Fix nbopen standard output and error handling in notebook generation - #89

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fix-nbopen-stdout-stderr-4118980527979395642
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Fix nbopen standard output and error handling in notebook generation#89
akutuva21 merged 2 commits into
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fix-nbopen-stdout-stderr-4118980527979395642

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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.

PR created automatically by Jules for task 4118980527979395642 started by @akutuva21

@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Fix nbopen standard output and error handling in notebook generation - #89
Merged
akutuva21 merged 2 commits into
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fix-nbopen-stdout-stderr-4118980527979395642
Apr 13, 2026
Merged
Fix nbopen standard output and error handling in notebook generation#89
akutuva21 merged 2 commits into
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fix-nbopen-stdout-stderr-4118980527979395642
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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.
PR created automatically by Jules for task 4118980527979395642 started by @akutuva21
@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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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");
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} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Fix nbopen standard output and error handling in notebook generation - #89
Merged
akutuva21 merged 2 commits into
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fix-nbopen-stdout-stderr-4118980527979395642
Apr 13, 2026
Merged
Fix nbopen standard output and error handling in notebook generation#89
akutuva21 merged 2 commits into
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fix-nbopen-stdout-stderr-4118980527979395642
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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.
PR created automatically by Jules for task 4118980527979395642 started by @akutuva21
@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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merged commit 5e4fbe4
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@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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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('^' + ".*" + '

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Fix nbopen standard output and error handling in notebook generation - #89
Merged
akutuva21 merged 2 commits into
mainfrom 
fix-nbopen-stdout-stderr-4118980527979395642
Apr 13, 2026
Merged
Fix nbopen standard output and error handling in notebook generation#89
akutuva21 merged 2 commits into
mainfrom 
fix-nbopen-stdout-stderr-4118980527979395642
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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.
PR created automatically by Jules for task 4118980527979395642 started by @akutuva21
@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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fix-nbopen-stdout-stderr-4118980527979395642

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akutuva21 pushed a commit
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@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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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" + '

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Fix nbopen standard output and error handling in notebook generation - #89
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fix-nbopen-stdout-stderr-4118980527979395642
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Fix nbopen standard output and error handling in notebook generation#89
akutuva21 merged 2 commits into
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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.
PR created automatically by Jules for task 4118980527979395642 started by @akutuva21
@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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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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Fix nbopen standard output and error handling in notebook generation - #89
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fix-nbopen-stdout-stderr-4118980527979395642
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Fix nbopen standard output and error handling in notebook generation#89
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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.
PR created automatically by Jules for task 4118980527979395642 started by @akutuva21
@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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akutuva21 pushed a commit
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@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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, 'i');
if (__m === '*' || __re.test(location.href)) {
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Fix nbopen standard output and error handling in notebook generation - #89
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fix-nbopen-stdout-stderr-4118980527979395642
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Fix nbopen standard output and error handling in notebook generation#89
akutuva21 merged 2 commits into
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fix-nbopen-stdout-stderr-4118980527979395642
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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.
PR created automatically by Jules for task 4118980527979395642 started by @akutuva21
@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
Co-authored-by: akutuva21 <44119804+akutuva21@users.noreply.github.com>
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@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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Skip to content
Fix nbopen standard output and error handling in notebook generation - #89
Merged
akutuva21 merged 2 commits into
mainfrom 
fix-nbopen-stdout-stderr-4118980527979395642
Apr 13, 2026
Merged
Fix nbopen standard output and error handling in notebook generation#89
akutuva21 merged 2 commits into
mainfrom 
fix-nbopen-stdout-stderr-4118980527979395642
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This commit resolves the TODO comment in bionetgen/core/main.py regarding standard output and error handling for the nbopen command. It correctly retrieves the streams from the app.config (with robust error fallback using AttributeError and KeyError), replacing the custom run_command (which didn't easily support arbitrary output destinations) with a subprocess.Popen.wait() combination that achieves correct behavior while being robust to invalid config values.
PR created automatically by Jules for task 4118980527979395642 started by @akutuva21
@google-labs-jules@akutuva21
Fix nbopen standard output and error handling in notebook generation
0a606a1
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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merged commit 5e4fbe4
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13 of 18 checks passed

@akutuva21
akutuva21
deleted the

fix-nbopen-stdout-stderr-4118980527979395642

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April 13, 2026 14:34
akutuva21 pushed a commit
that referenced
this pull request
Jun 1, 2026
@jrfaeder
Merge pull request#89from wshlavacek/modelapi-b4-strip-unquoted-bac…
763888c
…kslashes
Strip stray unquoted backslashes in action normalization
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