Merge branch 'devel' into scripts/localhost_shebang_fix

Author: hturner

.devcontainer/devcontainer.json

@@ -7,13 +7,16 @@
     "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",
                 "r.rterm.linux": "/usr/bin/R",
                 "terminal.integrated.sendKeybindingsToShell": true,
                 "svn.multipleFolders.enabled": true,
-                "workbench.editorAssociations": {   
+                "workbench.editorAssociations": {
                     "*.md": "vscode.markdown.preview.editor"
                 },
                 "workbench.welcomePage.walkthroughs.openOnInstall": false

.github/ISSUE_TEMPLATE/release-new-version-of-devcontainer.md

@@ -9,12 +9,12 @@ assignees: ''
 
 Checklist for release:
 
- - [ ] Update NEWS file
- - [ ] Update CITATION.cff
- - [ ] Update VERSION
- - [ ] In devcontainer.json, update `"image": "ghcr.io/r-devel/r-dev-env:devel"` to `"image": "ghcr.io/r-devel/r-dev-env:main"`,,
- - [ ] Make PR to main branch - needs approving review!
- - [ ] Make sure docker container is rebuilt
- - [ ] Test container and fix any issues
- - [ ] Make GitHub release
- - [ ] Rebuild docs
+- [ ] Update NEWS file
+- [ ] Update CITATION.cff
+- [ ] Update VERSION
+- [ ] In devcontainer.json, update `"image": "ghcr.io/r-devel/r-dev-env:devel"`
+      to `"image": "ghcr.io/r-devel/r-dev-env:main"`,,
+- [ ] Make PR to main branch - needs approving review!
+- [ ] Make sure docker container is rebuilt
+- [ ] Test container and fix any issues
+- [ ] Make GitHub release

.github/README.md

@@ -1,40 +1,76 @@
 # R Dev Container
-![Release](https://img.shields.io/github/v/release/r-devel/r-dev-env)
 
+![Release](https://img.shields.io/github/v/release/r-devel/r-dev-env)
 
-The aim of the R Dev Container is to provide a standard environment for the exploration and development of the R source code. A prototype was developed under Google Summer of Code 2023 and development is continuing under Google Summer of Code 2024. 
+The aim of the R Dev Container is to provide a standard environment for the
+exploration and development of the R source code. A prototype was developed
+under Google Summer of Code 2023 and development is continuing under Google
+Summer of Code 2024.
 
 ## Getting started
 
 ### Run in a web browser with GitHub Codespace
 
-Click on the button below followed by "Create Codespace" to create and enter your own web based containerised develoment environment.
+Click on the button below followed by "Create Codespace" to create and enter
+your own web based containerised develoment environment.
+
+[![Open in GitHub
+Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new?hide_repo_select=true&ref=main&repo=647768262&machine=premiumLinux&devcontainer_path=.devcontainer%2Fdevcontainer.json&location=WestUs2)
 
-[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://github.com/codespaces/new?hide_repo_select=true&ref=main&repo=647768262&machine=premiumLinux&devcontainer_path=.devcontainer%2Fdevcontainer.json&location=WestUs2)
+The [Starting Codespace
+section](https://contributor.r-project.org/r-dev-env/container_setup/github_codespace/creating_codespace/)
+of the R Dev Container Docs will walk you through the process. Then you can work
+through the tutorials in the docs to lean how to use the codespace for R
+development.
 
-The [Starting Codespace section](https://contributor.r-project.org/r-dev-env/container_setup/creating_codespace/) of the R Dev Container Docs will walk you through the process. Then you can work through the tutorials in the docs to lean how to use the codespace for R development.
+More details about GitHub codespaces can be found in the [GitHub Codespaces
+Docs](https://docs.github.com/en/codespaces/overview). GitHub currently offers
+up to 60 hours for free on dual core codespaces.
 
-More details about GitHub codespaces can be found in the [GitHub Codespaces Docs](https://docs.github.com/en/codespaces/overview). GitHub currently offers up to 60 hours for free on dual core codespaces.
+[![Open in Gitpod](https://img.shields.io/badge/Gitpod-Open%20in%20Gitpod-blue?logo=gitpod&style=for-the-badge)](https://gitpod.io/github.com/r-devel/r-dev-env/tree/main)
+
+The [Starting Gitpod
+section](https://contributor.r-project.org/r-dev-env/container_setup/gitpod_workspace/workspacestart/)
+of the R Dev Container Docs will walk you through the process. Then you can
+work through the tutorials in the docs to lean how to use the codespace for R
+development.
+
+More details about Gitpod Workspaces can be found in the
+[Gitpod Workspace Docs](https://www.gitpod.io/docs/introduction). Gitpod
+currently offers Up to 896 cores, 12,000 GB RAM & GPUs in free tier.
 
 ### Run on your local computer
 
-The R Dev Container can also be run locally on your computer. 
-Running the environment requires you to have Docker, VSCode, and the VSCode Dev Containers extension installed. 
-Upon opening a copy of the [r-dev-env repository](https://github.com/r-devel/r-dev-env) in VSCode you will be prompted to start the dev container. 
+The R Dev Container can also be run locally on your computer.  Running the
+environment requires you to have Docker, VSCode, and the VSCode Dev Containers
+extension installed.  Upon opening a copy of the [r-dev-env
+repository](https://github.com/r-devel/r-dev-env) in VSCode you will be prompted
+to start the dev container.
 
-The [Local setup section](https://contributor.r-project.org/r-dev-env/tutorials/localsetup/) of the R Dev Container Docs will walk you through the process. 
-Then you can work through the following the tutorials in the docs to learn how to use the codespace for R development.
+The [Local setup
+section](https://contributor.r-project.org/r-dev-env/container_setup/local_setup/localsetup/)
+of the R Dev Container Docs will walk you through the process.  Then you can
+work through the following the tutorials in the docs to learn how to use the
+codespace for R development.
 
-More information about Dev Containers can be found in the [Microsoft Documentation](https://code.visualstudio.com/docs/devcontainers/containers).
+More information about Dev Containers can be found in the [Microsoft
+Documentation](https://code.visualstudio.com/docs/devcontainers/containers).
 
 ## Project Background
 
-The standard development process used by members of the R Core Team involves an iterative process of making changes to the source code, re-building R and exploring/testing the changes made. 
-This process presents a big hurdle for new contributors to R, as setting up their system to build R can be non-trivial, requiring a lot of trouble-shooting, especially on Windows and macOS. 
-On Linux and macOS, it is not straight-forward to work with different versions of R side-by-side and care needs to be taken not to corrupt or over-write the user's existing version of R/R packages.
-
-For these reasons, we propose to create containerized development environments for R. 
-Our focus will be on creating a complete environment, including an IDE, that will provide a familiar space for R developers to work on contributions to base R.
+The standard development process used by members of the R Core Team involves an
+iterative process of making changes to the source code, re-building R and
+exploring/testing the changes made.  This process presents a big hurdle for new
+contributors to R, as setting up their system to build R can be non-trivial,
+requiring a lot of trouble-shooting, especially on Windows and macOS.  On Linux
+and macOS, it is not straight-forward to work with different versions of R
+side-by-side and care needs to be taken not to corrupt or over-write the user's
+existing version of R/R packages.
+
+For these reasons, we propose to create containerized development environments
+for R.  Our focus will be on creating a complete environment, including an IDE,
+that will provide a familiar space for R developers to work on contributions to
+base R.
 
 ## Contributors
 

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

@@ -1,7 +1,7 @@
-# This workflow uses actions that are not certified by GitHub.  
+# 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.  
+# documentation.
 
 name: Build and publish Docker image
 
@@ -15,19 +15,21 @@ on:
       - 'Dockerfile'
       - '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

@@ -1,7 +1,7 @@
-# This workflow uses actions that are not certified by GitHub.  
+# 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.  
+# documentation.
 
 name: Build and publish Gitpod Docker image
 
@@ -16,19 +16,21 @@ on:
       - '.gitpod.yml'
       - '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

@@ -12,29 +12,58 @@ on:
 
 jobs:
   build-and-deploy:
-    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: 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 
+          python-version: 3.x
 
       - name: Install dependencies
         run: pip install mkdocs mkdocs-material[imaging]
 
+      - name: Determine deployment settings
+        id: config
+        run: |
+          if [[ "${{ github.ref_name }}" == "main" ]]; then
+            echo "target_repo=${{ github.repository }}" >> "$GITHUB_OUTPUT"
+            echo "url=https://contributor.r-project.org/r-dev-env" >> "$GITHUB_OUTPUT"
+          else
+            echo "target_repo=r-devel/r-dev-env-devel" >> "$GITHUB_OUTPUT"
+            echo "url=https://contributor.r-project.org/r-dev-env-devel" >> "$GITHUB_OUTPUT"
+          fi
+
+      - name: Modify site_url in mkdocs.yml
+        run: |
+          echo "Setting site_url to ${{ steps.config.outputs.url }}"
+          sed -i "s|^site_url:.*|site_url: '${{ steps.config.outputs.url }}'|" mkdocs.yml
+
       - name: Build MkDocs
         run: mkdocs build
 
-      - name: Deploy to GitHub Pages
+      - name: Validate PAT
+        env:
+          GH_PAT: ${{ secrets.R_DEV_ENV_DOCS }}
         run: |
-           mkdocs gh-deploy --force
-           git push origin gh-pages
+          curl -H "Authorization: token $GH_PAT" https://api.github.com/user || {
+            echo "PAT is invalid or expired" >&2
+            exit 1
+          }
+
+      - name: Deploy to GitHub Pages
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GH_PAT: ${{ secrets.R_DEV_ENV_DOCS }}
+        run: |
+           echo "Deploying from branch: ${{ github.ref_name }}"
+           echo "Commit: ${{ github.sha }}"
+           git remote set-url origin https://x-access-token:${GH_PAT}@github.com/${{ steps.config.outputs.target_repo }}
+           mkdocs gh-deploy --config-file mkdocs.yml --remote-branch gh-pages --force

.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]

.markdownlint-cli2.yaml

@@ -0,0 +1,23 @@
+config:
+
+# MD013 - line-length
+  line_length:
+    line_length: 80
+    code_blocks: false
+    tables: false
+  html:
+    allowed_elements:
+      - div
+      - figure
+# MD029 - ol-prefix disabled as ordered lists are interspersed wit code in multiple places
+  ol-prefix: false
+# MD041 - first-line-heading disable due to splitting of sections across multiple files
+  first-line-h1: false
+
+globs:
+
+- "docs/**/*.md"
+- "*.md"
+
+
+fix: true

.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v5.0.0
+  hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+
+- repo: https://github.com/DavidAnson/markdownlint-cli2
+  rev: v0.18.1
+  hooks:
+    - id: markdownlint-cli2
+      args: []
+
+ci:
+ autofix_prs: true
+ autofix_commit_msg: '[pre-commit.ci] Fixing issues with pre-commit'
+ autoupdate_schedule: weekly
+ autoupdate_commit_msg: '[pre-commit.ci] pre-commit-autoupdate'
+ skip: [] # Optionally list ids of hooks to skip on CI