chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21
, '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" + '
Skip to content

chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21
, '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('^' + ".*" + '
Skip to content

chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21
, '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('^' + ".*" + '
Skip to content

chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21
, '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" + '
Skip to content

chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21
, '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('^' + ".*" + '
Skip to content

chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21
, '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('^' + ".*" + '
Skip to content

chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21
, '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); } })(); })();
Skip to content

chore: Restructure RuleHub directories and improve metadata categories - #1

Merged
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453
Mar 31, 2026
Merged

chore: Restructure RuleHub directories and improve metadata categories#1
akutuva21 merged 1 commit into
masterfrom
refactor-categories-635465190162969453

Conversation

@akutuva21

Copy link
Copy Markdown
Owner

This PR refactors the RuleHub directory structure and updates metadata categories according to the latest requirements.

Key Changes

  1. Restructured Top-Level Directories: Simplified the repository to mainly three directories: Published, Examples, and Tutorials.
  2. Reorganized Models:
    • Moved AI-generated playground examples to the new Examples directory.
    • Moved previously grouped PyBioNetGen published models to Published/PyBioNetGen.
    • Moved all published models adhering to the AuthorYear format from Contributed/ to Published/.
    • Re-distributed BNGPlayground_Validation models based on their origin (published vs. tutorials).
  3. Updated Metadata and Categories:
    • Addressed models grouped ambiguously under "category: other".
    • Introduced descriptive categories (mechanistic-modeling, feature-demos, compartments, wacky, energy, etc.) to the metadata-schema.yaml.
    • Updated corresponding metadata.yaml files.
  4. Updated Scripts:
    • generate-manifest.js and validate-metadata.js modified to scan the new root directories.
  5. Validation and Generation: Re-ran the manifest generation to reflect the correct paths and categories.

PR created automatically by Jules for task 635465190162969453 started by @akutuva21

- Create \`Examples\`, \`Published\`, and \`Tutorials\` root directories.
- Move \`Contributed/BNGPlayground_Examples\` to \`Examples\`.
- Move published model subdirectories (e.g., PyBioNetGen models, Contributed/Hlavacek2018, Contributed/Mitra2019, Validation models like Korwek2023, MyrtleBeach) to \`Published\`.
- Move remaining items in \`Contributed/BNGPlayground_Validation\` and \`BNGPlayground_PublicRuntime\` to \`Tutorials\`.
- Update \`metadata-schema.yaml\` to add explicit domains (\`compartments\`, \`energy\`, \`wacky\`, \`mechanistic-modeling\`, etc.).
- Update \`metadata.yaml\` files previously labeled as \`other\` with the new, specific categories.
- Update \`scripts/generate-manifest.js\` and \`scripts/validate-metadata.js\` with new \`SEARCH_ROOTS\` and categories.
- Regenerate \`manifest.json\`.
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

Copy link
Copy Markdown

👋 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 merged commit b2ad06c into masterMar 31, 2026
1 check passed
@akutuva21
akutuva21 deleted the refactor-categories-635465190162969453 branch March 31, 2026 22:58
Sign up for freeto join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant

@akutuva21