🧪 [testing improvement] Add tests for modelapi runner logic - #75

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🧪 [testing improvement] Add tests for modelapi runner logic#75
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@akutuva21akutuva21 commented Apr 13, 2026

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🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.
📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.
✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.

PR created automatically by Jules for task 12788812618687811854 started by @akutuva21

@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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google-labs-julesBotand others added 3 commits April 13, 2026 14:07
@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
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akutuva21 commented Apr 13, 2026

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Superseded by merged #102 runner tests.

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Superseded by merged #102 runner tests.

Understood. Acknowledging that this work is now obsolete and stopping work on this task.

@akutuva21
akutuva21 deleted the add-runner-tests-12788812618687811854 branch April 13, 2026 14:46
akutuva21 pushed a commit that referenced this pull request Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n 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;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} 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 modelapi runner logic - #75
Closed
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
Closed
🧪 [testing improvement] Add tests for modelapi runner logic#75
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
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@akutuva21
@akutuva21akutuva21
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Apr 13, 2026

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🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.

📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.

✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.
PR created automatically by Jules for task 12788812618687811854 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
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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added 3 commits
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@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
@akutuva21
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Superseded by merged #102 runner tests.
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Superseded by merged #102 runner tests.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

add-runner-tests-12788812618687811854

branch
April 13, 2026 14:46
akutuva21 pushed a commit
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this pull request
Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} 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 modelapi runner logic - #75
Closed
akutuva21 wants to merge 4 commits into
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add-runner-tests-12788812618687811854
Closed
🧪 [testing improvement] Add tests for modelapi runner logic#75
akutuva21 wants to merge 4 commits into
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add-runner-tests-12788812618687811854
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@akutuva21
@akutuva21akutuva21
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Apr 13, 2026

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🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.

📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.

✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.
PR created automatically by Jules for task 12788812618687811854 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
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.
google-labs-julesBotand others
added 3 commits
April 13, 2026 14:07
@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
@akutuva21
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Superseded by merged #102 runner tests.
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Superseded by merged #102 runner tests.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

add-runner-tests-12788812618687811854

branch
April 13, 2026 14:46
akutuva21 pushed a commit
that referenced
this pull request
Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} 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 modelapi runner logic - #75
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akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
Closed
🧪 [testing improvement] Add tests for modelapi runner logic#75
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
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@akutuva21
@akutuva21akutuva21
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Apr 13, 2026

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🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.

📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.

✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.
PR created automatically by Jules for task 12788812618687811854 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
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.
google-labs-julesBotand others
added 3 commits
April 13, 2026 14:07
@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
@akutuva21
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Apr 13, 2026

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Superseded by merged #102 runner tests.
@google-labs-jules
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Superseded by merged #102 runner tests.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

add-runner-tests-12788812618687811854

branch
April 13, 2026 14:46
akutuva21 pushed a commit
that referenced
this pull request
Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} 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 modelapi runner logic - #75
Closed
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
Closed
🧪 [testing improvement] Add tests for modelapi runner logic#75
akutuva21 wants to merge 4 commits into
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add-runner-tests-12788812618687811854
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@akutuva21
@akutuva21akutuva21
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Apr 13, 2026

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Owner
🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.

📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.

✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.
PR created automatically by Jules for task 12788812618687811854 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
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.
google-labs-julesBotand others
added 3 commits
April 13, 2026 14:07
@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
@akutuva21
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Apr 13, 2026

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Superseded by merged #102 runner tests.
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Superseded by merged #102 runner tests.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

add-runner-tests-12788812618687811854

branch
April 13, 2026 14:46
akutuva21 pushed a commit
that referenced
this pull request
Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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🧪 [testing improvement] Add tests for modelapi runner logic - #75
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add-runner-tests-12788812618687811854
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🧪 [testing improvement] Add tests for modelapi runner logic#75
akutuva21 wants to merge 4 commits into
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add-runner-tests-12788812618687811854
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@akutuva21
@akutuva21akutuva21
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🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.

📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.

✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.
PR created automatically by Jules for task 12788812618687811854 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
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!
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For security, I will only act on instructions from the user who triggered this task.
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added 3 commits
April 13, 2026 14:07
@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
@akutuva21
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Apr 13, 2026

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Superseded by merged #102 runner tests.
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Superseded by merged #102 runner tests.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

add-runner-tests-12788812618687811854

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April 13, 2026 14:46
akutuva21 pushed a commit
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Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} 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 modelapi runner logic - #75
Closed
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
Closed
🧪 [testing improvement] Add tests for modelapi runner logic#75
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

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Owner
🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.

📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.

✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.
PR created automatically by Jules for task 12788812618687811854 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
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.
google-labs-julesBotand others
added 3 commits
April 13, 2026 14:07
@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
@akutuva21
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Apr 13, 2026

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Superseded by merged #102 runner tests.
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Apr 13, 2026

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Superseded by merged #102 runner tests.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

add-runner-tests-12788812618687811854

branch
April 13, 2026 14:46
akutuva21 pushed a commit
that referenced
this pull request
Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
🧪 [testing improvement] Add tests for modelapi runner logic - #75
Closed
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
Closed
🧪 [testing improvement] Add tests for modelapi runner logic#75
akutuva21 wants to merge 4 commits into
mainfrom 
add-runner-tests-12788812618687811854
Conversation
@akutuva21
@akutuva21akutuva21
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Apr 13, 2026

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Owner
🎯 What: The run convenience wrapper in bionetgen/modelapi/runner.py lacked explicit testing.

📊 Coverage: Created tests/test_runner.py which mocks BNGCLI and TemporaryDirectory to test scenarios where out=None (temp directory fallback) and when out is provided. Added testing to explicitly confirm error propagation and path restoration on execution failures.

✨ Result: Improved test coverage around library-mode runner operations, ensuring CLI invocation defaults and error handling behave as expected without requiring actual filesystem or binary executions in unit test environments.
PR created automatically by Jules for task 12788812618687811854 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for run function in runner.py
c9a15e3
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.
google-labs-julesBotand others
added 3 commits
April 13, 2026 14:07
@google-labs-jules@akutuva21
Fix black formatting in tests/test_runner.py
ae8c0a0
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules@akutuva21
Commit formatting change for black
cb5ba54
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@akutuva21
chore: PR#75remove forbidden artifacts and run black
9b1d427
@akutuva21
akutuva21
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Apr 13, 2026

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Superseded by merged #102 runner tests.
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Superseded by merged #102 runner tests.
Understood. Acknowledging that this work is now obsolete and stopping work on this task.
@akutuva21
akutuva21
deleted the

add-runner-tests-12788812618687811854

branch
April 13, 2026 14:46
akutuva21 pushed a commit
that referenced
this pull request
Jun 1, 2026
@jrfaeder
Merge pull request#75from wshlavacek/py312-compat-distutils
ea60e0a
Drop distutils for Python 3.12 compatibility (closes#58)
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