Quarto (#12)

* feat: remove github pages config

* feat: quarto support added

* ci: quarto ci improvment

* ci: test

* docs: Quarto added

* ci: update labeler

* fix: merge conflict

* fix: implement dual licensing

* feat: improve rendering by changing licenses file format

---------

Co-authored-by: mtwente <[email protected]>

.github/workflows/label.yml

@@ -7,6 +7,6 @@ jobs:
   triage:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/labeler@v4
+      - uses: actions/labeler@v5
         with:
           repo-token: '${{ secrets.GITHUB_TOKEN }}'

.github/workflows/quarto-publish.yml

@@ -0,0 +1,80 @@
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+name: Render and Publish
+
+# you need these permissions to publish to GitHub pages
+permissions:
+  contents: write
+  pages: write
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        # with:
+        # To install LaTeX to build PDF book outputs, uncomment below
+        # tinytex: true
+        # uncomment below and fill to pin a version
+        # version: SPECIFIC-QUARTO-VERSION-HERE
+
+      # add software dependencies here and any libraries
+
+      # From https://github.com/actions/setup-python
+      # - name: Setup Python
+      #   uses: actions/setup-python@v3
+
+      # From https://github.com/r-lib/actions/tree/v2-branch/setup-r
+      # - name: Setup R
+      #   uses: r-lib/actions/setup-r@v2
+
+      # From https://github.com/julia-actions/setup-julia
+      # - name: Setup Julia
+      #   uses: julia-actions/setup-julia@v1
+
+      # See more at https://github.com/quarto-dev/quarto-actions/blob/main/examples/example-03-dependencies.md
+
+      # To publish to Netlify, RStudio Connect, or GitHub Pages, uncomment
+      # the appropriate block below
+
+      # - name: Publish to Netlify (and render)
+      #   uses: quarto-dev/quarto-actions/publish@v2
+      #   with:
+      #     target: netlify
+      #     NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+
+      # - name: Publish to RStudio Connect (and render)
+      #   uses: quarto-dev/quarto-actions/publish@v2
+      #   with:
+      #     target: connect
+      #     CONNECT_SERVER: enter-the-server-url-here
+      #     CONNECT_API_KEY: ${{ secrets.CONNECT_API_KEY }}
+
+      # NOTE: If Publishing to GitHub Pages, set the permissions correctly (see top of this yaml)
+      - name: Publish to GitHub Pages (and render)
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # this secret is always available for github actions
+
+
+      # - name: Publish to confluence
+      #   uses: quarto-dev/quarto-actions/publish@v2
+      #   with:
+      #     target: confluence
+      #   env:
+      #     CONFLUENCE_USER_EMAIL: ${{ secrets.CONFLUENCE_USER_EMAIL }}
+      #     CONFLUENCE_AUTH_TOKEN: ${{ secrets.CONFLUENCE_AUTH_TOKEN }}
+      #     CONFLUENCE_DOMAIN: ${{ secrets.CONFLUENCE_DOMAIN }}

.gitignore

@@ -1,3 +1,7 @@
+# Quarto
+.quarto/
+_site/
+
 # Exclude example.env
 !example.env
 

README.md

@@ -30,7 +30,7 @@ This GitHub template is independent of the (research) data and its format. It fo
 - [CHANGELOG.md](CHANGELOG.md) according to [keepachangelog.com](https://keepachangelog.com/)
 - Automated [CHANGELOG.md](CHANGELOG.md) via [git-cliff](https://github.com/orhun/git-cliff)
 - [package.json](package.json) via [npm docs](https://docs.npmjs.com/cli/v7/configuring-npm/package-json)
-- Accessible documentation via [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages)
+- Accessible documentation via [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages) and [Quarto](https://quarto.org/)
 
 ### Consistency
 
@@ -79,6 +79,7 @@ npm run prepare
 - [ ] run `npm run commit` to commit all changes
 - [ ] run `npm run changelog` and include the output in [CHANGELOG.md](CHANGELOG.md)
 - [ ] enable [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages)
+- [ ] customize the documentation with [Quarto](https://quarto.org/docs/websites/#workflow)
 
 3. optional tasks:
 
@@ -140,5 +141,6 @@ See also the list of [contributors](https://github.com/maehr/open-research-data-
 
 ## License
 
-The data in this repository is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) License - see the [LICENSE-CCBY](LICENSE-CCBY) file for details. By using this data, you agree to give appropriate credit to the original author(s) and to indicate if any modifications have been made.
-The code in this repository is released under the GNU Affero General Public License v3.0 - see the [LICENSE-AGPL](LICENSE-AGPL) file for details. By using this code, you agree to make any modifications available under the same license.
+The data in this repository is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) License - see the [LICENSE-CCBY](LICENSE-CCBY.md) file for details. By using this data, you agree to give appropriate credit to the original author(s) and to indicate if any modifications have been made.
+
+The code in this repository is released under the GNU Affero General Public License v3.0 - see the [LICENSE-AGPL](LICENSE-AGPL.md) file for details. By using this code, you agree to make any modifications available under the same license.

README.template.md

@@ -81,6 +81,6 @@ See also the list of [contributors](https://github.com/USERNAME/REPO_NAME/graphs
 
 ## License
 
-The data in this repository is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) License - see the [LICENSE-CCBY](LICENSE-CCBY) file for details. By using this data, you agree to give appropriate credit to the original author(s) and to indicate if any modifications have been made.
+The data in this repository is released under the Creative Commons Attribution 4.0 International (CC BY 4.0) License - see the [LICENSE-CCBY](LICENSE-CCBY.md) file for details. By using this data, you agree to give appropriate credit to the original author(s) and to indicate if any modifications have been made.
 
-The code in this repository is released under the GNU Affero General Public License v3.0 - see the [LICENSE-AGPL](LICENSE-AGPL) file for details. By using this code, you agree to make any modifications available under the same license.
+The code in this repository is released under the GNU Affero General Public License v3.0 - see the [LICENSE-AGPL](LICENSE-AGPL.md) file for details. By using this code, you agree to make any modifications available under the same license.

_quarto.yml

@@ -0,0 +1,62 @@
+project:
+  type: website
+
+website:
+  title: REPO_NAME
+  favicon: android-chrome-512x512.png
+  open-graph: true
+  twitter-card: true
+  site-url: https://USERNAME.github.io/REPO_NAME/
+  repo-url: https://github.com/USERNAME/REPO_NAME/
+  issue-url: https://github.com/USERNAME/REPO_NAME/issues/new/choose
+  repo-actions: [edit, issue]
+  page-navigation: true
+  bread-crumbs: true
+  back-to-top-navigation: true
+  search:
+    show-item-context: true
+    type: overlay
+  navbar:
+    logo: android-chrome-512x512.png
+    logo-alt: ''
+    title: REPO_NAME
+    tools:
+      - icon: github
+        url: https://github.com/USERNAME/REPO_NAME/
+    left:
+      - text: Readme
+        href: index.qmd
+      - text: Report
+        href: report.md
+
+  sidebar:
+    contents:
+      - section: REPO_NAME
+        href: index.qmd
+        contents:
+          - text: Changelog
+            href: CHANGELOG.md
+          - text: Code of Conduct
+            href: CODE_OF_CONDUCT.md
+          - text: Contributing
+            href: CONTRIBUTING.md
+          - text: License (Data)
+            href: LICENSE-CCBY.md
+          - text: License (Code)
+            href: LICENSE-AGPL.md
+          - text: Security
+            href: SECURITY.md
+      - href: report.md
+        contents: project-management/*
+
+format:
+  html:
+    toc: true
+    theme: cosmo
+    code-copy: true
+    code-overflow: wrap
+    css: styles.css
+
+freeze: true
+
+editor: visual

index.qmd

@@ -0,0 +1 @@
+{{< include README.md >}}

project-management/communication.md

@@ -1,3 +1,5 @@
-# TODO
+<!-- TODO -->
+
+# Communication
 
 Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.

project-management/people.md

@@ -1,3 +1,5 @@
-# TODO
+<!-- TODO -->
+
+# People
 
 Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.

project-management/project-report.md

@@ -1,3 +1,5 @@
-# TODO
+<!-- TODO -->
+
+# Project Report
 
 Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.

project-management/tools.md

@@ -1,3 +1,5 @@
-# TODO
+<!-- TODO -->
+
+# Tools
 
 Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.

report.md

@@ -1,3 +1,5 @@
-# TODO
+<!-- TODO -->
+
+# Report
 
 Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet. Lorem ipsum dolor sit amet, consetetur sadipscing elitr, sed diam nonumy eirmod tempor invidunt ut labore et dolore magna aliquyam erat, sed diam voluptua. At vero eos et accusam et justo duo dolores et ea rebum. Stet clita kasd gubergren, no sea takimata sanctus est Lorem ipsum dolor sit amet.

styles.css

@@ -0,0 +1 @@
+/* css styles */