Landing page

.github/ISSUE_TEMPLATE/bids_apps_submission.yml

@@ -11,10 +11,10 @@ body:
 -   type: markdown
     attributes:
         value: |
-            - Have you checked our [contributing guide](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html)?
+            - Have you checked our [contributing guide](https://bids.neuroimaging.io/collaboration/bids_github/CONTRIBUTING.html)?
               It's a helpful resource.
 
-            - Have you checked our [FAQ](https://bids-website.readthedocs.io/en/latest/faq/bids-apps.html)?
+            - Have you checked our [FAQ](https://bids.neuroimaging.io/faq/bids-apps.html)?
 
 -   type: textarea
     attributes:

.github/PULL_REQUEST_TEMPLATE/bep.md

@@ -0,0 +1,11 @@
+This is a suggested pull request template for to add BEP to the BIDS website.
+It's designed to capture information we've found to be useful in reviewing pull requests.
+
+If there is other information that would be helpful to include, please don't hesitate to add it!
+
+---
+
+- [ ] indicate the issue in the BIDS specification repository that you opened for your BEP.
+  BIDS specification issue: https://github.com/bids-standard/bids-specification/issues/????
+- [ ] update the `data/beps/beps.yml` document using the template entry described [here](https://github.com/bids-standard/bids-website/tree/main/.github/PULL_REQUEST_TEMPLATE/bep_template.yml)
+- [ ] ensure that BEP leads are listed among BIDS contributors in [the wiki of the BIDS specification](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors#adding-yourself-as-a-contributor)

.github/PULL_REQUEST_TEMPLATE/bep_template.yml

@@ -0,0 +1,29 @@
+---
+-   number:
+    title: # full title
+    display: ' ' # short title for display
+    google_doc: ' '
+    pull_request: ' ' # pull request for the BEP on the BIDS specification repo
+    html_preview: ' ' # link to the html render of the pull request
+                     #  for the BEP on the BIDS specification repo
+    leads:
+  # MUST match given-names and family-names
+  #  from the bids specification citation.cff
+  # Update the list of contributors via the BIDS specification
+  #  if necessary.
+  # See: https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors#adding-yourself-as-a-contributor
+    -   given-names: ' '
+        family-names: ' '
+    bids_maintainers:
+    -   given-names: ' '
+        family-names: ' '
+    status: # updates
+    -   '  ' # add updates
+    -   '  ' # with items
+    blocking: # potential blockers for this BEP
+    -   ' ' # add blocker
+    -   ' ' # with items
+    communication_channel: # mattermost, matrix, slack, discord...
+    google_doc_created: # date when the BEP draft was started: format 'YYYY-MM'
+    pull_request_created: # date when the Proposed BEP was started: format 'YYYY-MM'
+    pull_request_merged: # date when the Proposed BEP was merged: format 'YYYY-MM'

.github/PULL_REQUEST_TEMPLATE/website.md

@@ -0,0 +1,43 @@
+<!--- Until this PR is ready for review, you can include [WIP] in the title, or create a draft PR. -->
+
+
+<!---
+Below is a suggested pull request template. Feel free to add more details you feel are relevant/necessary.
+
+-->
+
+<!--
+Please indicate after the # which issue you're closing with this PR, if applicable.
+If the PR closes multiple issues, include "Closes" before each one is listed.
+You can also link to other issues if necessary, e.g. "See also #1234".
+
+https://help.github.com/articles/closing-issues-using-keywords
+-->
+- Closes #
+
+<!--
+Please give a brief overview of what has changed or been added in the PR.
+This can include anything specific the maintainers should be looking for when they review the PR.
+-->
+Changes proposed in this pull request:
+-
+
+## Checklist for contributor
+
+- [ ] PR has an interpretable title with a prefix (e.g. `[BUG]`, `[DOC]`, `[ENH]`, `[MAINT]`)\
+Refer to [NumPy Development Guide](https://numpy.org/doc/stable/dev/development_workflow.html#writing-the-commit-message) for a full list
+- [ ] PR links to GitHub issue with mention `Closes #XXXX`
+- [ ] My changes generate no new warnings
+- [ ] I have added tests that prove my fix is effective or that my feature works
+- [ ] New and existing unit tests pass locally with my changes
+- [ ] Any dependent changes have been merged and published in downstream modules
+
+<!-- To be checked off by reviewers -->
+## Checklist for reviewers
+_This section is for the PR reviewer_
+
+For new features:
+- [ ] Tests have been added
+
+For bug fixes:
+- [ ] There is at least one test that would fail under the original bug conditions

.github/workflows/deploy.yml

@@ -0,0 +1,46 @@
+---
+name: Publish docs via GitHub Pages
+
+on:
+    push:
+        branches:
+        -   main
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+# Force to use color
+env:
+    FORCE_COLOR: true
+
+jobs:
+    build:
+        name: Deploy docs
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Checkout
+            uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
+
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: 3.12
+
+        -   name: Set up node
+            uses: actions/setup-node@v4
+            with:
+                node-version: 14
+
+        -   name: Install dependencies and update content from submodules
+            run: make all
+
+        -   name: Deploy docs
+            uses: mhausenblas/mkdocs-deploy-gh-pages@master
+            env:
+                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+                CONFIG_FILE: mkdocs.yml
+                REQUIREMENTS: requirements.txt

.github/workflows/linkcheck.yml

@@ -0,0 +1,48 @@
+---
+name: Checklinks
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+# Force to use color
+env:
+    FORCE_COLOR: true
+
+jobs:
+    # check links
+    link-check:
+        runs-on: ubuntu-latest
+        steps:
+
+        -   name: Checkout
+            uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
+
+        -   name: Set up Python
+            uses: actions/setup-python@v5
+            with:
+                python-version: 3.12
+
+        -   name: Set up node
+            uses: actions/setup-node@v4
+            with:
+                node-version: 14
+
+        -   name: Install dependencies and update content from submodules
+            run: make all
+
+        -   uses: tcort/github-action-markdown-link-check@v1
+            with:
+                use-quiet-mode: yes
+                # use-verbose-mode: no
+                config-file: md_link_check_config.json
+                folder-path: docs
+                file-path: ./README.md

.github/workflows/validation.yml

@@ -69,18 +69,3 @@ jobs:
         -   name: Check bep lead metadata
             run: python validate_apps.py
             working-directory: tools/ci
-
-    # check links
-    link-check:
-        runs-on: ubuntu-latest
-        steps:
-        -   uses: actions/checkout@v4
-            with:
-                submodules: true
-        -   uses: gaurav-nelson/github-action-markdown-link-check@v1
-            with:
-                use-quiet-mode: yes
-                # use-verbose-mode: no
-                config-file: md_link_check_config.json
-                folder-path: docs
-                file-path: ./README.md

.gitmodules

@@ -1,10 +1,13 @@
 [submodule "specification"]
 	path = specification
 	url = https://github.com/bids-standard/bids-specification.git
+	branch = master
 [submodule "data/datasets/examples"]
 	path = data/datasets/examples
 	url = https://github.com/bids-standard/bids-examples
 	datalad-url = https://github.com/bids-standard/bids-examples
+	branch = master
 [submodule "docs/collaboration/bids_github"]
 	path = docs/collaboration/bids_github
 	url = https://github.com/bids-standard/.github
+	branch = main

.pre-commit-config.yaml

@@ -1,7 +1,11 @@
 ---
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
-exclude: tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json
+exclude: |
+    (?x)^(
+        tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json
+        | CNAME
+    )$
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
@@ -20,7 +24,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.4.1
     hooks:
     -   id: codespell
         args: [--toml, pyproject.toml]
@@ -38,23 +42,23 @@ repos:
             )$
 
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-    rev: v2.13.0
+    rev: v2.15.0
     hooks:
     -   id: pretty-format-toml
         args: [--autofix, --indent, '4']
 
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    rev: 25.1.0
     hooks:
     -   id: black
 
 -   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.1
     hooks:
     -   id: isort
 
 -   repo: https://github.com/PyCQA/flake8
-    rev: 7.0.0
+    rev: 7.3.0
     hooks:
     -   id: flake8
         args: [--config, .flake8, --verbose, tools]

.readthedocs.yaml

@@ -2,11 +2,20 @@
 version: 2
 
 build:
-    os: ubuntu-22.04
+    os: ubuntu-lts-latest
     tools:
         python: '3.12'
         nodejs: '20'
     jobs:
+        pre_create_environment:
+        -   asdf plugin add uv
+        -   asdf install uv latest
+        -   asdf global uv latest
+        create_environment:
+        -   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
         pre_build:
         -   make update
 
@@ -16,7 +25,3 @@ submodules:
 
 mkdocs:
     configuration: mkdocs.yml
-
-python:
-    install:
-    -   requirements: requirements.txt

CONTRIBUTING.md

@@ -8,8 +8,8 @@ We hope that these guidelines are designed to make it as easy as possible to get
 If you have any questions that aren't discussed below, please let us know
 by [opening an issue](https://github.com/bids-standard/bids-website/issues/new).
 
-If you are not familiar with Git ansd GitHub,
-check our [generic contributing guidelines](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html).
+If you are not familiar with Git and GitHub,
+check our [generic contributing guidelines](https://bids.neuroimaging.io/collaboration/bids_github/CONTRIBUTING.html).
 
 If you want to contribute to the BIDS website,
 make sure you also read the instructions below.
@@ -19,9 +19,14 @@ make sure you also read the instructions below.
 ### Requirements
 
 - python >= 3.10
+- node.js >= ???
+- npm >= ???
 
-Even though this is not required, having `make` installed
-will make it easier to easily serve the website locally.
+<!-- TODO find minimal version of node and npm
+For some quality checks and rare operations, you will need node.js and npm. -->
+
+Even though this is not required,
+having `make` installed will make it easier to easily serve the website locally.
 
 ### Install and serve
 
@@ -39,7 +44,18 @@ Install all the dependencies.
 pip install -r requirements.txt
 ```
 
-Generate all the content required for the build.
+Generate all the content required for the build:
+
+-   copies some pages from the specification repo
+
+-   updates the list of contributors
+
+-   generates the page for each BEP based on its metadata
+
+-   updates the list of BIDS examples
+
+-   generates all the 'plotly' interactive plots as html files in the `tmp` folder
+    that will be 'injected' in the website as snippets (with `--8<--`)
 
 ```bash
 make update
@@ -60,8 +76,6 @@ Same as for the install but you will also need to install `tox`.
 ```bash
 pip install tox
 ```
-<!-- TODO find minimal version of node and npm -->
-For some quality checks and rare operations, you will need node.js and npm.
 
 ## Update all files
 
@@ -75,3 +89,12 @@ make update
 tox
 make remark
 ```
+
+## Updating the `requirements.txt`
+
+Update the appropriate line `requirements.in` and run:
+
+```bash
+python -m pip install pip-tools
+pip-compile --strip-extras requirements.in
+```