ci: upgrade to biocthis::use_bioc_github_action('devel')

sgibb · sgibb · commit a85947b60d7b · 2024-04-24T10:15:30.000+02:00
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -5,7 +5,7 @@
 ## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
 ##
 ## You can add this workflow to other packages using:
-## > biocthis::use_bioc_github_action()
+## > biocthis::use_bioc_github_action("devel", testthat = TRUE, pkgdown = TRUE)
 ##
 ## Using GitHub Actions exposes you to many details about how R packages are
 ## compiled and installed in several operating system.s
@@ -52,10 +52,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
-          - { os: windows-latest, r: '4.2', bioc: '3.16'}
-          ## Check https://github.com/r-lib/actions/tree/v2/examples
+          - { os: ubuntu-latest, r: 'devel', bioc: '3.19', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: 'devel', bioc: '3.19'}
+          - { os: windows-latest, r: 'devel', bioc: '3.19'}
+          ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -76,10 +76,10 @@ jobs:
           echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
 
       ## Most of these steps are the same as the ones in
-      ## https://github.com/r-lib/actions/blob/v2/examples/check-standard.yaml
+      ## 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
@@ -102,26 +102,26 @@ 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-devel-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
       - 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-devel-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
 
-      - name: Install Linux system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
-          echo $sysreqs
-          sudo -s eval "$sysreqs"
+      # - name: Install Linux system dependencies
+      #   if: runner.os == 'Linux'
+      #   run: |
+      #     sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
+      #     echo $sysreqs
+      #     sudo -s eval "$sysreqs"
 
       - name: Install macOS system dependencies
         if: matrix.config.os == 'macOS-latest'
@@ -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/3.16/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}
@@ -210,15 +194,15 @@ 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")
+          remotes::install_github("r-lib/pkgdown")
         shell: Rscript {0}
 
       - name: Session info
@@ -266,46 +250,89 @@ 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()
+          covr::codecov(coverage = covr::package_coverage(type = "all"))
         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 "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          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-devel-r-4.2-results
+          name: ${{ runner.os }}-biocversion-devel-r-devel-results
           path: check
 
-        ## Note that DOCKER_PASSWORD is really a token for your dockerhub
-        ## account, not your actual dockerhub account password.
-        ## This comes from
-        ## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
-        ## Check https://github.com/docker/build-push-action/tree/releases/v1
-        ## for more details.
-      - 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: sgibb/cleaver
-          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
