upgrade docker steps

neurogenomics · Oct 12, 2023 · 19a7bd1 · 19a7bd1
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commit 19a7bd1
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diff --git a/action.yml b/action.yml
@@ -70,9 +70,9 @@ inputs:
     description: >
       Docker container registry. 
       Options include:
-      - ghcr.io/ : [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry}{GitHub Container Registry)
-      - docker.io/ : [DockerHub](https://hub.docker.com/) 
-    default: 'ghcr.io/'
+      - ghcr.io : [GitHub Container Registry](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry}{GitHub Container Registry)
+      - docker.io : [DockerHub](https://hub.docker.com/) 
+    default: 'ghcr.io'
   docker_user: 
     description: >
       DockerHub username. 
@@ -154,7 +154,7 @@ inputs:
 runs:
   using: 'composite'
   steps:
-    - name: Set GitHub environment variables ️🌎
+    - name: 🌎 Set environment variables 
       run: | 
         echo "GITHUB_TOKEN=${{ inputs.GITHUB_TOKEN }}" >> $GITHUB_ENV
         echo "RGL_USE_NULL=TRUE" >> $GITHUB_ENV
@@ -168,7 +168,7 @@ runs:
       uses: runforesight/workflow-telemetry-action@v1
       continue-on-error: true
 
-    ## Setup Miniconda 🐍
+    ## 🐍 Setup Miniconda 
     - name: Setup Miniconda
       if: inputs.miniforge_variant != 'false'
       uses: conda-incubator/setup-miniconda@v2
@@ -183,7 +183,7 @@ runs:
 
     ## Set the R library to the directory matching the
     ## R packages cache step further below when running on Docker (Linux).
-    - name: Set R library home on Linux 📚
+    - name: 📚 Set R library home on Linux 
       if: runner.os == 'Linux'
       run: |
         mkdir -p /__w/_temp/Library
@@ -194,51 +194,51 @@ runs:
     ## Most of these steps are the same as the ones in
     ## 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 ⏬
+    - name: ⏬ Checkout repository 
       uses: actions/checkout@v4
 
     ## R/Bioc are already installed on the Bioc Docker container, 
     ## and reinstalling them causes errors.
-    - name: Setup R and Bioconductor 🛠
+    - name: 🛠 Setup R and Bioconductor 
       if: runner.os != 'Linux'
       uses: grimbough/bioc-actions/setup-bioc@v1
       with:
         bioc-version: ${{ matrix.config.bioc }}
 
     ## pandoc is already included in the Bioconductor docker images
-    - name: Install Pandoc 🛠
+    - name: 🛠 Install Pandoc 
       if: inputs.pandoc_version != 'false' && runner.os != 'Linux'
       uses: r-lib/actions/setup-pandoc@v2
       with: 
         pandoc-version: ${{ inputs.pandoc_version }} 
 
-    - name: Query dependencies ❔
+    - name: ❔ Query dependencies 
       run: |
         options(crayon.enabled = TRUE)
         install.packages('remotes')
         remotes::install_github("r-lib/remotes")
         saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
       shell: Rscript {0}
 
-    - name: Restore R package cache 🏦
+    - name: 🏦 Restore R package cache 
       if: |
-        !contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'
+        !contains(github.event.head_commit.message, '[nocache]') && runner.os != 'Linux'
       uses: actions/cache@v3
       with:
         path: ${{ env.R_LIBS_USER }}
         key: ${{ inputs.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
         restore-keys: ${{ inputs.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-
 
-    - name: Cache R packages on Linux 🏦
+    - name: 🏦 Cache R packages on Linux 
       if: |
-        !contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux'
+        !contains(github.event.head_commit.message, '[nocache]') && runner.os == 'Linux'
       uses: actions/cache@v3
       with:
         path: /home/runner/work/_temp/Library
         key: ${{ inputs.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }}
         restore-keys: ${{ inputs.cache_version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-
 
-    - name: Install Linux system dependencies 🛠 
+    - 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 = " "))')
@@ -247,7 +247,7 @@ runs:
         sudo apt-get install -y qpdf rsync
       shell: bash {0}
 
-    - name: Install macOS system dependencies 🛠
+    - name: 🛠 Install macOS system dependencies 
       if: runner.os == 'macOS'
       run: |
         #### --- Justifications for each package --- ####
@@ -276,21 +276,21 @@ runs:
         echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
       shell: bash {0}
 
-    - name: Install Windows system dependencies 🛠
+    - name: 🛠 Install Windows system dependencies 
       if: inputs.has_latex == 'true' && runner.os == 'Windows'
       run: |
         #### npm ####
         npm install curl
       shell: pwsh {0}
 
-    - name: Install latex 🛠
+    - name: 🛠 Install latex 
       if: inputs.has_latex == 'true'
       uses: r-lib/actions/setup-tinytex@v2
       env: 
         TINYTEX_INSTALLER: ${{ inputs.tinytex_installer }}
         TINYTEX_VERSION: ${{ inputs.tinytex_version }}
 
-    - name: Install latex packages 🛠
+    - name: 🛠 Install latex packages 
       if: inputs.has_latex == 'true'
       env:
         tinytex_installer: ${{ inputs.tinytex_installer }}
@@ -304,7 +304,7 @@ runs:
         tinytex::tlmgr_install(pkgs = extra_packages)
       shell: Rscript {0} 
 
-    - name: Install dependencies pass 1 🛠
+    - name: 🛠 Install dependencies pass 1 
       env:
         timeout: ${{ inputs.timeout }}
       run: |
@@ -318,7 +318,7 @@ runs:
       continue-on-error: true
       shell: Rscript {0}
 
-    - name: Install dependencies pass 2 🛠
+    - name: 🛠 Install dependencies pass 2 
       env:
         timeout: ${{ inputs.timeout }}
       run: |
@@ -328,28 +328,28 @@ runs:
         remotes::install_local(repos=repos, dependencies=TRUE, build_vignettes=FALSE, upgrade=TRUE, force=TRUE)
       shell: Rscript {0}
 
-    - name: Install RUnit (via BiocGenerics) 🛠
+    - name: 🛠 Install RUnit (via BiocGenerics) 
       if:  inputs.has_runit == 'true'
       run: |
         options(crayon.enabled = TRUE)
         BiocManager::install("BiocGenerics")
       shell: Rscript {0}
 
-    - name: Install covr 🛠
+    - name: 🛠 Install covr 
       if: inputs.run_covr == 'true' && runner.os == 'Linux'
       run: |
         options(crayon.enabled = TRUE)
         install.packages("covr")
       shell: Rscript {0}
 
-    - name: Install pkgdown 🛠
+    - name: 🛠 Install pkgdown 
       if: inputs.run_pkgdown == 'true' && runner.os == 'Linux'
       run: |
         options(crayon.enabled = TRUE)
         install.packages("pkgdown")
       shell: Rscript {0}
 
-    - name: Session info ℹ️
+    - name: ℹ️ Session info ️
       run: |
         options(width = 100, crayon.enabled = TRUE)
         pkgs <- installed.packages()[,"Package"]
@@ -359,7 +359,7 @@ runs:
         }, error = function(x){utils::sessionInfo()})
       shell: Rscript {0}
 
-    - name: Run CMD check ✅
+    - name: ✅ Run CMD check 
       if: inputs.run_rcmdcheck == 'true'
       env:
         _R_CHECK_CRAN_INCOMING_: false
@@ -381,13 +381,13 @@ runs:
             check_dir = "check")
       shell: Rscript {0}
 
-    - name: Reveal testthat details 📋
+    - name: 📋 Reveal testthat details 
       if: inputs.has_testthat == 'true'
       run: |
         find . -name testthat.Rout -exec cat '{}' ';'
       shell: bash {0}
 
-    - name: Run RUnit tests (via BiocGenerics) 📋
+    - name: 📋 Run RUnit tests (via BiocGenerics) 
       if: inputs.has_runit == 'true'
       env:
         timeout: ${{ inputs.timeout }}
@@ -396,7 +396,7 @@ runs:
         BiocGenerics:::testPackage()
       shell: Rscript {0}
 
-    - name: Run BiocCheck ✅
+    - name: ✅ Run BiocCheck 
       if: inputs.run_bioccheck == 'true'
       env:
         DISPLAY: 99.0
@@ -422,18 +422,18 @@ runs:
             `no-check-bioc-help` = as_cran)
       shell: Rscript {0}
 
-    - name: Test coverage 📋
+    - name: 📋 Test coverage 
       if: inputs.run_covr == 'true' && runner.os == 'Linux'
       run: |
         covr::codecov()
       shell: Rscript {0} 
 
-    - name: Install package 🛠️
+    - name: 🛠 Install package ️
       if: inputs.run_pkgdown == 'true' && runner.os == 'Linux'
       run: R CMD INSTALL .
       shell: bash {0}
 
-    - name: Get R package info ℹ️
+    - name: ℹ️ Get R package info 
       if: runner.os == 'Linux'
       run: |
         #### DockerHub repos must be lowercase (,,) ####
@@ -446,7 +446,7 @@ runs:
         echo $version
       shell: bash {0}
 
-    - name: Render README 📦
+    - name: 📦 Render README 
       if: inputs.run_pkgdown == 'true' && runner.os == 'Linux'
       env:
         DISPLAY: 99.0
@@ -458,14 +458,14 @@ runs:
         }
       shell: Rscript {0} 
 
-    - name: Build pkgdown site 📦
+    - name: 📦 Build pkgdown site 
       if: inputs.run_pkgdown == 'true' && runner.os == 'Linux'
       run: |
         options(crayon.enabled = TRUE)
         pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
       shell: Rscript {0}
 
-    - name: Deploy pkgdown site to GitHub pages 📦 🚀
+    - name: 📦🚀 Deploy pkgdown site to GitHub pages 
       if: inputs.run_pkgdown == 'true' && runner.os == 'Linux'
       uses: JamesIves/github-pages-deploy-action@releases/v4
       with:
@@ -474,32 +474,61 @@ runs:
         folder: docs
         token: ${{ inputs.GITHUB_TOKEN }}
 
-    - name: Upload check results ⏫
+    - name: ⏫ Upload check results 
       if: failure()
       uses: actions/upload-artifact@v3
       with:
         name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{  matrix.config.r }}-results
         path: check 
 
-    ## DockerHub steps
-    - name: Create Docker file 🐳
+    #### Docker registry steps ####
+    - name: 🐳🛠 Set up Docker Buildx
       if: |
-        (!contains(github.event.head_commit.message, '/nodocker')) && inputs.run_docker == 'true' && runner.os == 'Linux'
+        (!contains(github.event.head_commit.message, '[nodocker]')) && inputs.run_docker == 'true' && runner.os == 'Linux'
+      uses: docker/setup-buildx-action@v3
+
+    - name: 🐳🛠 Set up QEMU
+      if: |
+        (!contains(github.event.head_commit.message, '[nodocker]')) && inputs.run_docker == 'true' && runner.os == 'Linux'
+      uses: docker/setup-qemu-action@v3
+
+    - name: 🐳🔐 Log in to the Github Container registry - ghcr.io
+      if : |
+        (!contains(github.event.head_commit.message, '[nodocker]')) && inputs.run_docker == 'true' && runner.os == 'Linux' && inputs.docker_registry == 'ghcr.io'
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ env.owner }}
+        password: ${{ inputs.GITHUB_TOKEN }}
+
+    - name: 🐳🔐 Log in to the Github Container registry - docker.io
+      if: |
+        (!contains(github.event.head_commit.message, '[nodocker]')) && inputs.run_docker == 'true' && runner.os == 'Linux' && inputs.docker_registry == 'docker.io'
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ inputs.docker_user }}
+        password: ${{ inputs.DOCKER_TOKEN }} 
+
+    - name: 🐳✏️ Create Docker file 
+      if: |
+        (!contains(github.event.head_commit.message, '[nodocker]')) && inputs.run_docker == 'true' && runner.os == 'Linux'
       run: |
         options(crayon.enabled = TRUE)
         if(!require("rworkflows", quietly=TRUE)) remotes::install_github("neurogenomics/rworkflows")
         path <- rworkflows::use_dockerfile()
       shell: Rscript {0} 
 
-    - name: Build and push to Docker registry 🐳 🚀
+    - name: 🐳🚀 Build and push to Docker registry 
       if: |
-        (!contains(github.event.head_commit.message, '/nodocker')) && inputs.run_docker == 'true' && runner.os == 'Linux'
-      uses: docker/build-push-action@v1
+        (!contains(github.event.head_commit.message, '[nodocker]')) && inputs.run_docker == 'true' && runner.os == 'Linux'
+      uses: docker/build-push-action@v5
       with:
-        username: ${{ inputs.docker_user }}
-        password: ${{ inputs.DOCKER_TOKEN }}
-        repository: ${{ inputs.docker_registry }}/${{ inputs.docker_org }}/${{ env.packageName }}
-        tag_with_ref: true
-        tag_with_sha: false
-        tags: ${{ env.packageVersion }},latest
-        build_args: PKG=${{ env.packageNameOrig }}
+        repository: 
+        push: true
+        tags: |
+          ${{ inputs.docker_registry }}/${{ inputs.docker_org }}/${{ env.packageName }}:${{ env.packageVersion }},
+          ${{ inputs.docker_registry }}/${{ inputs.docker_org }}/${{ env.packageName }}:latest
+        build_args: |
+          PKG=${{ env.packageNameOrig }},
+          CONT=${{ matrix.config.cont }}
diff --git a/inst/templates/Dockerfile b/inst/templates/Dockerfile
@@ -18,7 +18,7 @@
 # and you can set the password to whatever you like,
 #
 # This DockerFile was partly adapted from the [scFlow Dockerfile](https://github.com/combiz/scFlow/blob/master/Dockerfile).
-FROM bioconductor/bioconductor_docker:devel
+FROM $CONT
 RUN apt-get update && \
     apt-get install -y \
     git-core \
@@ -29,13 +29,13 @@ RUN apt-get update && \
     make pandoc \
     pandoc-citeproc \
     zlib1g-dev \
-	xfonts-100dpi \
-	xfonts-75dpi \
-	biber \
-	libsbml5-dev \
-	qpdf \
-	cmake \
-	&& apt-get clean \
+  	xfonts-100dpi \
+  	xfonts-75dpi \
+  	biber \
+  	libsbml5-dev \
+  	qpdf \
+  	cmake \
+  	&& apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 # Create a buildzone folder named after the R package
 # BiocCheck requires the buildzone to have the same name as the R package