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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -52,9 +52,9 @@ jobs: | |
| fail-fast: false | ||
| matrix: | ||
| config: | ||
| - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
| - { os: macOS-latest, r: '4.1', bioc: '3.14'} | ||
| - { os: windows-latest, r: '4.1', bioc: '3.14'} | ||
| - { os: ubuntu-latest, r: '4.3', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } | ||
| - { os: macOS-latest, r: '4.3', bioc: '3.17'} | ||
| - { os: windows-latest, r: '4.3', bioc: '3.17'} | ||
| ## Check https://github.com/r-lib/actions/tree/master/examples | ||
| ## for examples using the http-user-agent | ||
| env: | ||
|
|
@@ -79,20 +79,20 @@ jobs: | |
| ## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | ||
| ## If they update their steps, we will also need to update ours. | ||
| - name: Checkout Repository | ||
| uses: actions/checkout@v2 | ||
| uses: actions/checkout@v3 | ||
|
|
||
| ## R is already included in the Bioconductor docker images | ||
| - name: Setup R from r-lib | ||
| if: runner.os != 'Linux' | ||
| uses: r-lib/actions/setup-r@master | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: ${{ matrix.config.r }} | ||
| http-user-agent: ${{ matrix.config.http-user-agent }} | ||
|
|
||
| ## pandoc is already included in the Bioconductor docker images | ||
| - name: Setup pandoc from r-lib | ||
| if: runner.os != 'Linux' | ||
| uses: r-lib/actions/setup-pandoc@master | ||
| uses: r-lib/actions/setup-pandoc@v2 | ||
|
|
||
| - name: Query dependencies | ||
| run: | | ||
|
|
@@ -102,19 +102,19 @@ jobs: | |
|
|
||
| - name: Restore R package cache | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | ||
| uses: actions/cache@v2 | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: ${{ env.R_LIBS_USER }} | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1- | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3- | ||
|
|
||
| - name: Cache R packages on Linux | ||
| if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | ||
| uses: actions/cache@v2 | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: /home/runner/work/_temp/Library | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1- | ||
| key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-${{ hashFiles('.github/depends.Rds') }} | ||
| restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3- | ||
|
|
||
| - name: Install Linux system dependencies | ||
| if: runner.os == 'Linux' | ||
|
|
@@ -169,35 +169,19 @@ jobs: | |
| ## https://github.com/r-lib/remotes/issues/296 | ||
| ## Ideally, all dependencies should get installed in the first pass. | ||
| ## Set the repos source depending on the OS | ||
| ## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/ | ||
| ## though based on https://bit.ly/bioc2021-package-binaries | ||
| ## the Azure link will be the main one going forward. | ||
| gha_repos <- if( | ||
| .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin" | ||
| ) c( | ||
| "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.14/bioc", | ||
| BiocManager::repositories() | ||
| ) else BiocManager::repositories() | ||
| ## For running the checks | ||
| message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | ||
| install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos) | ||
| install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) | ||
| ## Pass #1 at installing dependencies | ||
| ## This pass uses AnVIL-powered fast binaries | ||
| ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries | ||
| ## The speed gains only apply to the docker builds. | ||
| message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | ||
| remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE) | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE) | ||
| continue-on-error: true | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install dependencies pass 2 | ||
| run: | | ||
| ## Pass #2 at installing dependencies | ||
| ## This pass does not use AnVIL and will thus update any packages | ||
| ## that have seen been updated in Bioconductor | ||
| message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****')) | ||
| remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | ||
| shell: Rscript {0} | ||
|
|
@@ -210,13 +194,13 @@ jobs: | |
| shell: Rscript {0} | ||
|
|
||
| - name: Install covr | ||
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| remotes::install_cran("covr") | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install pkgdown | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| remotes::install_cran("pkgdown") | ||
| shell: Rscript {0} | ||
|
|
@@ -267,40 +251,89 @@ jobs: | |
| shell: Rscript {0} | ||
|
|
||
| - name: Test coverage | ||
| if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| covr::codecov() | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Install package | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: R CMD INSTALL . | ||
|
|
||
| - name: Build and deploy pkgdown site | ||
| if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| git config --local user.name "$GITHUB_ACTOR" | ||
| git config --local user.email "[email protected]" | ||
| Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" | ||
| shell: bash {0} | ||
| - name: Build pkgdown site | ||
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
| ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) | ||
| ## at least one locally before this will work. This creates the gh-pages | ||
| ## branch (erasing anything you haven't version controlled!) and | ||
| ## makes the git history recognizable by pkgdown. | ||
|
|
||
| - name: Install deploy dependencies | ||
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| run: | | ||
| apt-get update && apt-get -y install rsync | ||
| - name: Deploy pkgdown site to GitHub pages 🚀 | ||
| if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
| uses: JamesIves/github-pages-deploy-action@releases/v4 | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs | ||
|
|
||
| - name: Upload check results | ||
| if: failure() | ||
| uses: actions/upload-artifact@master | ||
| with: | ||
| name: ${{ runner.os }}-biocversion-RELEASE_3_14-r-4.1-results | ||
| name: ${{ runner.os }}-biocversion-RELEASE_3_17-r-4.3-results | ||
| path: check | ||
|
|
||
| - uses: docker/build-push-action@v1 | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " | ||
|
|
||
| ## Code adapted from | ||
| ## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92 | ||
| docker-build-and-push: | ||
| runs-on: ubuntu-latest | ||
| needs: build-check | ||
| steps: | ||
| - name: Checkout Repository | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Register repo name | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| id: reg_repo_name | ||
| run: | | ||
| echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV | ||
| - name: Set up QEMU | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: docker/setup-qemu-action@v2 | ||
|
|
||
| - name: Set up Docker Buildx | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: docker/setup-buildx-action@v2 | ||
|
|
||
| - name: Login to Docker Hub | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'" | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKERHUB_USERNAME }} | ||
| password: ${{ secrets.DOCKERHUB_TOKEN }} | ||
| ## Note that DOCKERHUB_TOKEN is really a token for your dockerhub | ||
| ## account, not your actual dockerhub account password. You can get it | ||
| ## from https://hub.docker.com/settings/security. | ||
| ## Check https://github.com/docker/build-push-action/tree/v4.0.0 | ||
| ## for more details. | ||
| ## Alternatively, try checking | ||
| ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html. | ||
|
|
||
| - name: Build and Push Docker | ||
| if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()" | ||
| uses: docker/build-push-action@v4 | ||
| with: | ||
| username: ${{ secrets.DOCKER_USERNAME }} | ||
| password: ${{ secrets.DOCKER_PASSWORD }} | ||
| repository: lieberinstitute/megadepth | ||
| tag_with_ref: true | ||
| tag_with_sha: true | ||
| tags: latest | ||
| context: . | ||
| push: true | ||
| tags: > | ||
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest, | ||
| ${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel | ||