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 similarity index 100% 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 similarity index 100% rename from images/.xdp-logo_docker.png-xLc53c rename to src/images/.xdp-logo_docker.png-xLc53c diff --git a/images/R_logo.svg b/src/images/R_logo.svg similarity index 100% rename from images/R_logo.svg rename to src/images/R_logo.svg diff --git a/images/logo-matlab.svg b/src/images/logo-matlab.svg similarity index 100% rename from images/logo-matlab.svg rename to src/images/logo-matlab.svg diff --git a/images/logo_R.png b/src/images/logo_R.png similarity index 100% rename from images/logo_R.png rename to src/images/logo_R.png diff --git a/images/logo_docker.png b/src/images/logo_docker.png similarity index 100% rename from images/logo_docker.png rename to src/images/logo_docker.png diff --git a/images/logo_docker.svg b/src/images/logo_docker.svg similarity index 100% rename from images/logo_docker.svg rename to src/images/logo_docker.svg diff --git a/images/logo_matlab.png b/src/images/logo_matlab.png similarity index 100% rename from images/logo_matlab.png rename to src/images/logo_matlab.png diff --git a/images/logo_octave.png b/src/images/logo_octave.png similarity index 100% rename from images/logo_octave.png rename to src/images/logo_octave.png diff --git a/images/logo_octave.svg b/src/images/logo_octave.svg similarity index 100% rename from images/logo_octave.svg rename to src/images/logo_octave.svg diff --git a/images/logo_python.png b/src/images/logo_python.png similarity index 100% rename from images/logo_python.png rename to src/images/logo_python.png diff --git a/images/logo_python.svg b/src/images/logo_python.svg similarity index 100% rename from images/logo_python.svg rename to src/images/logo_python.svg 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())