Merge branch 'devel' into update/dynamic-url

Author: hturner

.devcontainer/devcontainer.json

@@ -7,6 +7,9 @@
     "customizations": {
         "vscode": {
             "settings": {
+                "editor.tabSize": 8,
+                "editor.indentSize": 4,
+                "editor.detectIndentation": false,
                 "r.lsp.diagnostics": false,
                 "r.plot.useHttpgd": true,
                 "r.rpath.linux": "/usr/bin/R",

.github/workflows/build-and-publish-image.yml

@@ -16,18 +16,20 @@ on:
       - 'reinstall-cmake.sh'
       - 'VERSION'
 
+permissions:
+  contents: read
+  packages: write
 
 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}}
+    if:  |
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'pull_request' && github.event.pull_request.merged == true)
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
 
     steps:
       - name: Checkout repository

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

@@ -17,18 +17,20 @@ on:
       - 'reinstall-cmake.sh'
       - 'VERSION'
 
+permissions:
+  contents: read
+  packages: write
 
 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}}
+    if:  |
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'pull_request' && github.event.pull_request.merged == true)
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
 
     steps:
       - name: Checkout repository

.github/workflows/build-mkdocs-website.yml

@@ -10,34 +10,49 @@ on:
       - 'docs/**/**'
       - 'mkdocs.yml'
 
-permissions:
-  contents: write
-
 jobs:
   build-and-deploy:
     if: |
       github.event_name == 'workflow_dispatch' ||
       (github.event_name == 'pull_request' && github.event.pull_request.merged == true)
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.x
 
       - name: Install dependencies
         run: pip install mkdocs mkdocs-material[imaging]
 
+      - name: Determine deployment path
+        id: path
+        run: |
+          if [[ "${{ github.ref_name }}" == "main" ]]; then
+            echo "url=https://contributor.r-project.org/r-dev-env" >> "$GITHUB_OUTPUT"
+          else
+            echo "url=https://contributor.r-project.org/r-dev-env/devel" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Modify site_url in mkdocs.yml
+        run: |
+          echo "Setting site_url to ${{ steps.path.outputs.url }}"
+          sed -i "s|^site_url:.*|site_url: '${{ steps.path.outputs.url }}'|" mkdocs.yml
+
+
       - name: Build MkDocs
         run: mkdocs build
 
       - name: Deploy to GitHub Pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
+           git remote set-url origin https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}
            mkdocs gh-deploy --force
            git push origin gh-pages
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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

@@ -1,6 +1,7 @@
 name: Optimize Docs Images
 
 on:
+  workflow_dispatch:
   pull_request:
     branches: ["main","devel"]
     types: [closed]
@@ -9,7 +10,9 @@ on:
 
 jobs:
   optimize-images:
-    if: ${{github.event_name == 'pull_request' && github.event.action == 'closed' && github.event.pull_request.merged == true}}
+    if:  |
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'pull_request' && github.event.pull_request.merged == true)
     runs-on: ubuntu-latest
 
     steps:

.github/workflows/schedule-docker-build.yml

@@ -4,6 +4,9 @@ on:
   schedule:
     - cron: '0 0 1,15 * *'
 
+permissions:
+  contents: read
+  packages: write
 
 env:
   REGISTRY: ghcr.io
@@ -12,9 +15,6 @@ env:
 jobs:
   build-and-push-image:
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
     strategy:
       matrix:
         branch: [main, devel]

Dockerfile

@@ -18,6 +18,7 @@ RUN sed -i.bak "/^#.*deb-src.*universe$/s/^# //g" /etc/apt/sources.list \
       subversion \
     && add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0" \
     && wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc \
+    && apt -y build-dep r-base-dev \
     && apt-get install -y r-base-dev \
     && rm -rf /var/lib/apt/lists/*
 
@@ -32,16 +33,5 @@ RUN Rscript -e "runiverse <- sprintf('r-universe.dev/bin/linux/%s-%s/%s/', \
                            nx10 = paste0('https://nx10.', runiverse))); \
                 print('Packages installed.')"
 
-
-# Install ShellCheck using apt-get from the PPA
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends \
-    shellcheck
-
-# Install ccache
-RUN apt-get install -y --no-install-recommends \
-    ccache \
-    && rm -rf /var/lib/apt/lists/*
-
 ARG CONTAINER_VERSION
-ENV CONTAINER_VERSION=${CONTAINER_VERSION}
+ENV CONTAINER_VERSION=${CONTAINER_VERSION}

mkdocs.yml

@@ -1,4 +1,5 @@
 site_name: R Devel Container Docs
+site_url: ''
 repo_name: r-devel/r-dev-env
 repo_url: https://github.com/r-devel/r-dev-env
 nav: