Various fixes

.github/_quarto.yml

@@ -0,0 +1,62 @@
+project:
+  type: website
+
+website:
+  title: GitHub template for FAIR and open research data
+  favicon: android-chrome-512x512.png
+  open-graph: true
+  twitter-card: true
+  site-url: https://maehr.github.io/open-research-data-template/
+  repo-url: https://github.com/maehr/open-research-data-template/
+  issue-url: https://github.com/maehr/open-research-data-template/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: open-research-data-template
+    tools:
+      - icon: github
+        url: https://github.com/maehr/open-research-data-template/
+    left:
+      - text: Readme
+        href: index.qmd
+      - text: Report
+        href: report.md
+
+  sidebar:
+    contents:
+      - section: open-research-data-template
+        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

.github/labeler.yml

@@ -1,35 +1,48 @@
 data:
-  - analysis/*
-  - build/*
-  - data/*
+  any:
+    changed-files:
+      any-glob-to-any-file:
+        - analysis/*
+        - build/*
+        - data/*
 
 docs:
-  - _layouts/*
-  - assets/*
-  - docs/*
-  - project-management/*
-  - _config.yml
-  - android-chrome-192x192.png
-  - android-chrome-512x512.png
-  - apple-touch-icon.png
-  - CODE_OF_CONDUCT.md
-  - CONTRIBUTING.md
-  - favicon-16x16.png
-  - favicon-32x32.png
-  - favicon.ico
-  - LICENSE.md
-  - README.md
-  - SECURITY.md
-  - site.webmanifest
+  any:
+    changed-files:
+      any-glob-to-any-file:
+        - _layouts/*
+        - assets/*
+        - docs/*
+        - project-management/*
+        - _config.yml
+        - android-chrome-192x192.png
+        - android-chrome-512x512.png
+        - apple-touch-icon.png
+        - CODE_OF_CONDUCT.md
+        - CONTRIBUTING.md
+        - favicon-16x16.png
+        - favicon-32x32.png
+        - favicon.ico
+        - LICENSE-AGPL.md
+        - LICENSE-CCBY.md
+        - README.md
+        - SECURITY.md
+        - site.webmanifest
 
 github:
-  - .github/*
-  - .husky/*
+  any:
+    changed-files:
+      any-glob-to-any-file:
+        - .github/*
+        - .husky/*
 
 src:
-  - .dockerignore
-  - .gitattributes
-  - .gitignore
-  - example.env
-  - src/*
-  - test/*
+  any:
+    changed-files:
+      any-glob-to-any-file:
+        - .dockerignore
+        - .gitattributes
+        - .gitignore
+        - example.env
+        - src/*
+        - test/*

.github/workflows/quarto-publish.yml

@@ -19,6 +19,10 @@ jobs:
       - name: Check out repository
         uses: actions/checkout@v4
 
+      - name: Overwrite _quarto.yml
+        run: |
+          cp .github/_quarto.yml _quarto.yml
+
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
         env:

README.md

@@ -5,7 +5,9 @@ This GitHub template is independent of the (research) data and its format. It fo
 [![GitHub issues](https://img.shields.io/github/issues/maehr/open-research-data-template.svg)](https://github.com/maehr/open-research-data-template/issues)
 [![GitHub forks](https://img.shields.io/github/forks/maehr/open-research-data-template.svg)](https://github.com/maehr/open-research-data-template/network)
 [![GitHub stars](https://img.shields.io/github/stars/maehr/open-research-data-template.svg)](https://github.com/maehr/open-research-data-template/stargazers)
-[![GitHub license](https://img.shields.io/github/license/maehr/open-research-data-template.svg)](https://github.com/maehr/open-research-data-template/blob/main/LICENSE.md)
+[![Code license](https://img.shields.io/github/license/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/blob/main/LICENSE-AGPL.md)
+[![Data license](https://img.shields.io/github/license/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/blob/main/LICENSE-CCBY.md)
+[![DOI](https://zenodo.org/badge/ZENODO_RECORD.svg)](https://zenodo.org/badge/latestdoi/ZENODO_RECORD)
 
 ## Why use a template (even for small datasets)?
 
@@ -21,7 +23,7 @@ This GitHub template is independent of the (research) data and its format. It fo
 
 - Citeable via [DOI](https://www.doi.org/) (and [CITATION.cff](https://citation-file-format.github.io/))
 - Automatic long-term archiving via [Zenodo](https://zenodo.org/)
-- Licensed under a non-restrictive [CC BY 4.0 license](LICENSE.md) according to [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-sharing.html#step-3-choose-a-licence-and-link-to-your-paper-and-code)
+- Licensed under a non-restrictive [AGPL 3.0](LICENSE-AGPL.md) and [CC BY 4.0](LICENSE-CCBY.md) license according to [The Turing Way](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-sharing.html#step-3-choose-a-licence-and-link-to-your-paper-and-code)
 - Templates for reporting data issues using a [custom template](.github/ISSUE_TEMPLATE/data_issue_report.md)
 
 ### Documentation

README.template.md

@@ -5,7 +5,8 @@ This repository contains SHORT_DESCRIPTION. The data in this repository is openl
 [![GitHub issues](https://img.shields.io/github/issues/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/issues)
 [![GitHub forks](https://img.shields.io/github/forks/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/network)
 [![GitHub stars](https://img.shields.io/github/stars/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/stargazers)
-[![GitHub license](https://img.shields.io/github/license/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/blob/main/LICENSE.md)
+[![Code license](https://img.shields.io/github/license/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/blob/main/LICENSE-AGPL.md)
+[![Data license](https://img.shields.io/github/license/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/blob/main/LICENSE-CCBY.md)
 [![DOI](https://zenodo.org/badge/ZENODO_RECORD.svg)](https://zenodo.org/badge/latestdoi/ZENODO_RECORD)
 
 ## Repository Structure

package.json

@@ -5,29 +5,24 @@
 	"url": "https://github.com/USERNAME/REPO_NAME/issues",
 	"license": "AGPL-3.0",
 	"scripts": {
-		"check": "prettier --ignore-path .gitignore  --check . '!{CODE_OF_CONDUCT.md,LICENSE.md,_layouts/default.html,package-lock.json,pnpm-lock.yaml,yarn.lock}'",
+		"check": "prettier --ignore-path .gitignore  --check . '!{CODE_OF_CONDUCT.md,LICENSE-AGPL.md,LICENSE-CCBY.md,_layouts/default.html,package-lock.json,pnpm-lock.yaml,yarn.lock}'",
 		"commit": "cz",
-		"format": "prettier --ignore-path .gitignore --write . '!{CODE_OF_CONDUCT.md,LICENSE.md,_layouts/default.html,package-lock.json,pnpm-lock.yaml,yarn.lock}'",
-		"prepare": "husky install",
+		"format": "prettier --ignore-path .gitignore --write . '!{CODE_OF_CONDUCT.md,LICENSE-AGPL.md,LICENSE-CCBY.md,_layouts/default.html,package-lock.json,pnpm-lock.yaml,yarn.lock}'",
+		"prepare": "husky",
 		"changelog": "npm exec git-cliff -- --config cliff.toml"
 	},
 	"devDependencies": {
 		"commitizen": "^4.3.0",
 		"cz": "^1.8.2",
 		"cz-conventional-changelog": "^3.3.0",
-		"git-cliff": "^1.3.1",
-		"husky": "^8.0.3",
-		"prettier": "^3.0.3"
+		"git-cliff": "^2.2.1",
+		"husky": "^9.0.11",
+		"prettier": "^3.2.5"
 	},
 	"type": "module",
 	"config": {
 		"commitizen": {
 			"path": "./node_modules/cz-conventional-changelog"
-		},
-		"husky": {
-			"hooks": {
-				"prepare-commit-msg": "exec < /dev/tty && git cz --hook || true"
-			}
 		}
 	}
 }