Skip to content

Subset of anndata leads to broken graph connectivity - #354

Merged
newmana merged 4 commits into
masterfrom
newmana/fix_paths
Jun 26, 2026
Merged

Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom
newmana/fix_paths

Conversation

@newmana

@newmananewmana commented Jun 26, 2026•
edited
Loading

Copy link
Copy Markdown
Collaborator

This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.

Changes:

  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.

Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.

@newmana
newmana merged commit 4dd71bc into masterJun 26, 2026
3 checks passed
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

No milestone

Development

Successfully merging this pull request may close these issues.

1 participant

@newmana
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
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;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Subset of anndata leads to broken graph connectivity by newmana · Pull Request #354 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Subset of anndata leads to broken graph connectivity  - #354
Merged
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Jun 26, 2026
Merged
Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Conversation
@newmana
@newmananewmana
commented
Jun 26, 2026•

edited

Loading

Copy link


Copy Markdown

Collaborator
This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.
Changes:
  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.
Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.
@newmana
newmana
merged commit 4dd71bc
into
masterJun 26, 2026

3 checks passed

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


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@newmana

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Subset of anndata leads to broken graph connectivity by newmana · Pull Request #354 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Subset of anndata leads to broken graph connectivity  - #354
Merged
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Jun 26, 2026
Merged
Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Conversation
@newmana
@newmananewmana
commented
Jun 26, 2026•

edited

Loading

Copy link


Copy Markdown

Collaborator
This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.
Changes:
  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.
Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.
@newmana
newmana
merged commit 4dd71bc
into
masterJun 26, 2026

3 checks passed

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


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@newmana

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Subset of anndata leads to broken graph connectivity by newmana · Pull Request #354 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Subset of anndata leads to broken graph connectivity  - #354
Merged
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Jun 26, 2026
Merged
Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Conversation
@newmana
@newmananewmana
commented
Jun 26, 2026•

edited

Loading

Copy link


Copy Markdown

Collaborator
This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.
Changes:
  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.
Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.
@newmana
newmana
merged commit 4dd71bc
into
masterJun 26, 2026

3 checks passed

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


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@newmana

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
Subset of anndata leads to broken graph connectivity by newmana · Pull Request #354 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Subset of anndata leads to broken graph connectivity  - #354
Merged
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Jun 26, 2026
Merged
Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Conversation
@newmana
@newmananewmana
commented
Jun 26, 2026•

edited

Loading

Copy link


Copy Markdown

Collaborator
This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.
Changes:
  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.
Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.
@newmana
newmana
merged commit 4dd71bc
into
masterJun 26, 2026

3 checks passed

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


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@newmana

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Subset of anndata leads to broken graph connectivity by newmana · Pull Request #354 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Subset of anndata leads to broken graph connectivity  - #354
Merged
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Jun 26, 2026
Merged
Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Conversation
@newmana
@newmananewmana
commented
Jun 26, 2026•

edited

Loading

Copy link


Copy Markdown

Collaborator
This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.
Changes:
  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.
Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.
@newmana
newmana
merged commit 4dd71bc
into
masterJun 26, 2026

3 checks passed

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


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@newmana

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
Subset of anndata leads to broken graph connectivity by newmana · Pull Request #354 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Subset of anndata leads to broken graph connectivity  - #354
Merged
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Jun 26, 2026
Merged
Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Conversation
@newmana
@newmananewmana
commented
Jun 26, 2026•

edited

Loading

Copy link


Copy Markdown

Collaborator
This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.
Changes:
  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.
Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.
@newmana
newmana
merged commit 4dd71bc
into
masterJun 26, 2026

3 checks passed

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


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@newmana

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Subset of anndata leads to broken graph connectivity by newmana · Pull Request #354 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Subset of anndata leads to broken graph connectivity  - #354
Merged
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Jun 26, 2026
Merged
Subset of anndata leads to broken graph connectivity #354
newmana merged 4 commits into
masterfrom 
newmana/fix_paths
Conversation
@newmana
@newmananewmana
commented
Jun 26, 2026•

edited

Loading

Copy link


Copy Markdown

Collaborator
This fixes issue #340 - the cause is that the graph can be disconnected when subsetted and kNN needs to be re-calculated.
Changes:
  • Calling pseudotime without a kNN causes an error - requires it to be run first.
  • When AnnData is subset the neighbourhood graph can become disconnected and running pseudotime on it creates NaN/Infinite distance nodes - both were kept in the old code - in the new code any node touching these will be removed.
  • The fall through if there is equal pseudotime is arbitrary - just picks the node with lowest node number.
Also added some small changes around Xenium data downloading - start of support for zarr in zips and files in subdirectories.
@newmana
newmana
merged commit 4dd71bc
into
masterJun 26, 2026

3 checks passed

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


No milestone


Development

Successfully merging this pull request may close these issues.

1 participant

@newmana