🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551

Merged
akutuva21 merged 2 commits into
mainfrom
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged

🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom
test-improvement-repl-18377354034072662518

Conversation

@akutuva21

@akutuva21akutuva21 commented Jun 15, 2026

Copy link
Copy Markdown
Owner

🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.

📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.

✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.

PR created automatically by Jules for task 18377354034072662518 started by @akutuva21

@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

google-labs-julesBot commented Jun 15, 2026

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 marked this pull request as ready for review June 16, 2026 14:57
@akutuva21
akutuva21 merged commit 1f7af3d into mainJun 16, 2026
1 check passed
@akutuva21
akutuva21 deleted the test-improvement-repl-18377354034072662518 branch July 20, 2026 17:52
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

@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
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551
Merged
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

Copy link


Copy Markdown

Owner
🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.
📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.
✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.
PR created automatically by Jules for task 18377354034072662518 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Jun 15, 2026

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
marked this pull request as ready for review
June 16, 2026 14:57
@akutuva21
akutuva21
merged commit 1f7af3d
into
mainJun 16, 2026

1 check passed

@akutuva21
akutuva21
deleted the

test-improvement-repl-18377354034072662518

branch
July 20, 2026 17:52
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

@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
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551
Merged
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

Copy link


Copy Markdown

Owner
🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.
📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.
✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.
PR created automatically by Jules for task 18377354034072662518 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Jun 15, 2026

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
marked this pull request as ready for review
June 16, 2026 14:57
@akutuva21
akutuva21
merged commit 1f7af3d
into
mainJun 16, 2026

1 check passed

@akutuva21
akutuva21
deleted the

test-improvement-repl-18377354034072662518

branch
July 20, 2026 17:52
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

@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
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551
Merged
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

Copy link


Copy Markdown

Owner
🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.
📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.
✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.
PR created automatically by Jules for task 18377354034072662518 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Jun 15, 2026

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
marked this pull request as ready for review
June 16, 2026 14:57
@akutuva21
akutuva21
merged commit 1f7af3d
into
mainJun 16, 2026

1 check passed

@akutuva21
akutuva21
deleted the

test-improvement-repl-18377354034072662518

branch
July 20, 2026 17:52
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

@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
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551
Merged
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

Copy link


Copy Markdown

Owner
🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.
📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.
✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.
PR created automatically by Jules for task 18377354034072662518 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Jun 15, 2026

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
marked this pull request as ready for review
June 16, 2026 14:57
@akutuva21
akutuva21
merged commit 1f7af3d
into
mainJun 16, 2026

1 check passed

@akutuva21
akutuva21
deleted the

test-improvement-repl-18377354034072662518

branch
July 20, 2026 17:52
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

@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
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551
Merged
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

Copy link


Copy Markdown

Owner
🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.
📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.
✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.
PR created automatically by Jules for task 18377354034072662518 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Jun 15, 2026

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
marked this pull request as ready for review
June 16, 2026 14:57
@akutuva21
akutuva21
merged commit 1f7af3d
into
mainJun 16, 2026

1 check passed

@akutuva21
akutuva21
deleted the

test-improvement-repl-18377354034072662518

branch
July 20, 2026 17:52
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

@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
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551
Merged
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

Copy link


Copy Markdown

Owner
🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.
📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.
✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.
PR created automatically by Jules for task 18377354034072662518 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Jun 15, 2026

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
marked this pull request as ready for review
June 16, 2026 14:57
@akutuva21
akutuva21
merged commit 1f7af3d
into
mainJun 16, 2026

1 check passed

@akutuva21
akutuva21
deleted the

test-improvement-repl-18377354034072662518

branch
July 20, 2026 17:52
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

@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
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function - #551
Merged
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Jun 16, 2026
Merged
🧪 Testing improvement: Add tests for _replace_nv_ith_s inner repl function#551
akutuva21 merged 2 commits into
mainfrom 
test-improvement-repl-18377354034072662518
Conversation
@akutuva21
@akutuva21akutuva21
commented
Jun 15, 2026

Copy link


Copy Markdown

Owner
🎯 What: Added tests to cover the untested repl inner method within _replace_nv_ith_s in bionetgen/modelapi/sympy_odes.py.
📊 Coverage: The new tests in tests/test_sympy_odes.py now cover all logic branches within _replace_nv_ith_s, including the "species", "expressions", "observables", "ratelaws", and "Dspecies" checks, as well as bounds checking and the unknown variable fallback.
✨ Result: Increased test reliability and coverage for the core ODE substitution logic, ensuring future refactoring won't silently break mathematical variable mappings. Extraneous scratchpad scripts created during development were also removed.
PR created automatically by Jules for task 18377354034072662518 started by @akutuva21
@google-labs-jules@akutuva21
Add tests for _replace_nv_ith_s inner repl function
2826a54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Jun 15, 2026

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
marked this pull request as ready for review
June 16, 2026 14:57
@akutuva21
akutuva21
merged commit 1f7af3d
into
mainJun 16, 2026

1 check passed

@akutuva21
akutuva21
deleted the

test-improvement-repl-18377354034072662518

branch
July 20, 2026 17:52
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

@akutuva21