Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Zethson wants to merge 5 commits into
base:main
Choose a base branch
from
Open

Link to the interoperability docs from the packages and learn pages #263

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
98bd4a5
Link to AnnData interoperability docs from packages and learn pages
Zethson Aug 23, 2026
ee8a5ef
Cover all three data structures consistently
Zethson Aug 23, 2026
0538c9e
Point the spatialdata link at stable
Zethson Aug 23, 2026
3feb88e
Update content/learn/_index.md
Zethson Aug 24, 2026
9697b6a
Merge remote-tracking branch 'origin/main' into interoperability-links
Zethson Aug 25, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions content/learn/_index.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down
12 changes: 11 additions & 1 deletion content/packages/_index.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++
5 changes: 3 additions & 2 deletions layouts/packages/list.html
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
<h1>{{ .Title }}</h1>
<article class="post">
{{ $sections := index .Params.sections 0 }}
{{ $interop := .Params.interoperability | default dict }}
<div class="post-content" id="packages-content">
{{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
{{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
{{ $sections.datastructures | markdownify }}
<div class="packages-list">
{{ range . }}
{{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
{{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
{{ end }}
</div>
{{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
{{ $sections.frameworks | markdownify }}
<div class="packages-list">
{{ range . }}
{{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
{{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
{{ end }}
</div>
{{ end }}
Expand Down
5 changes: 4 additions & 1 deletion layouts/partials/package-section.html
View file
Open in desktop
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
{{ with $p.tutorials_home }}
<a href="{{ . }}" target="_blank">Tutorials</a>
{{ end }}
{{ with .interop }}
<a href="{{ . }}" target="_blank">Interoperability</a>
{{ end }}
{{ with $p.install }}
{{ with .pypi }}
<a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

Zethson
wants to merge
5
commits into

base:main
Choose a base branch

from

 Open


Link to the interoperability docs from the packages and learn pages
#263
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


5 commits


Select commit
Hold shift + click to select a range
98bd4a5

Link to AnnData interoperability docs from packages and learn pages


Zethson Aug 23, 2026
ee8a5ef

Cover all three data structures consistently


Zethson Aug 23, 2026
0538c9e

Point the spatialdata link at stable


Zethson Aug 23, 2026
3feb88e

Update content/learn/_index.md


Zethson Aug 24, 2026
9697b6a

Merge remote-tracking branch 'origin/main' into interoperability-links


Zethson Aug 25, 2026

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down

12 changes: 11 additions & 1 deletion
content/packages/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
	core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
	datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
	datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
	datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
	frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
	ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
	anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
	mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
	spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++

5 changes: 3 additions & 2 deletions
layouts/packages/list.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
 <h1>{{ .Title }}</h1>
 <article class="post">
 {{ $sections := index .Params.sections 0 }}
 {{ $interop := .Params.interoperability | default dict }}
 <div class="post-content" id="packages-content">
 {{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
 {{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
 {{ $sections.datastructures | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
 {{ $sections.frameworks | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand Down

5 changes: 4 additions & 1 deletion
layouts/partials/package-section.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
 {{ with $p.tutorials_home }}
 <a href="{{ . }}" target="_blank">Tutorials</a>
 {{ end }}
 {{ with .interop }}
 <a href="{{ . }}" target="_blank">Interoperability</a>
 {{ end }}
 {{ with $p.install }}
 {{ with .pypi }}
 <a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

Zethson
wants to merge
5
commits into

base:main
Choose a base branch

from

 Open


Link to the interoperability docs from the packages and learn pages
#263
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


5 commits


Select commit
Hold shift + click to select a range
98bd4a5

Link to AnnData interoperability docs from packages and learn pages


Zethson Aug 23, 2026
ee8a5ef

Cover all three data structures consistently


Zethson Aug 23, 2026
0538c9e

Point the spatialdata link at stable


Zethson Aug 23, 2026
3feb88e

Update content/learn/_index.md


Zethson Aug 24, 2026
9697b6a

Merge remote-tracking branch 'origin/main' into interoperability-links


Zethson Aug 25, 2026

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down

12 changes: 11 additions & 1 deletion
content/packages/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
	core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
	datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
	datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
	datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
	frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
	ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
	anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
	mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
	spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++

5 changes: 3 additions & 2 deletions
layouts/packages/list.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
 <h1>{{ .Title }}</h1>
 <article class="post">
 {{ $sections := index .Params.sections 0 }}
 {{ $interop := .Params.interoperability | default dict }}
 <div class="post-content" id="packages-content">
 {{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
 {{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
 {{ $sections.datastructures | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
 {{ $sections.frameworks | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand Down

5 changes: 4 additions & 1 deletion
layouts/partials/package-section.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
 {{ with $p.tutorials_home }}
 <a href="{{ . }}" target="_blank">Tutorials</a>
 {{ end }}
 {{ with .interop }}
 <a href="{{ . }}" target="_blank">Interoperability</a>
 {{ end }}
 {{ with $p.install }}
 {{ with .pypi }}
 <a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

Zethson
wants to merge
5
commits into

base:main
Choose a base branch

from

 Open


Link to the interoperability docs from the packages and learn pages
#263
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


5 commits


Select commit
Hold shift + click to select a range
98bd4a5

Link to AnnData interoperability docs from packages and learn pages


Zethson Aug 23, 2026
ee8a5ef

Cover all three data structures consistently


Zethson Aug 23, 2026
0538c9e

Point the spatialdata link at stable


Zethson Aug 23, 2026
3feb88e

Update content/learn/_index.md


Zethson Aug 24, 2026
9697b6a

Merge remote-tracking branch 'origin/main' into interoperability-links


Zethson Aug 25, 2026

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down

12 changes: 11 additions & 1 deletion
content/packages/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
	core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
	datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
	datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
	datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
	frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
	ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
	anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
	mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
	spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++

5 changes: 3 additions & 2 deletions
layouts/packages/list.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
 <h1>{{ .Title }}</h1>
 <article class="post">
 {{ $sections := index .Params.sections 0 }}
 {{ $interop := .Params.interoperability | default dict }}
 <div class="post-content" id="packages-content">
 {{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
 {{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
 {{ $sections.datastructures | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
 {{ $sections.frameworks | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand Down

5 changes: 4 additions & 1 deletion
layouts/partials/package-section.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
 {{ with $p.tutorials_home }}
 <a href="{{ . }}" target="_blank">Tutorials</a>
 {{ end }}
 {{ with .interop }}
 <a href="{{ . }}" target="_blank">Interoperability</a>
 {{ end }}
 {{ with $p.install }}
 {{ with .pypi }}
 <a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

Zethson
wants to merge
5
commits into

base:main
Choose a base branch

from

 Open


Link to the interoperability docs from the packages and learn pages
#263
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


5 commits


Select commit
Hold shift + click to select a range
98bd4a5

Link to AnnData interoperability docs from packages and learn pages


Zethson Aug 23, 2026
ee8a5ef

Cover all three data structures consistently


Zethson Aug 23, 2026
0538c9e

Point the spatialdata link at stable


Zethson Aug 23, 2026
3feb88e

Update content/learn/_index.md


Zethson Aug 24, 2026
9697b6a

Merge remote-tracking branch 'origin/main' into interoperability-links


Zethson Aug 25, 2026

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down

12 changes: 11 additions & 1 deletion
content/packages/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
	core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
	datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
	datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
	datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
	frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
	ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
	anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
	mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
	spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++

5 changes: 3 additions & 2 deletions
layouts/packages/list.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
 <h1>{{ .Title }}</h1>
 <article class="post">
 {{ $sections := index .Params.sections 0 }}
 {{ $interop := .Params.interoperability | default dict }}
 <div class="post-content" id="packages-content">
 {{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
 {{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
 {{ $sections.datastructures | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
 {{ $sections.frameworks | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand Down

5 changes: 4 additions & 1 deletion
layouts/partials/package-section.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
 {{ with $p.tutorials_home }}
 <a href="{{ . }}" target="_blank">Tutorials</a>
 {{ end }}
 {{ with .interop }}
 <a href="{{ . }}" target="_blank">Interoperability</a>
 {{ end }}
 {{ with $p.install }}
 {{ with .pypi }}
 <a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

Zethson
wants to merge
5
commits into

base:main
Choose a base branch

from

 Open


Link to the interoperability docs from the packages and learn pages
#263
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


5 commits


Select commit
Hold shift + click to select a range
98bd4a5

Link to AnnData interoperability docs from packages and learn pages


Zethson Aug 23, 2026
ee8a5ef

Cover all three data structures consistently


Zethson Aug 23, 2026
0538c9e

Point the spatialdata link at stable


Zethson Aug 23, 2026
3feb88e

Update content/learn/_index.md


Zethson Aug 24, 2026
9697b6a

Merge remote-tracking branch 'origin/main' into interoperability-links


Zethson Aug 25, 2026

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down

12 changes: 11 additions & 1 deletion
content/packages/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
	core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
	datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
	datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
	datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
	frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
	ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
	anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
	mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
	spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++

5 changes: 3 additions & 2 deletions
layouts/packages/list.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
 <h1>{{ .Title }}</h1>
 <article class="post">
 {{ $sections := index .Params.sections 0 }}
 {{ $interop := .Params.interoperability | default dict }}
 <div class="post-content" id="packages-content">
 {{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
 {{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
 {{ $sections.datastructures | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
 {{ $sections.frameworks | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand Down

5 changes: 4 additions & 1 deletion
layouts/partials/package-section.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
 {{ with $p.tutorials_home }}
 <a href="{{ . }}" target="_blank">Tutorials</a>
 {{ end }}
 {{ with .interop }}
 <a href="{{ . }}" target="_blank">Interoperability</a>
 {{ end }}
 {{ with $p.install }}
 {{ with .pypi }}
 <a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

Zethson
wants to merge
5
commits into

base:main
Choose a base branch

from

 Open


Link to the interoperability docs from the packages and learn pages
#263
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


5 commits


Select commit
Hold shift + click to select a range
98bd4a5

Link to AnnData interoperability docs from packages and learn pages


Zethson Aug 23, 2026
ee8a5ef

Cover all three data structures consistently


Zethson Aug 23, 2026
0538c9e

Point the spatialdata link at stable


Zethson Aug 23, 2026
3feb88e

Update content/learn/_index.md


Zethson Aug 24, 2026
9697b6a

Merge remote-tracking branch 'origin/main' into interoperability-links


Zethson Aug 25, 2026

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down

12 changes: 11 additions & 1 deletion
content/packages/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
	core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
	datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
	datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
	datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
	frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
	ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
	anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
	mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
	spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++

5 changes: 3 additions & 2 deletions
layouts/packages/list.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
 <h1>{{ .Title }}</h1>
 <article class="post">
 {{ $sections := index .Params.sections 0 }}
 {{ $interop := .Params.interoperability | default dict }}
 <div class="post-content" id="packages-content">
 {{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
 {{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
 {{ $sections.datastructures | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
 {{ $sections.frameworks | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand Down

5 changes: 4 additions & 1 deletion
layouts/partials/package-section.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
 {{ with $p.tutorials_home }}
 <a href="{{ . }}" target="_blank">Tutorials</a>
 {{ end }}
 {{ with .interop }}
 <a href="{{ . }}" target="_blank">Interoperability</a>
 {{ end }}
 {{ with $p.install }}
 {{ with .pypi }}
 <a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Link to the interoperability docs from the packages and learn pages#263

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Open

Zethson
wants to merge
5
commits into

base:main
Choose a base branch

from

 Open


Link to the interoperability docs from the packages and learn pages
#263
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


5 commits


Select commit
Hold shift + click to select a range
98bd4a5

Link to AnnData interoperability docs from packages and learn pages


Zethson Aug 23, 2026
ee8a5ef

Cover all three data structures consistently


Zethson Aug 23, 2026
0538c9e

Point the spatialdata link at stable


Zethson Aug 23, 2026
3feb88e

Update content/learn/_index.md


Zethson Aug 24, 2026
9697b6a

Merge remote-tracking branch 'origin/main' into interoperability-links


Zethson Aug 25, 2026

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


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

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,7 @@ tutorials_intro = """\
If you are new to the scverse, get started with this set of tutorials covering basic analysis and functionality of the core packages.
For more tutorials as well as API documentation and user guides, see the sites of [individual packages](/packages/).
Beyond the core packages, the scverse [ecosystem](/packages/#ecosystem) contains many community-maintained packages that build on scverse data structures and integrate into standard workflows.
If you work primarily in another language, the scverse on-disk formats can be read from R, Rust, Julia, and beyond, as covered by the interoperability pages for [AnnData](https://anndata.scverse.org/en/stable/interoperability.html), [MuData](https://mudata.readthedocs.io/stable/interoperability.html), and [SpatialData](https://spatialdata.scverse.org/en/latest/interoperability.html).

You can also find recordings of past talks and workshops on our [YouTube channel](https://www.youtube.com/channel/UCpsvsIAW3R5OdftJKKuLNMA).
"""
Expand Down

12 changes: 11 additions & 1 deletion
content/packages/_index.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,10 +5,20 @@ aliases = ["/projects/"]

[[sections]]
	core_packages = "These packages are considered foundational in that many other packages build upon them. Joint maintenance by the core team guarantees long-term stability."
	datastructures = "Data structures are the foundational building block for all scverse packages. Building upon common data structures ensures interoperability."
	datastructures = """\
Data structures are the foundational building block for all scverse packages.
Building upon common data structures ensures interoperability.
The on-disk formats are language-agnostic as well: each can be read from R, Julia, and other languages, as listed on the interoperability pages linked below."""
	datastructures_post = "In addition to these packages, we define standards on how to represent certain data types in these data structures. For now, such a specification is available for [Adaptive Immune Receptor Repertoire (AIRR) data](https://scirpy.scverse.org/en/latest/data-structure.html#storing-airr-rearrangement-data-in-anndata)."
	frameworks = "Frameworks provide essential algorithms and plotting functions for specific analysis steps, building on our data structures."
	ecosystem = "Many popular packages rely on scverse functionality. For instance, they take advantage of established data format standards such as AnnData and MuData, or are designed to be integrated into the workflow of analysis frameworks. Here, we list ecosystem packages following development best practices (continuous testing, documented, available through standard distribution tools).\n\n *See [scverse/ecosystem-packages](https://github.com/scverse/ecosystem-packages) for inclusion criteria, and to submit more packages.*"


# The registry schema has no interoperability field, so the core data structures map theirs here.
# Keys are the registry's package name, lowercased.
[interoperability]
	anndata = "https://anndata.scverse.org/en/stable/interoperability.html"
	mudata = "https://mudata.readthedocs.io/stable/interoperability.html"
	spatialdata = "https://spatialdata.scverse.org/en/latest/interoperability.html"

+++

5 changes: 3 additions & 2 deletions
layouts/packages/list.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,6 +5,7 @@
 <h1>{{ .Title }}</h1>
 <article class="post">
 {{ $sections := index .Params.sections 0 }}
 {{ $interop := .Params.interoperability | default dict }}
 <div class="post-content" id="packages-content">
 {{ $registryBase := "https://scverse.org/ecosystem-packages/" }}
 {{ $data := resources.GetRemote (printf "%spackages.json" $registryBase) }}
Expand All@@ -25,7 +26,7 @@ <h3 id="datastructures">Data structures</h3>
 {{ $sections.datastructures | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand All@@ -36,7 +37,7 @@ <h3 id="frameworks">Frameworks</h3>
 {{ $sections.frameworks | markdownify }}
 <div class="packages-list">
 {{ range . }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase) }}
 {{ partial "package-section.html" (dict "pkg" . "base" $registryBase "interop" (index $interop (lower .name))) }}
 {{ end }}
 </div>
 {{ end }}
Expand Down

5 changes: 4 additions & 1 deletion
layouts/partials/package-section.html

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base */}}
{{/* One core package row on /packages, from an ecosystem-registry entry. Params: pkg, base, interop */}}
{{ $base := .base }}
{{ $p := .pkg }}
<div class="package-section">
Expand All@@ -24,6 +24,9 @@
 {{ with $p.tutorials_home }}
 <a href="{{ . }}" target="_blank">Tutorials</a>
 {{ end }}
 {{ with .interop }}
 <a href="{{ . }}" target="_blank">Interoperability</a>
 {{ end }}
 {{ with $p.install }}
 {{ with .pypi }}
 <a href="https://pypi.org/project/{{ . }}/" target="_blank">PyPI</a>
Expand Down