Merge branch 'main' of https://github.com/UofUEpiBio/PHS7045-advanced…

…-programming

.github/ISSUE_TEMPLATE/weekly-entry.md

@@ -0,0 +1,16 @@
+---
+name: Course week
+about: GitHub issue template for course week
+title: 'Week [#]'
+---
+
+Welcome to week [#] of the course! You can access this week's content in the following links:
+
+- Lecture notes ([link](https://UofUEpiBio.github.io/PHS7045-advanced-programming/week-01-slides.html)|[source]())
+- Lab ([link]()|[source]())
+
+## Additional resources
+
+- Reading 1
+- Reading 2
+- ...

.github/workflows/examples.yml

@@ -5,9 +5,10 @@ on: [push, pull_request]
 jobs:
   test-ubuntu:
     runs-on: Ubuntu-latest
+    container: ghcr.io/uofuepibio/phs7045-advanced-programming:fall2024
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Execute
         run: |
@@ -16,7 +17,8 @@ jobs:
 
       - name: Commit results
         run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
+          git config --global user.name "github-actions[bot]"
+          git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git config --global --add safe.directory "$GITHUB_WORKSPACE"
           git commit -a -m 'Re-build examples' || echo Nothing has changed
           git push origin || echo "No changes to commit"

.github/workflows/website.yml

@@ -3,24 +3,41 @@ name: Render website
 on: [push, pull_request]
 
 jobs:
-  quarto-ubuntu:
+  upload:
     runs-on: Ubuntu-latest
+    container: ghcr.io/uofuepibio/phs7045-advanced-programming:fall2024
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - name: Getting the docker
+      - name: preping
         run: |
-          docker pull gvegayon/phs7045:latest
+          mkdir _site
+          cp -R 0* _site
+          quarto render README.qmd --to=html
+          mv README.html _site/index.html
 
-      - name: Render
-        run: |
-          docker run -i --rm -v$(pwd):/home/docs -w/home/docs gvegayon/phs7045:latest make -B README.md
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: "_site"
+
+  website:
+    if: ${{ github.event_name != 'pull_request' }}
+    needs: upload
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Deploy to GitHub pages
+        uses: actions/deploy-pages@v4
+
+
 
-      - name: Commit results
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          git add docs/* || echo Nothing to be added
-          git commit -a -m 'Re-build examples' || echo Nothing has changed
-          git push origin || echo "No changes to commit"

.gitignore

@@ -7,4 +7,5 @@
 libs
 *.gz
 *.docx
-*.xlsx
+*.xlsx
+_site

.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+    "grammarly.selectors": [
+        {
+            "language": "quarto",
+            "scheme": "file"
+        }
+    ]
+}