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Refactor actionable unit split heuristic in analyzeSBML - #540

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refactor-split-heuristic-12583549134731861659
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Refactor actionable unit split heuristic in analyzeSBML#540
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refactor-split-heuristic-12583549134731861659

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Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.

PR created automatically by Jules for task 12583549134731861659 started by @akutuva21

@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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akutuva21 marked this pull request as ready for review June 16, 2026 15:13
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akutuva21 merged commit 37deb95 into mainJun 16, 2026
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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" + '
Refactor actionable unit split heuristic in analyzeSBML by akutuva21 · Pull Request #540 · akutuva21/PyBioNetGen · GitHub
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Refactor actionable unit split heuristic in analyzeSBML - #540
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akutuva21 merged 1 commit into
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refactor-split-heuristic-12583549134731861659
Jun 16, 2026
Merged
Refactor actionable unit split heuristic in analyzeSBML#540
akutuva21 merged 1 commit into
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refactor-split-heuristic-12583549134731861659
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Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.
PR created automatically by Jules for task 12583549134731861659 started by @akutuva21
@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
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For security, I will only act on instructions from the user who triggered this task.
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marked this pull request as ready for review
June 16, 2026 15:13
@akutuva21
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merged commit 37deb95
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refactor-split-heuristic-12583549134731861659

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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('^' + ".*" + '
Refactor actionable unit split heuristic in analyzeSBML by akutuva21 · Pull Request #540 · akutuva21/PyBioNetGen · GitHub
Skip to content
Refactor actionable unit split heuristic in analyzeSBML - #540
Merged
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
Jun 16, 2026
Merged
Refactor actionable unit split heuristic in analyzeSBML#540
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
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Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.
PR created automatically by Jules for task 12583549134731861659 started by @akutuva21
@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
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For security, I will only act on instructions from the user who triggered this task.
@akutuva21
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marked this pull request as ready for review
June 16, 2026 15:13
@akutuva21
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merged commit 37deb95
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mainJun 16, 2026

18 checks passed

@akutuva21
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deleted the

refactor-split-heuristic-12583549134731861659

branch
July 20, 2026 17:52
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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('^' + ".*" + '
Refactor actionable unit split heuristic in analyzeSBML by akutuva21 · Pull Request #540 · akutuva21/PyBioNetGen · GitHub
Skip to content
Refactor actionable unit split heuristic in analyzeSBML - #540
Merged
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
Jun 16, 2026
Merged
Refactor actionable unit split heuristic in analyzeSBML#540
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
Conversation
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Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.
PR created automatically by Jules for task 12583549134731861659 started by @akutuva21
@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
@akutuva21
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marked this pull request as ready for review
June 16, 2026 15:13
@akutuva21
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merged commit 37deb95
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mainJun 16, 2026

18 checks passed

@akutuva21
akutuva21
deleted the

refactor-split-heuristic-12583549134731861659

branch
July 20, 2026 17:52
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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" + '
Refactor actionable unit split heuristic in analyzeSBML by akutuva21 · Pull Request #540 · akutuva21/PyBioNetGen · GitHub
Skip to content
Refactor actionable unit split heuristic in analyzeSBML - #540
Merged
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
Jun 16, 2026
Merged
Refactor actionable unit split heuristic in analyzeSBML#540
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
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Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.
PR created automatically by Jules for task 12583549134731861659 started by @akutuva21
@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
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For security, I will only act on instructions from the user who triggered this task.
@akutuva21
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marked this pull request as ready for review
June 16, 2026 15:13
@akutuva21
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merged commit 37deb95
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18 checks passed

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deleted the

refactor-split-heuristic-12583549134731861659

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, '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('^' + ".*" + '
Refactor actionable unit split heuristic in analyzeSBML by akutuva21 · Pull Request #540 · akutuva21/PyBioNetGen · GitHub
Skip to content
Refactor actionable unit split heuristic in analyzeSBML - #540
Merged
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
Jun 16, 2026
Merged
Refactor actionable unit split heuristic in analyzeSBML#540
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
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Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.
PR created automatically by Jules for task 12583549134731861659 started by @akutuva21
@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
@akutuva21
akutuva21
marked this pull request as ready for review
June 16, 2026 15:13
@akutuva21
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merged commit 37deb95
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mainJun 16, 2026

18 checks passed

@akutuva21
akutuva21
deleted the

refactor-split-heuristic-12583549134731861659

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July 20, 2026 17:52
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, '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('^' + ".*" + '
Refactor actionable unit split heuristic in analyzeSBML by akutuva21 · Pull Request #540 · akutuva21/PyBioNetGen · GitHub
Skip to content
Refactor actionable unit split heuristic in analyzeSBML - #540
Merged
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
Jun 16, 2026
Merged
Refactor actionable unit split heuristic in analyzeSBML#540
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
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Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.
PR created automatically by Jules for task 12583549134731861659 started by @akutuva21
@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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June 16, 2026 15:13
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, 'i');
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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;
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/* 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; }
';
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var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
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if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
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console.log('[Universal Dark Mode] Disabled');
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if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
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observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
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} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Refactor actionable unit split heuristic in analyzeSBML by akutuva21 · Pull Request #540 · akutuva21/PyBioNetGen · GitHub
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Refactor actionable unit split heuristic in analyzeSBML - #540
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refactor-split-heuristic-12583549134731861659
Jun 16, 2026
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Refactor actionable unit split heuristic in analyzeSBML#540
akutuva21 merged 1 commit into
mainfrom 
refactor-split-heuristic-12583549134731861659
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

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Owner
Refactored the split heuristic in analyzeSBML.py when actionable unit extraction natively fails. It now checks for direct matches or uses greedyModificationMatching() before falling back to string splitting.
PR created automatically by Jules for task 12583549134731861659 started by @akutuva21
@google-labs-jules@akutuva21
Refactor split heuristic using greedyModificationMatching
9b7a270
Instead of doing a simple split by `_` when extracting actionable units, we now compare against `strippedMolecules` and split by smallest actionable units utilizing `self.greedyModificationMatching()`. If `greedyModificationMatching()` fails to find a valid match, we fall back to splitting the string by `_`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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Jun 15, 2026

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👋 Jules, reporting for duty! I'm here to lend a hand with this pull request.
When you start a review, I'll add a 👀 emoji to each comment to let you know I've read it. I'll focus on feedback directed at me and will do my best to stay out of conversations between you and other bots or reviewers to keep the noise down.
I'll push a commit with your requested changes shortly after. Please note there might be a delay between these steps, but rest assured I'm on the job!
For more direct control, you can switch me to Reactive Mode. When this mode is on, I will only act on comments where you specifically mention me with @jules. You can find this option in the Pull Request section of your global Jules UI settings. You can always switch back!
New to Jules? Learn more at jules.google/docs.
For security, I will only act on instructions from the user who triggered this task.
@akutuva21
akutuva21
marked this pull request as ready for review
June 16, 2026 15:13
@akutuva21
akutuva21
merged commit 37deb95
into
mainJun 16, 2026

18 checks passed

@akutuva21
akutuva21
deleted the

refactor-split-heuristic-12583549134731861659

branch
July 20, 2026 17:52
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