Deploy 🚀 | |
| uses: JamesIves/github-pages-deploy-action@releases/v4 | |
| with: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| BRANCH: gh-pages # The branch the action should deploy to. | |
| FOLDER: docs # The folder the action should deploy. | |
| docker-build-and-push: | |
| #needs: r-build-and-check | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| # This is used to complete the identity challenge | |
| # with sigstore/fulcio when running outside of PRs. | |
| id-token: write | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set Environment Variables | |
| run: | | |
| REPO_LOWER="$(echo "${{ github.repository }}" | tr '[:upper:]' '[:lower:]')" | |
| REGISTRY=ghcr.io | |
| echo "BUILD_DATE=$(date +'%Y-%m-%d %H:%M:%S')" >> $GITHUB_ENV | |
| echo "GIT_SHA=$(echo ${{ github.sha }} | cut -c1-7)" >> $GITHUB_ENV | |
| echo "REGISTRY=${REGISTRY}" >> $GITHUB_ENV | |
| echo "IMAGE=${REGISTRY}/${REPO_LOWER}" >> $GITHUB_ENV | |
| - name: Show environment | |
| run: | | |
| env | |
| # Install the cosign tool except on PR | |
| # https://github.com/sigstore/cosign-installer | |
| - name: Install cosign | |
| if: github.event_name != 'pull_request' | |
| uses: sigstore/cosign-installer@1e95c1de343b5b0c23352d6417ee3e48d5bcd422 | |
| with: | |
| cosign-release: 'v1.4.0' | |
| # Workaround: https://github.com/docker/build-push-action/issues/461 | |
| - name: Setup Docker buildx | |
| uses: docker/setup-buildx-action@79abd3f86f79a9d68a23c75a09a9a85889262adf | |
| # Login against a Docker registry except on PR | |
| # https://github.com/docker/login-action | |
| - name: Log into registry ${{ env.REGISTRY }} | |
| if: github.event_name != 'pull_request' | |
| uses: docker/login-action@28218f9b04b4f3f62068d7b6ce6ca5b26e35336c | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| # Extract metadata (tags, labels) for Docker | |
| # https://github.com/docker/metadata-action | |
| - name: Extract Docker metadata | |
| id: meta | |
| uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 | |
| with: | |
| images: ${{ env.IMAGE }} | |
| # Build and push Docker image with Buildx (don't push on PR) | |
| # https://github.com/docker/build-push-action | |
| - name: Build and push Docker image | |
| id: build-and-push | |
| uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc | |
| with: | |
| context: . | |
| push: ${{ github.event_name != 'pull_request' }} | |
| tags: | | |
| ${{ env.IMAGE }}:latest | |
| ${{ env.IMAGE }}:${{ env.GIT_SHA }} | |