Fusion site ssplab

.github/workflows/auto_fetch.yaml

@@ -0,0 +1,47 @@
+name: "Update external data"
+
+on:
+  workflow_dispatch:
+  # push:
+  #   branches:
+  #     - fusion_site_ssplab
+  # schedule:
+  #   - cron: '42 10 7 * *'  # Runs once a month (the 7th) at 10h42 UTC to avoid GHA overload
+
+jobs:
+  fetching-data:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Set up Git
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "actions@github.com"
+
+      - name: Install jq
+        run: sudo apt-get install jq
+
+      - name: Run synchronization script
+        id: run_script
+        run: |
+          chmod +x scripts/2_synchronize.sh
+          ./scripts/2_synchronize.sh
+          if [ -n "$(git branch --list auto_fetch)" ]; then
+            echo "branch_created=true" >> $GITHUB_OUTPUT
+          else
+            echo "branch_created=false" >> $GITHUB_OUTPUT
+          fi
+
+      - name: Create Pull Request
+        if: steps.run_script.outputs.branch_created == 'true'
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Update based on latest commits"
+          title: "Update projects with latest external docs"
+          body: "This PR updates the projects external docs based on the latest commits from these repositories."
+          branch: "auto_fetch"
+          base: "main"

.github/workflows/dev.yaml

@@ -1,59 +1,60 @@
 name: Build and deploy preview
 
 on:
-  workflow_dispatch:  # To allow for manuel trigger of this workflow. Cf
+  workflow_dispatch: # To allow for manuel trigger of this workflow. Cf
   # https://docs.github.com/en/actions/reference/workflows-and-actions/events-that-trigger-workflows#workflow_dispatch
   pull_request:
     types:
       - opened
       - reopened
-      - synchronize  # When the ref of the branch is updated (= commit to the branch to merge)
-      - closed   # Including closed to remove preview when PR is closed.
+      - synchronize # When the ref of the branch is updated (= commit to the branch to merge)
+      - closed # Including closed to remove preview when PR is closed.
     branches:
-      - main  # PR to main only
+      - main # PR to main only
 
 env:
   PREVIEW_BRANCH: gh-pages
 
 concurrency:
-  group: preview-${{ github.ref }}  # preview followed by the reference of the branch or tag that triggered the workflow
+  group: preview-${{ github.ref }} # preview followed by the reference of the branch or tag that triggered the workflow
   cancel-in-progress: true
 
 jobs:
   build-render:
-    if: github.event.action != 'closed'  # If closing the PR, no publishing
+    if: github.event.action != 'closed' # If closing the PR, no publishing
     runs-on: ubuntu-latest
     # To cancel previous actions that could run on this PR
     steps:
       - name: Check out repository
         uses: actions/checkout@v5
         with:
-          fetch-depth: 0  # To enable full access to Git repo
-          ref: ${{ github.event.pull_request.head.ref }}  # Reference of the commit to checkout to. To ensure it's the one of the PR
-          repository: ${{github.event.pull_request.head.repo.full_name}}  # Reference to the branch to checkout to. Useful with PR from forks
+          fetch-depth: 0 # To enable full access to Git repo
+          ref: ${{ github.event.pull_request.head.ref }} # Reference of the commit to checkout to. To ensure it's the one of the PR
+          repository: ${{github.event.pull_request.head.repo.full_name}} # Reference to the branch to checkout to. Useful with PR from forks
 
       # add software dependencies here and any libraries
       # See more at https://github.com/quarto-dev/quarto-actions/blob/main/examples/example-03-dependencies.md
-      - name: Configure safe.directory  # Workaround for actions/checkout#760
+      - name: Configure safe.directory # Workaround for actions/checkout#760
         run: git config --global --add safe.directory /__w/ssphub/ssphub
 
       - name: Install npm
         if: ${{ github.event.pull_request.head.repo.full_name == github.repository }}
         uses: actions/setup-node@v2
         with:
-          node-version: '18'
+          node-version: "18"
 
-      - uses: actions/setup-python@v4  # for post on onyxia
-        with:
-          python-version: '3.10' # Version range or exact version of a Python version to use, using SemVer's version range syntax
-
-      - run: pip install jupyter nbformat  # for post on onyxia
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
 
-      - name: Set up Quarto
-        uses: quarto-dev/quarto-actions/setup@v2
+      - name: Install babelquarto
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: |
+            github::ropensci-review-tools/babelquarto@a485fea
 
-      - name: Render Quarto Project
-        uses: quarto-dev/quarto-actions/render@v2
+      - name: Render bilingual project
+        run: |
+          Rscript scripts/1_render.R
 
       - name: Deploy preview
         id: deploy-preview
@@ -63,7 +64,6 @@ jobs:
           preview-branch: ${{ env.PREVIEW_BRANCH }}
           action: deploy
           comment: false
-          pr_number: ${{ github.event.pull_request.number }}
 
       - name: Comment PR (custom)
         uses: marocchino/sticky-pull-request-comment@v2
@@ -74,15 +74,15 @@ jobs:
             <h6>Built to branch [`${{ env.PREVIEW_BRANCH }}`](${{ github.server_url }}/${{ github.repository }}/tree/${{ env.PREVIEW_BRANCH }}) at ${{ steps.deploy-preview.outputs.action-start-time }}. <br> Preview will be ready when the [GitHub Pages deployment](${{ github.server_url }}/${{ github.repository }}/deployments) is complete. <br> </h6>
 
   delete-preview:
-    if: github.event.action == 'closed'  # Only run when PR is closed
+    if: github.event.action == 'closed' # Only run when PR is closed
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
         uses: actions/checkout@v5
         with:
-          fetch-depth: 0  # To enable full access to Git repo
-          ref: ${{ github.event.pull_request.head.ref }}  # Reference of the commit to checkout to. To ensure it's the one of the PR
-          repository: ${{github.event.pull_request.head.repo.full_name}}  # Reference to the branch to checkout to. Useful with PR from forks
+          fetch-depth: 0 # To enable full access to Git repo
+          ref: ${{ github.event.pull_request.head.ref }} # Reference of the commit to checkout to. To ensure it's the one of the PR
+          repository: ${{github.event.pull_request.head.repo.full_name}} # Reference to the branch to checkout to. Useful with PR from forks
 
       - name: Remove preview
         id: remove-preview
@@ -97,5 +97,3 @@ jobs:
           message: |
             Preview removed because the pull request was closed.
             ${{ steps.remove-preview.outputs.action-start-time }}
-
-

.github/workflows/prod.yaml

@@ -33,3 +33,5 @@ jobs:
           target: netlify
           NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
           NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+
+

.gitignore

@@ -9,7 +9,25 @@ node_modules/
 go.sum
 .hugo_build.lock
 
+# Quarto
+_freeze/
+*.html
+*.json
+!scripts/2_repo_fetch.json
+*.feed*
+site_libs/
+
+# For gh-pages
 /.quarto/
 _site/
+
 rp_parquet/
+*.quarto_ipynb
 **/*.quarto_ipynb
+course_files/
+
+# Venv
+.venv/
+*/.venv/
+__pycache__/
+*/__pycache__/