chore: stale AnnData.concatenate references - #4201

Merged
ilan-gold merged 2 commits into
scverse:mainfrom
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged

chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom
rwbaber:doc/fix-stale-concatenate-links

Conversation

@rwbaber

@rwbaberrwbaber commented Jul 8, 2026

Copy link
Copy Markdown
Contributor

This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.

Changes:

  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  • Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.

@codecov

codecovBot commented Jul 8, 2026•
edited
Loading

Copy link
Copy Markdown

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).
✅ All tests successful. No failed tests found.

Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)

... and 1 file with indirect coverage changes

@rwbaberrwbaber mentioned this pull request Jul 8, 2026
Open
3 tasks
@ilan-goldilan-gold changed the title Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold added this to the 1.12.3 milestone Jul 8, 2026
@ilan-gold
ilan-gold enabled auto-merge (squash) July 8, 2026 14:04
@ilan-gold
ilan-gold merged commit a7868fe into scverse:mainJul 8, 2026
16 of 18 checks passed
@meeseeksmachinemeeseeksmachine mentioned this pull request Jul 8, 2026
Merged
flying-sheep pushed a commit that referenced this pull request Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

No reviews

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold
, '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
chore: stale AnnData.concatenate references - #4201
Merged
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged
chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Conversation
@rwbaber
@rwbaberrwbaber
commented
Jul 8, 2026

Copy link


Copy Markdown

Contributor
This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.
Changes:
  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  •  Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.
@codecov
codecovBot
commented
Jul 8, 2026•

edited

Loading

Copy link


Copy Markdown

Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).

✅ All tests successful. No failed tests found.
Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1 
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️
Flags with carried forward coverage won't be shown. Click here to find out more.
Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)
... and 1 file with indirect coverage changes
@rwbaberrwbaber
mentioned this pull request
Jul 8, 2026
 Open

3 tasks
@ilan-goldilan-gold
changed the title
Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold
added this to the 1.12.3 milestone
Jul 8, 2026
@ilan-gold
ilan-gold
enabled auto-merge (squash)
July 8, 2026 14:04
@ilan-gold
ilan-gold
merged commit a7868fe
into
scverse:mainJul 8, 2026

16 of 18 checks passed

@meeseeksmachinemeeseeksmachine
mentioned this pull request
Jul 8, 2026
 Merged

flying-sheep pushed a commit
that referenced
this pull request
Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold

, '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
chore: stale AnnData.concatenate references - #4201
Merged
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged
chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Conversation
@rwbaber
@rwbaberrwbaber
commented
Jul 8, 2026

Copy link


Copy Markdown

Contributor
This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.
Changes:
  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  •  Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.
@codecov
codecovBot
commented
Jul 8, 2026•

edited

Loading

Copy link


Copy Markdown

Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).

✅ All tests successful. No failed tests found.
Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1 
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️
Flags with carried forward coverage won't be shown. Click here to find out more.
Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)
... and 1 file with indirect coverage changes
@rwbaberrwbaber
mentioned this pull request
Jul 8, 2026
 Open

3 tasks
@ilan-goldilan-gold
changed the title
Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold
added this to the 1.12.3 milestone
Jul 8, 2026
@ilan-gold
ilan-gold
enabled auto-merge (squash)
July 8, 2026 14:04
@ilan-gold
ilan-gold
merged commit a7868fe
into
scverse:mainJul 8, 2026

16 of 18 checks passed

@meeseeksmachinemeeseeksmachine
mentioned this pull request
Jul 8, 2026
 Merged

flying-sheep pushed a commit
that referenced
this pull request
Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold

, '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
chore: stale AnnData.concatenate references - #4201
Merged
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged
chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Conversation
@rwbaber
@rwbaberrwbaber
commented
Jul 8, 2026

Copy link


Copy Markdown

Contributor
This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.
Changes:
  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  •  Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.
@codecov
codecovBot
commented
Jul 8, 2026•

edited

Loading

Copy link


Copy Markdown

Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).

✅ All tests successful. No failed tests found.
Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1 
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️
Flags with carried forward coverage won't be shown. Click here to find out more.
Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)
... and 1 file with indirect coverage changes
@rwbaberrwbaber
mentioned this pull request
Jul 8, 2026
 Open

3 tasks
@ilan-goldilan-gold
changed the title
Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold
added this to the 1.12.3 milestone
Jul 8, 2026
@ilan-gold
ilan-gold
enabled auto-merge (squash)
July 8, 2026 14:04
@ilan-gold
ilan-gold
merged commit a7868fe
into
scverse:mainJul 8, 2026

16 of 18 checks passed

@meeseeksmachinemeeseeksmachine
mentioned this pull request
Jul 8, 2026
 Merged

flying-sheep pushed a commit
that referenced
this pull request
Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold

, '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
chore: stale AnnData.concatenate references - #4201
Merged
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged
chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Conversation
@rwbaber
@rwbaberrwbaber
commented
Jul 8, 2026

Copy link


Copy Markdown

Contributor
This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.
Changes:
  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  •  Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.
@codecov
codecovBot
commented
Jul 8, 2026•

edited

Loading

Copy link


Copy Markdown

Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).

✅ All tests successful. No failed tests found.
Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1 
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️
Flags with carried forward coverage won't be shown. Click here to find out more.
Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)
... and 1 file with indirect coverage changes
@rwbaberrwbaber
mentioned this pull request
Jul 8, 2026
 Open

3 tasks
@ilan-goldilan-gold
changed the title
Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold
added this to the 1.12.3 milestone
Jul 8, 2026
@ilan-gold
ilan-gold
enabled auto-merge (squash)
July 8, 2026 14:04
@ilan-gold
ilan-gold
merged commit a7868fe
into
scverse:mainJul 8, 2026

16 of 18 checks passed

@meeseeksmachinemeeseeksmachine
mentioned this pull request
Jul 8, 2026
 Merged

flying-sheep pushed a commit
that referenced
this pull request
Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold

, '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
chore: stale AnnData.concatenate references - #4201
Merged
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged
chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Conversation
@rwbaber
@rwbaberrwbaber
commented
Jul 8, 2026

Copy link


Copy Markdown

Contributor
This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.
Changes:
  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  •  Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.
@codecov
codecovBot
commented
Jul 8, 2026•

edited

Loading

Copy link


Copy Markdown

Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).

✅ All tests successful. No failed tests found.
Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1 
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️
Flags with carried forward coverage won't be shown. Click here to find out more.
Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)
... and 1 file with indirect coverage changes
@rwbaberrwbaber
mentioned this pull request
Jul 8, 2026
 Open

3 tasks
@ilan-goldilan-gold
changed the title
Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold
added this to the 1.12.3 milestone
Jul 8, 2026
@ilan-gold
ilan-gold
enabled auto-merge (squash)
July 8, 2026 14:04
@ilan-gold
ilan-gold
merged commit a7868fe
into
scverse:mainJul 8, 2026

16 of 18 checks passed

@meeseeksmachinemeeseeksmachine
mentioned this pull request
Jul 8, 2026
 Merged

flying-sheep pushed a commit
that referenced
this pull request
Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold

, '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
chore: stale AnnData.concatenate references - #4201
Merged
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged
chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Conversation
@rwbaber
@rwbaberrwbaber
commented
Jul 8, 2026

Copy link


Copy Markdown

Contributor
This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.
Changes:
  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  •  Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.
@codecov
codecovBot
commented
Jul 8, 2026•

edited

Loading

Copy link


Copy Markdown

Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).

✅ All tests successful. No failed tests found.
Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1 
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️
Flags with carried forward coverage won't be shown. Click here to find out more.
Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)
... and 1 file with indirect coverage changes
@rwbaberrwbaber
mentioned this pull request
Jul 8, 2026
 Open

3 tasks
@ilan-goldilan-gold
changed the title
Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold
added this to the 1.12.3 milestone
Jul 8, 2026
@ilan-gold
ilan-gold
enabled auto-merge (squash)
July 8, 2026 14:04
@ilan-gold
ilan-gold
merged commit a7868fe
into
scverse:mainJul 8, 2026

16 of 18 checks passed

@meeseeksmachinemeeseeksmachine
mentioned this pull request
Jul 8, 2026
 Merged

flying-sheep pushed a commit
that referenced
this pull request
Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold

, '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
chore: stale AnnData.concatenate references - #4201
Merged
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Jul 8, 2026
Merged
chore: stale AnnData.concatenate references#4201
ilan-gold merged 2 commits into
scverse:mainfrom 
rwbaber:doc/fix-stale-concatenate-links
Conversation
@rwbaber
@rwbaberrwbaber
commented
Jul 8, 2026

Copy link


Copy Markdown

Contributor
This PR fixes stale references to AnnData.concatenate, which was removed from anndata (scverse/anndata#2370) and is no longer available in the hosted intersphinx inventory. These stale references were causing the Read the Docs build to fail.
Changes:
  • Replace broken Sphinx AnnData.concatenate method links with plain literal text.
  • Update the Harmony time-series example and test to use anndata.concat.
  • Preserve the previous unique-index behavior with index_unique="-".
  •  Closes #
  • Tests included or not required because:
  • Release notes not necessary because: this is just a fix for stale historical references caused by an upstream anndata API removal.
@codecov
codecovBot
commented
Jul 8, 2026•

edited

Loading

Copy link


Copy Markdown

Codecov Report
✅ All modified and coverable lines are covered by tests.

✅ Project coverage is 79.87%. Comparing base (af6de2e) to head (860ac8f).

✅ All tests successful. No failed tests found.
Additional details and impacted files
@@ Coverage Diff @@## main #4201 +/- ##
==========================================
- Coverage 79.87% 79.87% -0.01% 
==========================================
Files 121 121 Lines 12932 12932 ==========================================
- Hits 10330 10329 -1 - Misses 2602 2603 +1 
FlagCoverage Δ
hatch-test.low-vers78.97% <ø> (-0.04%)⬇️
hatch-test.pre79.82% <ø> (-0.01%)⬇️
Flags with carried forward coverage won't be shown. Click here to find out more.
Files with missing linesCoverage Δ
src/scanpy/external/pp/_mnn_correct.py22.22% <ø> (ø)
src/scanpy/external/tl/_harmony_timeseries.py28.57% <ø> (ø)
... and 1 file with indirect coverage changes
@rwbaberrwbaber
mentioned this pull request
Jul 8, 2026
 Open

3 tasks
@ilan-goldilan-gold
changed the title
Fix stale AnnData.concatenate referenceschore: stale AnnData.concatenate referencesJul 8, 2026
@ilan-goldilan-gold
added this to the 1.12.3 milestone
Jul 8, 2026
@ilan-gold
ilan-gold
enabled auto-merge (squash)
July 8, 2026 14:04
@ilan-gold
ilan-gold
merged commit a7868fe
into
scverse:mainJul 8, 2026

16 of 18 checks passed

@meeseeksmachinemeeseeksmachine
mentioned this pull request
Jul 8, 2026
 Merged

flying-sheep pushed a commit
that referenced
this pull request
Jul 8, 2026
@meeseeksmachine@rwbaber
Backport PR#4201on branch 1.12.x (chore: stale AnnData.concatenate …
5989241
…references) (#4203)
Co-authored-by: rwbaber <97636743+rwbaber@users.noreply.github.com>
Sign up for freeto join this conversation on GitHub.
Already have an account?
Sign in to comment

Reviewers


No reviews


Assignees


No one assigned


Labels


None yet


Projects


None yet


Milestone

1.12.3

Development

Successfully merging this pull request may close these issues.

2 participants

@rwbaber@ilan-gold