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code-cite

This project started at Springer Nature Hackday in November 2017.

The goal is to investigate how often code is cited in academic publications.

It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.

Contributing

We would love for you to join us on this journey!

Check out the contributing guidelines or our list of issues to see how you can help.

Contributors

Thank you to everyone who has contributed so far!


Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔

This project follows the all-contributors specification and this emoji key explains the different contributions.

Secrets

Some scripts may require the use of secrets you don't want to be stored in this public Github repository (e.g. web service API keys). You can create a "secrets" folder in the top level of this repository to store these. This "secrets" folder and all comments will be ignored by Git.

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Investigating code cited in published papers

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MIT license

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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" + '

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code-cite
This project started at Springer Nature Hackday in November 2017.
The goal is to investigate how often code is cited in academic publications.
It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.
Contributing
We would love for you to join us on this journey!
Check out the contributing guidelines or our list of issues to see how you can help.
Contributors
Thank you to everyone who has contributed so far!

Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔
This project follows the all-contributors specification and this emoji key explains the different contributions.
Secrets
Some scripts may require the use of secrets you don't want to be stored in this public
Github repository (e.g. web service API keys). You can create a "secrets" folder
in the top level of this repository to store these. This "secrets" folder and
all comments will be ignored by Git.
About
Investigating code cited in published papers
Resources
Readme
MIT license
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
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0 forks
Report repository
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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('^' + ".*" + '

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BranchesTags
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code-cite
This project started at Springer Nature Hackday in November 2017.
The goal is to investigate how often code is cited in academic publications.
It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.
Contributing
We would love for you to join us on this journey!
Check out the contributing guidelines or our list of issues to see how you can help.
Contributors
Thank you to everyone who has contributed so far!

Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔
This project follows the all-contributors specification and this emoji key explains the different contributions.
Secrets
Some scripts may require the use of secrets you don't want to be stored in this public
Github repository (e.g. web service API keys). You can create a "secrets" folder
in the top level of this repository to store these. This "secrets" folder and
all comments will be ignored by Git.
About
Investigating code cited in published papers
Resources
Readme
MIT license
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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Packages
Contributors
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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
BranchesTags
Repository files navigation
code-cite
This project started at Springer Nature Hackday in November 2017.
The goal is to investigate how often code is cited in academic publications.
It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.
Contributing
We would love for you to join us on this journey!
Check out the contributing guidelines or our list of issues to see how you can help.
Contributors
Thank you to everyone who has contributed so far!

Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔
This project follows the all-contributors specification and this emoji key explains the different contributions.
Secrets
Some scripts may require the use of secrets you don't want to be stored in this public
Github repository (e.g. web service API keys). You can create a "secrets" folder
in the top level of this repository to store these. This "secrets" folder and
all comments will be ignored by Git.
About
Investigating code cited in published papers
Resources
Readme
MIT license
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
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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
BranchesTags
Repository files navigation
code-cite
This project started at Springer Nature Hackday in November 2017.
The goal is to investigate how often code is cited in academic publications.
It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.
Contributing
We would love for you to join us on this journey!
Check out the contributing guidelines or our list of issues to see how you can help.
Contributors
Thank you to everyone who has contributed so far!

Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔
This project follows the all-contributors specification and this emoji key explains the different contributions.
Secrets
Some scripts may require the use of secrets you don't want to be stored in this public
Github repository (e.g. web service API keys). You can create a "secrets" folder
in the top level of this repository to store these. This "secrets" folder and
all comments will be ignored by Git.
About
Investigating code cited in published papers
Resources
Readme
MIT license
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
code-cite
This project started at Springer Nature Hackday in November 2017.
The goal is to investigate how often code is cited in academic publications.
It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.
Contributing
We would love for you to join us on this journey!
Check out the contributing guidelines or our list of issues to see how you can help.
Contributors
Thank you to everyone who has contributed so far!

Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔
This project follows the all-contributors specification and this emoji key explains the different contributions.
Secrets
Some scripts may require the use of secrets you don't want to be stored in this public
Github repository (e.g. web service API keys). You can create a "secrets" folder
in the top level of this repository to store these. This "secrets" folder and
all comments will be ignored by Git.
About
Investigating code cited in published papers
Resources
Readme
MIT license
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
code-cite
This project started at Springer Nature Hackday in November 2017.
The goal is to investigate how often code is cited in academic publications.
It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.
Contributing
We would love for you to join us on this journey!
Check out the contributing guidelines or our list of issues to see how you can help.
Contributors
Thank you to everyone who has contributed so far!

Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔
This project follows the all-contributors specification and this emoji key explains the different contributions.
Secrets
Some scripts may require the use of secrets you don't want to be stored in this public
Github repository (e.g. web service API keys). You can create a "secrets" folder
in the top level of this repository to store these. This "secrets" folder and
all comments will be ignored by Git.
About
Investigating code cited in published papers
Resources
Readme
MIT license
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
BranchesTags
Repository files navigation
code-cite
This project started at Springer Nature Hackday in November 2017.
The goal is to investigate how often code is cited in academic publications.
It was inspired by Yo Yehudi'sCode is Science project and seeks to complement the work by that community by providing some numbers associated with the prevalence of code citations in the published literature.
Contributing
We would love for you to join us on this journey!
Check out the contributing guidelines or our list of issues to see how you can help.
Contributors
Thank you to everyone who has contributed so far!

Martin O'Reilly
💻 🤔
Isla Staden
💻 🤔
Kirstie Whitaker
📖 🤔
This project follows the all-contributors specification and this emoji key explains the different contributions.
Secrets
Some scripts may require the use of secrets you don't want to be stored in this public
Github repository (e.g. web service API keys). You can create a "secrets" folder
in the top level of this repository to store these. This "secrets" folder and
all comments will be ignored by Git.
About
Investigating code cited in published papers
Resources
Readme
MIT license
Contributing
Contributing
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages