Merge branch 'landing_page' of github.com:julia-pfarr/bids-website into landing_page

Author: julia-pfarr

.github/dependabot.yml

@@ -2,13 +2,36 @@
 # Documentation
 # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
 version: 2
+enable-beta-ecosystems: true
 updates:
 -   package-ecosystem: github-actions
     directory: /
     schedule:
         interval: monthly
+    groups:
+        actions-infrastructure:
+            patterns:
+            -   actions/*
 
 -   package-ecosystem: gitsubmodule
     directory: /
     schedule:
         interval: monthly
+
+-   package-ecosystem: uv
+    directory: /
+    schedule:
+        interval: monthly
+    groups:
+        python:
+            patterns:
+            -   '*'
+
+-   package-ecosystem: npm
+    directory: /
+    schedule:
+        interval: weekly
+    groups:
+        npm:
+            patterns:
+            -   '*'

.github/workflows/.add-doc-link.yaml

@@ -0,0 +1,17 @@
+---
+name: Read the Docs PR preview
+on:
+    pull_request_target:
+        types:
+        -   opened
+
+permissions:
+    pull-requests: write
+
+jobs:
+    pr-preview-link:
+        runs-on: ubuntu-latest
+        steps:
+        -   uses: readthedocs/actions/preview@v1
+            with:
+                project-slug: bids-website

.github/workflows/deploy.yml

@@ -1,10 +1,11 @@
 ---
-name: Publish docs via GitHub Pages
+name: Build for gh-pages
 
 on:
     push:
         branches:
         -   main
+    pull_request:
 
 concurrency:
     group: ${{ github.workflow }}-${{ github.ref }}
@@ -20,27 +21,32 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         -   name: Checkout
-            uses: actions/checkout@v4
+            uses: actions/checkout@v5
             with:
                 submodules: recursive
                 fetch-depth: 0
 
         -   name: Set up Python
-            uses: actions/setup-python@v5
+            uses: astral-sh/setup-uv@v6
             with:
                 python-version: 3.12
 
         -   name: Set up node
-            uses: actions/setup-node@v4
+            uses: actions/setup-node@v5
             with:
-                node-version: 14
+                node-version: 24
 
         -   name: Install dependencies and update content from submodules
             run: make all
 
-        -   name: Deploy docs
-            uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        -   name: Build site
+            run: uv run mkdocs build
+
+        -   name: Deploy pages
+            if: github.event_name == 'push'
+            run: |
+                git remote set-url origin https://x-access-token:${GITHUB_TOKEN}@github.com/${GITHUB_REPOSITORY}.git
+                uv run mkdocs gh-deploy --force
             env:
                 GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-                CONFIG_FILE: mkdocs.yml
-                REQUIREMENTS: requirements.txt
+                GITHUB_REPOSITORY: bids-standard/bids-website

.github/workflows/linkcheck.yml

@@ -21,20 +21,20 @@ jobs:
         steps:
 
         -   name: Checkout
-            uses: actions/checkout@v4
+            uses: actions/checkout@v5
             with:
                 submodules: recursive
                 fetch-depth: 0
 
         -   name: Set up Python
-            uses: actions/setup-python@v5
+            uses: actions/setup-python@v6
             with:
                 python-version: 3.12
 
         -   name: Set up node
-            uses: actions/setup-node@v4
+            uses: actions/setup-node@v5
             with:
-                node-version: 14
+                node-version: 22
 
         -   name: Install dependencies and update content from submodules
             run: make all

.github/workflows/validation.yml

@@ -19,8 +19,8 @@ jobs:
     latin-phrases:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
-        -   uses: actions/setup-python@v5
+        -   uses: actions/checkout@v5
+        -   uses: actions/setup-python@v6
             with:
                 python-version: 3.12
         -   name: Install dependencies
@@ -33,21 +33,21 @@ jobs:
     remark:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
-        -   uses: actions/setup-node@v4
+        -   uses: actions/checkout@v5
+        -   uses: actions/setup-node@v5
             with:
-                node-version: 14
+                node-version: 22
         -   name: Run markdown style checks
             run: make remark
 
     # validate bep leads metadata
     bep-leads:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
+        -   uses: actions/checkout@v5
             with:
                 submodules: true
-        -   uses: actions/setup-python@v5
+        -   uses: actions/setup-python@v6
             with:
                 python-version: 3.12
         -   name: Install dependencies
@@ -56,12 +56,12 @@ jobs:
             run: python validate_people.py
             working-directory: tools/ci
 
-    # validate bep leads metadata
+    # validate apps metadata
     apps:
         runs-on: ubuntu-latest
         steps:
-        -   uses: actions/checkout@v4
-        -   uses: actions/setup-python@v5
+        -   uses: actions/checkout@v5
+        -   uses: actions/setup-python@v6
             with:
                 python-version: 3.12
         -   name: Install dependencies

.gitignore

@@ -31,4 +31,3 @@ vendor/
 
 # node
 node_modules
-package*json

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ exclude: |
     )$
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -45,15 +45,15 @@ repos:
     rev: v2.15.0
     hooks:
     -   id: pretty-format-toml
-        args: [--autofix, --indent, '4']
+        args: [--autofix, --indent, '4', --no-sort, --trailing-commas]
 
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.1.0
+    rev: 25.9.0
     hooks:
     -   id: black
 
 -   repo: https://github.com/pycqa/isort
-    rev: 6.0.1
+    rev: 7.0.0
     hooks:
     -   id: isort
 

.readthedocs.yaml

@@ -15,7 +15,7 @@ build:
         -   uv venv $READTHEDOCS_VIRTUALENV_PATH
         install:
         # Use a cache dir in the same mount to halve the install time
-        -   VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache -r requirements.txt
+        -   VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv sync --active --frozen --cache-dir $READTHEDOCS_VIRTUALENV_PATH/../../uv_cache
         pre_build:
         -   make update
 

.remarkrc

@@ -1,18 +1,29 @@
 {
+  "settings": {
+    "bullet": "-",
+    "commonmark": true,
+    "emphasis": "*",
+    "fences": true,
+    "incrementListMarker": false,
+    "listItemIndent": "tab",
+    "rule": "-",
+    "strong": "*"
+  },
   "plugins": [
     "preset-lint-markdown-style-guide",
     "preset-lint-recommended",
     "remark-gfm",
-    ["lint-no-duplicate-headings", false],
-    ["lint-list-item-indent", "tab-size"],
     ["lint-emphasis-marker", "consistent"],
+    ["lint-list-item-indent", "tab"],
     ["lint-maximum-line-length", 500],
     ["lint-maximum-heading-length", false],
+    ["lint-no-duplicate-headings", false],
     ["lint-no-shortcut-reference-link", false],
-    ["remark-lint-unordered-list-marker-style", "-"],
     ["lint-no-trailing-spaces"],
-    ["remark-lint-code-block-style", false],
     ["lint-no-undefined-references", false],
-    ["remark-lint-heading-style", false]
+    ["remark-lint-code-block-style", false],
+    ["remark-lint-heading-style", false],
+    ["remark-lint-list-item-spacing", 1],
+    ["remark-lint-unordered-list-marker-style", "-"]
   ]
 }

CONTRIBUTING.md

@@ -18,8 +18,8 @@ make sure you also read the instructions below.
 
 ### Requirements
 
-- python >= 3.10
-- node.js >= ???
+- [uv](https://docs.astral.sh/uv/)
+- node.js >= 14
 - npm >= ???
 
 <!-- TODO find minimal version of node and npm
@@ -36,12 +36,10 @@ Fork and clone the repository and its submodules
 git clone https://github.com/YOUR_USER_NAME/bids-website.git --recurse-submodules
 ```
 
-Create a virtual environment using `conda`, `venv` of what other environment management tool you prefer.
-
-Install all the dependencies.
+Run `uv` to create a virtual environment in `.venv/`.
 
 ```bash
-pip install -r requirements.txt
+uv sync --frozen
 ```
 
 Generate all the content required for the build:
@@ -64,7 +62,7 @@ make update
 Serve the website with the mkdocs.
 
 ```bash
-mkdocs serve
+uv run mkdocs serve
 ```
 
 ## Maintenance
@@ -74,7 +72,7 @@ mkdocs serve
 Same as for the install but you will also need to install `tox`.
 
 ```bash
-pip install tox
+uv run tox
 ```
 
 ## Update all files
@@ -90,11 +88,21 @@ tox
 make remark
 ```
 
-## Updating the `requirements.txt`
+### Using remark to format a file
+
+If you have a completely new file that you want to lint,
+you can use the following to get most of the markdown formatting done.
+
+Some will still need some manual work.
+
+```bash
+npm run format -- path_to_file --ouput
+```
+
+## Upgrading dependencies
 
-Update the appropriate line `requirements.in` and run:
+Rerun `uv sync`:
 
 ```bash
-python -m pip install pip-tools
-pip-compile --strip-extras requirements.in
+uv sync --upgrade
 ```