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Keep User Cluster Colours if Possible - #359

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Keep User Cluster Colours if Possible#359
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@newmananewmana commented Jul 12, 2026

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Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.

@newmananewmana changed the title Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana

newmana commented Jul 12, 2026

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Fix for issue #356

@newmana
newmana merged commit f60364c into masterJul 12, 2026
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@newmana
newmana deleted the newmana/fix_plotting_colours branch July 12, 2026 09:19
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, '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" + '
Keep User Cluster Colours if Possible by newmana · Pull Request #359 · BiomedicalMachineLearning/stLearn · GitHub
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Keep User Cluster Colours if Possible - #359
Merged
newmana merged 2 commits into
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newmana/fix_plotting_colours
Jul 12, 2026
Merged
Keep User Cluster Colours if Possible#359
newmana merged 2 commits into
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newmana/fix_plotting_colours
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@newmana
@newmananewmana
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Jul 12, 2026

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Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.
@newmananewmana
changed the title
Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana
newmana
commented
Jul 12, 2026

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Fix for issue #356
@newmana
newmana
merged commit f60364c
into
masterJul 12, 2026

3 checks passed

@newmana
newmana
deleted the

newmana/fix_plotting_colours

branch
July 12, 2026 09:19
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, '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('^' + ".*" + '
Keep User Cluster Colours if Possible by newmana · Pull Request #359 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Keep User Cluster Colours if Possible - #359
Merged
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Jul 12, 2026
Merged
Keep User Cluster Colours if Possible#359
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
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@newmana
@newmananewmana
commented
Jul 12, 2026

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Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.
@newmananewmana
changed the title
Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana
newmana
commented
Jul 12, 2026

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CollaboratorAuthor
Fix for issue #356
@newmana
newmana
merged commit f60364c
into
masterJul 12, 2026

3 checks passed

@newmana
newmana
deleted the

newmana/fix_plotting_colours

branch
July 12, 2026 09:19
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, '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('^' + ".*" + '
Keep User Cluster Colours if Possible by newmana · Pull Request #359 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Keep User Cluster Colours if Possible - #359
Merged
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Jul 12, 2026
Merged
Keep User Cluster Colours if Possible#359
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
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@newmana
@newmananewmana
commented
Jul 12, 2026

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Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.
@newmananewmana
changed the title
Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana
newmana
commented
Jul 12, 2026

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CollaboratorAuthor
Fix for issue #356
@newmana
newmana
merged commit f60364c
into
masterJul 12, 2026

3 checks passed

@newmana
newmana
deleted the

newmana/fix_plotting_colours

branch
July 12, 2026 09:19
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, '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" + '
Keep User Cluster Colours if Possible by newmana · Pull Request #359 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Keep User Cluster Colours if Possible - #359
Merged
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Jul 12, 2026
Merged
Keep User Cluster Colours if Possible#359
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Conversation
@newmana
@newmananewmana
commented
Jul 12, 2026

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Collaborator
Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.
@newmananewmana
changed the title
Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana
newmana
commented
Jul 12, 2026

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CollaboratorAuthor
Fix for issue #356
@newmana
newmana
merged commit f60364c
into
masterJul 12, 2026

3 checks passed

@newmana
newmana
deleted the

newmana/fix_plotting_colours

branch
July 12, 2026 09:19
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@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('^' + ".*" + '
Keep User Cluster Colours if Possible by newmana · Pull Request #359 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Keep User Cluster Colours if Possible - #359
Merged
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Jul 12, 2026
Merged
Keep User Cluster Colours if Possible#359
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Conversation
@newmana
@newmananewmana
commented
Jul 12, 2026

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Collaborator
Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.
@newmananewmana
changed the title
Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana
newmana
commented
Jul 12, 2026

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CollaboratorAuthor
Fix for issue #356
@newmana
newmana
merged commit f60364c
into
masterJul 12, 2026

3 checks passed

@newmana
newmana
deleted the

newmana/fix_plotting_colours

branch
July 12, 2026 09:19
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@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('^' + ".*" + '
Keep User Cluster Colours if Possible by newmana · Pull Request #359 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Keep User Cluster Colours if Possible - #359
Merged
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Jul 12, 2026
Merged
Keep User Cluster Colours if Possible#359
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Conversation
@newmana
@newmananewmana
commented
Jul 12, 2026

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Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.
@newmananewmana
changed the title
Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana
newmana
commented
Jul 12, 2026

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CollaboratorAuthor
Fix for issue #356
@newmana
newmana
merged commit f60364c
into
masterJul 12, 2026

3 checks passed

@newmana
newmana
deleted the

newmana/fix_plotting_colours

branch
July 12, 2026 09:19
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@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); }
})();
})();
Keep User Cluster Colours if Possible by newmana · Pull Request #359 · BiomedicalMachineLearning/stLearn · GitHub
Skip to content
Keep User Cluster Colours if Possible - #359
Merged
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Jul 12, 2026
Merged
Keep User Cluster Colours if Possible#359
newmana merged 2 commits into
masterfrom 
newmana/fix_plotting_colours
Conversation
@newmana
@newmananewmana
commented
Jul 12, 2026

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Collaborator
Change behaviour of how we deal with user provided clustering colours - use to remove them all and regenerate to ensure we had the right number of colours. Now it will keep the user's colours and if there isn't enough add them to the end of list.
@newmananewmana
changed the title
Keep colours - if user supplies to few - add them - used to remove al…Keep User Cluster Colours if PossibleJul 12, 2026
@newmana
newmana
commented
Jul 12, 2026

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CollaboratorAuthor
Fix for issue #356
@newmana
newmana
merged commit f60364c
into
masterJul 12, 2026

3 checks passed

@newmana
newmana
deleted the

newmana/fix_plotting_colours

branch
July 12, 2026 09:19
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@newmana