Merge pull request #186 from r-devel/devel

Version 0.3 release

.devcontainer/devcontainer.json

@@ -1,45 +1,31 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the 
-// README at: https://github.com/devcontainers/templates/tree/main/src/cpp 
 {
-	"name": "R-Dev-Env",
-	"image": "ghcr.io/r-devel/r-dev-env:main",
-	"hostRequirements": {
-		"cpus": 4
-	},
-
-	"customizations": {
-	    "vscode": {
-			"settings": {
-			    "r.lsp.diagnostics": false,
-			    "r.plot.useHttpgd": true,
-				"r.rpath.linux": "/usr/bin/R",
-				"r.rterm.linux": "/usr/bin/R",
-				"terminal.integrated.sendKeybindingsToShell": true,
-				"svn.multipleFolders.enabled": true,
+    "name": "R-Dev-Env",
+    "image": "ghcr.io/r-devel/r-dev-env:main",
+    "hostRequirements": {
+        "cpus": 4
+    },
+    "customizations": {
+        "vscode": {
+            "settings": {
+                "r.lsp.diagnostics": false,
+                "r.plot.useHttpgd": true,
+                "r.rpath.linux": "/usr/bin/R",
+                "r.rterm.linux": "/usr/bin/R",
+                "terminal.integrated.sendKeybindingsToShell": true,
+                "svn.multipleFolders.enabled": true,
                 "workbench.editorAssociations": {   
                     "*.md": "vscode.markdown.preview.editor"
                 },
                 "workbench.welcomePage.walkthroughs.openOnInstall": false
-			},
-			"extensions": [
-				"REditorSupport.r",
-				"mads-hartmann.bash-ide-vscode",
-				"johnstoncode.svn-scm",
-				"ms-vscode.cpptools",
-				"MS-vsliveshare.vsliveshare"
-			]
-		}
-
-	},
-	"postCreateCommand":"cat /workspaces/r-dev-env/scripts/welcome_msg.sh >> ~/.bashrc && cat /workspaces/r-dev-env/scripts/set_build_r.sh >> ~/.bashrc && bash /workspaces/r-dev-env/scripts/localscript.sh"
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	// "features": {},
-	// Use 'forwardPorts' to make a list of ports inside the container available locally.
-	// "forwardPorts": [],
-	// Use 'postCreateCommand' to run commands after the container is created.
-	// "postCreateCommand": "gcc -v",
-	// Configure tool-specific properties.
-	// "customizations": {},
-	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
-	// "remoteUser": "root"
+            },
+            "extensions": [
+                "REditorSupport.r",
+                "mads-hartmann.bash-ide-vscode",
+                "johnstoncode.svn-scm",
+                "ms-vscode.cpptools",
+                "MS-vsliveshare.vsliveshare"
+            ]
+        }
+    },
+    "postCreateCommand": "chown -R vscode:vscode /workspaces/r-dev-env && sh /workspaces/r-dev-env/scripts/localscript.sh"
 }

.github/workflows/build-gitpod-image.yml

@@ -0,0 +1,69 @@
+# This workflow uses actions that are not certified by GitHub.  
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.  
+
+name: Build and publish Gitpod Docker image
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: ["main","devel"]
+    types: [closed]
+    paths:
+      - '.github/workflows/build-gitpod-image.yml'
+      - '.gitpod.Dockerfile'
+      - '.gitpod.yml'
+      - 'reinstall-cmake.sh'
+      - 'VERSION'
+
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    if: ${{github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true}}
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Extract version number
+        run: |
+          VER=$(cat VERSION)
+          echo "VERSION=$VER" >> $GITHUB_ENV
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ github.repository }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{ env.VERSION }}
+            type=sha
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: .gitpod.Dockerfile
+          push: true
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:gitpod.${{ github.ref_name }}
+          build-args: |
+            CONTAINER_VERSION=${{ env.VERSION }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/optimize-docs-images.yml

@@ -0,0 +1,44 @@
+name: Optimize Docs Images
+
+on:
+  pull_request:
+    branches: ["main","devel"]
+    types: [closed]
+    paths:
+      - 'docs/assets/**'
+
+jobs:
+  optimize-images:
+    if: ${{github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true}}
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Setup R
+      uses: r-lib/actions/setup-r@v2
+
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libmagick++-dev libcurl4-openssl-dev
+
+    - name: Install R packages
+      run: |
+        R -e 'install.packages(c("magick"), repos = "https://cloud.r-project.org/")'
+
+    - name: Optimize images
+      run: |
+        Rscript ./scripts/optimize.R
+
+    - name: Commit and push optimized images
+      if: github.ref == 'refs/heads/devel' && github.event_name == 'push'
+      run: |
+        git config --global user.name "github-actions[bot]"
+        git config --global user.email "github-actions[bot]@users.noreply.github.com"
+        git add docs/assets
+        git commit -m 'Optimize docs images'
+        git push
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitpod.Dockerfile

@@ -0,0 +1,34 @@
+FROM gitpod/workspace-full:latest
+
+USER root
+
+ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="none"
+
+# Optionally install the cmake for vcpkg
+COPY ./reinstall-cmake.sh /tmp/
+
+RUN if [ "${REINSTALL_CMAKE_VERSION_FROM_SOURCE}" != "none" ]; then \
+    chmod +x /tmp/reinstall-cmake.sh && /tmp/reinstall-cmake.sh ${REINSTALL_CMAKE_VERSION_FROM_SOURCE}; \
+    fi \
+    && rm -f /tmp/reinstall-cmake.sh
+
+RUN sed -i.bak "/^#.*deb-src.*universe$/s/^# //g" /etc/apt/sources.list \
+    && echo "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/" >> /etc/apt/sources.list \
+    && wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
+    && apt update \
+    && apt -y install subversion \
+    && apt -y build-dep r-base-dev \
+    && apt -y install r-base-dev \
+    && apt -y install valgrind \
+    && Rscript -e "install.packages('languageserver', repos='https://cran.rstudio.com')" \
+    && Rscript -e "install.packages('httpgd', repos='https://cran.rstudio.com')"
+
+RUN apt install -y shellcheck
+RUN apt install -y ccache
+RUN apt install -y rsync
+#RUN /usr/sbin/update-ccache-symlinks
+#RUN echo 'export PATH="/usr/lib/ccache:$PATH"' | tee -a /home/vscode/.bashrc
+
+
+ARG CONTAINER_VERSION
+ENV CONTAINER_VERSION ${CONTAINER_VERSION}

.gitpod.yml

@@ -0,0 +1,13 @@
+image: ghcr.io/r-devel/r-dev-env:gitpod.devel
+
+tasks:
+    - name: Initial Setup for R-dev-env Gitpod Workspace
+      before: |
+         bash /workspace/r-dev-env/scripts/localscript.sh
+         source ~/.bashrc
+
+
+vscode:
+    extensions:
+     - REditorSupport.r
+     - johnstoncode.svn-scm

CITATION.cff

@@ -1,15 +1,20 @@
-cff-version: 1.2.0
-message: "If you use this software, please cite it as below."
-authors:
-  - family-names: Shirdhankar
-    given-names: Atharva
-  - family-names: Turner
-    given-names: Heather
-  - family-names: Tripp
-    given-names: James
-  - family-name: Emsley
-    given-names: Iain
-title: "R Development Container"
-version: 0.2.0
-doi: 
-date-released: 28-06-2024
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: Shirdhankar
+    given-names: Atharva
+  - family-names: Turner
+    given-names: Heather
+  - family-names: Tripp
+    given-names: James
+  - family-name: Emsley
+    given-names: Iain
+  - family-names: Crespo
+    given-names: Lorena
+  - family-names: Campitelli
+    given-names: Elio
+
+title: "R Development Container"
+version: 0.3.0
+doi: 
+date-released: 04-09-2024

Dockerfile

@@ -26,8 +26,6 @@ RUN apt install -y ccache
 #RUN echo 'export PATH="/usr/lib/ccache:$PATH"' | tee -a /home/vscode/.bashrc
 
 
-ENV BUILDDIR="/workspaces/r-dev-env/build/r-devel"
-ENV TOP_SRCDIR="/workspaces/r-dev-env/svn/r-devel"
-ENV PATCHDIR='/workspaces/r-dev-env/patches'
+
 ARG CONTAINER_VERSION
 ENV CONTAINER_VERSION ${CONTAINER_VERSION}

INDEX.md

@@ -3,9 +3,27 @@
 If you haven't seen them yet, you can find the
 [R Dev Container Docs](https://contributor.r-project.org/r-dev-env/) online.
 
+This index links to underlying markdown files for key sections of the docs, so you can preview them right here in VS Code. 
+
+## Working with the container
+
+The links below give more information on using the container via GitHub Codespaces or Gitpod Workspaces.
+Take a moment to review how to stop and restart your container, so you can continue your work.
+If you are collaborating with others, you may want to use Live Share so that you can share the same workspace.
+
+### Github Codespace
+
+- [Stopping and Restarting Codespace](docs/container_setup/github_codespace/codespacestartstop.md)
+- [Collaborating with Live Share](docs/container_setup/github_codespace/live_share.md)
+
+### Gitpod Workspace
+
+- [Stopping and Restarting Codespace](docs/container_setup/gitpod_workspace/workspacestop_and_restart.md)
+- [Collaborating with Live Share](docs/container_setup/gitpod_workspace/live_share.md)
+
 ## Tutorials
 
-You can also preview the tutorials right here in VSCode, making them easier to work through. 
+Learn how to use the container with these mini tutorials. 
 If you have used R in VSCode before, you can skip Tutorial 1. 
 Tutorials 2 and 3 are the minimum to get started with R development. 
 You can run through these in about 30 minutes. 
@@ -19,9 +37,6 @@ You can refer to the remaining sections as needed!
 6. [Multiple R versions](docs/tutorials/multi_r_compilation.md)
 7. [SVN Help](docs/tutorials/svn_help.md)
 
-## Other Docs
+## Further docs
 
-- [Restarting And Stopping Codespace](docs/container_setup/codespacestartstop.md)
-- [Collaborating with Live Share]((docs/container_setup/live_share.md))
-- [Using R Dev Container Locally](docs/container_setup/localsetup.md)
-- [Useful Resources](docs/resources.md)
+See the [full documentation](https://contributor.r-project.org/r-dev-env/) for background information on this project, how to contribute to the [documentation](docs/contributor_guide/contributing_to_docs.md) or the [codebase](docs/contributor_guide/contributing_to_codebase.md), [external resources](docs/resources.md) and [troubleshooting](docs/troubleshoot.md).

NEWS.md

@@ -1,3 +1,13 @@
+## R Development Container 0.3
+
+- Implemented Gitpod setup with GitHub Actions workflow to build Docker images for the Gitpod workspace.
+- Improved `which_r` script with version choice validation and updated both `which_r` and `set_build_r` scripts for enhanced functionality.
+- Resolved local setup permission issues to ensure smoother operation within the devcontainer environment on Linux.
+- Restructured documentation to incorporate Gitpod alternative setup.
+- Implemented a workflow to optimize images so that documentation files are more lightweight.
+
+
+
 ## R Development Container 0.2
 
 - Documentation split into set of markdown files. These are used to create the documentation website https://contributor.r-project.org/r-dev-env/ and the user-focused pages can be accessed directly within the codespace, linked from an index that opens when the codespace first starts. New documentation pages/topics:

VERSION

@@ -1 +1 @@
-0.2.0
+0.3.0