2410 rerender 2

cambiotraining · Oct 24, 2024 · 85c123e · 85c123e
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Showing 229 changed files with 564 additions and 15 deletions.
diff --git a/...ambiotraining/courseformat/_extension.yml → _extensions/courseformat/_extension.yml b/...ambiotraining/courseformat/_extension.yml → _extensions/courseformat/_extension.yml
diff --git a/...raining/courseformat/callout_exercise.lua → ...ensions/courseformat/callout_exercise.lua b/...raining/courseformat/callout_exercise.lua → ...ensions/courseformat/callout_exercise.lua
diff --git a/...biotraining/courseformat/citation_cff.lua → _extensions/courseformat/citation_cff.lua b/...biotraining/courseformat/citation_cff.lua → _extensions/courseformat/citation_cff.lua
diff --git a/...s/cambiotraining/courseformat/footer.html → _extensions/courseformat/footer.html b/...s/cambiotraining/courseformat/footer.html → _extensions/courseformat/footer.html
diff --git a/...t/img/university-of-cambridge-favicon.ico → ...t/img/university-of-cambridge-favicon.ico b/...t/img/university-of-cambridge-favicon.ico → ...t/img/university-of-cambridge-favicon.ico
diff --git a/...eformat/img/university_crest_reversed.png → ...eformat/img/university_crest_reversed.png b/...eformat/img/university_crest_reversed.png → ...eformat/img/university_crest_reversed.png
diff --git a/...mbiotraining/courseformat/star_levels.lua → _extensions/courseformat/star_levels.lua b/...mbiotraining/courseformat/star_levels.lua → _extensions/courseformat/star_levels.lua
diff --git a/...ns/cambiotraining/courseformat/theme.scss → _extensions/courseformat/theme.scss b/...ns/cambiotraining/courseformat/theme.scss → _extensions/courseformat/theme.scss
diff --git a/...cambiotraining/fontawesome/_extension.yml → _extensions/fontawesome/_extension.yml b/...cambiotraining/fontawesome/_extension.yml → _extensions/fontawesome/_extension.yml
diff --git a/...iotraining/fontawesome/assets/css/all.css → _extensions/fontawesome/assets/css/all.css b/...iotraining/fontawesome/assets/css/all.css → _extensions/fontawesome/assets/css/all.css
diff --git a/...fontawesome/assets/css/latex-fontsize.css → ...fontawesome/assets/css/latex-fontsize.css b/...fontawesome/assets/css/latex-fontsize.css → ...fontawesome/assets/css/latex-fontsize.css
diff --git a/...awesome/assets/webfonts/fa-brands-400.ttf → ...awesome/assets/webfonts/fa-brands-400.ttf b/...awesome/assets/webfonts/fa-brands-400.ttf → ...awesome/assets/webfonts/fa-brands-400.ttf
diff --git a/...esome/assets/webfonts/fa-brands-400.woff2 → ...esome/assets/webfonts/fa-brands-400.woff2 b/...esome/assets/webfonts/fa-brands-400.woff2 → ...esome/assets/webfonts/fa-brands-400.woff2
diff --git a/...wesome/assets/webfonts/fa-regular-400.ttf → ...wesome/assets/webfonts/fa-regular-400.ttf b/...wesome/assets/webfonts/fa-regular-400.ttf → ...wesome/assets/webfonts/fa-regular-400.ttf
diff --git a/...some/assets/webfonts/fa-regular-400.woff2 → ...some/assets/webfonts/fa-regular-400.woff2 b/...some/assets/webfonts/fa-regular-400.woff2 → ...some/assets/webfonts/fa-regular-400.woff2
diff --git a/...tawesome/assets/webfonts/fa-solid-900.ttf → ...tawesome/assets/webfonts/fa-solid-900.ttf b/...tawesome/assets/webfonts/fa-solid-900.ttf → ...tawesome/assets/webfonts/fa-solid-900.ttf
diff --git a/...wesome/assets/webfonts/fa-solid-900.woff2 → ...wesome/assets/webfonts/fa-solid-900.woff2 b/...wesome/assets/webfonts/fa-solid-900.woff2 → ...wesome/assets/webfonts/fa-solid-900.woff2
diff --git a/...me/assets/webfonts/fa-v4compatibility.ttf → ...me/assets/webfonts/fa-v4compatibility.ttf b/...me/assets/webfonts/fa-v4compatibility.ttf → ...me/assets/webfonts/fa-v4compatibility.ttf
diff --git a/.../assets/webfonts/fa-v4compatibility.woff2 → .../assets/webfonts/fa-v4compatibility.woff2 b/.../assets/webfonts/fa-v4compatibility.woff2 → .../assets/webfonts/fa-v4compatibility.woff2
diff --git a/...ambiotraining/fontawesome/fontawesome.lua → _extensions/fontawesome/fontawesome.lua b/...ambiotraining/fontawesome/fontawesome.lua → _extensions/fontawesome/fontawesome.lua
diff --git a/_quarto.yml b/_quarto.yml
@@ -8,16 +8,18 @@ project:
   output-dir: _site
   render:
     - index.md
-    - setup.qmd
-    - materials.qmd
+    - setup.md
+    - materials.md
     - materials/*
-    - "!materials/*/_no-render"
+    - "!materials/*/no_render"
 
 format: courseformat-html
+exercises:
+  number: true
+  hide-answers: false
 
-metadata-files:
-  - "materials/_chapters.yml"
-  # - "materials/_sidebar.yml"
+filters:
+  - courseformat
 
 execute:
   freeze: auto
@@ -26,25 +28,34 @@ knitr:
   opts_knit:
     cache.path: .knitr_cache
 
+metadata-files:
+  - "materials/_chapters.yml"
+  # - "materials/_sidebar.yml"
+
 book:
-  favicon: "_extensions/cambiotraining/courseformat/img/university-of-cambridge-favicon.ico"
-  page-navigation: true
+  search:
+    location: sidebar
+  favicon: "_extensions/courseformat/img/university-of-cambridge-favicon.ico"
   bread-crumbs: false
+  page-navigation: true
   page-footer:
     center: |
       Licensed [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/)
       ![](https://creativecommons.org/images/deed/cc_icon_black_x2.png){width=25px}
       Bioinformatics Training Facility
   navbar:
     pinned: true
-    logo: "_extensions/cambiotraining/courseformat/img/university_crest_reversed.png"
+    logo: "_extensions/courseformat/img/university_crest_reversed.png"
     right:
       - icon: github
         href: https://github.com/cambiotraining/corestats/
         aria-label: Bioinformatics Training Facility GitHub
       - icon: twitter
         href: https://twitter.com/bioinfocambs
         aria-label: Bioinformatics Training Facility Twitter
+      - icon: mastodon
+        href: https://genomic.social/@BioInfoCambs
+        aria-label: Bioinformatics Training Facility Mastodon
     title: "Core statistics"
   chapters:
     - part: "Welcome"