Multiple fixes 2603 (#71)

maehr · web-flow · commit 37b324913579 · 2026-03-06T10:55:22.000+01:00
* feat: update devcontainer configuration, add maintainers guide, and enhance CI workflows

* chore: update package-lock.json and uv.lock files

* fix: update concurrency group in workflow and enhance link checking exclusions

* fix: add missing permissions for lint jobs in workflow

---------

Co-authored-by: Moritz Mähr &lt;14755525+maehr@users.noreply.github.com&gt;
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,43 +1,43 @@
 {
-	"name": "Open-Research-Data Template",
-	"image": "mcr.microsoft.com/devcontainers/universal:2-linux",
-	"remoteUser": "codespace",
-	"features": {
-		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
-			"version": "4.5.2",
-			"vscodeRSupport": "basic",
-			"installREnv": "true"
-		},
-		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
-			"version": "release",
-			"installTinyTex": "true",
-			"installChromium": "false"
-		},
-		"ghcr.io/va-h/devcontainers-features/uv:1": {
-			"version": "latest",
-			"shellautocompletion": "true"
-		}
-	},
-	"postCreateCommand": "uv sync && Rscript -e 'renv::restore()'",
-	"customizations": {
-		"vscode": {
-			"extensions": [
-				"quarto.quarto",
-				"REditorSupport.r",
-				"astral-sh.uv",
-				"astral-sh.ty",
-				"ms-toolsai.jupyter",
-				"Posit.air-vscode"
-			],
-			"settings": {
-				"r.rterm.option": ["--no-save", "--no-restore-data", "--quiet"],
-				"r.useRenvLibPath": true,
-				"[r]": {
-					"editor.defaultFormatter": "Posit.air-vscode",
-					"editor.formatOnSave": true
-				}
-			},
-			"openFiles": ["README.md", "README.template.md"]
-		}
-	}
+  "name": "Open-Research-Data Template",
+  "image": "mcr.microsoft.com/devcontainers/universal:2-linux",
+  "remoteUser": "codespace",
+  "features": {
+    "ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+      "version": "4.5.2",
+      "vscodeRSupport": "basic",
+      "installREnv": "true"
+    },
+    "ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
+      "version": "release",
+      "installTinyTex": "true",
+      "installChromium": "false"
+    },
+    "ghcr.io/va-h/devcontainers-features/uv:1": {
+      "version": "latest",
+      "shellautocompletion": "true"
+    }
+  },
+  "postCreateCommand": "uv sync && Rscript -e 'renv::restore()'",
+  "customizations": {
+    "vscode": {
+      "extensions": [
+        "quarto.quarto",
+        "REditorSupport.r",
+        "astral-sh.uv",
+        "astral-sh.ty",
+        "ms-toolsai.jupyter",
+        "Posit.air-vscode"
+      ],
+      "settings": {
+        "r.rterm.option": ["--no-save", "--no-restore-data", "--quiet"],
+        "r.useRenvLibPath": true,
+        "[r]": {
+          "editor.defaultFormatter": "Posit.air-vscode",
+          "editor.formatOnSave": true
+        }
+      },
+      "openFiles": ["README.md", "README.template.md"]
+    }
+  }
 }
diff --git a/.github/MAINTAINERS.md b/.github/MAINTAINERS.md
@@ -0,0 +1,7 @@
+# Maintainers Guide
+
+## `_quarto.yml` Override Mechanism
+
+The CI workflow (`.github/workflows/quarto-publish.yml`) contains a step that copies `.github/_quarto.yml` over the root `_quarto.yml` **only** when the repository is `maehr/open-research-data-template`. This override customizes the Quarto configuration for the template's own documentation site.
+
+**Template instances** (repositories created from this template) are not affected by this override. If you need to customize the Quarto configuration for your project, edit the root `_quarto.yml` directly.
diff --git a/.github/workflows/changelog.yaml b/.github/workflows/changelog.yaml
@@ -1,6 +1,8 @@
 name: Create changelog
 
-on: [push]
+on:
+  push:
+    branches: [main]
 
 jobs:
   changelog:
diff --git a/.github/workflows/greetings.yml b/.github/workflows/greetings.yml
@@ -6,7 +6,7 @@ jobs:
   greeting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/first-interaction@v1
+      - uses: actions/first-interaction@v3
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           issue-message: 'Hi there! Thanks for opening your first issue!'
diff --git a/.github/workflows/quarto-publish.yml b/.github/workflows/quarto-publish.yml
@@ -14,10 +14,16 @@ permissions:
   pages: write
   id-token: write
 
+concurrency:
+  group: '${{ github.workflow }}-${{ github.ref }}'
+  cancel-in-progress: true
+
 jobs:
   lint:
     name: Lint with Prettier
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
 
     steps:
       - name: Check out repository
@@ -34,6 +40,46 @@ jobs:
       - name: Check for linting errors
         run: npm run check
 
+  lint-python:
+    name: Lint Python
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Run ruff check
+        run: uv run ruff check
+
+      - name: Run ty check
+        run: uv run ty check
+
+  lint-r:
+    name: Lint R
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v5
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: renv
+
+      - name: Setup renv
+        uses: r-lib/actions/setup-renv@v2
+
+      - name: Run lintr
+        run: Rscript -e 'lintr::lint_dir(".")'
+
   build-optimize:
     name: Build, Optimize, and Upload Artifacts
     runs-on: ubuntu-latest
@@ -103,7 +149,7 @@ jobs:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
-    needs: [build-optimize]
+    needs: [lint, lint-python, lint-r, build-optimize]
     if: github.event_name != 'pull_request'
 
     steps:
diff --git a/.gitignore b/.gitignore
@@ -5,7 +5,7 @@
 _site/
 
 # Lychee link checker cache
-.lycheecache/
+.lycheecache
 
 # Jampack
 .jampack/
diff --git a/.lycheerc.toml b/.lycheerc.toml
@@ -12,6 +12,8 @@ exclude = [
   "https://www.gnu.org/licenses/",
   "https://www.gnu.org/licenses/agpl-3.0.html",
   "https://www.makeareadme.com/",
+  "https://fsf.org/",
+  "https://book.the-turing-way.org/",
 ]
 
 # Timeout for requests (seconds)
diff --git a/.nvmrc b/.nvmrc
@@ -0,0 +1 @@
+24
diff --git a/.prettierrc b/.prettierrc
@@ -1,6 +1,6 @@
 {
-	"useTabs": true,
-	"singleQuote": true,
-	"trailingComma": "none",
-	"printWidth": 100
+  "useTabs": false,
+  "singleQuote": true,
+  "trailingComma": "none",
+  "printWidth": 100
 }
diff --git a/AGENTS.md b/AGENTS.md
@@ -55,7 +55,6 @@ Aligned with _The Turing Way_ advanced structure:
 
 - `analysis/` — notebooks and analysis scripts
 - `assets/` — images and media
-- `build/` — data build/processing scripts
 - `data/` — datasets (FAIR-aligned)
 - `documentation/` — extended docs beyond README
 - `project-management/` — planning and minutes
@@ -102,7 +101,7 @@ Place new files accordingly.
 - `styler::style_dir(".")` for R formatting
 - `lintr::lint_dir(".")` for R linting
 - `quarto preview` to detect rendering issues
-- Run and validate scripts in `src/`, `build/`, and `analysis/`
+- Run and validate scripts in `src/` and `analysis/`
 - Confirm `.github/workflows/` still pass for changes
 
 ## 9) GitHub Features and Security (Project instances)
diff --git a/CITATION.cff b/CITATION.cff
@@ -1 +1,13 @@
-# Go to https://citation-file-format.github.io/ to learn more about the Citation File Format.
+cff-version: 1.2.0
+title: REPO_NAME
+message: >-
+  If you use this dataset, please cite it using the
+  metadata from this file.
+type: dataset
+authors:
+  - given-names: FULLNAME
+    email: '[INSERT CONTACT METHOD]'
+repository-code: 'https://github.com/USERNAME/REPO_NAME'
+license: AGPL-3.0
+version: 0.1.0
+abstract: SHORT_DESCRIPTION
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -5,6 +5,14 @@ email, or any other method with the owners of this repository before making a ch
 
 Please note we have a [code of conduct](CODE_OF_CONDUCT.md), please follow it in all your interactions with the project.
 
+## Environment Setup
+
+This project uses an `example.env` file for local configuration. To set up your environment:
+
+1. Copy `example.env` to `.env`: `cp example.env .env`
+2. Fill in the values in `.env` with your actual configuration
+3. `.env` is git-ignored and will not be committed
+
 ## Pull Request Process
 
 1. Ensure any install or build dependencies are removed before the end of the layer when doing a
diff --git a/README.template.md b/README.template.md
@@ -15,7 +15,6 @@ The structure of this repository follows the [Advanced Structure for Data Analys
 
 - `analysis/`: scripts and notebooks used to analyze the data
 - `assets/`: images, logos, etc. used in the README and other documentation
-- `build/`: scripts and notebooks used to build the data
 - `data/`: data files
 - `documentation/`: documentation for the data and the repository
 - `project-management/`: project management documents (e.g., meeting notes, project plans, etc.)
diff --git a/TODO.md b/TODO.md
@@ -21,6 +21,7 @@ Complete the following steps after creating your project from this template to c
 - [ ] **Add Zenodo DOI to README**: After creating your first release and obtaining a Zenodo DOI, replace `ZENODO_RECORD` in README.md with your actual Zenodo record number (found in your Zenodo deposit URL).
 - [ ] **Add Favicons**: Generate and add favicon files to the root directory using [favicon.io](https://favicon.io/) or a similar service. Include `favicon.ico`, `favicon-16x16.png`, `favicon-32x32.png`, `apple-touch-icon.png`, and Android icons.
 - [ ] **Address TODO Comments**: Search for `TODO` comments throughout all project files using `grep -r "TODO" .` and complete or remove each task as appropriate for your project.
+- [ ] **Update Citation File**: Edit `CITATION.cff` with your project's citation metadata (authors, title, version, DOI, and repository URL). See the [Citation File Format guide](https://citation-file-format.github.io/) for details.
 - [ ] **Finalize README**: Once all customization is complete, delete the template README.md and rename `README.template.md` to `README.md` to make it your project's main README.
 - [ ] **Format Files**: Run `npm run format` to apply consistent formatting to all files using Prettier before committing changes.
 - [ ] **Commit Changes**: Use `npm run commit` to create a properly formatted commit message following Conventional Commits standards (e.g., "chore: initial project setup").
@@ -31,9 +32,10 @@ Complete the following steps after creating your project from this template to c
 
 ## Optional Enhancements
 
-- [ ] **Add Citation File**: Create a `CITATION.cff` file with your project's citation metadata using the [Citation File Format guide](https://citation-file-format.github.io/). Include authors, title, version, DOI, and repository URL.
 - [ ] **Add Zenodo Metadata File**: Create a `.zenodo.json` file to control metadata sent to Zenodo during archival. Include custom creators, contributors, keywords, and license information. See [Zenodo developer documentation](https://developers.zenodo.org/?python#add-metadata-to-your-github-repository-release) for schema details.
 
+- [ ] **Review Project-Management Files**: Populate or remove the files in `project-management/` before publishing. These are placeholder templates for meeting notes and project plans.
+
 ## Verification Steps
 
 After completing the checklist:
diff --git a/example.env b/example.env
@@ -1 +1,5 @@
-ENV_VAR="Value"
+# Copy this file to .env and fill in the values.
+# .env is ignored by git and used for local configuration.
+
+# Example: API key for an external service
+# API_KEY="your-api-key-here"
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
diff --git a/pyproject.toml b/pyproject.toml
diff --git a/site.webmanifest b/site.webmanifest
diff --git a/test/conftest.py b/test/conftest.py
diff --git a/uv.lock b/uv.lock

Original file line number	Diff line number	Diff line change
`@@ -12,6 +12,8 @@ exclude = [`
`12`	`12`	`"https://www.gnu.org/licenses/",`
`13`	`13`	`"https://www.gnu.org/licenses/agpl-3.0.html",`
`14`	`14`	`"https://www.makeareadme.com/",`
	`15`	`+ "https://fsf.org/",`
	`16`	`+ "https://book.the-turing-way.org/",`
`15`	`17`	`]`
`16`	`18`
`17`	`19`	`# Timeout for requests (seconds)`
Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`		`- "useTabs": true,`
`3`		`- "singleQuote": true,`
`4`		`- "trailingComma": "none",`
`5`		`- "printWidth": 100`
	`2`	`+ "useTabs": false,`
	`3`	`+ "singleQuote": true,`
	`4`	`+ "trailingComma": "none",`
	`5`	`+ "printWidth": 100`
`6`	`6`	`}`