Merge branch 'devel' into dockefile/misc

Author: hturner

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

@@ -31,28 +31,39 @@ jobs:
       - name: Install dependencies
         run: pip install mkdocs mkdocs-material[imaging]
 
-      - name: Determine deployment path
-        id: path
+      - 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 "url=https://contributor.r-project.org/r-dev-env/devel" >> "$GITHUB_OUTPUT"
+            echo "target_repo=r-devel/r-dev-env-devel" >> "$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 ${{ steps.path.outputs.url }}"
-          sed -i "s|^site_url:.*|site_url: '${{ steps.path.outputs.url }}'|" mkdocs.yml
-
+          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: Validate PAT
+        env:
+          GH_PAT: ${{ secrets.R_DEV_ENV_DOCS }}
+        run: |
+          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: ${{ secrets.R_DEV_ENV_DOCS }}
         run: |
-           git remote set-url origin https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}
-           mkdocs gh-deploy --force
-           git push origin gh-pages
+           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

docs/tutorials/running_r.md

@@ -1,5 +1,5 @@
 
-1) Create a file in VS Code ending with a .R extension. You can create new files
+1) Create a file in VS Code ending with a `.R` extension. You can create new files
 by clicking on the new file icon in VS Code Explorer, or use the `code` command
 in the terminal to create and open an R file
 
@@ -10,11 +10,25 @@ code R/test.R
 ![alt text](../assets/rdev4.png)
 
 2) You should see `R:(not attached)` in the Status Bar at the bottom of the
-VSCode window.
+VSCode window:
 
 ![alt text](../assets/rdev11.png)
 
-3) Click on the `R:(not attached)` link to launch an R terminal. You can then
-send code from the `.R` file to the R terminal by pressing `cmd/ctrl + enter`.
+Click on the `R:(not attached)` link to launch an R terminal.
 
-![alt text](../assets/rdev12.png) ![alt text](../assets/rdev5.png)
+![alt text](../assets/rdev12.png)
+
+<!-- markdownlint-disable MD046 -->
+!!! Note
+    If you don't see the `R:(not attached)` link in the status
+    bar, you can open an R terminal using the VS Code Command Palette. Click the
+    cog icon ('Manage') in the bottom left of the VS Code window, then click
+    `Command Palette` (note the keyboard shortcut displayed next to this menu
+    item for future use). This starts a prompt at the top of the VS Code window.
+    Type `R terminal` and select the command `R: Create R terminal`.
+<!-- markdownlint-enable MD046 -->
+
+3) You can then send code from the `.R` file to the R terminal by pressing
+`cmd/ctrl + enter`.
+
+![alt text](../assets/rdev5.png)