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  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

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  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

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Milestones · WhitakerLab/scona · GitHub
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Milestones

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  • No due date
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  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

    No due date
    5/10 issues closed
  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

    No due date
    2/2 issues closed
, 'i'); if (__m === '*' || __re.test(location.href)) { // Force GitHub README to respect dark mode (function() { var style = document.createElement('style'); style.textContent = ' .markdown-body { color-scheme: dark light; } .markdown-body pre { background: #161b22 !important; } .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; } .markdown-body table th, .markdown-body table td { border-color: #30363d !important; } .markdown-body img { background: #0d1117; } .markdown-body blockquote { border-left-color: #8b949e; } .markdown-body hr { border-color: #30363d; } '; document.head.appendChild(style); })(); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Milestones · WhitakerLab/scona · GitHub
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Milestones

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  • No due date
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  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

    No due date
    5/10 issues closed
  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

    No due date
    2/2 issues closed
, 'i'); if (__m === '*' || __re.test(location.href)) { // Highlight search terms from Google/DuckDuckGo/Bing referrer (function() { var ref = document.referrer; var terms = []; if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) { var url = new URL(ref); var q = url.searchParams.get('q') || url.searchParams.get('p'); if (q) { terms = q.split(/\s+/).filter(function(t) { return t.length > 2; }); } } if (terms.length === 0) return; var style = document.createElement('style'); style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }'; document.head.appendChild(style); function highlight(node) { if (node.nodeType === 3) { // text node var text = node.textContent; var found = false; terms.forEach(function(term) { var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi'); if (regex.test(text)) { found = true; var frag = document.createDocumentFragment(); var parts = text.split(regex); parts.forEach(function(part, i) { if (i % 2 === 0) { frag.appendChild(document.createTextNode(part)); } else { var span = document.createElement('span'); span.className = 'userscript-highlight'; span.textContent = part; frag.appendChild(span); } }); node.parentNode.replaceChild(frag, node); } }); } else if (node.nodeType === 1 && node.childNodes) { // element var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT']; if (!skipTags.includes(node.tagName)) { Array.from(node.childNodes).forEach(highlight); } } } highlight(document.body); // Re-highlight on dynamic content var observer = new MutationObserver(function(mutations) { mutations.forEach(function(m) { m.addedNodes.forEach(function(node) { if (node.nodeType === 1 || node.nodeType === 3) highlight(node); }); }); }); observer.observe(document.body, { childList: true, subtree: true }); })(); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Milestones · WhitakerLab/scona · GitHub
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  • No due date
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  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

    No due date
    5/10 issues closed
  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

    No due date
    2/2 issues closed
, 'i'); if (__m === '*' || __re.test(location.href)) { // Strip utm_, fbclid, gclid, etc. from all links on page (function() { var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content', 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid', 'ref', 'ref_src', 'source', 'medium', 'campaign']; function cleanUrl(url) { try { var u = new URL(url, window.location.origin); var changed = false; trackingParams.forEach(function(p) { if (u.searchParams.has(p)) { u.searchParams.delete(p); changed = true; } }); return changed ? u.toString() : url; } catch (e) { return url; } } function cleanLinks() { document.querySelectorAll('a[href]').forEach(function(a) { var clean = cleanUrl(a.href); if (clean !== a.href) a.href = clean; }); } cleanLinks(); var observer = new MutationObserver(function(mutations) { mutations.forEach(function(m) { m.addedNodes.forEach(function(node) { if (node.nodeType === 1) { if (node.tagName === 'A') cleanLinks(); node.querySelectorAll('a[href]').forEach(function(a) { var clean = cleanUrl(a.href); if (clean !== a.href) a.href = clean; }); } }); }); }); observer.observe(document.body, { childList: true, subtree: true }); })(); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + ' Milestones · WhitakerLab/scona · GitHub
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Milestones

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  • No due date
    0/5 issues closed
  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

    No due date
    5/10 issues closed
  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

    No due date
    2/2 issues closed
, 'i'); if (__m === '*' || __re.test(location.href)) { // Auto-enable theater mode on YouTube (function() { function tryTheater() { var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]'); if (btn && !btn.classList.contains('activated')) { btn.click(); } } // Try immediately tryTheater(); // Try after navigation (SPA) var lastUrl = location.href; setInterval(function() { if (location.href !== lastUrl) { lastUrl = location.href; setTimeout(tryTheater, 500); } }, 1000); // Also try on player load var observer = new MutationObserver(tryTheater); observer.observe(document.body, { childList: true, subtree: true }); })(); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Milestones · WhitakerLab/scona · GitHub
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Milestones

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  • No due date
    0/5 issues closed
  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

    No due date
    5/10 issues closed
  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

    No due date
    2/2 issues closed
, 'i'); if (__m === '*' || __re.test(location.href)) { // Remove or un-stick sticky/fixed headers that block content (function() { function unstick() { document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) { if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') { el.style.position = 'static'; el.style.top = 'auto'; el.style.zIndex = 'auto'; } }); } unstick(); var observer = new MutationObserver(unstick); observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] }); })(); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + ' Milestones · WhitakerLab/scona · GitHub
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Milestones

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  • No due date
    0/5 issues closed
  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

    No due date
    5/10 issues closed
  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

    No due date
    2/2 issues closed
, 'i'); if (__m === '*' || __re.test(location.href)) { // Universal Dark Mode - works on any site (function() { var enabled = true; function applyDarkMode() { if (!enabled) return; // Create style element if it doesn't exist var style = document.getElementById('universal-dark-mode-style'); if (!style) { style = document.createElement('style'); style.id = 'universal-dark-mode-style'; document.head.appendChild(style); } // Dark mode CSS - inverts colors but preserves images/video style.textContent = ' /* Invert everything except media */ html { filter: invert(1) hue-rotate(180deg) !important; background: #1a1a2e !important; } /* Restore images, videos, iframes, canvas */ img, video, iframe, canvas, svg, picture, [style*="background-image"] { filter: invert(1) hue-rotate(180deg) !important; } /* Preserve specific elements that should not be inverted */ .no-dark-mode, .no-dark-mode *, [data-theme="light"], [data-theme="light"], .ace_editor, .ace_editor *, .CodeMirror, .CodeMirror *, .monaco-editor, .monaco-editor *, .markdown-body pre, .markdown-body pre *, .highlight, .highlight *, pre code, pre code * { filter: none !important; } /* Fix common UI elements */ .modal, .popup, .dropdown-menu, .tooltip, .popover { filter: invert(1) hue-rotate(180deg) !important; background: #2d2d44 !important; border-color: #444 !important; } /* Scrollbars */ ::-webkit-scrollbar { background: #1a1a2e !important; } ::-webkit-scrollbar-thumb { background: #444 !important; } ::-webkit-scrollbar-thumb:hover { background: #555 !important; } /* Selection */ ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; } ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; } '; } function removeDarkMode() { var style = document.getElementById('universal-dark-mode-style'); if (style) style.remove(); } // Toggle with Alt+Shift+D document.addEventListener('keydown', function(e) { if (e.altKey && e.shiftKey && e.key === 'D') { e.preventDefault(); enabled = !enabled; if (enabled) { applyDarkMode(); console.log('[Universal Dark Mode] Enabled'); } else { removeDarkMode(); console.log('[Universal Dark Mode] Disabled'); } } }); // Apply on load applyDarkMode(); // Re-apply on dynamic content var observer = new MutationObserver(function(mutations) { if (enabled && !document.getElementById('universal-dark-mode-style')) { applyDarkMode(); } }); observer.observe(document.head, { childList: true }); console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle'); })(); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })(); Milestones · WhitakerLab/scona · GitHub
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Milestones

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  • No due date
    0/5 issues closed
  • Brain Networks In Python started off as legacy code written by Dr Kirstie Whitaker for the analyses done in the Neuroscience in Psychiatry Network publication "Adolescence is associated with genomically patterned consolidation of the hubs of the human brain connectome" published in PNAS in 2016 ([Whitaker*, Vertes* et al, 2016](http://dx.doi.org/10.1073/pnas.1601745113)). Brain Networks In Python needs to be refactored to break down the conceptual steps for a network analysis to allow the user to re-combine them as they see fit and, as we are fond of repeating, "The second best time to add in tests for software is when refactoring. (The optimum time would have been when the code was written in the first place)".

    No due date
    5/10 issues closed
  • In the fullness of time, we plan to release Brain Networks In Python as a Python package. Let's keep track of what needs to be done here.

    No due date
    2/2 issues closed