🧪 [Add tests for bionetgen.modelapi.runner.run] - #102

Merged
akutuva21 merged 2 commits into
mainfrom
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged

🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom
testing-improvement-runner-15698129411844816542

Conversation

@akutuva21

@akutuva21akutuva21 commented Apr 13, 2026

Copy link
Copy Markdown
Owner

🎯 What: The testing gap addressed
This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.

📊 Coverage: What scenarios are now tested

  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.

✨ Result: The improvement in test coverage
The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.

PR created automatically by Jules for task 15698129411844816542 started by @akutuva21

@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules

google-labs-julesBot commented Apr 13, 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 merged commit 7b29521 into mainApr 13, 2026
14 of 18 checks passed
@akutuva21
akutuva21 deleted the testing-improvement-runner-15698129411844816542 branch April 13, 2026 14:26
This was referenced Apr 13, 2026
Closed
Closed
akutuva21 pushed a commit that referenced this pull request Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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)) { 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
🧪 [Add tests for bionetgen.modelapi.runner.run] - #102
Merged
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged
🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

Copy link


Copy Markdown

Owner
🎯 What: The testing gap addressed

This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.
📊 Coverage: What scenarios are now tested
  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.
✨ Result: The improvement in test coverage

The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.
PR created automatically by Jules for task 15698129411844816542 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 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
merged commit 7b29521
into
mainApr 13, 2026

14 of 18 checks passed

@akutuva21
akutuva21
deleted the

testing-improvement-runner-15698129411844816542

branch
April 13, 2026 14:26

This was referenced Apr 13, 2026
 Closed

 Closed

akutuva21 pushed a commit
that referenced
this pull request
Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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)) {
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
🧪 [Add tests for bionetgen.modelapi.runner.run] - #102
Merged
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged
🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

Copy link


Copy Markdown

Owner
🎯 What: The testing gap addressed

This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.
📊 Coverage: What scenarios are now tested
  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.
✨ Result: The improvement in test coverage

The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.
PR created automatically by Jules for task 15698129411844816542 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 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
merged commit 7b29521
into
mainApr 13, 2026

14 of 18 checks passed

@akutuva21
akutuva21
deleted the

testing-improvement-runner-15698129411844816542

branch
April 13, 2026 14:26

This was referenced Apr 13, 2026
 Closed

 Closed

akutuva21 pushed a commit
that referenced
this pull request
Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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)) {
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
🧪 [Add tests for bionetgen.modelapi.runner.run] - #102
Merged
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged
🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

Copy link


Copy Markdown

Owner
🎯 What: The testing gap addressed

This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.
📊 Coverage: What scenarios are now tested
  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.
✨ Result: The improvement in test coverage

The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.
PR created automatically by Jules for task 15698129411844816542 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 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
merged commit 7b29521
into
mainApr 13, 2026

14 of 18 checks passed

@akutuva21
akutuva21
deleted the

testing-improvement-runner-15698129411844816542

branch
April 13, 2026 14:26

This was referenced Apr 13, 2026
 Closed

 Closed

akutuva21 pushed a commit
that referenced
this pull request
Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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)) {
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
🧪 [Add tests for bionetgen.modelapi.runner.run] - #102
Merged
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged
🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

Copy link


Copy Markdown

Owner
🎯 What: The testing gap addressed

This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.
📊 Coverage: What scenarios are now tested
  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.
✨ Result: The improvement in test coverage

The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.
PR created automatically by Jules for task 15698129411844816542 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 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
merged commit 7b29521
into
mainApr 13, 2026

14 of 18 checks passed

@akutuva21
akutuva21
deleted the

testing-improvement-runner-15698129411844816542

branch
April 13, 2026 14:26

This was referenced Apr 13, 2026
 Closed

 Closed

akutuva21 pushed a commit
that referenced
this pull request
Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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)) {
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('^' + ".*" + '

Skip to content
🧪 [Add tests for bionetgen.modelapi.runner.run] - #102
Merged
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged
🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

Copy link


Copy Markdown

Owner
🎯 What: The testing gap addressed

This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.
📊 Coverage: What scenarios are now tested
  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.
✨ Result: The improvement in test coverage

The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.
PR created automatically by Jules for task 15698129411844816542 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 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
merged commit 7b29521
into
mainApr 13, 2026

14 of 18 checks passed

@akutuva21
akutuva21
deleted the

testing-improvement-runner-15698129411844816542

branch
April 13, 2026 14:26

This was referenced Apr 13, 2026
 Closed

 Closed

akutuva21 pushed a commit
that referenced
this pull request
Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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)) {
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
🧪 [Add tests for bionetgen.modelapi.runner.run] - #102
Merged
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged
🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

Copy link


Copy Markdown

Owner
🎯 What: The testing gap addressed

This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.
📊 Coverage: What scenarios are now tested
  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.
✨ Result: The improvement in test coverage

The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.
PR created automatically by Jules for task 15698129411844816542 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 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
merged commit 7b29521
into
mainApr 13, 2026

14 of 18 checks passed

@akutuva21
akutuva21
deleted the

testing-improvement-runner-15698129411844816542

branch
April 13, 2026 14:26

This was referenced Apr 13, 2026
 Closed

 Closed

akutuva21 pushed a commit
that referenced
this pull request
Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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)) {
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
🧪 [Add tests for bionetgen.modelapi.runner.run] - #102
Merged
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Apr 13, 2026
Merged
🧪 [Add tests for bionetgen.modelapi.runner.run]#102
akutuva21 merged 2 commits into
mainfrom 
testing-improvement-runner-15698129411844816542
Conversation
@akutuva21
@akutuva21akutuva21
commented
Apr 13, 2026

Copy link


Copy Markdown

Owner
🎯 What: The testing gap addressed

This PR provides test coverage for the previously untested run function in bionetgen.modelapi.runner.py. The run function acts as a wrapper around the BNGCLI object. Additionally, some test dependencies that were completely broken in Python 3.12 due to the removal of distutils were patched to fallback to standard libraries (shutil), enabling the test suite to run.
📊 Coverage: What scenarios are now tested
  1. Calling run(inp, out=...) explicitly with an output directory.
  2. Calling run(inp) without providing an output directory, testing the temp dir context logic.
  3. Simulating an exception during cli.run(), ensuring that os.chdir() cleans up the working directory and the exception is appropriately raised.
✨ Result: The improvement in test coverage

The core flow of the modelapi.runner.run utility is now robustly tested, safeguarding against regressions. Additionally, the test suite is now significantly more robust to run in modern Python >=3.12 versions.
PR created automatically by Jules for task 15698129411844816542 started by @akutuva21
@google-labs-jules@akutuva21
Add unit tests for bionetgen.modelapi.runner.run
1da7dbf
- Implemented tests using `unittest.mock` to stub out `BNGCLI` and `TemporaryDirectory`.
- Added tests covering happy path (with out dir, without out dir) and exception flow.
- Added a compatibility fix in `csimulator.py` and `utils.py` for Python 3.12, replacing `distutils` with standard library equivalents (`shutil`).
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
@google-labs-jules
google-labs-julesBot
commented
Apr 13, 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
merged commit 7b29521
into
mainApr 13, 2026

14 of 18 checks passed

@akutuva21
akutuva21
deleted the

testing-improvement-runner-15698129411844816542

branch
April 13, 2026 14:26

This was referenced Apr 13, 2026
 Closed

 Closed

akutuva21 pushed a commit
that referenced
this pull request
Jun 5, 2026
@jrfaeder
Merge pull request#102from wshlavacek/pr66-bngsim-integration
5109a46
Optional BNGsim integration: in-process simulation + multi-format input
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