adds quarto website

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.github/workflows/publish.yml

@@ -0,0 +1,47 @@
+# on:
+#   # manually trigger
+#   workflow_dispatch:
+#   # pushing to main
+#   push:
+#     branches: main
+#     paths: 
+#       - *.qmd
+#       - custom.scss
+#       - renv.lock
+#       - _quarto.yml
+#   # every week on sunday
+#   schedule:
+#     - cron: "0 0 * * SUN"
+# 
+# name: Quarto Publish
+# 
+# jobs:
+#   build-deploy:
+#     runs-on: ubuntu-latest
+#     permissions:
+#       contents: write
+#     steps:
+#       - name: Check out repository
+#         uses: actions/checkout@v4
+# 
+#       - name: Set up Quarto
+#         uses: quarto-dev/quarto-actions/setup@v2
+#         
+#       - name: Install R
+#         uses: r-lib/actions/setup-r@v2
+#         with:
+#           r-version: '4.3.1'
+# 
+#       - name: Install R Dependencies
+#         uses: r-lib/actions/setup-renv@v2
+#         with:
+#           cache-version: 1
+# 
+#       - name: Render and Publish
+#         uses: quarto-dev/quarto-actions/publish@v2
+#         with:
+#           target: gh-pages
+#         env:
+#           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#           PAT: ${{ secrets.PAT }}
+#           GOOGLE_API_KEY: ${{ secrets.GOOGLE_API_KEY }}

.gitignore

@@ -47,3 +47,17 @@ po/*~
 
 # RStudio Connect folder
 rsconnect/
+
+/.quarto/
+
+# rstudio server files
+var-lib-rstudio-server/
+run/
+database.conf
+
+# quarto large dirs
+_freeze/
+_site/
+
+# analysis dir
+analysis/

_quarto.yml

@@ -0,0 +1,48 @@
+project:
+  type: website
+  execute-dir: project
+  render:
+    - "*.qmd"
+    - "!CONTRIBUTIONG.md"
+    - "!LICENSE.md"
+
+website:
+  title: "Spatial transcriptomics"
+  favicon: assets/SIB_logo.svg
+  search: true
+  page-navigation: true
+  navbar:
+    background: "#003eaa"
+    left:
+      - href: index.qmd
+        text: Home
+      - href: precourse_preparations.qmd
+      - href: course_schedule.qmd
+      - text: "Course material"
+        menu:
+          - href: "quality_control.qmd"
+          - href: "normalization_scaling.qmd"
+    right:
+      - icon: github
+        href: https://github.com/sib-swiss/spatial-transcriptomics-training/
+        aria-label: GitHub
+  sidebar:
+    logo: assets/SIB_LogoQ_GBv.svg
+
+format:
+  html:
+    code-link: true
+    theme: 
+      - default
+      - custom.scss
+    toc: true
+    header-includes: |
+      <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Source+Sans+Pro">
+
+execute:
+  freeze: auto 
+  cache: true
+  tidy: true
+
+
+