diff --git a/.github/workflows/jekyll-gh-pages.yml b/.github/workflows/jekyll-gh-pages.yml
deleted file mode 100644
index 008e476..0000000
--- a/.github/workflows/jekyll-gh-pages.yml
+++ /dev/null
@@ -1,52 +0,0 @@
----
-# Sample workflow for building and deploying a Jekyll site to GitHub Pages
-name: Deploy Jekyll with GitHub Pages dependencies preinstalled
-
-on:
- # Runs on pushes targeting the default branch
- push:
- branches: [main]
-
- # Allows you to run this workflow manually from the Actions tab
- workflow_dispatch:
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
-permissions:
- contents: read
- pages: write
- id-token: write
-
-# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
-# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
-concurrency:
- group: pages
- cancel-in-progress: false
-
-jobs:
- # Build job
- build:
- runs-on: ubuntu-latest
- steps:
- - name: Checkout
- uses: actions/checkout@v4
- - name: Setup Pages
- uses: actions/configure-pages@v3
- - name: Build with Jekyll
- uses: actions/jekyll-build-pages@v1
- with:
- source: ./
- destination: ./_site
- - name: Upload artifact
- uses: actions/upload-pages-artifact@v2
-
- # Deployment job
- deploy:
- environment:
- name: github-pages
- url: ${{ steps.deployment.outputs.page_url }}
- runs-on: ubuntu-latest
- needs: build
- steps:
- - name: Deploy to GitHub Pages
- id: deployment
- uses: actions/deploy-pages@v2
diff --git a/.github/workflows/publishdocs.yaml b/.github/workflows/publishdocs.yaml
new file mode 100644
index 0000000..cdf75bd
--- /dev/null
+++ b/.github/workflows/publishdocs.yaml
@@ -0,0 +1,19 @@
+---
+name: Publish docs via GitHub Pages
+on:
+ push:
+ branches:
+ - main
+
+jobs:
+ build:
+ name: Deploy docs
+ runs-on: ubuntu-latest
+ steps:
+ - name: Checkout master
+ uses: actions/checkout@v4
+
+ - name: Deploy docs
+ uses: mhausenblas/mkdocs-deploy-gh-pages@master
+ env:
+ GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/README.md b/README.md
index 98dba3b..1639602 100644
--- a/README.md
+++ b/README.md
@@ -20,7 +20,7 @@ Documentation related to BIDS.
- The [FieldTrip](https://www.fieldtriptoolbox.org/example/bids/) websites contains
many BIDS tips and examples, mainly for MEG, EEG, fNIRS, etc.
- If you help to mention BIDS in one of your grant,
- make sure that to check out the [BIDS grant writing kit](https://github.com/bids-standard/grant_writing_kit)
+ make sure that to check out the [BIDS grant writing kit](https://github.com/bids-standard/grant_writing_kit#bids-grant-writing-kit).
## Community
@@ -62,7 +62,7 @@ Tools for converting data to/from BIDS from other standard or custom formats and
- ### MRI
+### MRI
- [Autobids](https://github.com/khanlab/autobids): Automated Dicom to BIDS and pipelines using compute canada. From the Center for Functional and Metabolic Mapping (CFMM) at Western’s Robarts Research Institute.
[![Last commit](https://img.shields.io/github/last-commit/khanlab/autobids?style=plastic)](https://github.com/khanlab/autobids)
@@ -111,7 +111,7 @@ Tools for converting data to/from BIDS from other standard or custom formats and
- [XNAT2BIDS](https://github.com/kamillipi/2bids): Simple xnat pipeline to convert DICOM scans to BIDS-compatible output (nii+json).
![](https://img.shields.io/badge/shell-black.svg?style=plastic)[![Last commit](https://img.shields.io/github/last-commit/kamillipi/2bids?style=plastic)](https://github.com/kamillipi/2bids)
- ### MEEG
+### MEEG
- [BIDSme](https://gitlab.uliege.be/CyclotronResearchCentre/Public/bidstools/bidsme/bidsme_example/-/tree/master/example1):
[![Last commit](https://img.shields.io/github/last-commit/nbeliy/bidsme?style=plastic)](https://github.com/nbeliy/bidsme)[![License: GPL-2.0](https://img.shields.io/badge/License-GPLv2-blue.svg?style=plastic)](https://www.gnu.org/licenses/gpl-2.0)
@@ -128,7 +128,7 @@ Tools for converting data to/from BIDS from other standard or custom formats and
- [sovabids](https://sovabids.readthedocs.io/en/latest/): A Python package for the automatic conversion of EEG datasets to the BIDS standard, with a focus on making the most out of metadata.
[![Last commit](https://img.shields.io/github/last-commit/yjmantilla/sovabids?style=plastic)](https://github.com/yjmantilla/sovabids)
- ### physiological
+### physiological
- [BIDScoin](https://bidscoin.readthedocs.io/en/stable/): BIDScoin converts your source-level neuroimaging data to BIDS
[![Last commit](https://img.shields.io/github/last-commit/Donders-Institute/bidscoin?style=plastic)](https://github.com/Donders-Institute/bidscoin)[![PyPI version](https://badge.fury.io/py/bidscoin.svg)](https://pypi.org/project/bidscoin)
@@ -137,7 +137,7 @@ Tools for converting data to/from BIDS from other standard or custom formats and
- [phys2bids](https://phys2bids.readthedocs.io/en/latest/): Python3 library to format physiological files in BIDS.
[![Last commit](https://img.shields.io/github/last-commit/physiopy/phys2bids?style=plastic)](https://github.com/physiopy/phys2bids)[![PyPI version](https://badge.fury.io/py/phys2bids.svg)](https://pypi.org/project/phys2bids)
- ### others
+### others
- [convert-eprime](https://github.com/tsalo/convert-eprime): Python functions to convert E-Prime files to csvs. Not currently being developed.
[![Last commit](https://img.shields.io/github/last-commit/tsalo/convert-eprime?style=plastic)](https://github.com/tsalo/convert-eprime)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
@@ -149,6 +149,13 @@ Tools for converting data to/from BIDS from other standard or custom formats and
[![Last commit](https://img.shields.io/github/last-commit/dissagaliyeva/sim2bids?style=plastic)](https://github.com/dissagaliyeva/sim2bids)[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg?style=plastic)](https://opensource.org/licenses/MIT)
+## Validation
+
+Make sure you use to validate any BIDS dataset you are working with.
+
+You can [use it in a browser](https://bids-standard.github.io/bids-validator/)
+or [install the package](https://github.com/bids-standard/bids-validator#quickstart)
+and use it as a command line tool.
## BIDS Apps
@@ -329,7 +336,7 @@ make sure to check our [documentation regarding the BIDS extension proposal proc
- ### raw
+### raw
- [BEP004](https://bids.neuroimaging.io/bep004): Susceptibility Weighted Imaging (SWI)
- [BEP020](https://bids.neuroimaging.io/bep020): Eye Tracking including Gaze Position and Pupil Size
@@ -344,7 +351,7 @@ make sure to check our [documentation regarding the BIDS extension proposal proc
- [BEP039](https://bids.neuroimaging.io/bep039): Dimensionality reduction-based networks
- [BEP040](https://bids.neuroimaging.io/bep040): Functional Ultrasound (fUS)
- ### derivative
+### derivative
- [BEP011](https://bids.neuroimaging.io/bep011): Structural preprocessing derivatives
- [BEP012](https://bids.neuroimaging.io/bep012): Functional preprocessing derivatives
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..0a66185
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,49 @@
+---
+site_name: Awesome BIDS
+repo_url: https://github.com/bids-standard/awesome-bids.git
+
+nav:
+- Home: index.md
+- Contributing: contributing.md
+- Code of conduct: code-of-conduct.md
+
+theme:
+ name: material
+ features:
+ - navigation.top
+ - content.action.edit
+ icon:
+ repo: fontawesome/brands/github
+ edit: material/pencil
+ palette:
+ # Palette toggle for automatic mode
+ - media: (prefers-color-scheme)
+ toggle:
+ icon: material/brightness-auto
+ name: Switch to light mode
+ # Palette toggle for light mode
+ - media: '(prefers-color-scheme: light)'
+ scheme: default
+ toggle:
+ icon: material/brightness-7
+ name: Switch to dark mode
+ # Palette toggle for dark mode
+ - media: '(prefers-color-scheme: dark)'
+ scheme: slate
+ toggle:
+ icon: material/brightness-4
+ name: Switch to system preference
+
+edit_uri: edit/main/src/
+
+markdown_extensions:
+- toc:
+ anchorlink: true
+- pymdownx.superfences
+
+plugins:
+- search
+
+docs_dir: src
+
+use_directory_urls: false
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..da59789
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,6 @@
+mkdocs>=1.1
+mkdocs-material>=5.4
+pre-commit
+black
+codespell
+reorder-python-imports
diff --git a/code-of-conduct.md b/src/code-of-conduct.md
similarity index 100%
rename from code-of-conduct.md
rename to src/code-of-conduct.md
diff --git a/contributing.md b/src/contributing.md
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rename from contributing.md
rename to src/contributing.md
diff --git a/images/.xdp-logo_docker.png-xLc53c b/src/images/.xdp-logo_docker.png-xLc53c
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rename from images/.xdp-logo_docker.png-xLc53c
rename to src/images/.xdp-logo_docker.png-xLc53c
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diff --git a/images/logo-matlab.svg b/src/images/logo-matlab.svg
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diff --git a/images/logo_R.png b/src/images/logo_R.png
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diff --git a/images/logo_docker.png b/src/images/logo_docker.png
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similarity index 100%
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rename to src/images/logo_matlab.png
diff --git a/images/logo_octave.png b/src/images/logo_octave.png
similarity index 100%
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rename to src/images/logo_octave.png
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similarity index 100%
rename from images/logo_octave.svg
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diff --git a/images/logo_python.png b/src/images/logo_python.png
similarity index 100%
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diff --git a/images/logo_python.svg b/src/images/logo_python.svg
similarity index 100%
rename from images/logo_python.svg
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diff --git a/src/index.md b/src/index.md
new file mode 120000
index 0000000..32d46ee
--- /dev/null
+++ b/src/index.md
@@ -0,0 +1 @@
+../README.md
\ No newline at end of file
diff --git a/tools/update_bep_listing.py b/tools/update_bep_listing.py
index 2e55d0b..b800024 100644
--- a/tools/update_bep_listing.py
+++ b/tools/update_bep_listing.py
@@ -13,7 +13,7 @@ def write_beps(f, beps: list[dict]) -> None:
f.write("\n")
for section in ["raw", "derivative"]:
- f.write(f"\n ### {section}\n\n")
+ f.write(f"\n### {section}\n\n")
subset = [x for x in beps if section in x["content"]]
for bep_ in subset:
diff --git a/tools/update_converters_listing.py b/tools/update_converters_listing.py
index 66b686f..799d68b 100644
--- a/tools/update_converters_listing.py
+++ b/tools/update_converters_listing.py
@@ -39,7 +39,7 @@ def docker_badge(converter: dict):
def write_converters(readme, converters: list[dict], section: str):
# for a section of converters write info about each converter with badges below
- readme.write(f"\n ### {section}\n\n")
+ readme.write(f"\n### {section}\n\n")
converters = converters[0]["members"]
sorted_converters = sorted(converters, key=lambda x: x["name"].lower())