[MAINT] clean up after moving to new website (#623)

bids-standard · Feb 21, 2025 · b7b729b · b7b729b
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diff --git a/.github/ISSUE_TEMPLATE/bids_apps_submission.yml b/.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:

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -12,6 +12,9 @@ jobs:
         steps:
         -   name: Checkout
             uses: actions/checkout@v4
+            with:
+                submodules: recursive
+                fetch-depth: 0
 
         -   name: Set up Python
             uses: actions/setup-python@v5

diff --git a/.github/workflows/linkcheck.yml b/.github/workflows/linkcheck.yml
@@ -0,0 +1,30 @@
+---
+name: Validation
+
+on:
+    push:
+        branches: [main]
+
+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:
+        -   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
diff --git a/.github/workflows/validation.yml b/.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
diff --git a/CNAME b/CNAME
@@ -1 +1 @@
-bids.neuroimaging.io
+bids.neuroimaging.io
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -9,7 +9,7 @@ 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 and GitHub,
-check our [generic contributing guidelines](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html).
+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.

diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![Documentation Status](https://readthedocs.org/projects/bids-website/badge/?version=latest)](https://bids-website.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/bids-website/badge/?version=latest)](https://bids.neuroimaging.io/?badge=latest)
 [![Validation](https://github.com/bids-standard/bids-website/actions/workflows/validation.yml/badge.svg?branch=main)](https://github.com/bids-standard/bids-website/actions/workflows/validation.yml)
 [![Bluesky Follow](https://img.shields.io/badge/bluesky-Follow_bidsstandard-blue?logo=bluesky)](https://bsky.app/profile/bidsstandard.bsky.social)
 ![YouTube Channel Subscribers](https://img.shields.io/youtube/channel/subscribers/UCxZUcYfd_nvIVWAbzRB1tlw)
@@ -20,7 +20,7 @@
 
 <!-- This is the repository for the Brain Imaging Data Structure (BIDS) website that is hosted at <https://bids.neuroimaging.io>. -->
 
-View it here: https://bids-website.readthedocs.io/en/latest/?badge=latest
+View it here: https://bids.neuroimaging.io/?badge=latest
 
 ## Contributing to the BIDS website
 
@@ -42,5 +42,5 @@ on the [bids-specification][specification_gh] repository.
 If you have questions how to apply BIDS to your dataset,
 how to use a shared BIDS dataset,
 or about tools to convert and/or handle BIDS datasets,
-please see the [getting started section](https://bids-website.readthedocs.io/en/latest/getting_started/index.html) page,
-and our [FAQ](https://bids-website.readthedocs.io/en/latest/faq/index.html).
+please see the [getting started section](https://bids.neuroimaging.io/getting_started/index.html) page,
+and our [FAQ](https://bids.neuroimaging.io/faq/index.html).
diff --git a/docs/blog/posts/2024-08-08-steering-group-minutes.md b/docs/blog/posts/2024-08-08-steering-group-minutes.md
@@ -64,7 +64,7 @@ New meeting in Boston, not sure that there will be BIDS representation there.
         If not, how should the general inquiries be routed?"
 
     -   Could the contributing page help identify where to direct queries (e.g. a contact for interviews, press...)?
-        We currently have a contact page [on the new website](https://bids-website.readthedocs.io/en/latest/contact/index.html)
+        We currently have a contact page [on the new website](https://bids.neuroimaging.io/contact/index.html)
         (which might not be sufficient)
 
 ## BIDS Virtual Meeting?

diff --git a/docs/blog/posts/2024-08-30-steering-group-minutes.md b/docs/blog/posts/2024-08-30-steering-group-minutes.md
@@ -96,13 +96,13 @@ categories:
 
 -   website has been consolidated
 
--   [main webite restructure](https://bids-website.readthedocs.io/) needs mentor review (goal September 15)
+-   main webite restructure needs mentor review (goal September 15)
 
 -   would like community feedback starting October 1
     -   [Steering group feedback right now](https://docs.google.com/document/d/1O3trMc2-9MdLwj-RhRnUyQYe8ciWbvBYTeHqm63PcBg/edit#heading=h.w8lni71xnxbp)
 
 -   TODO: Steering group to visit/review the website
-    -   in particular [impact page](https://bids-website.readthedocs.io/en/latest/impact/index.html )
+    -   in particular impact page
 
     -   Yarik:
         IMHO Grantsmanship better goes under "Collaboration",

diff --git a/docs/blog/posts/bids-news-september-2024.md b/docs/blog/posts/bids-news-september-2024.md
@@ -43,7 +43,7 @@ You can also provide feedback now with our [BIDS website survey](https://cryptpa
 Per BIDS governance, the steering group members have a term of 3 years.
 This year, Ariel Rokem's term ends. Keep an eye out for the upcoming election which BIDS contributors can vote upon. And on behalf of the community, thank you so much Ariel for your service\!
 
-You can find more [about BIDS governance](https://bids-website.readthedocs.io/en/latest/collaboration/governance.html) here.
+You can find more [about BIDS governance](https://bids.neuroimaging.io/collaboration/governance.html) here.
 
 ## Recent venues BIDS presented
 
@@ -58,7 +58,7 @@ The BEPs carry on to help us all update the standard with new and previously une
 -   [BEP043](https://bids.neuroimaging.io/bep043): Term mapping (Chris Markiewicz & Eric Earl)
 -   [BEP044](https://bids.neuroimaging.io/bep044): Stimuli (Seyed Yahya Shirazi)
 
-Other BEPs are listed on [the BIDS website](https://bids-website.readthedocs.io/en/latest/extensions/beps.html).
+Other BEPs are listed on [the BIDS website](https://bids.neuroimaging.io/extensions/beps.html).
 
 ## New working groups
 

diff --git a/docs/collaboration/bids_github b/docs/collaboration/bids_github
diff --git a/docs/collaboration/contributors.md b/docs/collaboration/contributors.md
@@ -9,7 +9,7 @@ hide:
 ## Adding yourself as a contributors
 
 To know more about if you can qualify as a BIDS contributor, how to add your name to the list of contributors, and why you should,
-check our [contributing guidelines about this](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html#recognizing-contributions).
+check our [contributing guidelines about this](https://bids.neuroimaging.io/collaboration/bids_github/CONTRIBUTING.html#recognizing-contributions).
 
 ## List of contributors
 

diff --git a/docs/collaboration/governance.md b/docs/collaboration/governance.md
@@ -60,7 +60,7 @@ users to confirm that a given dataset complies with the current edition
 of the standard, the [PyBIDS](https://github.com/bids-standard/pybids)
 Python and [bids-matlab](https://github.com/bids-standard/bids-matlab)
 libraries allow querying and manipulating BIDS-compliant datasets,
-[BIDS-Apps](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html) for running portable
+[BIDS-Apps](https://bids.neuroimaging.io/tools/bids-apps.html) for running portable
 pipelines on validated BIDS datasets, and platforms like
 [OpenNeuro][openneuro] store and serve BIDS datasets. Note
 that the associated software does not fall under the same governance

diff --git a/docs/collaboration/index.md b/docs/collaboration/index.md
@@ -39,7 +39,7 @@ Below is a list of common resources where users can get involved in making the B
 There are so many ways to help us build this community.
 
 -   You could help someone else learn the benefits of BIDS by giving a talk in your local organization
--   Or you could work on [building a BIDS App](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html){:target="_blank"}!
+-   Or you could work on [building a BIDS App](https://bids.neuroimaging.io/tools/bids-apps.html){:target="_blank"}!
 
 <b>The only requirement is that everyone who contributes adheres to our [BIDS Code of Conduct](./bids_github/CODE_OF_CONDUCT.md).</b>
 

diff --git a/docs/collaboration/reports/google_summer/2024-gsod.md b/docs/collaboration/reports/google_summer/2024-gsod.md
@@ -96,7 +96,7 @@ And finally, October and November brought the BIDS Impact page together to wrap
 | ----------------------------------------------------------------------- | ---------- | -------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | Consolidate into one website                                            | 100%       | [new BIDS website](https://bids-website.readthedocs.io/)                                           | Dev site - Planning launch in Q1 2025 to replace the old BIDS website at <https://bids.neuroimaging.io/>                                                |
 | Implement a more friendly main website structure and improve navigation | 100%       | [mkdocs TOC configuration](https://github.com/bids-standard/bids-website/blob/main/mkdocs.yml#L88) | User feedback indicates this created significant improvement ( See: [Metrics](#metrics))                                                                |
-| New BIDS Impact page                                                    | 100%       | [new impact page](https://bids-website.readthedocs.io/en/latest/impact/index.html)                 | Expanded and improved with more metrics and relevant context                                                                                            |
+| New BIDS Impact page                                                    | 100%       | [new impact page](https://bids.neuroimaging.io/impact/index.html)                                  | Expanded and improved with more metrics and relevant context                                                                                            |
 | Categorize and add clear summaries to each webpage                      | 100%       | [Pull request #498](https://github.com/bids-standard/bids-website/pull/498)                        | Each page now has a lead paragraph.                                                                                                                     |
 | Synthesized and enabled gathering of user-feedback and user-testing     | 100%       |                                                                                                    | Developed a follow-up survey and collated findings from all community feedback. Helped synthesize metrics and inputs for annual community presentation. |
 | Add a feedback form within the main website                             | 100%       |                                                                                                    | Giscus at the bottom of the front page was re-scoped and implemented by a mentor                                                                        |

diff --git a/docs/faq/bids-apps.md b/docs/faq/bids-apps.md
@@ -149,7 +149,7 @@ to have a repo created for you.
 If you base your code on <https://github.com/bids-apps/example> deployment
 on docker hub will happen automatically via Circle-ci.
 
-If you want your App to show on the [BIDS website](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html),
+If you want your App to show on the [BIDS website](https://bids.neuroimaging.io/tools/bids-apps.html),
 you will have to update the `data/tools/apps.yml` in the
 [BIDS website repository](https://github.com/bids-standard/bids-website/tree/main).
 

diff --git a/docs/faq/general.md b/docs/faq/general.md
@@ -138,7 +138,7 @@ The BIDS schema is available in two machine readable formats:
 -   as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/tree/master/src/schema)
 -   as a [single json file](https://bids-specification.readthedocs.io/en/stable/schema.json)
 
-A light-weight introduction to the schema can be found [here](https://bids-extensions.readthedocs.io/en/latest/schema/).
+A light-weight introduction to the schema can be found [here](https://bids.neuroimaging.io/standards/schema/index.html#what-is-the-schema).
 
 A full description of the schema can be found on this [website](https://bidsschematools.readthedocs.io/en/latest/?badge=latest)
 where you will also find the documentation for the python package

diff --git a/docs/impact/measuring.md b/docs/impact/measuring.md
@@ -57,7 +57,7 @@ we can quantify which BIDS-associated tools are of the highest interest to the r
 | statistical model | ![PyPI - Downloads](https://img.shields.io/pypi/dm/bsmschema)                                                            |
 
 For the number of docker pulls of specific BIDS apps, please check the
-[BIDS app dashboard](https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html).
+[BIDS app dashboard](https://bids.neuroimaging.io/tools/bids-apps.html).
 
 ## Contributors
 

diff --git a/docs/overrides/main.html b/docs/overrides/main.html
@@ -15,11 +15,13 @@
       margin: 0
     }
   </style>
-  <div class="announcement">
-    <p><b>THIS SITE IS UNDER DEVELOPMENT</b></p>
+
+  <!-- <div class="announcement"> -->
+
+    <!-- <p><b>THIS SITE IS UNDER DEVELOPMENT</b></p>
     <p>
       Please leave your feedback at <a href="https://cryptpad.fr/form/#/2/form/view/f3b2wVPL5VK1HhvBNwtW3-4LXeEpJ9xMY+uOaoahyqQ/">the survey linked here</a>.
-    </p>
+    </p> -->
 
   <!--
     <h2><b>BIDS steering group election</b></h2>
@@ -59,10 +61,10 @@ <h3>
     </p>
     -->
 
-    <p>
+    <!-- <p>
       If you have any questions, please feel free to reach out to
       <a href="mailto:[email protected]">the BIDS maintainers</a>.
-    </p>
+    </p> -->
 
     <!--
     <div class="iframe-container">
@@ -76,6 +78,7 @@ <h3>
     </div>
   -->
 
-  </div>
+  <!-- </div> -->
+
 </div>
 {% endblock %}
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,7 +1,7 @@
 ---
 site_name: The Brain Imaging Data Structure
 repo_url: https://github.com/bids-standard/bids-website/tree/main
-site_url: https://bids-website.readthedocs.io
+site_url: https://bids.neuroimaging.io/
 
 plugins:
   - search

diff --git a/pyproject.toml b/pyproject.toml
@@ -8,7 +8,7 @@ description = "Utility package for bids website"
 dynamic = ["version"]
 name = "bids_website"
 readme = "README.md"
-requires-python = ">=3.10"
+requires-python = ">=3.12"
 
 [tool.black]
 line-length = 79

diff --git a/requirements.in b/requirements.in
@@ -1,5 +1,6 @@
 gender_guesser
 geopy
+jinja2>=3.1.5
 markdown-it-py
 mkdocs-material[imaging]
 mkdocs-macros-plugin
@@ -8,9 +9,10 @@ mkdocs-redirects
 mkdocs-rss-plugin
 plotly>=5.3.1
 pybids
+pyzotero
 rich
 ruamel.yaml
 tabulate
-pyzotero
+urllib3>=2.2.2
 bidsschematools[render]
 -e file:tools
diff --git a/requirements.txt b/requirements.txt
@@ -73,8 +73,9 @@ idna==3.7
     # via requests
 interface-meta==1.3.0
     # via formulaic
-jinja2==3.1.4
+jinja2==3.1.5
     # via
+    #   -r requirements.in
     #   mkdocs
     #   mkdocs-macros-plugin
     #   mkdocs-material
@@ -212,13 +213,17 @@ requests==2.32.3
     #   mkdocs-material
     #   pyzotero
 rich==12.6.0
-    # via -r requirements.in
+    # via
+    #   -r requirements.in
+    #   bids-website
 rpds-py==0.18.1
     # via
     #   jsonschema
     #   referencing
 ruamel-yaml==0.18.6
-    # via -r requirements.in
+    # via
+    #   -r requirements.in
+    #   bids-website
 ruamel-yaml-clib==0.2.8
     # via ruamel-yaml
 scipy==1.13.1
@@ -253,8 +258,10 @@ typing-extensions==4.12.2
     #   sqlalchemy
 tzdata==2024.1
     # via pandas
-urllib3==2.2.1
-    # via requests
+urllib3==2.3.0
+    # via
+    #   -r requirements.in
+    #   requests
 watchdog==4.0.1
     # via mkdocs
 webencodings==0.5.1