From fc33deb3b8c825a142bd627c807eabdaf68ca8d0 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Thu, 9 Jan 2025 18:12:53 +0100 Subject: [PATCH 01/31] [DATALAD] Recorded changes --- docs/index.md | 118 +++++++++++++++++++++++----------------- docs/standards/index.md | 9 ++- makefile | 2 +- 3 files changed, 77 insertions(+), 52 deletions(-) diff --git a/docs/index.md b/docs/index.md index badf5bbb..6f2db60d 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,27 +1,43 @@ --- -title: BIDS +hide: + - navigation --- -Neuroimaging experiments result in complex data that can be arranged in many different ways. -For a long time, there was no consensus how to organize and share -data obtained in neuroimaging experiments. -Even two researchers working in the same lab could opt to arrange their data in a different way. -Lack of consensus (or a standard) leads to misunderstandings and time wasted on rearranging data -or rewriting scripts expecting certain structure. -With the Brain Imaging Data Structure (BIDS), -we describe a simple and easy to adopt way of organizing neuroimaging and behavioral data. +## What is BIDS? + +The Brain Imaging Data Structure (BIDS) is a community-led set of standards +for organizing, describing, sharing and analyze neuroimaging data. + +It is organized around 3 pilars: + +1. standards +1. collaboration +1. tools + +Its goal is to make neuroimaging data more accessible, shareable, and usable by researchers. +To achieve this goal, BIDS provides a simple and intuitive way to organize and describe neuroimaging data and associated data and metadata. +BIDS is based on simple file formats (often text-based) and folder structures that can easily be adopted by any researcher around the world with minimum effort. +BIDS is not a file format, but instead relies upon common standard file formats (e.g. nifti, json, tsv). +BIDS has two major components. +First, it specifies a naming convention for files and directories. +Second, it specifies conventions for the organization of metadata. +A robust validator allows researchers to easily check whether a dataset meets the standard. + + + +### BIDS as a set of standards + + + +The [BIDS specification][specification] is intentionally based on simple file formats and folder structures +to reflect current lab practices and make it accessible to a wide range of scientists coming from different backgrounds. ![BIDS-folder-organization](./assets/img/dicom-reorganization-transparent-black_1000x477.png#only-light) ![BIDS-folder-organization](./assets/img/dicom-reorganization-transparent-white_1000x477.png#only-dark) -BIDS was heavily inspired by the format used internally by the OpenfMRI repository -that is now known as [OpenNeuro][openneuro]. -While working on BIDS we consulted many neuroscientists to make sure it covers most common experiments, -but at the same time is intuitive and easy to adopt. -The specification is intentionally based on simple file formats and folder structures -to reflect current lab practices and make it accessible to a wide range of scientists coming from different backgrounds. +### BIDS as a community effort -## BIDS is a community effort + BIDS is developed by the community for the community and everybody can [become a part of the community](./extensions/index.md). @@ -34,33 +50,28 @@ if more people use it, more data will be shared and the more powerful it will be Since BIDS is platform independent and still an adapting, growing tool, the greater the community, the better it will be. -## Specification vs. Ecosystem +### BIDS as an ecosystem of tools + + Since the inception of the BIDS specification that documents how to organize neuroimaging data, a large ecosystem of tools and resources has evolved around BIDS. A few of the key elements of this ecosystem are -the [BIDS specification](http://bids-specification.readthedocs.io/) with the nitty-gritty details, - +the [BIDS specification][specification] with the nitty-gritty details, the [starter kit](./getting_started/index.md) with a simple explanation how to work with it, - -the [BIDS validator](https://github.com/bids-standard/bids-validator) to automatically check datasets for adherence to the specification, -[BIDS Apps](https://doi.org/10.1371/journal.pcbi.1005209), a collection of portable neuroimaging pipelines that understand BIDS datasets, -and [OpenNeuro][openneuro] as a database for BIDS formatted datasets. +the [BIDS validator][bids_validator_gh] to automatically check datasets for adherence to the specification, +[BIDS Apps](./tools/bids-apps.md), a collection of portable neuroimaging pipelines that understand BIDS datasets. A non-exhaustive list of further tools can be found in the [tools](./tools/index.md) section. With the ongoing development of new tools and resources it is important to keep in mind -that the [BIDS specification](http://bids-specification.readthedocs.io/) remains -the standard according to which the entire ecosystem must adhere. - -## Philosophy +that the [BIDS specification][specification] +remains the standard according to which the entire ecosystem must adhere. -Another part is that BIDS is striving to not reinventing other standards and metadata ontologies but reuse them: +## Why use BIDS? -![BIDS-minder](./assets/img/BIDS-minder.svg) - -## Benefits +1) Efficient data usage: The use of a common format allows data to be more easily reused by other researchers, maximizing its utility. 2) Analysis pipelines: there is a growing number of data analysis software packages (BIDS-Apps) that can automatically process data organized according to BIDS; 3) Data sharing: Use of BIDS makes sharing by major repositories (e.g. OpenNeuro) very simple, enabling rapid and effective data sharing.
@@ -98,33 +109,40 @@ By using this standard you will benefit in the following ways: - There is a growing number of [data analysis software packages](./tools/index.md) that can understand data organized according to BIDS. -- Databases such as [OpenNeuro.org](http://openneuro.org), [LORIS](http://www.loris.ca), [COINS](https://coins.trendscenter.org), [XNAT](https://central.xnat.org/), [SciTran](https://scitran.github.io/), and others will accept and export datasets organized according to BIDS. +- Databases such as [OpenNeuro.org][openneuro], [LORIS](http://www.loris.ca), [COINS](https://coins.trendscenter.org), [XNAT](https://central.xnat.org/), [SciTran](https://scitran.github.io/), and others will accept and export datasets organized according to BIDS. If you ever plan to share your data publicly (nowadays some journals require this) you can speed up the curation process by using BIDS. -- There are [validation tools](https://github.com/bids-standard/bids-validator) (also available [online](http://bids-standard.github.io/bids-validator/)) that can check your dataset integrity and let you easily spot missing values. +- There are [validation tools][bids_validator_gh] (also available [online][bids_validator]) that can check your dataset integrity and let you easily spot missing values. -## Further information +## Foundational principles -- Good introductions to the BIDS standard can be found in the initial - [paper published in Nature Scientific Data](https://www.nature.com/articles/sdata201644), - as well as in the follow up papers on specific modalities: - [MEG](https://www.nature.com/articles/sdata2018110), - [EEG](https://www.nature.com/articles/s41597-019-0104-8), - [iEEG](https://www.nature.com/articles/s41597-019-0105-7), - [genetics](https://doi.org/10.1093/gigascience/giaa104), - [PET](https://doi.org/10.1038/s41597-022-01164-1), - [microscopy](https://doi.org/10.3389/fnins.2022.871228), - and [qMRI](https://doi.org/10.1038/s41597-022-01571-4). +### Reuse existing standards -- Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/). +BIDS strives to reuse existing standares, formats, methods and technologies +whenever possible to minimize complexity and facilitate adoption. + +![BIDS-minder](./assets/img/BIDS-minder.svg) + +### Tackle most common use cases -- Take a look at how the community [uses BIDS](https://medium.com/stanford-center-for-reproducible-neuroscience/bids-usage-survey-results-72637ff039c4). +BIDS aims to tackle the most commonly used neuroimaging data, derivatives, and models +(inspired by the [Pareto principle](https://en.wikipedia.org/wiki/Pareto_principle)). -- We have constructed a [grant writing kit](./impact/index.md) - to assist you in putting together BIDS-related grant proposals. +### Community engagement + +BIDS should enable and maximize community engagement in the creation and extension of the specification, +to ensure maximal adoption by the research community. + +## Further information + +- Good introductions to the BIDS standard can be found in the initial BIDS paper + as well as in the follow up papers for BIDS extensions. + All of those are listed in [the BIDS specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids). + +- Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/). -- We submitted an application to [The Neuro Open Science in action prize 2020](https://www.mcgill.ca/neuro/open-science/neuro-open-science-action-prize-2020). - Please find our [associated application](./assets/BIDS-materials/2020_TheNeuro_OpenScienceInAction_application.pdf). +- To assist you in putting together BIDS-related grant proposals, + check our [impact section that contains numbers and statistics about BIDS](./impact/index.md). **Leave comments about the site below:** diff --git a/docs/standards/index.md b/docs/standards/index.md index e114284c..36c5db27 100644 --- a/docs/standards/index.md +++ b/docs/standards/index.md @@ -1,7 +1,14 @@ # BIDS Standards +Neuroimaging experiments result in complex data that can be arranged in many different ways. +For a long time, there was no consensus how to organize and share +data obtained in neuroimaging experiments. +Even two researchers working in the same lab could opt to arrange their data in a different way. +Lack of consensus (or a standard) leads to misunderstandings and time wasted on rearranging data +or rewriting scripts expecting certain structure. + The current set of BIDS Standards provide outlines and guidance -for file naming and organization, statistical modeling of neuroimaging data, +for file and metaddata naming and organization, statistical modeling of neuroimaging data, and applications created to be used with BIDS data. These standards are intended to be updated and evolve as methods and data types change, but current documentation on BIDS standards can be found in the sections below. diff --git a/makefile b/makefile index fe5952b3..c44fe91b 100644 --- a/makefile +++ b/makefile @@ -1,7 +1,7 @@ all: update serve: update - mkdocs serve -a localhost:8080 + mkdocs serve -a localhost:8060 update: update_from_spec update_contributors update_datasets_examples tmp_figures update_bep_pages From 98ac33ae8cc5341d272141d9bf169aee307fb502 Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Thu, 21 Aug 2025 16:31:31 -0400 Subject: [PATCH 02/31] first updates to landing page --- docs/assets/img/logos/BIDS_logo_black.svg | 1 + docs/index.md | 1 + docs/overrides/home.html | 190 +++++++++ docs/stylesheets/extra.css | 464 ++++++++++++++++++++++ mkdocs.yml | 64 ++- 5 files changed, 708 insertions(+), 12 deletions(-) create mode 100644 docs/assets/img/logos/BIDS_logo_black.svg create mode 100644 docs/overrides/home.html diff --git a/docs/assets/img/logos/BIDS_logo_black.svg b/docs/assets/img/logos/BIDS_logo_black.svg new file mode 100644 index 00000000..9f1718f7 --- /dev/null +++ b/docs/assets/img/logos/BIDS_logo_black.svg @@ -0,0 +1 @@ +Ресурс 2 diff --git a/docs/index.md b/docs/index.md index c81c89bd..a8b7b386 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,5 @@ --- +template: home.html title: BIDS --- diff --git a/docs/overrides/home.html b/docs/overrides/home.html new file mode 100644 index 00000000..00817f6f --- /dev/null +++ b/docs/overrides/home.html @@ -0,0 +1,190 @@ +{% extends "main.html" %} + +{% block tabs %} + {{ super() }} + + + +
+
+
+
+ BIDS Logo Background +
+
+

Data standardization that simply works.

+
+ + Get started + + + Learn more + +
+
+
+
+
+ + +
+
+
+ + +
+

BIDS in a nutshell

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+ + +
+ +
+
+
+ {% include ".icons/material/file-tree.svg" %} +
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Standardized Organization

+

BIDS provides a consistent way to organize your neuroimaging data, making it easy to understand and share across research groups and institutions.

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+ +
+
+
+ {% include ".icons/material/account-group.svg" %} +
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+

Community Driven

+

Developed by the neuroscience community for the community. BIDS continues to evolve based on real-world research needs and feedback.

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+ +
+
+
+ {% include ".icons/material/tools.svg" %} +
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Rich Ecosystem

+

A growing collection of BIDS Apps, validators, and analysis tools that work seamlessly with BIDS-formatted datasets.

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+ +
+
+
+ {% include ".icons/material/open-source-initiative.svg" %} +
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Open Science

+

Promotes reproducible research and data sharing through standardized formats that are platform-independent and openly documented.

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+ +
+
+
+ {% include ".icons/material/check-decagram.svg" %} +
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Validation Tools

+

Built-in validation ensures your datasets comply with BIDS standards, catching issues early and improving data quality.

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+ +
+
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+ {% include ".icons/material/brain.svg" %} +
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Multi-Modal Support

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Supports a wide range of neuroimaging modalities including fMRI, EEG, MEG, iEEG, PET, and behavioral data.

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Public BIDS Datasets
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BIDS Research Papers
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BIDS Apps and Tools
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Supported by

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+ Sponsor 1 +
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+
+{% endblock %} + +{% block content %}{% endblock %} +{% block footer %}{% endblock %} \ No newline at end of file diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index 994124de..412703da 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -38,3 +38,467 @@ p { text-align: justify; } } .md-footer__inner.md-grid { display: none; } + +/* Hero section styles - Complete rewrite */ +.mdx-container { + padding-top: 1rem !important; + background: linear-gradient(to bottom, var(--bd24-olive), #f7c794 99%, #fff 99%) !important; + position: relative !important; + overflow: hidden !important; + min-height: 300px !important; +} + +.mdx-hero { + margin: 1rem 0 !important; + color: var(--md-primary-bg-color) !important; + position: relative !important; + z-index: 2 !important; + min-height: 280px !important; + display: flex !important; + align-items: center !important; +} + +.mdx-hero__logo-bg { + position: absolute !important; + top: -475px !important; + left: -200px !important; + transform: none !important; + z-index: 1 !important; + width: auto !important; + height: 120% !important; +} + +.mdx-hero__logo-bg img { + height: 400px !important; + width: auto !important; + opacity: 0.15 !important; + object-fit: contain !important; + pointer-events: none !important; + display: block !important; +} + +.mdx-hero__content { + position: relative !important; + z-index: 3 !important; + max-width: 600px !important; + padding-left: 0 !important; + margin-left: 0 !important; +} + +/* Mobile adjustments */ +@media screen and (max-width: 44.9375em) { + .mdx-container { + min-height: 300px !important; + } + + .mdx-hero { + min-height: 280px !important; + } + + .mdx-hero__logo-bg { + left: -50px !important; + height: 100% !important; + } + + .mdx-hero__logo-bg img { + height: 480px !important; + opacity: 0.15 !important; + } + + .mdx-hero__content { + max-width: 100% !important; + } +} + +/* Tablet adjustments */ +@media screen and (min-width: 60em) { + .mdx-container { + min-height: 400px !important; + } + + .mdx-hero { + min-height: 350px !important; + } + + .mdx-hero__logo-bg { + left: -150px !important; + } + + .mdx-hero__logo-bg img { + height: 680px !important; + } +} + +/* Desktop adjustments */ +@media screen and (min-width: 76.25em) { + .mdx-container { + min-height: 625px !important; + } + + .mdx-hero { + min-height: 575px !important; + } + + .mdx-hero__content { + padding-top: 75px !important; /* Add padding to push text back down */ + } + + .mdx-hero__logo-bg { + left: -100px !important; + } + + .mdx-hero__logo-bg img { + height: 1500px !important; + opacity: 0.1 !important; + } +} + +.mdx-hero h1 { + margin-bottom: 1rem; + color: currentColor; + font-weight: 700; + font-size: 2.5rem; + line-height: 1.2; +} + +.mdx-hero__content p { + margin-bottom: 2rem; + font-size: 1.125rem; + opacity: 0.8; +} + +.mdx-hero__actions { + display: flex; + gap: 1rem; + flex-wrap: wrap; +} + +.mdx-hero__actions .md-button { + margin-right: 0.5rem; + margin-bottom: 0.5rem; +} + +@media screen and (min-width: 60em) { + .mdx-hero { + display: block; + } + + .mdx-hero__content { + max-width: 50rem; + margin-top: 3.5rem; + padding-bottom: 14vw; + } +} + +@media screen and (min-width: 76.25em) { + .mdx-hero__content { + max-width: 50rem; + } +} + +/* Features section with headline above and full-width grid */ +.mdx-features-section { + margin: 4rem 0; +} + +.mdx-features-headline { + text-align: center; + margin-bottom: 3rem; + max-width: 800px; + margin-left: auto; + margin-right: auto; +} + +.mdx-features-headline h2 { + font-size: 2.5rem; + font-weight: 700; + margin-bottom: 1rem; + color: var(--md-default-fg-color); + line-height: 1.2; +} + +.mdx-features-headline p { + font-size: 1.125rem; + color: var(--md-default-fg-color--light); + line-height: 1.6; + margin: 0; +} + +.mdx-features { + display: grid; + grid-template-columns: repeat(auto-fit, minmax(16rem, 1fr)); + gap: 2rem; +} + +/* Responsive adjustments for features section */ +@media screen and (max-width: 44.9375em) { + .mdx-features-section { + margin: 2rem 0; + } + + .mdx-features-headline { + margin-bottom: 2rem; + } + + .mdx-features-headline h2 { + font-size: 2rem; + } + + .mdx-features { + grid-template-columns: 1fr; + gap: 1.5rem; + } +} + +.mdx-feature__item { + display: flex; + flex-direction: column; + padding: 2rem; + background: var(--md-default-bg-color); + border-radius: 0.5rem; + box-shadow: var(--md-shadow-z1); + transition: transform 0.2s, box-shadow 0.2s; + height: 280px; +} + +.mdx-feature__item:hover { + transform: translateY(-0.25rem); + box-shadow: var(--md-shadow-z2); +} + +.mdx-feature__icon { + width: 3rem; + height: 3rem; + margin-bottom: 1rem; + color: var(--md-primary-fg-color); +} + +.mdx-feature__icon svg { + width: 100%; + height: 100%; +} + +.mdx-feature__content h2 { + margin: 0 0 1rem; + font-weight: 700; + font-size: 1.25rem; +} + +.mdx-feature__content { + flex-grow: 1; + display: flex; + flex-direction: column; +} + +.mdx-feature__content p { + margin: 0; + color: var(--md-default-fg-color--light); + flex-grow: 1; +} + +/* Stats section */ +.mdx-stats { + display: grid; + grid-template-columns: repeat(auto-fit, minmax(8rem, 1fr)); + gap: 2rem; + margin: 4rem 0 2rem; + text-align: center; +} + +.mdx-stats__item { + color: var(--md-primary-bg-color); +} + +.mdx-stats__number { + font-weight: 700; + font-size: 2rem; + line-height: 1.2; +} + +.mdx-stats__label { + font-size: 0.875rem; + opacity: 0.8; +} + +/* Responsive adjustments */ +@media screen and (max-width: 44.9375em) { + .mdx-hero h1 { + font-size: 2rem; + } + + .mdx-hero__actions { + flex-direction: column; + } + + .mdx-hero__actions .md-button { + width: 100%; + margin-right: 0; + } +} + +/* Sponsors section */ +.mdx-sponsors { + background: var(--md-default-bg-color) !important; + padding: 4rem 0 !important; + border-top: 1px solid var(--md-default-fg-color--lightest) !important; +} + +.mdx-sponsors__content { + text-align: center !important; + max-width: 1200px !important; + margin: 0 auto !important; + padding: 0 2rem !important; +} + +.mdx-sponsors__content h2 { + margin-bottom: 1rem !important; + font-weight: 700 !important; + font-size: 2rem !important; + color: var(--md-default-fg-color) !important; +} + +.mdx-sponsors__content p { + margin-bottom: 3rem !important; + font-size: 1.125rem !important; + color: var(--md-default-fg-color--light) !important; + max-width: 600px !important; + margin-left: auto !important; + margin-right: auto !important; +} + +.mdx-sponsors__grid { + display: flex !important; + justify-content: center !important; + align-items: center !important; + gap: 1.5rem !important; + flex-wrap: wrap !important; +} + +.mdx-sponsors__item { + display: flex !important; + align-items: center !important; + justify-content: center !important; + padding: 1.5rem !important; + background: white !important; + border-radius: 0.5rem !important; + box-shadow: 0 2px 8px rgba(0,0,0,0.1) !important; + transition: all 0.3s ease !important; + width: 200px !important; + height: 120px !important; + border: 1px solid #eee !important; +} + +.mdx-sponsors__item:hover { + transform: translateY(-2px) !important; + box-shadow: 0 4px 16px rgba(0,0,0,0.15) !important; +} + +.mdx-sponsors__item img { + max-width: 180px !important; + max-height: 80px !important; + width: auto !important; + height: auto !important; + object-fit: contain !important; + filter: grayscale(100%) opacity(0.7) !important; + transition: filter 0.3s ease !important; +} + +.mdx-sponsors__item:hover img { + filter: grayscale(0%) opacity(1) !important; +} + +/* Sponsors responsive adjustments */ +@media screen and (max-width: 44.9375em) { + .mdx-sponsors { + padding: 3rem 0 !important; + } + + .mdx-sponsors__content { + padding: 0 1rem !important; + } + + .mdx-sponsors__content h2 { + font-size: 1.5rem !important; + } + + .mdx-sponsors__grid { + grid-template-columns: repeat(2, 1fr) !important; + gap: 1.5rem !important; + } + + .mdx-sponsors__item { + height: 100px !important; + max-width: none !important; + } + + .mdx-sponsors__item img { + max-width: 140px !important; + max-height: 60px !important; + } +} + +@media screen and (min-width: 60em) { + .mdx-sponsors__grid { + flex-wrap: nowrap !important; + } +} + +/* BrewDistrict24 inspired pastel color scheme */ +:root { + --bd24-raspberry: #d47b8a; + --bd24-sage-green: #a8b5a0; + --bd24-teal: #7db5b0; + --bd24-dusty-pink: #e8b4c0; + --bd24-blue-gray: #8a9ba8; + --bd24-peach: #f4a572; + --bd24-olive: #969b66; + --bd24-navbar: #6c704a; + --bd24-light-orange: #f7c794; + --bd24-cream: #f8f6f0; + --bd24-soft-white: #fefefe; +} + +/* Override Material Design color variables */ +:root { + --md-primary-fg-color: var(--bd24-navbar); + --md-primary-fg-color--light: var(--bd24-navbar); + --md-primary-fg-color--dark: var(--bd24-navbar); + --md-accent-fg-color: var(--bd24-raspberry); + --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); +} + +/* Custom button styling with pastel colors */ +.md-button--primary { + background-color: var(--bd24-navbar) !important; + border-color: var(--bd24-navbar) !important; + color: white !important; + font-weight: 500 !important; +} + +.md-button--primary:hover { + background-color: var(--bd24-dusty-pink) !important; + border-color: var(--bd24-dusty-pink) !important; + color: white !important; + transform: translateY(-1px) !important; +} + +.md-button--primary:focus { + background-color: var(--bd24-raspberry) !important; + border-color: var(--bd24-raspberry) !important; + color: white !important; +} + +/* Secondary button styling */ +.md-button { + border: 2px solid white !important; + color: white !important; + font-weight: 500 !important; + background-color: var(--bd24-navbar) !important; +} + +.md-button:hover { + background-color: var(--bd24-peach) !important; + border: 2px solid white !important; + color: white !important; + transform: translateY(-1px) !important; +} \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index cd8e7d6b..3a2e2016 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -4,7 +4,10 @@ repo_url: https://github.com/bids-standard/bids-website/tree/main site_url: https://bids.neuroimaging.io/ plugins: - - search + - search: + separator: '[\s\u200b\-_,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])' + - minify: + minify_html: true - tags # - social - blog @@ -191,21 +194,26 @@ theme: logo: assets/img/logos/logo.png features: - announce.dismiss - - content.action.edit + - content.code.annotate - content.code.copy - content.tabs.link - content.tooltips - - footnotes - header.autohide + - navigation.expand - navigation.footer - navigation.indexes - navigation.instant + - navigation.instant.prefetch + - navigation.instant.progress + - navigation.prune - navigation.sections - navigation.tabs - navigation.tabs.sticky - navigation.top - - search.suggest + - navigation.tracking - search.highlight + - search.share + - search.suggest - toc.follow icon: repo: fontawesome/brands/github @@ -217,15 +225,15 @@ theme: icon: material/brightness-auto name: Switch to light mode - media: "(prefers-color-scheme: light)" - primary: teal - accent: green + primary: custom + accent: custom scheme: default toggle: icon: material/brightness-7 name: Switch to dark mode - media: "(prefers-color-scheme: dark)" - primary: teal - accent: green + primary: custom + accent: custom scheme: slate toggle: icon: material/brightness-4 @@ -237,14 +245,38 @@ markdown_extensions: - abbr - admonition - attr_list + - def_list + - footnotes - md_in_html + - toc: + permalink: true + anchorlink: true + toc_depth: 3 + - pymdownx.arithmatex: + generic: true + - pymdownx.betterem: + smart_enable: all + - pymdownx.caret - pymdownx.details - pymdownx.emoji: emoji_generator: !!python/name:material.extensions.emoji.to_svg emoji_index: !!python/name:material.extensions.emoji.twemoji + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite + - pymdownx.keys + - pymdownx.magiclink: + normalize_issue_symbols: true + repo_url_shorthand: true + user: bids-standard + repo: bids-website + - pymdownx.mark + - pymdownx.smartsymbols - pymdownx.snippets: auto_append: - - includes/abbreviations.md + - includes/mkdocs.md - pymdownx.superfences: custom_fences: - name: mermaid @@ -252,14 +284,22 @@ markdown_extensions: format: !!python/name:pymdownx.superfences.fence_code_format - pymdownx.tabbed: alternate_style: true + combine_header_slug: true + slugify: !!python/object/apply:pymdownx.slugs.slugify + kwds: + case: lower + - pymdownx.tasklist: + custom_checkbox: true + - pymdownx.tilde - tables - - toc: - anchorlink: true - toc_depth: 3 + extra_javascript: - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js - javascripts/tablesort.js + - javascripts/mathjax.js + - https://polyfill.io/v3/polyfill.min.js?features=es6 + - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js extra_css: - stylesheets/extra.css From f5b8ce473004a8a5b7ab75a040bf534b35ba6b1c Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Wed, 1 Oct 2025 18:15:27 -0400 Subject: [PATCH 03/31] first modifications for landing page --- .github/PULL_REQUEST_TEMPLATE/website.md | 43 +++++++++++++++ docs/overrides/home.html | 5 +- docs/stylesheets/extra.css | 67 +++++++++++++++--------- 3 files changed, 88 insertions(+), 27 deletions(-) create mode 100644 .github/PULL_REQUEST_TEMPLATE/website.md diff --git a/.github/PULL_REQUEST_TEMPLATE/website.md b/.github/PULL_REQUEST_TEMPLATE/website.md new file mode 100644 index 00000000..74829e17 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/website.md @@ -0,0 +1,43 @@ + + + + + + +- Closes # + + +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 + + +## 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 diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 00817f6f..836a3123 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -47,7 +47,7 @@

Data standardization that simply works.

-
+
@@ -135,10 +135,9 @@

Multi-Modal Support

- -
+
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index 412703da..feef401b 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -42,12 +42,18 @@ p { text-align: justify; } /* Hero section styles - Complete rewrite */ .mdx-container { padding-top: 1rem !important; - background: linear-gradient(to bottom, var(--bd24-olive), #f7c794 99%, #fff 99%) !important; + padding-bottom: 8rem !important; + background: transparent !important; position: relative !important; overflow: hidden !important; min-height: 300px !important; } +/* Apply gradient only to first section */ +.mdx-container:first-of-type { + background: linear-gradient(to bottom, #984949, transparent 99%) !important; +} + .mdx-hero { margin: 1rem 0 !important; color: var(--md-primary-bg-color) !important; @@ -254,11 +260,15 @@ p { text-align: justify; } display: flex; flex-direction: column; padding: 2rem; - background: var(--md-default-bg-color); + background: #984949; + color: white; border-radius: 0.5rem; box-shadow: var(--md-shadow-z1); transition: transform 0.2s, box-shadow 0.2s; height: 280px; + justify-content: center; + align-items: center; + text-align: center; } .mdx-feature__item:hover { @@ -270,30 +280,31 @@ p { text-align: justify; } width: 3rem; height: 3rem; margin-bottom: 1rem; - color: var(--md-primary-fg-color); + color: white; } .mdx-feature__icon svg { width: 100%; height: 100%; + fill: white; } .mdx-feature__content h2 { margin: 0 0 1rem; font-weight: 700; font-size: 1.25rem; + color: white; } .mdx-feature__content { - flex-grow: 1; display: flex; flex-direction: column; + align-items: center; } .mdx-feature__content p { margin: 0; - color: var(--md-default-fg-color--light); - flex-grow: 1; + color: rgba(255, 255, 255, 0.8); } /* Stats section */ @@ -306,18 +317,27 @@ p { text-align: justify; } } .mdx-stats__item { - color: var(--md-primary-bg-color); + background: #743737; + color: white; + padding: 2rem; + border-radius: 0.5rem; + display: flex; + flex-direction: column; + justify-content: center; + align-items: center; + min-height: 150px; } .mdx-stats__number { font-weight: 700; font-size: 2rem; line-height: 1.2; + color: white; } .mdx-stats__label { font-size: 0.875rem; - opacity: 0.8; + color: rgba(255, 255, 255, 0.8); } /* Responsive adjustments */ @@ -338,9 +358,8 @@ p { text-align: justify; } /* Sponsors section */ .mdx-sponsors { - background: var(--md-default-bg-color) !important; - padding: 4rem 0 !important; - border-top: 1px solid var(--md-default-fg-color--lightest) !important; + background: #984949 !important; + padding: 1rem 0 3rem!important; } .mdx-sponsors__content { @@ -351,7 +370,7 @@ p { text-align: justify; } } .mdx-sponsors__content h2 { - margin-bottom: 1rem !important; + margin-bottom: 2rem !important; font-weight: 700 !important; font-size: 2rem !important; color: var(--md-default-fg-color) !important; @@ -460,31 +479,31 @@ p { text-align: justify; } /* Override Material Design color variables */ :root { - --md-primary-fg-color: var(--bd24-navbar); - --md-primary-fg-color--light: var(--bd24-navbar); - --md-primary-fg-color--dark: var(--bd24-navbar); - --md-accent-fg-color: var(--bd24-raspberry); + --md-primary-fg-color: #984949; + --md-primary-fg-color--light: #984949; + --md-primary-fg-color--dark: #984949; + --md-accent-fg-color: #984949; --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); } /* Custom button styling with pastel colors */ .md-button--primary { - background-color: var(--bd24-navbar) !important; - border-color: var(--bd24-navbar) !important; + background-color: #984949 !important; + border-color: white !important; color: white !important; font-weight: 500 !important; } .md-button--primary:hover { - background-color: var(--bd24-dusty-pink) !important; - border-color: var(--bd24-dusty-pink) !important; + background-color: #984949 !important; + border-color: white !important; color: white !important; transform: translateY(-1px) !important; } .md-button--primary:focus { - background-color: var(--bd24-raspberry) !important; - border-color: var(--bd24-raspberry) !important; + background-color: #984949 !important; + border-color: #984949 !important; color: white !important; } @@ -493,11 +512,11 @@ p { text-align: justify; } border: 2px solid white !important; color: white !important; font-weight: 500 !important; - background-color: var(--bd24-navbar) !important; + background-color: #743737 !important; } .md-button:hover { - background-color: var(--bd24-peach) !important; + background-color: #984949 !important; border: 2px solid white !important; color: white !important; transform: translateY(-1px) !important; From e76dd7d3340ab48761d186cebffe592332c9630c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 1 Oct 2025 22:19:47 +0000 Subject: [PATCH 04/31] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .github/PULL_REQUEST_TEMPLATE/website.md | 6 ++-- docs/overrides/home.html | 8 ++--- docs/stylesheets/extra.css | 44 ++++++++++++------------ 3 files changed, 29 insertions(+), 29 deletions(-) diff --git a/.github/PULL_REQUEST_TEMPLATE/website.md b/.github/PULL_REQUEST_TEMPLATE/website.md index 74829e17..af56a6f1 100644 --- a/.github/PULL_REQUEST_TEMPLATE/website.md +++ b/.github/PULL_REQUEST_TEMPLATE/website.md @@ -6,7 +6,7 @@ Below is a suggested pull request template. Feel free to add more details you fe --> - - Closes # - Changes proposed in this pull request: -- +- ## Checklist for contributor diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 836a3123..3e16c72c 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -23,7 +23,7 @@ } } - +
@@ -50,7 +50,7 @@

Data standardization that simply works.

- +

BIDS in a nutshell

@@ -58,7 +58,7 @@

BIDS in a nutshell

- +
@@ -186,4 +186,4 @@

Supported by

{% endblock %} {% block content %}{% endblock %} -{% block footer %}{% endblock %} \ No newline at end of file +{% block footer %}{% endblock %} diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index feef401b..a0e7e23d 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -96,21 +96,21 @@ p { text-align: justify; } .mdx-container { min-height: 300px !important; } - + .mdx-hero { min-height: 280px !important; } - + .mdx-hero__logo-bg { left: -50px !important; height: 100% !important; } - + .mdx-hero__logo-bg img { height: 480px !important; opacity: 0.15 !important; } - + .mdx-hero__content { max-width: 100% !important; } @@ -121,15 +121,15 @@ p { text-align: justify; } .mdx-container { min-height: 400px !important; } - + .mdx-hero { min-height: 350px !important; } - + .mdx-hero__logo-bg { left: -150px !important; } - + .mdx-hero__logo-bg img { height: 680px !important; } @@ -140,7 +140,7 @@ p { text-align: justify; } .mdx-container { min-height: 625px !important; } - + .mdx-hero { min-height: 575px !important; } @@ -148,11 +148,11 @@ p { text-align: justify; } .mdx-hero__content { padding-top: 75px !important; /* Add padding to push text back down */ } - + .mdx-hero__logo-bg { left: -100px !important; } - + .mdx-hero__logo-bg img { height: 1500px !important; opacity: 0.1 !important; @@ -241,15 +241,15 @@ p { text-align: justify; } .mdx-features-section { margin: 2rem 0; } - + .mdx-features-headline { margin-bottom: 2rem; } - + .mdx-features-headline h2 { font-size: 2rem; } - + .mdx-features { grid-template-columns: 1fr; gap: 1.5rem; @@ -345,11 +345,11 @@ p { text-align: justify; } .mdx-hero h1 { font-size: 2rem; } - + .mdx-hero__actions { flex-direction: column; } - + .mdx-hero__actions .md-button { width: 100%; margin-right: 0; @@ -431,25 +431,25 @@ p { text-align: justify; } .mdx-sponsors { padding: 3rem 0 !important; } - + .mdx-sponsors__content { padding: 0 1rem !important; } - + .mdx-sponsors__content h2 { font-size: 1.5rem !important; } - + .mdx-sponsors__grid { grid-template-columns: repeat(2, 1fr) !important; gap: 1.5rem !important; } - + .mdx-sponsors__item { height: 100px !important; max-width: none !important; } - + .mdx-sponsors__item img { max-width: 140px !important; max-height: 60px !important; @@ -471,7 +471,7 @@ p { text-align: justify; } --bd24-blue-gray: #8a9ba8; --bd24-peach: #f4a572; --bd24-olive: #969b66; - --bd24-navbar: #6c704a; + --bd24-navbar: #6c704a; --bd24-light-orange: #f7c794; --bd24-cream: #f8f6f0; --bd24-soft-white: #fefefe; @@ -520,4 +520,4 @@ p { text-align: justify; } border: 2px solid white !important; color: white !important; transform: translateY(-1px) !important; -} \ No newline at end of file +} From c5aea7fab64dc6d50d7b7925ea3b353e7c130e96 Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Wed, 1 Oct 2025 18:29:17 -0400 Subject: [PATCH 05/31] remove minify plugin; not needed --- mkdocs.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 3a2e2016..ddd4888a 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -6,8 +6,6 @@ site_url: https://bids.neuroimaging.io/ plugins: - search: separator: '[\s\u200b\-_,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])' - - minify: - minify_html: true - tags # - social - blog From 9c46d4d5735002e04eeb4430c6af3fce48b8554d Mon Sep 17 00:00:00 2001 From: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Date: Wed, 1 Oct 2025 18:44:26 -0400 Subject: [PATCH 06/31] Apply suggestions from code review Co-authored-by: Chris Markiewicz --- docs/overrides/home.html | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 3e16c72c..0e019511 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -29,7 +29,7 @@
- BIDS Logo Background + BIDS Logo Background

Data standardization that simply works.

@@ -168,16 +168,16 @@

Supported by

- Sponsor 1 + Sponsor 1
- Sponsor 2 + Sponsor 2
- Sponsor 3 + Sponsor 3
- Sponsor 4 + Sponsor 4
From 86bcd3787c515a4cf855180096859dcf6d2e1e16 Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Wed, 15 Oct 2025 16:14:35 -0400 Subject: [PATCH 07/31] first modifications based on review --- .github/PULL_REQUEST_TEMPLATE/bep.md | 11 -- .../PULL_REQUEST_TEMPLATE/bep_template.yml | 29 ---- .../{website.md => pull_request_template.md} | 14 -- docs/assets/img/logos/BIDS_logo_black.svg | 1 - docs/index.md | 158 +----------------- docs/overrides/home.html | 10 +- mkdocs.yml | 5 +- 7 files changed, 7 insertions(+), 221 deletions(-) delete mode 100644 .github/PULL_REQUEST_TEMPLATE/bep.md delete mode 100644 .github/PULL_REQUEST_TEMPLATE/bep_template.yml rename .github/PULL_REQUEST_TEMPLATE/{website.md => pull_request_template.md} (67%) delete mode 100644 docs/assets/img/logos/BIDS_logo_black.svg diff --git a/.github/PULL_REQUEST_TEMPLATE/bep.md b/.github/PULL_REQUEST_TEMPLATE/bep.md deleted file mode 100644 index 8f40ef43..00000000 --- a/.github/PULL_REQUEST_TEMPLATE/bep.md +++ /dev/null @@ -1,11 +0,0 @@ -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) diff --git a/.github/PULL_REQUEST_TEMPLATE/bep_template.yml b/.github/PULL_REQUEST_TEMPLATE/bep_template.yml deleted file mode 100644 index b48c2193..00000000 --- a/.github/PULL_REQUEST_TEMPLATE/bep_template.yml +++ /dev/null @@ -1,29 +0,0 @@ ---- -- 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' diff --git a/.github/PULL_REQUEST_TEMPLATE/website.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md similarity index 67% rename from .github/PULL_REQUEST_TEMPLATE/website.md rename to .github/PULL_REQUEST_TEMPLATE/pull_request_template.md index af56a6f1..88137e17 100644 --- a/.github/PULL_REQUEST_TEMPLATE/website.md +++ b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md @@ -27,17 +27,3 @@ Changes proposed in this pull request: - [ ] 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 - - -## 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 diff --git a/docs/assets/img/logos/BIDS_logo_black.svg b/docs/assets/img/logos/BIDS_logo_black.svg deleted file mode 100644 index 9f1718f7..00000000 --- a/docs/assets/img/logos/BIDS_logo_black.svg +++ /dev/null @@ -1 +0,0 @@ -Ресурс 2 diff --git a/docs/index.md b/docs/index.md index db0c1273..76ce3384 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,160 +1,4 @@ --- template: home.html title: BIDS ---- - -Neuroimaging experiments result in complex data that can be arranged in many different ways. -For a long time, there was no consensus how to organize and share -data obtained in neuroimaging experiments. -Even two researchers working in the same lab could opt to arrange their data in a different way. -Lack of consensus (or a standard) leads to misunderstandings and time wasted on rearranging data -or rewriting scripts expecting certain structure. -With the Brain Imaging Data Structure (BIDS), -we describe a simple and easy to adopt way of organizing neuroimaging and behavioral data. - -![BIDS-folder-organization](./assets/img/dicom-reorganization-transparent-black_1000x477.png#only-light) -![BIDS-folder-organization](./assets/img/dicom-reorganization-transparent-white_1000x477.png#only-dark) - -### BIDS as a community effort - - - -BIDS is developed by the community for the community -and everybody can [become a part of the community](./extensions/index.md). - -The most important part of BIDS are the users: -if more people use it, more data will be shared and the more powerful it will become. - -We want to make it easy to learn and more adopted. - -Since BIDS is platform independent -and still an adapting, growing tool, the greater the community, the better it will be. - -### BIDS as an ecosystem of tools - - - -Since the inception of the BIDS specification that documents how to organize neuroimaging data, -a large ecosystem of tools and resources has evolved around BIDS. - -A few of the key elements of this ecosystem are -the [BIDS specification][specification] with the nitty-gritty details, -the [starter kit](./getting_started/index.md) with a simple explanation how to work with it, -the [BIDS validator][bids_validator_gh] to automatically check datasets for adherence to the specification, -[BIDS Apps](./tools/bids-apps.md), a collection of portable neuroimaging pipelines that understand BIDS datasets. - -A non-exhaustive list of further tools can be found in the [tools](./tools/index.md) section. - -With the ongoing development of new tools and resources it is important to keep in mind -that the [BIDS specification][specification] -remains the standard according to which the entire ecosystem must adhere. - -## Why use BIDS? - -1) Efficient data usage: The use of a common format allows data to be more easily reused by other researchers, maximizing its utility. 2) Analysis pipelines: there is a growing number of data analysis software packages (BIDS-Apps) that can automatically process data organized according to BIDS; 3) Data sharing: Use of BIDS makes sharing by major repositories (e.g. OpenNeuro) very simple, enabling rapid and effective data sharing. - -
- -- :material-account-group:{ .lg .middle } **For the public good** - - --- - - - Lowers scientific waste - - Gives opportunity to less-funded researchers - - Improves efficiency - - Spurs innovation - -- :recycle:{ .lg .middle } **For yourself** - - --- - - - You are likely the future user of the data and data analysis pipelines you’ve developed - - - Enables and simplifies collaboration - - - Reviewers and funding agencies like to see reproducible results - - - Open-science based funding opportunities and awards available - (for instance: OHBM Replication Award, Mozilla Open Science Fellowship, - Google Summer of Code, and so on.) - -
- -By using this standard you will benefit in the following ways: - -- It will be easy for another researcher to work on your data. - To understand the organization of the files and their format you will only need to refer them to this document. - This is especially important if you are running your own lab and anticipate more than one person working on the same data over time. - By using BIDS you will save time trying to understand and reuse data acquired by a graduate student or postdoc that has already left the lab. - -- There is a growing number of [data analysis software packages](./tools/index.md) that can understand data organized according to BIDS. - -- Databases such as [OpenNeuro.org][openneuro], [LORIS](http://www.loris.ca), [COINS](https://coins.trendscenter.org), [XNAT](https://central.xnat.org/), [SciTran](https://scitran.github.io/), and others will accept and export datasets organized according to BIDS. - If you ever plan to share your data publicly (nowadays some journals require this) you can speed up the curation process by using BIDS. - -- There are [validation tools][bids_validator_gh] (also available [online][bids_validator]) that can check your dataset integrity and let you easily spot missing values. - -## Foundational principles - -### Reuse existing standards - -BIDS strives to reuse existing standares, formats, methods and technologies -whenever possible to minimize complexity and facilitate adoption. - -![BIDS-minder](./assets/img/BIDS-minder.svg) - -### Tackle most common use cases - -BIDS aims to tackle the most commonly used neuroimaging data, derivatives, and models -(inspired by the [Pareto principle](https://en.wikipedia.org/wiki/Pareto_principle)). - -### Community engagement - -BIDS should enable and maximize community engagement in the creation and extension of the specification, -to ensure maximal adoption by the research community. - -## Further information - -- Good introductions to the BIDS standard can be found in the initial BIDS paper - as well as in the follow up papers for BIDS extensions. - All of those are listed in [the BIDS specification](https://bids-specification.readthedocs.io/en/latest/introduction.html#citing-bids). - -- Look through some of the community's [presentations on BIDS](https://osf.io/yn93h/). - -- To assist you in putting together BIDS-related grant proposals, - check our [impact section that contains numbers and statistics about BIDS](./impact/index.md). - -**Leave comments about the site below:** - ---- - -
-
- - INCF - -
-
- - GSOC - -
-
- - NIH - -
-
- - Arnold Ventures - -
-
+--- \ No newline at end of file diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 3e16c72c..fbdd7199 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -29,7 +29,7 @@
- BIDS Logo Background + BIDS Logo Background

Data standardization that simply works.

@@ -168,16 +168,16 @@

Supported by

- Sponsor 1 + Sponsor 1
- Sponsor 2 + Sponsor 2
- Sponsor 3 + Sponsor 3
- Sponsor 4 + Sponsor 4
diff --git a/mkdocs.yml b/mkdocs.yml index ddd4888a..bf60e5bc 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -192,6 +192,7 @@ theme: logo: assets/img/logos/logo.png features: - announce.dismiss + - content.action.edit - content.code.annotate - content.code.copy - content.tabs.link @@ -201,7 +202,6 @@ theme: - navigation.footer - navigation.indexes - navigation.instant - - navigation.instant.prefetch - navigation.instant.progress - navigation.prune - navigation.sections @@ -272,9 +272,6 @@ markdown_extensions: repo: bids-website - pymdownx.mark - pymdownx.smartsymbols - - pymdownx.snippets: - auto_append: - - includes/mkdocs.md - pymdownx.superfences: custom_fences: - name: mermaid From 6ff0239f113028bff10d1a0d32bcba1be4558931 Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Wed, 15 Oct 2025 16:25:49 -0400 Subject: [PATCH 08/31] change logo path --- docs/overrides/home.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index fbdd7199..46d97616 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -29,7 +29,7 @@
- BIDS Logo Background + BIDS Logo Background

Data standardization that simply works.

From 3bebffb209e225c4e422c041d6e9c193497500eb Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Thu, 13 Nov 2025 13:43:29 +0100 Subject: [PATCH 09/31] modify landing page according to code review --- docs/overrides/home.html | 6 ++++-- docs/stylesheets/extra.css | 35 +++++++++++++++++------------------ 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 46d97616..55cc8103 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -33,11 +33,12 @@

Data standardization that simply works.

+

With the Brain Imaging Data Structure (BIDS), we describe a simple and easy to adopt way of organizing brain imaging and associated data.

Get started - + Learn more
@@ -142,7 +143,8 @@

Multi-Modal Support

2000+
-
Public BIDS Datasets
+
Public BIDS Datasets +
500+
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index a0e7e23d..49f5e4b6 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -39,10 +39,9 @@ p { text-align: justify; } .md-footer__inner.md-grid { display: none; } -/* Hero section styles - Complete rewrite */ +/* Hero section styles */ .mdx-container { padding-top: 1rem !important; - padding-bottom: 8rem !important; background: transparent !important; position: relative !important; overflow: hidden !important; @@ -51,7 +50,7 @@ p { text-align: justify; } /* Apply gradient only to first section */ .mdx-container:first-of-type { - background: linear-gradient(to bottom, #984949, transparent 99%) !important; + background: linear-gradient(to bottom, #124559, transparent 99%) !important; } .mdx-hero { @@ -260,7 +259,7 @@ p { text-align: justify; } display: flex; flex-direction: column; padding: 2rem; - background: #984949; + background: #124559; color: white; border-radius: 0.5rem; box-shadow: var(--md-shadow-z1); @@ -317,7 +316,7 @@ p { text-align: justify; } } .mdx-stats__item { - background: #743737; + background: #598392; color: white; padding: 2rem; border-radius: 0.5rem; @@ -358,7 +357,7 @@ p { text-align: justify; } /* Sponsors section */ .mdx-sponsors { - background: #984949 !important; + background: #124559 !important; padding: 1rem 0 3rem!important; } @@ -373,7 +372,7 @@ p { text-align: justify; } margin-bottom: 2rem !important; font-weight: 700 !important; font-size: 2rem !important; - color: var(--md-default-fg-color) !important; + color: white !important; } .mdx-sponsors__content p { @@ -479,31 +478,31 @@ p { text-align: justify; } /* Override Material Design color variables */ :root { - --md-primary-fg-color: #984949; - --md-primary-fg-color--light: #984949; - --md-primary-fg-color--dark: #984949; - --md-accent-fg-color: #984949; + --md-primary-fg-color: #124559; + --md-primary-fg-color--light: #124559; + --md-primary-fg-color--dark: #124559; + --md-accent-fg-color: #124559; --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); } -/* Custom button styling with pastel colors */ +/* Custom button styling */ .md-button--primary { - background-color: #984949 !important; + background-color: #124559 !important; border-color: white !important; color: white !important; font-weight: 500 !important; } .md-button--primary:hover { - background-color: #984949 !important; + background-color: #aec3b0 !important; border-color: white !important; color: white !important; transform: translateY(-1px) !important; } .md-button--primary:focus { - background-color: #984949 !important; - border-color: #984949 !important; + background-color: #aec3b0 !important; + border-color: #124559 !important; color: white !important; } @@ -512,11 +511,11 @@ p { text-align: justify; } border: 2px solid white !important; color: white !important; font-weight: 500 !important; - background-color: #743737 !important; + background-color: #124559 !important; } .md-button:hover { - background-color: #984949 !important; + background-color: #aec3b0!important; border: 2px solid white !important; color: white !important; transform: translateY(-1px) !important; From faa7c4cadc3c7ffae9c4a5fc80b77e50f7ba32a9 Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Thu, 13 Nov 2025 14:16:59 +0100 Subject: [PATCH 10/31] adjust heights and spaces --- docs/overrides/home.html | 16 ++++++++-------- docs/stylesheets/extra.css | 39 +++++++++++++++++++++++--------------- 2 files changed, 32 insertions(+), 23 deletions(-) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 55cc8103..59958df1 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -141,23 +141,23 @@

Multi-Modal Support

-
+
2000+
Public BIDS Datasets
-
-
+ +
500+
BIDS Research Papers
-
-
+ +
100+
BIDS Apps and Tools
-
-
+ +
300+
Contributors
-
+
diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index 49f5e4b6..10340b58 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -45,7 +45,7 @@ p { text-align: justify; } background: transparent !important; position: relative !important; overflow: hidden !important; - min-height: 300px !important; + min-height: 150px !important; } /* Apply gradient only to first section */ @@ -54,11 +54,11 @@ p { text-align: justify; } } .mdx-hero { - margin: 1rem 0 !important; + margin: 1rem 0 0 0 !important; color: var(--md-primary-bg-color) !important; position: relative !important; z-index: 2 !important; - min-height: 280px !important; + min-height: 150px !important; display: flex !important; align-items: center !important; } @@ -93,11 +93,11 @@ p { text-align: justify; } /* Mobile adjustments */ @media screen and (max-width: 44.9375em) { .mdx-container { - min-height: 300px !important; + min-height: 150px !important; } .mdx-hero { - min-height: 280px !important; + min-height: 150px !important; } .mdx-hero__logo-bg { @@ -118,11 +118,11 @@ p { text-align: justify; } /* Tablet adjustments */ @media screen and (min-width: 60em) { .mdx-container { - min-height: 400px !important; + min-height: 220px !important; } .mdx-hero { - min-height: 350px !important; + min-height: 200px !important; } .mdx-hero__logo-bg { @@ -137,15 +137,15 @@ p { text-align: justify; } /* Desktop adjustments */ @media screen and (min-width: 76.25em) { .mdx-container { - min-height: 625px !important; + min-height: 300px !important; } .mdx-hero { - min-height: 575px !important; + min-height: 280px !important; } .mdx-hero__content { - padding-top: 75px !important; /* Add padding to push text back down */ + padding-top: 0 !important; } .mdx-hero__logo-bg { @@ -190,8 +190,8 @@ p { text-align: justify; } .mdx-hero__content { max-width: 50rem; - margin-top: 3.5rem; - padding-bottom: 14vw; + margin-top: 3rem; + padding-bottom: 5rem; } } @@ -203,7 +203,7 @@ p { text-align: justify; } /* Features section with headline above and full-width grid */ .mdx-features-section { - margin: 4rem 0; + margin: 0 0 2rem 0; } .mdx-features-headline { @@ -311,7 +311,7 @@ p { text-align: justify; } display: grid; grid-template-columns: repeat(auto-fit, minmax(8rem, 1fr)); gap: 2rem; - margin: 4rem 0 2rem; + margin: 8rem 0 2rem; text-align: center; } @@ -325,6 +325,15 @@ p { text-align: justify; } justify-content: center; align-items: center; min-height: 150px; + text-decoration: none; + transition: all 0.3s ease; + cursor: pointer; +} + +.mdx-stats__item:hover { + transform: translateY(-4px); + box-shadow: 0 8px 16px rgba(0, 0, 0, 0.2); + background: #6b9aaa; } .mdx-stats__number { @@ -358,7 +367,7 @@ p { text-align: justify; } /* Sponsors section */ .mdx-sponsors { background: #124559 !important; - padding: 1rem 0 3rem!important; + padding: 0.5rem 0 3rem!important; } .mdx-sponsors__content { From 5d6d36b6e8fc69187d4cb23f5df6aee81beffa5a Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Thu, 13 Nov 2025 16:47:10 +0100 Subject: [PATCH 11/31] adjust spacing in feature boxes --- docs/stylesheets/extra.css | 25 +++++-------------------- 1 file changed, 5 insertions(+), 20 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index 10340b58..d412d630 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -258,14 +258,14 @@ p { text-align: justify; } .mdx-feature__item { display: flex; flex-direction: column; - padding: 2rem; + padding: 1rem 2rem 2rem 2rem; background: #124559; color: white; border-radius: 0.5rem; box-shadow: var(--md-shadow-z1); transition: transform 0.2s, box-shadow 0.2s; height: 280px; - justify-content: center; + justify-content: space-between; align-items: center; text-align: center; } @@ -470,21 +470,6 @@ p { text-align: justify; } } } -/* BrewDistrict24 inspired pastel color scheme */ -:root { - --bd24-raspberry: #d47b8a; - --bd24-sage-green: #a8b5a0; - --bd24-teal: #7db5b0; - --bd24-dusty-pink: #e8b4c0; - --bd24-blue-gray: #8a9ba8; - --bd24-peach: #f4a572; - --bd24-olive: #969b66; - --bd24-navbar: #6c704a; - --bd24-light-orange: #f7c794; - --bd24-cream: #f8f6f0; - --bd24-soft-white: #fefefe; -} - /* Override Material Design color variables */ :root { --md-primary-fg-color: #124559; @@ -503,14 +488,14 @@ p { text-align: justify; } } .md-button--primary:hover { - background-color: #aec3b0 !important; + background-color: #6b9aaa !important; border-color: white !important; color: white !important; transform: translateY(-1px) !important; } .md-button--primary:focus { - background-color: #aec3b0 !important; + background-color: #6b9aaa !important; border-color: #124559 !important; color: white !important; } @@ -524,7 +509,7 @@ p { text-align: justify; } } .md-button:hover { - background-color: #aec3b0!important; + background-color: #6b9aaa!important; border: 2px solid white !important; color: white !important; transform: translateY(-1px) !important; From e705068705c3274e28c20c60fa7ab1632efd3ee7 Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Thu, 13 Nov 2025 17:02:05 +0100 Subject: [PATCH 12/31] adjust mobile specs --- docs/stylesheets/extra.css | 55 +++++++++++++------------------------- 1 file changed, 18 insertions(+), 37 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index d412d630..d931b46a 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -1,24 +1,3 @@ -/* https://colorbrewer2.org/#type=qualitative&scheme=Paired&n=12 */ -:root { - --mri: #a6cee3; - --pet: #1f78b4; - --micr: #33a02c; - --meeg: #6a3d9a; - --beh: #fb9a99; - --nirs: #b2df8a; - --motion: #e31a1c; - --mrs: #fdbf6f; - --unused2: #ff7f00; - --unused3: #cab2d6; - --unused4: #ffff99; - --unused5: #b15928; - --key: #e41a1c; - --label: #377eb8; - --suffix: #4daf4a; - --ext: #984ea3; - --underscore: #ff7f00; -} - p { text-align: justify; } .iframe-container{ @@ -222,13 +201,6 @@ p { text-align: justify; } line-height: 1.2; } -.mdx-features-headline p { - font-size: 1.125rem; - color: var(--md-default-fg-color--light); - line-height: 1.6; - margin: 0; -} - .mdx-features { display: grid; grid-template-columns: repeat(auto-fit, minmax(16rem, 1fr)); @@ -255,6 +227,13 @@ p { text-align: justify; } } } +/* Tablet-specific adjustments for features */ +@media screen and (min-width: 45em) and (max-width: 76.24em) { + .mdx-features { + grid-template-columns: repeat(2, 1fr); + } +} + .mdx-feature__item { display: flex; flex-direction: column; @@ -362,6 +341,17 @@ p { text-align: justify; } width: 100%; margin-right: 0; } + + /* Stats section mobile optimization */ + .mdx-stats { + grid-template-columns: 1fr; + gap: 1rem; + margin: 4rem 0 1rem; + } + + .mdx-stats__item { + min-height: 120px; + } } /* Sponsors section */ @@ -384,15 +374,6 @@ p { text-align: justify; } color: white !important; } -.mdx-sponsors__content p { - margin-bottom: 3rem !important; - font-size: 1.125rem !important; - color: var(--md-default-fg-color--light) !important; - max-width: 600px !important; - margin-left: auto !important; - margin-right: auto !important; -} - .mdx-sponsors__grid { display: flex !important; justify-content: center !important; From 875aace0bc9e68e759a319e2cf5cf812cb5a7ccb Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 13 Nov 2025 16:14:14 +0000 Subject: [PATCH 13/31] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/stylesheets/extra.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index d931b46a..c7cd2745 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -348,7 +348,7 @@ p { text-align: justify; } gap: 1rem; margin: 4rem 0 1rem; } - + .mdx-stats__item { min-height: 120px; } From bfd17581ba0116b4f89feba790d53e2b0aa249b3 Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Thu, 13 Nov 2025 17:26:13 +0100 Subject: [PATCH 14/31] try other path for logo --- docs/overrides/home.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 59958df1..932fe01a 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -29,7 +29,7 @@
- BIDS Logo Background + BIDS Logo Background

Data standardization that simply works.

From 26a4add6819308ee4f8535696503d16a1f83810b Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Wed, 26 Nov 2025 19:52:40 +0100 Subject: [PATCH 15/31] code review and add logo --- docs/assets/img/logos/BIDS_logo_black.svg | 1 + docs/overrides/home.html | 18 +- docs/stylesheets/extra.css | 645 +++++++--------------- 3 files changed, 216 insertions(+), 448 deletions(-) create mode 100644 docs/assets/img/logos/BIDS_logo_black.svg diff --git a/docs/assets/img/logos/BIDS_logo_black.svg b/docs/assets/img/logos/BIDS_logo_black.svg new file mode 100644 index 00000000..9f1718f7 --- /dev/null +++ b/docs/assets/img/logos/BIDS_logo_black.svg @@ -0,0 +1 @@ +Ресурс 2 diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 932fe01a..f67641b4 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -27,10 +27,10 @@
+
+ +
-
- BIDS Logo Background -

Data standardization that simply works.

With the Brain Imaging Data Structure (BIDS), we describe a simple and easy to adopt way of organizing brain imaging and associated data.

@@ -142,19 +142,19 @@

Multi-Modal Support

-
2000+
-
Public BIDS Datasets +
1,500+
+
OpenNeuro Public Datasets
- -
500+
+ +
3,000+
BIDS Research Papers
 - +
100+
BIDS Apps and Tools
 - +
300+
Contributors
 diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index c7cd2745..45d6029a 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -1,497 +1,264 @@ -p { text-align: justify; } +/* Brand variables */ +:root { + --bids-brand: #124559; + --bids-accent: #6b9aaa; + --bids-stats-bg: #598392; + --white: #ffffff; -.iframe-container{ - position: relative; - width: 90%; - margin-left: 5%; - padding-bottom: 56.25%; - height: 0; + /* Material Design variable overrides (keep so top tabs/header use brand) */ + --md-primary-fg-color: #124559; + --md-primary-fg-color--light: #124559; + --md-primary-fg-color--dark: #124559; + --md-accent-fg-color: #124559; + --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); + --md-default-fg-color: #111; + --content-max: 1200px; } -.iframe-container > iframe{ - position: absolute; - top:0; - left: 0; - width: 100%; - height: 100%; +/* Basic */ +p { text-align: justify; } + +/* iframe helper */ +.iframe-container { + position: relative; + width: 90%; + margin: 0 5%; + padding-bottom: 56.25%; + height: 0; +} +.iframe-container > iframe { + position: absolute; + inset: 0; + width: 100%; + height: 100%; } -.md-footer__inner.md-grid { display: none; } +/* Hide material footer grid */ +.md-footer__inner.md-grid { display: none; } -/* Hero section styles */ +/* Hero section container */ .mdx-container { - padding-top: 1rem !important; - background: transparent !important; - position: relative !important; - overflow: hidden !important; - min-height: 150px !important; + padding-top: 1rem; + background: transparent; + position: relative; + overflow: visible; + min-height: 150px; } -/* Apply gradient only to first section */ .mdx-container:first-of-type { - background: linear-gradient(to bottom, #124559, transparent 99%) !important; + background: linear-gradient(to bottom, var(--bids-brand), transparent 99%); + overflow: hidden; /* clip logo to container bounds */ } +/* ======= HERO - content + responsive logo ======= */ .mdx-hero { - margin: 1rem 0 0 0 !important; - color: var(--md-primary-bg-color) !important; - position: relative !important; - z-index: 2 !important; - min-height: 150px !important; - display: flex !important; - align-items: center !important; + margin-top: 4rem; + color: var(--white); + position: relative; + z-index: 3; + display: flex; + align-items: center; + min-height: 150px; + padding-bottom: clamp(3rem, 6vw, 6rem); /* space to features */ + overflow: hidden; /* keep logo clipped to hero */ } .mdx-hero__logo-bg { - position: absolute !important; - top: -475px !important; - left: -200px !important; - transform: none !important; - z-index: 1 !important; - width: auto !important; - height: 120% !important; + position: absolute; + top: 0; + height: 100%; /* always as tall as hero */ + left: 50%; + transform: translateX(-50%); + z-index: 0; /* behind the hero content */ + pointer-events: none; + width: min(100%, var(--content-max)); + display: flex; + align-items: center; + justify-content: center; + margin: 0; + padding: 0; } +/* SVG/logo image: fill the wrapper while maintaining aspect ratio */ .mdx-hero__logo-bg img { - height: 400px !important; - width: auto !important; - opacity: 0.15 !important; - object-fit: contain !important; - pointer-events: none !important; - display: block !important; -} - -.mdx-hero__content { - position: relative !important; - z-index: 3 !important; - max-width: 600px !important; - padding-left: 0 !important; - margin-left: 0 !important; + width: 100%; + height: 100%; + opacity: 0.14; /* subtle background watermark */ + object-fit: contain; /* keeps aspect ratio, fits within container */ + object-position: center left; + pointer-events: none; + display: block; + filter: saturate(.95); } -/* Mobile adjustments */ -@media screen and (max-width: 44.9375em) { - .mdx-container { - min-height: 150px !important; - } - - .mdx-hero { - min-height: 150px !important; - } - +/* Small screens: keep the logo large relative to the content column but allow it to overflow a bit to the left + so it doesn't occlude the text while preserving the same width relationship with the features section. */ +@media (max-width: 44.9375em) { .mdx-hero__logo-bg { - left: -50px !important; - height: 100% !important; - } - - .mdx-hero__logo-bg img { - height: 480px !important; - opacity: 0.15 !important; - } - - .mdx-hero__content { - max-width: 100% !important; + /* on small screens, content width is basically 100% - keep full width */ + width: 100%; + left: 50%; + transform: translateX(-50%); + top: 0; + /* allow a little extra vertical breathing room */ + height: 120%; } + .mdx-hero__logo-bg img { opacity: 0.12; max-height: none; object-position: left center; } } -/* Tablet adjustments */ -@media screen and (min-width: 60em) { - .mdx-container { - min-height: 220px !important; - } - - .mdx-hero { - min-height: 200px !important; - } - +/* Mid / tablet screens slight tweaks */ +@media (min-width: 60em) and (max-width: 76.24em) { .mdx-hero__logo-bg { - left: -150px !important; - } - - .mdx-hero__logo-bg img { - height: 680px !important; + /* match the same max content width, but allow it to exceed slightly to create the "off to the side" feel */ + width: min(100%, var(--content-max)); + right: auto; + left: 50%; + transform: translateX(-50%); } + .mdx-hero__logo-bg img { opacity: 0.14; } } -/* Desktop adjustments */ -@media screen and (min-width: 76.25em) { - .mdx-container { - min-height: 300px !important; - } - - .mdx-hero { - min-height: 280px !important; - } - - .mdx-hero__content { - padding-top: 0 !important; - } - +/* Desktop: keep logo the same width as the content column but subtle and slightly shifted left/right by adjusting object-position */ +@media (min-width: 76.25em) { .mdx-hero__logo-bg { - left: -100px !important; + width: min(100%, var(--content-max)); + left: 50%; + transform: translateX(-50%); } + .mdx-hero__logo-bg img { opacity: 0.10; max-height: none; object-position: center left; } +} - .mdx-hero__logo-bg img { - height: 1500px !important; - opacity: 0.1 !important; - } +/* Hero content area */ +.mdx-hero__content { + position: relative; + z-index: 3; + max-width: 600px; + padding-left: 0; + margin-left: 0; } +/* Hero text - stable sizes to avoid 'stretched' look */ .mdx-hero h1 { margin-bottom: 1rem; - color: currentColor; font-weight: 700; font-size: 2.5rem; line-height: 1.2; + color: inherit; } - .mdx-hero__content p { margin-bottom: 2rem; font-size: 1.125rem; - opacity: 0.8; -} - -.mdx-hero__actions { - display: flex; - gap: 1rem; - flex-wrap: wrap; -} - -.mdx-hero__actions .md-button { - margin-right: 0.5rem; - margin-bottom: 0.5rem; -} - -@media screen and (min-width: 60em) { - .mdx-hero { - display: block; - } - - .mdx-hero__content { - max-width: 50rem; - margin-top: 3rem; - padding-bottom: 5rem; - } -} - -@media screen and (min-width: 76.25em) { - .mdx-hero__content { - max-width: 50rem; - } -} - -/* Features section with headline above and full-width grid */ -.mdx-features-section { - margin: 0 0 2rem 0; + opacity: 0.95; + color: rgba(255,255,255,0.95); } -.mdx-features-headline { - text-align: center; - margin-bottom: 3rem; - max-width: 800px; - margin-left: auto; - margin-right: auto; -} - -.mdx-features-headline h2 { - font-size: 2.5rem; - font-weight: 700; - margin-bottom: 1rem; - color: var(--md-default-fg-color); - line-height: 1.2; -} +/* Buttons */ +.mdx-hero__actions { display:flex; gap:1rem; flex-wrap:wrap; } +.mdx-hero__actions .md-button { margin-bottom: 0.5rem; } +.md-button--primary { + background-color: var(--bids-brand) !important; + border-color: var(--white) !important; + color: var(--white) !important; + font-weight: 500; +} +.md-button--primary:hover { background-color: var(--bids-accent) !important; transform: translateY(-1px); } + +/* Ensure header/tabs use brand */ +.md-header, +.md-header__inner, +.md-header-nav, +.md-tabs, +.md-nav { + background-color: var(--bids-brand) !important; + color: var(--white) !important; +} +.md-header a, +.md-tabs a, +.md-header-nav a, +.md-nav a { + color: var(--white) !important; +} + +/* Features & cards (kept equal-height) */ +.mdx-features-section { margin-bottom: 2rem; } +.mdx-features-headline { text-align: center; margin: 0 0 3rem; max-width: 800px; margin-left: auto; margin-right: auto; } +.mdx-features-headline h2 { font-size: clamp(1.6rem, 3.5vw, 2.5rem); font-weight: 700; color: var(--md-default-fg-color); line-height:1.2; } .mdx-features { display: grid; grid-template-columns: repeat(auto-fit, minmax(16rem, 1fr)); gap: 2rem; + align-items: stretch; } - -/* Responsive adjustments for features section */ -@media screen and (max-width: 44.9375em) { - .mdx-features-section { - margin: 2rem 0; - } - - .mdx-features-headline { - margin-bottom: 2rem; - } - - .mdx-features-headline h2 { - font-size: 2rem; - } - - .mdx-features { - grid-template-columns: 1fr; - gap: 1.5rem; - } -} - -/* Tablet-specific adjustments for features */ -@media screen and (min-width: 45em) and (max-width: 76.24em) { - .mdx-features { - grid-template-columns: repeat(2, 1fr); - } -} +.mdx-feature { display:flex; } .mdx-feature__item { - display: flex; - flex-direction: column; - padding: 1rem 2rem 2rem 2rem; - background: #124559; - color: white; - border-radius: 0.5rem; - box-shadow: var(--md-shadow-z1); - transition: transform 0.2s, box-shadow 0.2s; - height: 280px; + box-sizing: border-box; + display:flex; + flex-direction:column; justify-content: space-between; - align-items: center; - text-align: center; -} - -.mdx-feature__item:hover { - transform: translateY(-0.25rem); - box-shadow: var(--md-shadow-z2); -} - -.mdx-feature__icon { - width: 3rem; - height: 3rem; - margin-bottom: 1rem; - color: white; -} - -.mdx-feature__icon svg { - width: 100%; - height: 100%; - fill: white; -} - -.mdx-feature__content h2 { - margin: 0 0 1rem; - font-weight: 700; - font-size: 1.25rem; - color: white; + align-items:center; + text-align:center; + padding: clamp(1rem, 2vw, 2rem); + background: var(--bids-brand); + color: var(--white); + border-radius: .5rem; + box-shadow: var(--md-shadow-z1); + transition: transform .2s, box-shadow .2s; + flex:1 1 auto; + min-height: 220px; + height: auto; + overflow: visible; } +.mdx-feature__item:hover { transform: translateY(-0.25rem); box-shadow: var(--md-shadow-z2); } -.mdx-feature__content { - display: flex; - flex-direction: column; - align-items: center; -} +.mdx-feature__icon { width:3rem; height:3rem; margin-bottom:1rem; flex:0 0 auto; } +.mdx-feature__icon svg { width:100%; height:100%; fill:var(--white); } +.mdx-feature__content { display:flex; flex-direction:column; align-items:center; justify-content:center; width:100%; flex:1 1 auto; } +.mdx-feature__content h2 { margin:0 0 .75rem; font-weight:700; font-size: clamp(1.05rem,2vw,1.25rem); line-height:1.15; color:var(--white); } .mdx-feature__content p { - margin: 0; - color: rgba(255, 255, 255, 0.8); -} - -/* Stats section */ -.mdx-stats { - display: grid; - grid-template-columns: repeat(auto-fit, minmax(8rem, 1fr)); - gap: 2rem; - margin: 8rem 0 2rem; - text-align: center; -} - -.mdx-stats__item { - background: #598392; - color: white; - padding: 2rem; - border-radius: 0.5rem; - display: flex; - flex-direction: column; - justify-content: center; - align-items: center; - min-height: 150px; - text-decoration: none; - transition: all 0.3s ease; - cursor: pointer; -} - -.mdx-stats__item:hover { - transform: translateY(-4px); - box-shadow: 0 8px 16px rgba(0, 0, 0, 0.2); - background: #6b9aaa; -} - -.mdx-stats__number { - font-weight: 700; - font-size: 2rem; - line-height: 1.2; - color: white; -} - -.mdx-stats__label { - font-size: 0.875rem; - color: rgba(255, 255, 255, 0.8); -} - -/* Responsive adjustments */ -@media screen and (max-width: 44.9375em) { - .mdx-hero h1 { - font-size: 2rem; - } - - .mdx-hero__actions { - flex-direction: column; - } - - .mdx-hero__actions .md-button { - width: 100%; - margin-right: 0; - } - - /* Stats section mobile optimization */ - .mdx-stats { - grid-template-columns: 1fr; - gap: 1rem; - margin: 4rem 0 1rem; - } - - .mdx-stats__item { - min-height: 120px; - } -} - -/* Sponsors section */ -.mdx-sponsors { - background: #124559 !important; - padding: 0.5rem 0 3rem!important; -} - -.mdx-sponsors__content { - text-align: center !important; - max-width: 1200px !important; - margin: 0 auto !important; - padding: 0 2rem !important; -} - -.mdx-sponsors__content h2 { - margin-bottom: 2rem !important; - font-weight: 700 !important; - font-size: 2rem !important; - color: white !important; -} - -.mdx-sponsors__grid { - display: flex !important; - justify-content: center !important; - align-items: center !important; - gap: 1.5rem !important; - flex-wrap: wrap !important; -} - -.mdx-sponsors__item { - display: flex !important; - align-items: center !important; - justify-content: center !important; - padding: 1.5rem !important; - background: white !important; - border-radius: 0.5rem !important; - box-shadow: 0 2px 8px rgba(0,0,0,0.1) !important; - transition: all 0.3s ease !important; - width: 200px !important; - height: 120px !important; - border: 1px solid #eee !important; -} - -.mdx-sponsors__item:hover { - transform: translateY(-2px) !important; - box-shadow: 0 4px 16px rgba(0,0,0,0.15) !important; -} - -.mdx-sponsors__item img { - max-width: 180px !important; - max-height: 80px !important; - width: auto !important; - height: auto !important; - object-fit: contain !important; - filter: grayscale(100%) opacity(0.7) !important; - transition: filter 0.3s ease !important; -} - -.mdx-sponsors__item:hover img { - filter: grayscale(0%) opacity(1) !important; -} - -/* Sponsors responsive adjustments */ -@media screen and (max-width: 44.9375em) { - .mdx-sponsors { - padding: 3rem 0 !important; - } - - .mdx-sponsors__content { - padding: 0 1rem !important; - } - - .mdx-sponsors__content h2 { - font-size: 1.5rem !important; - } - - .mdx-sponsors__grid { - grid-template-columns: repeat(2, 1fr) !important; - gap: 1.5rem !important; - } - - .mdx-sponsors__item { - height: 100px !important; - max-width: none !important; - } - - .mdx-sponsors__item img { - max-width: 140px !important; - max-height: 60px !important; - } -} - -@media screen and (min-width: 60em) { - .mdx-sponsors__grid { - flex-wrap: nowrap !important; - } -} - -/* Override Material Design color variables */ -:root { - --md-primary-fg-color: #124559; - --md-primary-fg-color--light: #124559; - --md-primary-fg-color--dark: #124559; - --md-accent-fg-color: #124559; - --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); -} - -/* Custom button styling */ -.md-button--primary { - background-color: #124559 !important; - border-color: white !important; - color: white !important; - font-weight: 500 !important; -} - -.md-button--primary:hover { - background-color: #6b9aaa !important; - border-color: white !important; - color: white !important; - transform: translateY(-1px) !important; -} - -.md-button--primary:focus { - background-color: #6b9aaa !important; - border-color: #124559 !important; - color: white !important; -} - -/* Secondary button styling */ -.md-button { - border: 2px solid white !important; - color: white !important; - font-weight: 500 !important; - background-color: #124559 !important; -} - -.md-button:hover { - background-color: #6b9aaa!important; - border: 2px solid white !important; - color: white !important; - transform: translateY(-1px) !important; -} + margin:0; + color: rgba(255,255,255,0.92); + font-size: clamp(.9rem,1.5vw,1rem); + line-height:1.35; + word-break: break-word; + overflow-wrap:anywhere; + -webkit-hyphens:auto; + -ms-hyphens:auto; + hyphens:auto; +} + +/* Stats */ +.mdx-stats { display:grid; grid-template-columns: repeat(auto-fit, minmax(8rem, 1fr)); gap:2rem; margin:8rem 0 2rem; text-align:center; } +.mdx-stats__item { background: var(--bids-stats-bg); color: var(--white); padding:2rem; border-radius:.5rem; display:flex; flex-direction:column; justify-content:center; align-items:center; min-height:150px; text-decoration:none; transition: all .3s ease; } +.mdx-stats__item:hover { transform: translateY(-4px); box-shadow: 0 8px 16px rgba(0,0,0,.2); background: var(--bids-accent); } +.mdx-stats__number { font-weight:700; font-size:2rem; line-height:1.2; color: var(--white) !important; } +.mdx-stats__label { font-size:.875rem; color: rgba(255,255,255,.8); } + +/* Sponsors */ +.mdx-sponsors { background: var(--bids-brand); padding: .5rem 0 3rem; } +.mdx-sponsors__content { text-align:center; max-width:1200px; margin:0 auto; padding:0 2rem; } +.mdx-sponsors__content h2 { margin-bottom:2rem; font-weight:700; font-size:clamp(1.25rem,2.5vw,2rem); color:var(--white); } +.mdx-sponsors__grid { display:flex; justify-content:center; align-items:center; gap:1.5rem; flex-wrap:wrap; } +.mdx-sponsors__item { display:flex; align-items:center; justify-content:center; padding:1.5rem; background:var(--white); border-radius:.5rem; box-shadow:0 2px 8px rgba(0,0,0,.1); transition:all .3s ease; width:200px; height:120px; border:1px solid #eee; } +.mdx-sponsors__item img { max-width:180px; max-height:80px; object-fit:contain; filter:grayscale(100%) opacity(.7); transition:filter .3s; } +.mdx-sponsors__item:hover img { filter:none; opacity:1; } +.mdx-sponsors__item:hover { transform: translateY(-2px); box-shadow: 0 4px 16px rgba(0,0,0,.15); } + +/* Responsive adjustments grouped */ +@media (max-width: 44.9375em) { + .mdx-hero h1 { font-size: 2rem; } + .mdx-hero__actions .md-button { width:100%; } + .mdx-features { grid-template-columns: 1fr; gap: 1.5rem; } + .mdx-features-headline h2 { font-size: 2rem; } + .mdx-stats { grid-template-columns: 1fr; gap: 1rem; margin: 4rem 0 1rem; } + .mdx-stats__item { min-height: 120px; } + .mdx-sponsors { padding: 3rem 0; } + .mdx-sponsors__grid { gap: 1.5rem; } + .mdx-sponsors__item { height: 100px; width: auto; } + .mdx-sponsors__item img { max-width: 140px; max-height:60px; } +} + +/* Minimal theme overrides left as !important where required */ +.md-button--primary { background-color: var(--bids-brand) !important; border-color: var(--white) !important; color: var(--white) !important; } \ No newline at end of file From 033c9978ccc3f6d452d2292af2a8155b5c1ec238 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 26 Nov 2025 18:53:53 +0000 Subject: [PATCH 16/31] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/stylesheets/extra.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index 45d6029a..a6534d64 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -261,4 +261,4 @@ p { text-align: justify; } } /* Minimal theme overrides left as !important where required */ -.md-button--primary { background-color: var(--bids-brand) !important; border-color: var(--white) !important; color: var(--white) !important; } \ No newline at end of file +.md-button--primary { background-color: var(--bids-brand) !important; border-color: var(--white) !important; color: var(--white) !important; } From 450f141ffe4bc47eba1b2c7ac2531d8468508602 Mon Sep 17 00:00:00 2001 From: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Date: Wed, 26 Nov 2025 20:56:42 +0100 Subject: [PATCH 17/31] fix navigation sidebars --- docs/stylesheets/extra.css | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index a6534d64..d3089455 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -167,15 +167,13 @@ p { text-align: justify; } .md-header, .md-header__inner, .md-header-nav, -.md-tabs, -.md-nav { +.md-tabs{ background-color: var(--bids-brand) !important; color: var(--white) !important; } .md-header a, .md-tabs a, -.md-header-nav a, -.md-nav a { +.md-header-nav a { color: var(--white) !important; } From 68ba06dc7ef7134b86be675d370843827608690d Mon Sep 17 00:00:00 2001 From: julia-pfarr Date: Wed, 26 Nov 2025 21:56:10 +0100 Subject: [PATCH 18/31] change link for logo --- docs/overrides/home.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index f67641b4..1c0ade4f 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -28,7 +28,7 @@
- +
From 25c92f7e2d66461d64ef3946f508abb97defa58e Mon Sep 17 00:00:00 2001 From: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Date: Thu, 27 Nov 2025 16:40:22 +0100 Subject: [PATCH 19/31] Apply suggestions from code review MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Boris Clénet <117362283+bclenet@users.noreply.github.com> --- docs/overrides/home.html | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/overrides/home.html b/docs/overrides/home.html index 1c0ade4f..fe4fb100 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -150,11 +150,11 @@

Multi-Modal Support

3,000+
BIDS Research Papers
- +
100+
BIDS Apps and Tools
 - +
300+
Contributors
 From 1f7d49d70ccda223aaf92617a2f0a132539460c7 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 16:54:22 +0100 Subject: [PATCH 20/31] rm pr template changes --- .github/PULL_REQUEST_TEMPLATE/bep.md | 11 +++++++ .../PULL_REQUEST_TEMPLATE/bep_template.yml | 29 +++++++++++++++++++ .../pull_request_template.md | 29 ------------------- 3 files changed, 40 insertions(+), 29 deletions(-) create mode 100644 .github/PULL_REQUEST_TEMPLATE/bep.md create mode 100644 .github/PULL_REQUEST_TEMPLATE/bep_template.yml delete mode 100644 .github/PULL_REQUEST_TEMPLATE/pull_request_template.md diff --git a/.github/PULL_REQUEST_TEMPLATE/bep.md b/.github/PULL_REQUEST_TEMPLATE/bep.md new file mode 100644 index 00000000..8f40ef43 --- /dev/null +++ b/.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) diff --git a/.github/PULL_REQUEST_TEMPLATE/bep_template.yml b/.github/PULL_REQUEST_TEMPLATE/bep_template.yml new file mode 100644 index 00000000..b48c2193 --- /dev/null +++ b/.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' diff --git a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md b/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md deleted file mode 100644 index 88137e17..00000000 --- a/.github/PULL_REQUEST_TEMPLATE/pull_request_template.md +++ /dev/null @@ -1,29 +0,0 @@ - - - - - - -- Closes # - - -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` From a19cc22627cd25f966428b84c848480b9f9cbd94 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 16:58:04 +0100 Subject: [PATCH 21/31] rm logo and copy from spec on build --- .gitignore | 1 + Makefile | 1 + docs/assets/img/logos/BIDS_logo_black.svg | 1 - 3 files changed, 2 insertions(+), 1 deletion(-) delete mode 100644 docs/assets/img/logos/BIDS_logo_black.svg diff --git a/.gitignore b/.gitignore index 4d00cfcd..ae2c4f88 100644 --- a/.gitignore +++ b/.gitignore @@ -7,6 +7,7 @@ docs/extensions/beps # ignore for now files that are copied from the bids examples and spe docs/examples/ docs/extensions/macros_doc.md +docs/assets/img/logos/BIDS_logo_black.svg # folders *.DS_Store diff --git a/Makefile b/Makefile index 723cde75..26e5dd13 100644 --- a/Makefile +++ b/Makefile @@ -15,6 +15,7 @@ update_from_spec: rm -fr docs/specification mkdir -p docs/specification/ cp specification/macros_doc.md docs/extensions/macros_doc.md + cp -f specification/BIDS_logo/BIDS_logo_black.svg docs/assets/img/logos/ update_contributors: .venv node_modules @echo " ---------------------------------- " diff --git a/docs/assets/img/logos/BIDS_logo_black.svg b/docs/assets/img/logos/BIDS_logo_black.svg deleted file mode 100644 index 9f1718f7..00000000 --- a/docs/assets/img/logos/BIDS_logo_black.svg +++ /dev/null @@ -1 +0,0 @@ -Ресурс 2 From 30a6b947c72b05131cc57585714a9c8a6d6e77ea Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 17:15:55 +0100 Subject: [PATCH 22/31] format with djlint --- .pre-commit-config.yaml | 30 +++ docs/overrides/home.html | 402 +++++++++++++++++++++------------------ pyproject.toml | 9 + 3 files changed, 261 insertions(+), 180 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4e258a21..62e2bcd2 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -47,6 +47,36 @@ repos: - id: pretty-format-toml args: [--autofix, --indent, '4', --no-sort, --trailing-commas] +- repo: https://github.com/djlint/djLint + rev: v1.36.4 + hooks: + - id: djlint + exclude: | + (?x)^( + docs/overrides/main.html| + docs/overrides/404.html + )$ + - id: djlint-reformat + exclude: | + (?x)^( + docs/overrides/main.html| + docs/overrides/404.html + )$ + - id: djlint-jinja + exclude: | + (?x)^( + docs/overrides/main.html| + docs/overrides/404.html| + templates/.* + )$ + - id: djlint-reformat-jinja + exclude: | + (?x)^( + docs/overrides/main.html| + docs/overrides/404.html| + templates/.* + )$ + - repo: https://github.com/psf/black-pre-commit-mirror rev: 25.11.0 hooks: diff --git a/docs/overrides/home.html b/docs/overrides/home.html index fe4fb100..6734a2e2 100644 --- a/docs/overrides/home.html +++ b/docs/overrides/home.html @@ -1,191 +1,233 @@ {% extends "main.html" %} {% block tabs %} - {{ super() }} - - - -
-
-
- -
-
-
-

Data standardization that simply works.

-

With the Brain Imaging Data Structure (BIDS), we describe a simple and easy to adopt way of organizing brain imaging and associated data.

-
- - Get started - - - Learn more - -
-
-
-
-
- - -
-
-
- - -
-

BIDS in a nutshell

-
+ {{ super() }} + + +
+
+
+
-
- -
-
-
- {% include ".icons/material/open-source-initiative.svg" %} -
-
-

Open Science

-

Promotes reproducible research and data sharing through standardized formats that are platform-independent and openly documented.

-
+
+
+

Data standardization that simply works.

+

+ With the Brain Imaging Data Structure (BIDS), + we describe a simple way of organizing brain imaging and associated data. +

+
+ + Get started + + Learn more +
+
-
- -
-
-
- {% include ".icons/material/check-decagram.svg" %} -
-
-

Validation Tools

-

Built-in validation ensures your datasets comply with BIDS standards, catching issues early and improving data quality.

-
+
+
+ +
+
+
+ +
+

BIDS in a nutshell

+
+ +
+
+
+
+ + {% include ".icons/material/file-tree.svg" %} + +
+
+

Standardized Organization

+

+ BIDS provides a consistent way to organize your neuroimaging data, + making it easy to understand and share across research groups and institutions. +

+
+
+
+
+
+
+ + {% include ".icons/material/account-group.svg" %} + +
+
+

Community Driven

+

+ Developed by the neuroscience community for the community. + BIDS continues to evolve based on real-world research needs and feedback. +

+
+
+
+
+
+
+ + {% include ".icons/material/tools.svg" %} + +
+
+

Rich Ecosystem

+

+ A growing collection of BIDS Apps, validators, + and analysis tools that work seamlessly with BIDS-formatted datasets. +

+
+
+
+
+
+
+ + {% include ".icons/material/open-source-initiative.svg" %} + +
+
+

Open Science

+

+ Promotes reproducible research and data sharing + through standardized formats that are platform-independent and openly documented. +

+
+
+
+
+
+
+ + {% include ".icons/material/check-decagram.svg" %} + +
+
+

Validation Tools

+

+ Built-in validation ensures your datasets comply with BIDS standards, + catching issues early and improving data quality. +

+
+
+
+
+
+
+ + {% include ".icons/material/brain.svg" %} + +
+
+

Multi-Modal Support

+

+ Supports a wide range of neuroimaging modalities + including fMRI, EEG, MEG, iEEG, PET, and behavioral data. +

+
+
+
+
-
- -
-
-
- {% include ".icons/material/brain.svg" %} -
-
-

Multi-Modal Support

-

Supports a wide range of neuroimaging modalities including fMRI, EEG, MEG, iEEG, PET, and behavioral data.

-
+
+
+ +
+
+
+ +
1,500+
+
OpenNeuro Public Datasets
+ + +
3,000+
+
BIDS Research Papers
+ + +
100+
+
BIDS Apps and Tools
+ + +
300+
+
Contributors
+
-
-
-
-
-
- - -
-
-
- -
1,500+
-
OpenNeuro Public Datasets -
- - -
3,000+
-
BIDS Research Papers
- - -
100+
-
BIDS Apps and Tools
- - -
300+
-
Contributors
- -
-
-
- - -
-
-
-

Supported by

-
- -
- Sponsor 1 -
-
- Sponsor 2 -
-
- Sponsor 3 -
-
- Sponsor 4 -
+
+ +
+
+
+

Supported by

+
+ +
+ Sponsor 1 +
+
+ Sponsor 2 +
+
+ Sponsor 3 +
+
+ Sponsor 4 +
+
+
-
-
-
-{% endblock %} +
+{% endblock tabs %} + +{% block content %} +{% endblock content %} -{% block content %}{% endblock %} -{% block footer %}{% endblock %} +{% block footer %} +{% endblock footer %} diff --git a/pyproject.toml b/pyproject.toml index 1dbf978c..44766a96 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -45,3 +45,12 @@ combine_as_imports = true line_length = 79 profile = "black" skip_gitignore = true + +[tool.djlint] +profile = "django" +blank_line_after_tag = "load,extends,include,endblock,set" +blank_line_before_tag = "load,extends,include,block,set" +format_css = true +ignore = "H030,H031,H021,H006" +max_line_length = 79 +use_gitignore = true From 0e79749d46e68b90028b0a88469e215d2b394852 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 17:21:23 +0100 Subject: [PATCH 23/31] revert config changes --- mkdocs.yml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index bf60e5bc..d8103627 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -246,10 +246,6 @@ markdown_extensions: - def_list - footnotes - md_in_html - - toc: - permalink: true - anchorlink: true - toc_depth: 3 - pymdownx.arithmatex: generic: true - pymdownx.betterem: @@ -259,6 +255,9 @@ markdown_extensions: - pymdownx.emoji: emoji_generator: !!python/name:material.extensions.emoji.to_svg emoji_index: !!python/name:material.extensions.emoji.twemoji + - pymdownx.snippets: + auto_append: + - includes/abbreviations.md - pymdownx.highlight: anchor_linenums: true line_spans: __span @@ -287,7 +286,10 @@ markdown_extensions: custom_checkbox: true - pymdownx.tilde - tables - + - toc: + permalink: true + anchorlink: true + toc_depth: 3 extra_javascript: - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js From 51c6d5f489888b7572e59a9ab4c996689e45eace Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 17:29:45 +0100 Subject: [PATCH 24/31] revert --- docs/stylesheets/extra.css | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index d3089455..c41feea3 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -13,6 +13,25 @@ --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); --md-default-fg-color: #111; --content-max: 1200px; + + /* colors used in several places in the getting started section to identify datatypes */ + --mri: #a6cee3; + --pet: #1f78b4; + --micr: #33a02c; + --meeg: #6a3d9a; + --beh: #fb9a99; + --nirs: #b2df8a; + --motion: #e31a1c; + --mrs: #fdbf6f; + --unused2: #ff7f00; + --unused3: #cab2d6; + --unused4: #ffff99; + --unused5: #b15928; + --key: #e41a1c; + --label: #377eb8; + --suffix: #4daf4a; + --ext: #984ea3; + --underscore: #ff7f00; } /* Basic */ From 982c828e84b8dec1ccd97d86fc8c9476b2406268 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 17:30:54 +0100 Subject: [PATCH 25/31] mv --- docs/stylesheets/extra.css | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index c41feea3..7349a697 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -1,18 +1,4 @@ -/* Brand variables */ :root { - --bids-brand: #124559; - --bids-accent: #6b9aaa; - --bids-stats-bg: #598392; - --white: #ffffff; - - /* Material Design variable overrides (keep so top tabs/header use brand) */ - --md-primary-fg-color: #124559; - --md-primary-fg-color--light: #124559; - --md-primary-fg-color--dark: #124559; - --md-accent-fg-color: #124559; - --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); - --md-default-fg-color: #111; - --content-max: 1200px; /* colors used in several places in the getting started section to identify datatypes */ --mri: #a6cee3; @@ -32,6 +18,22 @@ --suffix: #4daf4a; --ext: #984ea3; --underscore: #ff7f00; + + --bids-brand: #124559; + --bids-accent: #6b9aaa; + --bids-stats-bg: #598392; + --white: #ffffff; + + /* Material Design variable overrides (keep so top tabs/header use brand) */ + --md-primary-fg-color: #124559; + --md-primary-fg-color--light: #124559; + --md-primary-fg-color--dark: #124559; + --md-accent-fg-color: #124559; + --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); + --md-default-fg-color: #111; + --content-max: 1200px; + + } /* Basic */ From db05f11badae382f495e9d447d62e4f8b99a4bab Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 17:31:58 +0100 Subject: [PATCH 26/31] mv --- docs/stylesheets/extra.css | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index 7349a697..fbbb2181 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -1,23 +1,23 @@ :root { - /* colors used in several places in the getting started section to identify datatypes */ - --mri: #a6cee3; - --pet: #1f78b4; - --micr: #33a02c; - --meeg: #6a3d9a; - --beh: #fb9a99; - --nirs: #b2df8a; - --motion: #e31a1c; - --mrs: #fdbf6f; - --unused2: #ff7f00; - --unused3: #cab2d6; - --unused4: #ffff99; - --unused5: #b15928; - --key: #e41a1c; - --label: #377eb8; - --suffix: #4daf4a; - --ext: #984ea3; - --underscore: #ff7f00; + /* colors used in several places in the getting started section to identify datatypes */ + --mri: #a6cee3; + --pet: #1f78b4; + --micr: #33a02c; + --meeg: #6a3d9a; + --beh: #fb9a99; + --nirs: #b2df8a; + --motion: #e31a1c; + --mrs: #fdbf6f; + --unused2: #ff7f00; + --unused3: #cab2d6; + --unused4: #ffff99; + --unused5: #b15928; + --key: #e41a1c; + --label: #377eb8; + --suffix: #4daf4a; + --ext: #984ea3; + --underscore: #ff7f00; --bids-brand: #124559; --bids-accent: #6b9aaa; From 68502f40dd620b9959ee67a70d0e3f1da5138e76 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 17:33:01 +0100 Subject: [PATCH 27/31] comment --- docs/stylesheets/extra.css | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index fbbb2181..b5b9e50b 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -1,6 +1,9 @@ :root { - /* colors used in several places in the getting started section to identify datatypes */ + /* colors used in several places in the getting started section to identify datatypes + obtained from https://colorbrewer2.org/#type=qualitative&scheme=Paired&n=12 + */ + --mri: #a6cee3; --pet: #1f78b4; --micr: #33a02c; From 7835a8cccaf7aeed0a2d2d65c3d7d9a237846b4a Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 17:33:37 +0100 Subject: [PATCH 28/31] mv --- docs/stylesheets/extra.css | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index b5b9e50b..a84bbb58 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -44,17 +44,17 @@ p { text-align: justify; } /* iframe helper */ .iframe-container { - position: relative; - width: 90%; - margin: 0 5%; - padding-bottom: 56.25%; - height: 0; + position: relative; + width: 90%; + margin: 0 5%; + padding-bottom: 56.25%; + height: 0; } .iframe-container > iframe { - position: absolute; - inset: 0; - width: 100%; - height: 100%; + position: absolute; + inset: 0; + width: 100%; + height: 100%; } /* Hide material footer grid */ From 3e2ed8d00a7d8ca9b2a763b2869cbaca83c69406 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 18:01:05 +0100 Subject: [PATCH 29/31] evert --- mkdocs.yml | 43 +++---------------------------------------- 1 file changed, 3 insertions(+), 40 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index d8103627..732e4cc7 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -4,8 +4,7 @@ repo_url: https://github.com/bids-standard/bids-website/tree/main site_url: https://bids.neuroimaging.io/ plugins: - - search: - separator: '[\s\u200b\-_,:!=\[\]()"`/]+|\.(?!\d)|&[lg]t;|(?!\b)(?=[A-Z][a-z])' + - search - tags # - social - blog @@ -193,25 +192,20 @@ theme: features: - announce.dismiss - content.action.edit - - content.code.annotate - content.code.copy - content.tabs.link - content.tooltips + - footnotes - header.autohide - - navigation.expand - navigation.footer - navigation.indexes - navigation.instant - - navigation.instant.progress - - navigation.prune - navigation.sections - navigation.tabs - navigation.tabs.sticky - navigation.top - - navigation.tracking - - search.highlight - - search.share - search.suggest + - search.highlight - toc.follow icon: repo: fontawesome/brands/github @@ -243,14 +237,7 @@ markdown_extensions: - abbr - admonition - attr_list - - def_list - - footnotes - md_in_html - - pymdownx.arithmatex: - generic: true - - pymdownx.betterem: - smart_enable: all - - pymdownx.caret - pymdownx.details - pymdownx.emoji: emoji_generator: !!python/name:material.extensions.emoji.to_svg @@ -258,19 +245,6 @@ markdown_extensions: - pymdownx.snippets: auto_append: - includes/abbreviations.md - - pymdownx.highlight: - anchor_linenums: true - line_spans: __span - pygments_lang_class: true - - pymdownx.inlinehilite - - pymdownx.keys - - pymdownx.magiclink: - normalize_issue_symbols: true - repo_url_shorthand: true - user: bids-standard - repo: bids-website - - pymdownx.mark - - pymdownx.smartsymbols - pymdownx.superfences: custom_fences: - name: mermaid @@ -278,25 +252,14 @@ markdown_extensions: format: !!python/name:pymdownx.superfences.fence_code_format - pymdownx.tabbed: alternate_style: true - combine_header_slug: true - slugify: !!python/object/apply:pymdownx.slugs.slugify - kwds: - case: lower - - pymdownx.tasklist: - custom_checkbox: true - - pymdownx.tilde - tables - toc: - permalink: true anchorlink: true toc_depth: 3 extra_javascript: - https://unpkg.com/tablesort@5.3.0/dist/tablesort.min.js - javascripts/tablesort.js - - javascripts/mathjax.js - - https://polyfill.io/v3/polyfill.min.js?features=es6 - - https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js extra_css: - stylesheets/extra.css From eeb836837514606bfdc49cdc40ccec8ee9c89795 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 18:44:55 +0100 Subject: [PATCH 30/31] fix contrast --- docs/stylesheets/extra.css | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index a84bbb58..d6793ed5 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -107,7 +107,7 @@ p { text-align: justify; } .mdx-hero__logo-bg img { width: 100%; height: 100%; - opacity: 0.14; /* subtle background watermark */ + opacity: 0.2; /* subtle background watermark */ object-fit: contain; /* keeps aspect ratio, fits within container */ object-position: center left; pointer-events: none; @@ -256,7 +256,7 @@ p { text-align: justify; } .mdx-stats__item { background: var(--bids-stats-bg); color: var(--white); padding:2rem; border-radius:.5rem; display:flex; flex-direction:column; justify-content:center; align-items:center; min-height:150px; text-decoration:none; transition: all .3s ease; } .mdx-stats__item:hover { transform: translateY(-4px); box-shadow: 0 8px 16px rgba(0,0,0,.2); background: var(--bids-accent); } .mdx-stats__number { font-weight:700; font-size:2rem; line-height:1.2; color: var(--white) !important; } -.mdx-stats__label { font-size:.875rem; color: rgba(255,255,255,.8); } +.mdx-stats__label { font-size:.875rem; color: rgba(255,255,255,.9); } /* Sponsors */ .mdx-sponsors { background: var(--bids-brand); padding: .5rem 0 3rem; } From 34978ffb967ddf0b14b82024bf15be7852bcbb44 Mon Sep 17 00:00:00 2001 From: Remi Gau Date: Sat, 29 Nov 2025 19:13:13 +0100 Subject: [PATCH 31/31] improve dark mode contrast --- docs/stylesheets/extra.css | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/stylesheets/extra.css b/docs/stylesheets/extra.css index d6793ed5..6135a69f 100644 --- a/docs/stylesheets/extra.css +++ b/docs/stylesheets/extra.css @@ -22,16 +22,16 @@ --ext: #984ea3; --underscore: #ff7f00; - --bids-brand: #124559; + --bids-brand: #1F7293; --bids-accent: #6b9aaa; - --bids-stats-bg: #598392; + --bids-stats-bg: #1f8193fb; --white: #ffffff; /* Material Design variable overrides (keep so top tabs/header use brand) */ - --md-primary-fg-color: #124559; - --md-primary-fg-color--light: #124559; - --md-primary-fg-color--dark: #124559; - --md-accent-fg-color: #124559; + --md-primary-fg-color: #1F7293; + --md-primary-fg-color--light: #1F7293; + --md-primary-fg-color--dark: #1F7293; + --md-accent-fg-color: #1F7293; --md-accent-fg-color--transparent: rgba(212, 123, 138, 0.1); --md-default-fg-color: #111; --content-max: 1200px;