Fix the issues found in the site audit#270

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Merged
Zethson merged 5 commits into from
Aug 23, 2026
Merged

Fix the issues found in the site audit #270

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0833987
Fix broken external links
Zethson Aug 23, 2026
69e16fe
Fix the page metadata in the document head
Zethson Aug 23, 2026
374edb6
Fix the accessibility problems on the site
Zethson Aug 23, 2026
14858e5
Cut the weight of the site from 22 MB to 7 MB
Zethson Aug 23, 2026
b800c2c
Fix the structural gaps in navigation and page chrome
Zethson Aug 23, 2026
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -9,9 +9,9 @@ repos:
- repo: https://github.com/ericmjl/webp-pre-commit
rev: v0.0.12
hooks:
# Convert blog and learn images
# img/logo is excluded on purpose: the media kit advertises PNG downloads.
- id: convert-to-webp
files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
- repo: https://github.com/oxipng/oxipng
rev: v10.2.0
hooks:
Expand Down
148 changes: 90 additions & 58 deletions assets/main.scss
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -59,11 +59,13 @@ $additionalInfoColor: #666666;
// Font stack: these two have well matching cap- and x-heights
@font-face {
font-family: "Inter";
src: url("fonts/Inter/Inter-VariableFont_slnt,wght.ttf");
src: url("fonts/Inter/Inter-VariableFont_slnt,wght.woff2") format("woff2");
font-display: swap;
}
@font-face {
font-family: "JetBrains Mono";
src: url("fonts/JetBrainsMono/JetBrainsMono[wght].ttf");
src: url("fonts/JetBrainsMono/JetBrainsMono[wght].woff2") format("woff2");
font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
#title {
#title-text {
#title-name {
margin: 0;
font-size: 6rem;
font-weight: 900;
letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
display: flex;
min-width: 6rem;
max-width: 6rem;
// Matches the img height below, so that a package
// without an icon still lines up with the others.
min-height: 4rem;
@media (max-width: 50rem) {
display: none;
}
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
// }
}
}
.page-item {
display: flex;
flex-direction: row;

@media (max-width: 50rem) {
flex-direction: column;
align-items: flex-start;
justify-content: center;
h2 {
margin: 0.5rem 0 !important;
}
margin: 0 -0.5rem;
padding: 0.5rem;
padding-bottom: 1.3rem;
}

margin: 0 -1rem;
padding: 1rem;

background-color: #ff000000;
transition: all 200ms ease-in-out;
border-radius: 0.5rem;

&:hover {
cursor: pointer;
background-color: $tilebg3;
}

@media (max-width: 50rem) {
background-color: $tilebg4;
}

h2 {
color: $tiletext;
margin: 0 0 0.5rem 0;
line-height: 1.5rem;
}
span {
font-size: 1rem;
color: $greydesc;
line-height: 1.3rem;
}
.page-item-date {
flex: 1;
line-height: 1.3rem;
}
.page-item-content {
flex: 2;
display: flex;
flex-direction: column;
font-size: 1rem;
h2 {
font-size: 1.4rem;
}
}
}
// TODO: Much of this does nothing AFAICT
.post {
.post-subtitle {
Expand DownExpand Up@@ -1175,6 +1125,9 @@ $eco-hues:
}

.eco-card {
// All 120 registry entries are in the DOM so the filter can work offline.
content-visibility: auto;
contain-intrinsic-size: auto 14rem;
position: relative;
display: flex;
flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
transition: width 1s ease-in-out;
pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
*,
*::before,
*::after {
animation-duration: 0.01ms !important;
animation-iteration-count: 1 !important;
transition-duration: 0.01ms !important;
scroll-behavior: auto !important;
}
}

.command-icon:focus-visible {
outline: 3px solid #1a73e8;
outline-offset: 2px;
}

// Hoisted out of #page-content: the landing page shows one of these and uses #cover.

.page-item {
display: flex;
flex-direction: row;

@media (max-width: 50rem) {
flex-direction: column;
align-items: flex-start;
justify-content: center;
h2 {
margin: 0.5rem 0 !important;
}
margin: 0 -0.5rem;
padding: 0.5rem;
padding-bottom: 1.3rem;
}

margin: 0 -1rem;
padding: 1rem;

background-color: #ff000000;
transition: all 200ms ease-in-out;
border-radius: 0.5rem;

&:hover {
cursor: pointer;
background-color: $tilebg3;
}

@media (max-width: 50rem) {
background-color: $tilebg4;
}

h2 {
color: $tiletext;
margin: 0 0 0.5rem 0;
line-height: 1.5rem;
}
span {
font-size: 1rem;
color: $greydesc;
line-height: 1.3rem;
}
.page-item-date {
flex: 1;
line-height: 1.3rem;
}
.page-item-content {
flex: 2;
display: flex;
flex-direction: column;
font-size: 1rem;
h2 {
font-size: 1.4rem;
}
}
}

.page-item-author {
font-weight: 600;
}
9 changes: 6 additions & 3 deletions config.toml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
Expand Down
2 changes: 1 addition & 1 deletion content/_index.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
name = "mudata"
description = "Multimodal data format"
url = "https://mudata.readthedocs.io/en/latest/"
url = "https://mudata.readthedocs.io/stable/"

[[packages]]
name = "spatialdata"
Expand Down
1 change: 1 addition & 0 deletions content/about/_index.md
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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
+++
title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
Expand Down
10 changes: 5 additions & 5 deletions content/about/code_of_conduct/_index.md
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -2,11 +2,11 @@
title = "Code of Conduct"
+++

# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct].

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
Expand Down
1 change: 1 addition & 0 deletions content/about/mission/_index.md
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Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
+++
title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
+++


Expand Down
1 change: 1 addition & 0 deletions content/about/roles/_index.md
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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
+++
title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
+++

## Roles and Responsibilities
Expand Down
2 changes: 1 addition & 1 deletion content/blog/2025-07-biomni.md
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Original file line numberDiff line numberDiff line change
Expand Up@@ -10,7 +10,7 @@ draft = false

Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

Expand Down
8 changes: 4 additions & 4 deletions content/blog/2025-11-biocontextai.md
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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,7 @@ author = "Malte Kuehl, Lukas Heumos"
draft = false
+++

# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

Expand Down
8 changes: 4 additions & 4 deletions content/blog/2025-anndata-012.md
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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,14 +6,14 @@ author = "Ilan Gold"
draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
Expand Down
2 changes: 1 addition & 1 deletion content/blog/2025-conference-summary.md
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Expand Up@@ -177,6 +177,6 @@ Each sponsor provided an outlook of the latest technologies in perturbation scre

### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
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Fix the issues found in the site audit#270

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to your account

 Merged

Zethson
merged 5 commits into

from

Aug 23, 2026
 Merged


Fix the issues found in the site audit
#270
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0833987

Fix broken external links


Zethson Aug 23, 2026
69e16fe

Fix the page metadata in the document head


Zethson Aug 23, 2026
374edb6

Fix the accessibility problems on the site


Zethson Aug 23, 2026
14858e5

Cut the weight of the site from 22 MB to 7 MB


Zethson Aug 23, 2026
b800c2c

Fix the structural gaps in navigation and page chrome


Zethson Aug 23, 2026

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4 changes: 2 additions & 2 deletions
.pre-commit-config.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -9,9 +9,9 @@ repos:
 - repo: https://github.com/ericmjl/webp-pre-commit
 rev: v0.0.12
 hooks:
 # Convert blog and learn images
 # img/logo is excluded on purpose: the media kit advertises PNG downloads.
 - id: convert-to-webp
 files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
 files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
 - repo: https://github.com/oxipng/oxipng
 rev: v10.2.0
 hooks:
Expand Down

148 changes: 90 additions & 58 deletions
assets/main.scss

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -59,11 +59,13 @@ $additionalInfoColor: #666666;
// Font stack: these two have well matching cap- and x-heights
@font-face {
 font-family: "Inter";
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.ttf");
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.woff2") format("woff2");
 font-display: swap;
}
@font-face {
 font-family: "JetBrains Mono";
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].ttf");
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].woff2") format("woff2");
 font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
 #title {
 #title-text {
 #title-name {
 margin: 0;
 font-size: 6rem;
 font-weight: 900;
 letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
 display: flex;
 min-width: 6rem;
 max-width: 6rem;
 // Matches the img height below, so that a package
 // without an icon still lines up with the others.
 min-height: 4rem;
 @media (max-width: 50rem) {
 display: none;
 }
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
 // }
 }
 }
 .page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
 }
 // TODO: Much of this does nothing AFAICT
 .post {
 .post-subtitle {
Expand DownExpand Up@@ -1175,6 +1125,9 @@ $eco-hues:
 }

 .eco-card {
 // All 120 registry entries are in the DOM so the filter can work offline.
 content-visibility: auto;
 contain-intrinsic-size: auto 14rem;
 position: relative;
 display: flex;
 flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
 transition: width 1s ease-in-out;
 pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
 *,
 *::before,
 *::after {
 animation-duration: 0.01ms !important;
 animation-iteration-count: 1 !important;
 transition-duration: 0.01ms !important;
 scroll-behavior: auto !important;
 }
}

.command-icon:focus-visible {
 outline: 3px solid #1a73e8;
 outline-offset: 2px;
}

// Hoisted out of #page-content: the landing page shows one of these and uses #cover.

.page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
}

.page-item-author {
 font-weight: 600;
}

9 changes: 6 additions & 3 deletions
config.toml

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Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
 series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
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content/_index.md

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Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
	name = "mudata"
	description = "Multimodal data format"
	url = "https://mudata.readthedocs.io/en/latest/"
	url = "https://mudata.readthedocs.io/stable/"

[[packages]]
	name = "spatialdata"
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title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
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title = "Code of Conduct"
+++

# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct]. 

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
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title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
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title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
+++

## Roles and Responsibilities
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content/blog/2025-07-biomni.md

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Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

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content/blog/2025-11-biocontextai.md

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Expand Up@@ -6,7 +6,7 @@ author = "Malte Kuehl, Lukas Heumos"
draft = false
+++

# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

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content/blog/2025-anndata-012.md

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Expand Up@@ -6,14 +6,14 @@ author = "Ilan Gold"
draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
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Expand Up@@ -177,6 +177,6 @@ Each sponsor provided an outlook of the latest technologies in perturbation scre

### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
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Fix the issues found in the site audit
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0833987

Fix broken external links


Zethson Aug 23, 2026
69e16fe

Fix the page metadata in the document head


Zethson Aug 23, 2026
374edb6

Fix the accessibility problems on the site


Zethson Aug 23, 2026
14858e5

Cut the weight of the site from 22 MB to 7 MB


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Fix the structural gaps in navigation and page chrome


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4 changes: 2 additions & 2 deletions
.pre-commit-config.yaml

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Expand Up@@ -9,9 +9,9 @@ repos:
 - repo: https://github.com/ericmjl/webp-pre-commit
 rev: v0.0.12
 hooks:
 # Convert blog and learn images
 # img/logo is excluded on purpose: the media kit advertises PNG downloads.
 - id: convert-to-webp
 files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
 files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
 - repo: https://github.com/oxipng/oxipng
 rev: v10.2.0
 hooks:
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Expand Up@@ -59,11 +59,13 @@ $additionalInfoColor: #666666;
// Font stack: these two have well matching cap- and x-heights
@font-face {
 font-family: "Inter";
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.ttf");
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.woff2") format("woff2");
 font-display: swap;
}
@font-face {
 font-family: "JetBrains Mono";
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].ttf");
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].woff2") format("woff2");
 font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
 #title {
 #title-text {
 #title-name {
 margin: 0;
 font-size: 6rem;
 font-weight: 900;
 letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
 display: flex;
 min-width: 6rem;
 max-width: 6rem;
 // Matches the img height below, so that a package
 // without an icon still lines up with the others.
 min-height: 4rem;
 @media (max-width: 50rem) {
 display: none;
 }
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
 // }
 }
 }
 .page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
 }
 // TODO: Much of this does nothing AFAICT
 .post {
 .post-subtitle {
Expand DownExpand Up@@ -1175,6 +1125,9 @@ $eco-hues:
 }

 .eco-card {
 // All 120 registry entries are in the DOM so the filter can work offline.
 content-visibility: auto;
 contain-intrinsic-size: auto 14rem;
 position: relative;
 display: flex;
 flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
 transition: width 1s ease-in-out;
 pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
 *,
 *::before,
 *::after {
 animation-duration: 0.01ms !important;
 animation-iteration-count: 1 !important;
 transition-duration: 0.01ms !important;
 scroll-behavior: auto !important;
 }
}

.command-icon:focus-visible {
 outline: 3px solid #1a73e8;
 outline-offset: 2px;
}

// Hoisted out of #page-content: the landing page shows one of these and uses #cover.

.page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
}

.page-item-author {
 font-weight: 600;
}

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config.toml

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Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
 series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
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content/_index.md

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Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
	name = "mudata"
	description = "Multimodal data format"
	url = "https://mudata.readthedocs.io/en/latest/"
	url = "https://mudata.readthedocs.io/stable/"

[[packages]]
	name = "spatialdata"
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+++
title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
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content/about/code_of_conduct/_index.md

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title = "Code of Conduct"
+++

# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct]. 

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
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title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
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title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
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## Roles and Responsibilities
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Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

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content/blog/2025-11-biocontextai.md

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Expand Up@@ -6,7 +6,7 @@ author = "Malte Kuehl, Lukas Heumos"
draft = false
+++

# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

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content/blog/2025-anndata-012.md

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Expand Up@@ -6,14 +6,14 @@ author = "Ilan Gold"
draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
Expand Down

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content/blog/2025-conference-summary.md

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Expand Up@@ -177,6 +177,6 @@ Each sponsor provided an outlook of the latest technologies in perturbation scre

### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
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Fix the issues found in the site audit
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Fix broken external links


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Fix the page metadata in the document head


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Fix the accessibility problems on the site


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4 changes: 2 additions & 2 deletions
.pre-commit-config.yaml

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Expand Up@@ -9,9 +9,9 @@ repos:
 - repo: https://github.com/ericmjl/webp-pre-commit
 rev: v0.0.12
 hooks:
 # Convert blog and learn images
 # img/logo is excluded on purpose: the media kit advertises PNG downloads.
 - id: convert-to-webp
 files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
 files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
 - repo: https://github.com/oxipng/oxipng
 rev: v10.2.0
 hooks:
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assets/main.scss

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Expand Up@@ -59,11 +59,13 @@ $additionalInfoColor: #666666;
// Font stack: these two have well matching cap- and x-heights
@font-face {
 font-family: "Inter";
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 font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
 #title {
 #title-text {
 #title-name {
 margin: 0;
 font-size: 6rem;
 font-weight: 900;
 letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
 display: flex;
 min-width: 6rem;
 max-width: 6rem;
 // Matches the img height below, so that a package
 // without an icon still lines up with the others.
 min-height: 4rem;
 @media (max-width: 50rem) {
 display: none;
 }
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
 // }
 }
 }
 .page-item {
 display: flex;
 flex-direction: row;

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 margin: 0.5rem 0 !important;
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 padding: 0.5rem;
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 .page-item-content {
 flex: 2;
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 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
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 // TODO: Much of this does nothing AFAICT
 .post {
 .post-subtitle {
Expand DownExpand Up@@ -1175,6 +1125,9 @@ $eco-hues:
 }

 .eco-card {
 // All 120 registry entries are in the DOM so the filter can work offline.
 content-visibility: auto;
 contain-intrinsic-size: auto 14rem;
 position: relative;
 display: flex;
 flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
 transition: width 1s ease-in-out;
 pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
 *,
 *::before,
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 padding: 1rem;

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.page-item-author {
 font-weight: 600;
}

9 changes: 6 additions & 3 deletions
config.toml

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Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
 series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
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content/_index.md

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Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
	name = "mudata"
	description = "Multimodal data format"
	url = "https://mudata.readthedocs.io/en/latest/"
	url = "https://mudata.readthedocs.io/stable/"

[[packages]]
	name = "spatialdata"
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content/about/_index.md

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@@ -1,5 +1,6 @@
+++
title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
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content/about/code_of_conduct/_index.md

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Expand Up@@ -2,11 +2,11 @@
title = "Code of Conduct"
+++

# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct]. 

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
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content/about/mission/_index.md

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@@ -1,5 +1,6 @@
+++
title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
+++


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content/about/roles/_index.md

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@@ -1,5 +1,6 @@
+++
title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
+++

## Roles and Responsibilities
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content/blog/2025-07-biomni.md

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Expand Up@@ -10,7 +10,7 @@ draft = false

Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

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content/blog/2025-11-biocontextai.md

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Expand Up@@ -6,7 +6,7 @@ author = "Malte Kuehl, Lukas Heumos"
draft = false
+++

# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

Expand Down

8 changes: 4 additions & 4 deletions
content/blog/2025-anndata-012.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,14 +6,14 @@ author = "Ilan Gold"
draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
Expand Down

2 changes: 1 addition & 1 deletion
content/blog/2025-conference-summary.md

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -177,6 +177,6 @@ Each sponsor provided an outlook of the latest technologies in perturbation scre

### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
Loading

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Fix the issues found in the site audit#270

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Zethson
merged 5 commits into

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Aug 23, 2026
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Fix the issues found in the site audit
#270
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0833987

Fix broken external links


Zethson Aug 23, 2026
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Fix the page metadata in the document head


Zethson Aug 23, 2026
374edb6

Fix the accessibility problems on the site


Zethson Aug 23, 2026
14858e5

Cut the weight of the site from 22 MB to 7 MB


Zethson Aug 23, 2026
b800c2c

Fix the structural gaps in navigation and page chrome


Zethson Aug 23, 2026

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4 changes: 2 additions & 2 deletions
.pre-commit-config.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -9,9 +9,9 @@ repos:
 - repo: https://github.com/ericmjl/webp-pre-commit
 rev: v0.0.12
 hooks:
 # Convert blog and learn images
 # img/logo is excluded on purpose: the media kit advertises PNG downloads.
 - id: convert-to-webp
 files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
 files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
 - repo: https://github.com/oxipng/oxipng
 rev: v10.2.0
 hooks:
Expand Down

148 changes: 90 additions & 58 deletions
assets/main.scss

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Original file line numberDiff line numberDiff line change
Expand Up@@ -59,11 +59,13 @@ $additionalInfoColor: #666666;
// Font stack: these two have well matching cap- and x-heights
@font-face {
 font-family: "Inter";
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.ttf");
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.woff2") format("woff2");
 font-display: swap;
}
@font-face {
 font-family: "JetBrains Mono";
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].ttf");
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].woff2") format("woff2");
 font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
 #title {
 #title-text {
 #title-name {
 margin: 0;
 font-size: 6rem;
 font-weight: 900;
 letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
 display: flex;
 min-width: 6rem;
 max-width: 6rem;
 // Matches the img height below, so that a package
 // without an icon still lines up with the others.
 min-height: 4rem;
 @media (max-width: 50rem) {
 display: none;
 }
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
 // }
 }
 }
 .page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
 }
 // TODO: Much of this does nothing AFAICT
 .post {
 .post-subtitle {
Expand DownExpand Up@@ -1175,6 +1125,9 @@ $eco-hues:
 }

 .eco-card {
 // All 120 registry entries are in the DOM so the filter can work offline.
 content-visibility: auto;
 contain-intrinsic-size: auto 14rem;
 position: relative;
 display: flex;
 flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
 transition: width 1s ease-in-out;
 pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
 *,
 *::before,
 *::after {
 animation-duration: 0.01ms !important;
 animation-iteration-count: 1 !important;
 transition-duration: 0.01ms !important;
 scroll-behavior: auto !important;
 }
}

.command-icon:focus-visible {
 outline: 3px solid #1a73e8;
 outline-offset: 2px;
}

// Hoisted out of #page-content: the landing page shows one of these and uses #cover.

.page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
}

.page-item-author {
 font-weight: 600;
}

9 changes: 6 additions & 3 deletions
config.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
 series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
Expand Down

2 changes: 1 addition & 1 deletion
content/_index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
	name = "mudata"
	description = "Multimodal data format"
	url = "https://mudata.readthedocs.io/en/latest/"
	url = "https://mudata.readthedocs.io/stable/"

[[packages]]
	name = "spatialdata"
Expand Down

1 change: 1 addition & 0 deletions
content/about/_index.md

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
+++
title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
Expand Down

10 changes: 5 additions & 5 deletions
content/about/code_of_conduct/_index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -2,11 +2,11 @@
title = "Code of Conduct"
+++

# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct]. 

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
Expand Down

1 change: 1 addition & 0 deletions
content/about/mission/_index.md

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
+++
title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
+++


Expand Down

1 change: 1 addition & 0 deletions
content/about/roles/_index.md

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Original file line numberDiff line numberDiff line change
@@ -1,5 +1,6 @@
+++
title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
+++

## Roles and Responsibilities
Expand Down

2 changes: 1 addition & 1 deletion
content/blog/2025-07-biomni.md

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Expand Up@@ -10,7 +10,7 @@ draft = false

Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

Expand Down

8 changes: 4 additions & 4 deletions
content/blog/2025-11-biocontextai.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,7 +6,7 @@ author = "Malte Kuehl, Lukas Heumos"
draft = false
+++

# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

Expand Down

8 changes: 4 additions & 4 deletions
content/blog/2025-anndata-012.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,14 +6,14 @@ author = "Ilan Gold"
draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
Expand Down

2 changes: 1 addition & 1 deletion
content/blog/2025-conference-summary.md

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Expand Up@@ -177,6 +177,6 @@ Each sponsor provided an outlook of the latest technologies in perturbation scre

### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
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if (__m === '*' || __re.test(location.href)) {
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 Merged

Zethson
merged 5 commits into

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Aug 23, 2026
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Fix the issues found in the site audit
#270
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0833987

Fix broken external links


Zethson Aug 23, 2026
69e16fe

Fix the page metadata in the document head


Zethson Aug 23, 2026
374edb6

Fix the accessibility problems on the site


Zethson Aug 23, 2026
14858e5

Cut the weight of the site from 22 MB to 7 MB


Zethson Aug 23, 2026
b800c2c

Fix the structural gaps in navigation and page chrome


Zethson Aug 23, 2026

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4 changes: 2 additions & 2 deletions
.pre-commit-config.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -9,9 +9,9 @@ repos:
 - repo: https://github.com/ericmjl/webp-pre-commit
 rev: v0.0.12
 hooks:
 # Convert blog and learn images
 # img/logo is excluded on purpose: the media kit advertises PNG downloads.
 - id: convert-to-webp
 files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
 files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
 - repo: https://github.com/oxipng/oxipng
 rev: v10.2.0
 hooks:
Expand Down

148 changes: 90 additions & 58 deletions
assets/main.scss

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -59,11 +59,13 @@ $additionalInfoColor: #666666;
// Font stack: these two have well matching cap- and x-heights
@font-face {
 font-family: "Inter";
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.ttf");
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.woff2") format("woff2");
 font-display: swap;
}
@font-face {
 font-family: "JetBrains Mono";
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].ttf");
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].woff2") format("woff2");
 font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
 #title {
 #title-text {
 #title-name {
 margin: 0;
 font-size: 6rem;
 font-weight: 900;
 letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
 display: flex;
 min-width: 6rem;
 max-width: 6rem;
 // Matches the img height below, so that a package
 // without an icon still lines up with the others.
 min-height: 4rem;
 @media (max-width: 50rem) {
 display: none;
 }
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
 // }
 }
 }
 .page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
 }
 // TODO: Much of this does nothing AFAICT
 .post {
 .post-subtitle {
Expand DownExpand Up@@ -1175,6 +1125,9 @@ $eco-hues:
 }

 .eco-card {
 // All 120 registry entries are in the DOM so the filter can work offline.
 content-visibility: auto;
 contain-intrinsic-size: auto 14rem;
 position: relative;
 display: flex;
 flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
 transition: width 1s ease-in-out;
 pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
 *,
 *::before,
 *::after {
 animation-duration: 0.01ms !important;
 animation-iteration-count: 1 !important;
 transition-duration: 0.01ms !important;
 scroll-behavior: auto !important;
 }
}

.command-icon:focus-visible {
 outline: 3px solid #1a73e8;
 outline-offset: 2px;
}

// Hoisted out of #page-content: the landing page shows one of these and uses #cover.

.page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
}

.page-item-author {
 font-weight: 600;
}

9 changes: 6 additions & 3 deletions
config.toml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
 series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
Expand Down

2 changes: 1 addition & 1 deletion
content/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
	name = "mudata"
	description = "Multimodal data format"
	url = "https://mudata.readthedocs.io/en/latest/"
	url = "https://mudata.readthedocs.io/stable/"

[[packages]]
	name = "spatialdata"
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1 change: 1 addition & 0 deletions
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title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
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title = "Code of Conduct"
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# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct]. 

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
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title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
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title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
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## Roles and Responsibilities
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Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

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draft = false
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# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

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draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
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### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
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Fix the issues found in the site audit
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0833987

Fix broken external links


Zethson Aug 23, 2026
69e16fe

Fix the page metadata in the document head


Zethson Aug 23, 2026
374edb6

Fix the accessibility problems on the site


Zethson Aug 23, 2026
14858e5

Cut the weight of the site from 22 MB to 7 MB


Zethson Aug 23, 2026
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Fix the structural gaps in navigation and page chrome


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4 changes: 2 additions & 2 deletions
.pre-commit-config.yaml

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Expand Up@@ -9,9 +9,9 @@ repos:
 - repo: https://github.com/ericmjl/webp-pre-commit
 rev: v0.0.12
 hooks:
 # Convert blog and learn images
 # img/logo is excluded on purpose: the media kit advertises PNG downloads.
 - id: convert-to-webp
 files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
 files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
 - repo: https://github.com/oxipng/oxipng
 rev: v10.2.0
 hooks:
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// Font stack: these two have well matching cap- and x-heights
@font-face {
 font-family: "Inter";
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.ttf");
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.woff2") format("woff2");
 font-display: swap;
}
@font-face {
 font-family: "JetBrains Mono";
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].ttf");
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].woff2") format("woff2");
 font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
 #title {
 #title-text {
 #title-name {
 margin: 0;
 font-size: 6rem;
 font-weight: 900;
 letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
 display: flex;
 min-width: 6rem;
 max-width: 6rem;
 // Matches the img height below, so that a package
 // without an icon still lines up with the others.
 min-height: 4rem;
 @media (max-width: 50rem) {
 display: none;
 }
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
 // }
 }
 }
 .page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
 }
 // TODO: Much of this does nothing AFAICT
 .post {
 .post-subtitle {
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 }

 .eco-card {
 // All 120 registry entries are in the DOM so the filter can work offline.
 content-visibility: auto;
 contain-intrinsic-size: auto 14rem;
 position: relative;
 display: flex;
 flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
 transition: width 1s ease-in-out;
 pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
 *,
 *::before,
 *::after {
 animation-duration: 0.01ms !important;
 animation-iteration-count: 1 !important;
 transition-duration: 0.01ms !important;
 scroll-behavior: auto !important;
 }
}

.command-icon:focus-visible {
 outline: 3px solid #1a73e8;
 outline-offset: 2px;
}

// Hoisted out of #page-content: the landing page shows one of these and uses #cover.

.page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
}

.page-item-author {
 font-weight: 600;
}

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Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
 series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
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Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
	name = "mudata"
	description = "Multimodal data format"
	url = "https://mudata.readthedocs.io/en/latest/"
	url = "https://mudata.readthedocs.io/stable/"

[[packages]]
	name = "spatialdata"
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title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
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content/about/code_of_conduct/_index.md

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title = "Code of Conduct"
+++

# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct]. 

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
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title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
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title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
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## Roles and Responsibilities
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Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

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draft = false
+++

# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

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content/blog/2025-anndata-012.md

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draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
Expand Down

2 changes: 1 addition & 1 deletion
content/blog/2025-conference-summary.md

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Expand Up@@ -177,6 +177,6 @@ Each sponsor provided an outlook of the latest technologies in perturbation scre

### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
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Fix the issues found in the site audit
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0833987

Fix broken external links


Zethson Aug 23, 2026
69e16fe

Fix the page metadata in the document head


Zethson Aug 23, 2026
374edb6

Fix the accessibility problems on the site


Zethson Aug 23, 2026
14858e5

Cut the weight of the site from 22 MB to 7 MB


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Fix the structural gaps in navigation and page chrome


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4 changes: 2 additions & 2 deletions
.pre-commit-config.yaml

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Expand Up@@ -9,9 +9,9 @@ repos:
 - repo: https://github.com/ericmjl/webp-pre-commit
 rev: v0.0.12
 hooks:
 # Convert blog and learn images
 # img/logo is excluded on purpose: the media kit advertises PNG downloads.
 - id: convert-to-webp
 files: ^static/img/(blog|learn)/.*\.(png|jpe?g|gif|bmp|tiff)$
 files: ^static/img/(blog|learn|events)/.*\.(png|jpe?g|gif|bmp|tiff)$
 - repo: https://github.com/oxipng/oxipng
 rev: v10.2.0
 hooks:
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Expand Up@@ -59,11 +59,13 @@ $additionalInfoColor: #666666;
// Font stack: these two have well matching cap- and x-heights
@font-face {
 font-family: "Inter";
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.ttf");
 src: url("fonts/Inter/Inter-VariableFont_slnt,wght.woff2") format("woff2");
 font-display: swap;
}
@font-face {
 font-family: "JetBrains Mono";
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].ttf");
 src: url("fonts/JetBrainsMono/JetBrainsMono[wght].woff2") format("woff2");
 font-display: swap;
}

// Global
Expand DownExpand Up@@ -367,6 +369,7 @@ body {
 #title {
 #title-text {
 #title-name {
 margin: 0;
 font-size: 6rem;
 font-weight: 900;
 letter-spacing: 0.2rem;
Expand DownExpand Up@@ -532,6 +535,9 @@ body {
 display: flex;
 min-width: 6rem;
 max-width: 6rem;
 // Matches the img height below, so that a package
 // without an icon still lines up with the others.
 min-height: 4rem;
 @media (max-width: 50rem) {
 display: none;
 }
Expand DownExpand Up@@ -763,62 +769,6 @@ body {
 // }
 }
 }
 .page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
 }
 // TODO: Much of this does nothing AFAICT
 .post {
 .post-subtitle {
Expand DownExpand Up@@ -1175,6 +1125,9 @@ $eco-hues:
 }

 .eco-card {
 // All 120 registry entries are in the DOM so the filter can work offline.
 content-visibility: auto;
 contain-intrinsic-size: auto 14rem;
 position: relative;
 display: flex;
 flex-direction: column;
Expand DownExpand Up@@ -2749,3 +2702,82 @@ $eco-hues:
 transition: width 1s ease-in-out;
 pointer-events: none;
}

@media (prefers-reduced-motion: reduce) {
 *,
 *::before,
 *::after {
 animation-duration: 0.01ms !important;
 animation-iteration-count: 1 !important;
 transition-duration: 0.01ms !important;
 scroll-behavior: auto !important;
 }
}

.command-icon:focus-visible {
 outline: 3px solid #1a73e8;
 outline-offset: 2px;
}

// Hoisted out of #page-content: the landing page shows one of these and uses #cover.

.page-item {
 display: flex;
 flex-direction: row;

 @media (max-width: 50rem) {
 flex-direction: column;
 align-items: flex-start;
 justify-content: center;
 h2 {
 margin: 0.5rem 0 !important;
 }
 margin: 0 -0.5rem;
 padding: 0.5rem;
 padding-bottom: 1.3rem;
 }

 margin: 0 -1rem;
 padding: 1rem;

 background-color: #ff000000;
 transition: all 200ms ease-in-out;
 border-radius: 0.5rem;

 &:hover {
 cursor: pointer;
 background-color: $tilebg3;
 }

 @media (max-width: 50rem) {
 background-color: $tilebg4;
 }

 h2 {
 color: $tiletext;
 margin: 0 0 0.5rem 0;
 line-height: 1.5rem;
 }
 span {
 font-size: 1rem;
 color: $greydesc;
 line-height: 1.3rem;
 }
 .page-item-date {
 flex: 1;
 line-height: 1.3rem;
 }
 .page-item-content {
 flex: 2;
 display: flex;
 flex-direction: column;
 font-size: 1rem;
 h2 {
 font-size: 1.4rem;
 }
 }
}

.page-item-author {
 font-weight: 600;
}

9 changes: 6 additions & 3 deletions
config.toml

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Expand Up@@ -3,11 +3,14 @@ languageCode = "en-us"
title = "scverse"
description = "Foundational tools for omics data in the life sciences"

# CI publishes with --buildFuture so that events dated in the future are listed.
# Setting it here too keeps `hugo server` in step with production.
buildFuture = true
enableRobotsTXT = true

[params]
images = ["img/scverse-social-card.png"]

[taxonomies]
 series = 'series'
description = "Foundational tools for omics data in the life sciences"

[markup.goldmark.renderer]
unsafe= true
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content/_index.md

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Expand Up@@ -12,7 +12,7 @@ description = "Foundational tools for single-cell omics data analysis"
[[packages]]
	name = "mudata"
	description = "Multimodal data format"
	url = "https://mudata.readthedocs.io/en/latest/"
	url = "https://mudata.readthedocs.io/stable/"

[[packages]]
	name = "spatialdata"
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content/about/_index.md

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@@ -1,5 +1,6 @@
+++
title = "About scverse"
description = "Scverse is a consortium of foundational tools for the analysis of omics data in the life sciences."
+++

Scverse® is a consortium of foundational tools for analysis of omics data in life sciences. It has been founded to ensure the long-term maintenance of these core tools.
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content/about/code_of_conduct/_index.md

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Expand Up@@ -2,11 +2,11 @@
title = "Code of Conduct"
+++

# NUMFOCUS CODE OF CONDUCT
## NUMFOCUS CODE OF CONDUCT

You can find the whole document [here][NumFOCUS Code of Conduct]. 

## THE SHORT VERSION
### THE SHORT VERSION

NumFOCUS is dedicated to providing a harassment-free community for everyone, regardless of gender, sexual orientation, gender identity and expression, disability, physical appearance, body size, race, or religion.
We do not tolerate harassment of community members in any form.
Expand All@@ -20,15 +20,15 @@ Sexual language and imagery is not appropriate.

Thank you for helping make this a welcoming, friendly community for all.

## LONG VERSION
### LONG VERSION

You can find the long version of the Code of Conduct on the [NumFOCUS Code of Conduct][] page.

## HOW TO REPORT
### HOW TO REPORT

If you feel that the Code of Conduct has been violated, feel free to submit a report, by using the [NumFOCUS Code of Conduct Reporting Form](https://forms.monday.com/forms/f130e8cddb99568fa86cf077b8912a60?r=use1).

## WHO WILL RECEIVE YOUR REPORT
### WHO WILL RECEIVE YOUR REPORT

Your report will be received and handled by NumFOCUS Code of Conduct Working Group; trained, and experienced contributors with diverse backgrounds.
The group is making decisions independently from the project, PyData, NumFOCUS or any other organization.
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@@ -1,5 +1,6 @@
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title = "Mission statement"
description = "The goals, organization and vision of the scverse consortium."
+++


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content/about/roles/_index.md

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@@ -1,5 +1,6 @@
+++
title = "Roles and Decisions"
description = "How scverse is governed: the roles within the project and the process by which decisions are made."
+++

## Roles and Responsibilities
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content/blog/2025-07-biomni.md

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Expand Up@@ -10,7 +10,7 @@ draft = false

Single-cell and spatial omics have unlocked unprecedented insights into cellular diversity, tissue architecture, and drug responses.
Despite the remarkable progress in computational tools, the diversity and complexity of analyses can still pose challenges.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/en/latest/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.
While the scverse ecosystem provides powerful and interoperable tools such as [Scanpy](https://scanpy.scverse.org/), [scvi-tools](https://scvi-tools.org/), [Squidpy](https://squidpy.readthedocs.io/), [AnnData](https://anndata.scverse.org/), [MuData](https://mudata.readthedocs.io/stable/), and [SpatialData](https://spatialdata.scverse.org/en/latest/), researchers can sometimes face a steep learning curve, particularly when integrating multiple analytical steps or modalities.

Scverse is a community-driven, open-source initiative behind many of the most widely adopted Python tools in single-cell biology, known for promoting modular, interoperable, and scalable analysis across diverse modalities—from transcriptomics to spatial and immune profiling.

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content/blog/2025-11-biocontextai.md

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Expand Up@@ -6,7 +6,7 @@ author = "Malte Kuehl, Lukas Heumos"
draft = false
+++

# scverse × BioContextAI: Community Infrastructure for Agentic Analysis
## scverse × BioContextAI: Community Infrastructure for Agentic Analysis

We're excited to announce that we are partnering with [BioContextAI][biocontextai], a new open-source initiative for building agentic systems in biomedical research.
BioContextAI provides a community registry for Model Context Protocol (MCP) servers.
Expand All@@ -15,21 +15,21 @@ This project was recently published as a [Nature Biotechnology correspondence][N

<img src="/img/blog/biocontextai_overview.webp" style="max-width: 100%;" alt="BioContextAI overview" />

## What we're building
### What we're building

BioContextAI currently hosts over 40 community-built biomedical MCP servers with hundreds of tools, including the BioContextAI Knowledgebase MCP with access to resources like UniProt, Open Targets, and pathway databases.
There's a natural synergy here: while scverse packages handle computational analyses, these knowledge resources support the hypothesis generation and interpretation work that happens around those analyses.
By jointly building best practice scverse MCP servers, we hope to facilitate exploration of omics data and provide improved code generation for scverse ecosystem-enabled analyses, all while maintaining reproducibility and transparency.
This is early work and we are actively evaluating patterns for building MCP servers that integrate well with existing workflows and best practices.

## How to get involved
### How to get involved

Check out the Registry at [biocontext.ai][biocontextai] to explore community-built MCP servers.
If you're interested in building new servers, try the [cookiecutter template][biocontextai-cookiecutter] to get started.
Join the conversation on the [BioContextAI channel][biocontextai-zulip] within the scverse Zulip to connect with other developers and researchers working in this space.
We're excited to see what the community builds together.

## Learn more
### Learn more

Learn more about BioContextAI in the [Nature Biotechnology correspondence][Nature Biotechnology correspondence] and on the [BioContextAI website][biocontextai].

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content/blog/2025-anndata-012.md

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Expand Up@@ -6,14 +6,14 @@ author = "Ilan Gold"
draft = false
+++

# 0.12 released
## 0.12 released

We're happy to announce that `anndata` 0.12 is out now!
Check out [the changelog](https://anndata.scverse.org/page/release-notes/index.html#v0-12-0) for a full list of changes.
Here, we want to give our users a bit of a deep dive into the new functionality.
We have lots of great features, like zarr v3 support (package and format), full lazy loading, and new API customisability! Let’s dive in!

## Zarr v3
### Zarr v3

[Zarr v3 as a file format](https://zarr-specs.readthedocs.io/en/latest/v3/core/index.html) provides improved cloud support, support for sharding to reduce the number of files created in a zarr store, and improved support for extensibility.
Check out the following graphic from the zarr docs:
Expand All@@ -36,7 +36,7 @@ And of course, all of this new functionality has not broken our backwards compat
Anndata 0.12 is still fully zarr v2 compatible, both with the package and the file format.
Upgrade fearlessly!

## Fully lazy file access
### Fully lazy file access

Moving on, we have also replaced `anndata.experimental.read_elem_as_dask` with [`anndata.experimental.read_elem_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_lazy.html) and [`anndata.experimental.read_lazy`](https://anndata.scverse.org/page/generated/anndata.experimental.read_elem_lazy.html).
Why? Because now your dataframes can be lazy too thanks to support from [xarray](https://docs.xarray.dev/en/stable/user-guide/index.html)!
Expand All@@ -47,7 +47,7 @@ Mix this with zarr v3 for performant, fully lazy, fully remote (if needed) acces
Check out [our notebook](https://anndata.scverse.org/page/tutorials/notebooks/read_lazy.html) to learn more about the API – thanks to [Nils Gehlenborg’s HIDIVE lab](https://hidivelab.org/) for hosting the data, and be sure to check out the [Vitessce visualisation](https://tinyurl.com/jtan4nx7) of the very same data backing the notebook.
This dual-access really showcases the power of smart remote data access!

## Customizable API
### Customizable API

And if that wasn’t enough, we now have [a new way of extending the anndata API](https://anndata.scverse.org/page/generated/anndata.register_anndata_namespace.html) contributed by one of our community members, Sri Varra.
This contribution lets users extend the `AnnData` API easily, great for tinkering with new APIs and features but also for writing new methods directly into the `AnnData` object:
Expand Down

2 changes: 1 addition & 1 deletion
content/blog/2025-conference-summary.md

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Expand Up@@ -177,6 +177,6 @@ Each sponsor provided an outlook of the latest technologies in perturbation scre

### Conclusion

This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scaboranova), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).
This was the second time we organized the scverse conference — you can read about [the first edition in Munich](/blog/2024-conference-summary/). We're looking forward to seeing you at future scverse events! In the meantime, you can engage with the community on [Zulip](https://scverse.zulipchat.com/) and at our community meetings. Look out for announcements on our social media channels ([X](https://x.com/scverse_team), [Bluesky](https://bsky.app/profile/scverse.bsky.social), [LinkedIn](https://www.linkedin.com/company/scverse/)).

*Photo credits: Vivekanandan Ramalingam (Vivek), Research Scientist at Stanford Genetics.*
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