Merge branch 'master' into amplicon_extract

brendanf · Sep 26, 2024 · bd1e205 · bd1e205
2 parents 25c6260 + 51de0bc
commit bd1e205
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diff --git a/.github/.gitignore b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/check-bioc.yaml → .github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yaml → .github/workflows/check-bioc.yml
@@ -34,8 +34,8 @@ name: R-CMD-check-bioc
 ## Note that you can always run a GHA test without the cache by using the word
 ## "/nocache" in the commit message.
 env:
-  has_testthat: 'true'
-  run_covr: 'true'
+  has_testthat: 'false'
+  run_covr: 'false'
   run_pkgdown: 'false'
   has_RUnit: 'false'
   cache-version: 'cache-v1'
@@ -52,8 +52,10 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: '4.2', bioc: '3.16'}
+          - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
+          ## 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
       RSPM: ${{ matrix.config.rspm }}
@@ -102,24 +104,23 @@ jobs:
         uses: actions/cache@v3
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
 
       - name: Cache R packages on Linux
         if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
         uses: actions/cache@v3
         with:
           path: /home/runner/work/_temp/Library
-          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.0-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
+          key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-
 
-      - 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"
-          sudo apt-get install -y infernal
+      # - 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'
@@ -171,20 +172,9 @@ 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/{{biocvernum}}/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
@@ -212,13 +202,13 @@ 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}
@@ -268,13 +258,13 @@ 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 pkgdown site
@@ -303,21 +293,54 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@master
         with:
-          name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
+          name: ${{ runner.os }}-biocversion-RELEASE_3_18-r-4.3-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: brendanf/inferrnal
-          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