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LINCC Frameworks Python Project Template

GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs

DOI:10.3847/2515-5172/ad4da1

This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.

Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!

Our template works best with Copier v9.1 and above. For all the information, see the detailed user guide in readthedocs

Getting started

Choose where you would like to create your new project, and call copier with the template.

copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh

Contributing to the Template

GitHub issue custom search in repo

See full documentation at readthedocs

Citation

If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:

Acknowledgements

This project is supported by Schmidt Sciences.

About

LINCC Frameworks scaffolding for Python project best practices

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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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LINCC Frameworks Python Project Template
GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs
DOI:10.3847/2515-5172/ad4da1
This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.
Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!
Our template works best with Copier v9.1 and above.
For all the information, see the detailed user guide in
readthedocs
Getting started
Choose where you would like to create your new project, and call copier with the template.
copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh
Contributing to the Template
GitHub issue custom search in repo
See full documentation at readthedocs
Citation
If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:
Acknowledgements
This project is supported by Schmidt Sciences.
About
LINCC Frameworks scaffolding for Python project best practices
Resources
Readme
BSD-3-Clause license
Activity
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
LINCC Frameworks Python Project Template
GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs
DOI:10.3847/2515-5172/ad4da1
This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.
Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!
Our template works best with Copier v9.1 and above.
For all the information, see the detailed user guide in
readthedocs
Getting started
Choose where you would like to create your new project, and call copier with the template.
copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh
Contributing to the Template
GitHub issue custom search in repo
See full documentation at readthedocs
Citation
If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:
Acknowledgements
This project is supported by Schmidt Sciences.
About
LINCC Frameworks scaffolding for Python project best practices
Resources
Readme
BSD-3-Clause license
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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
LINCC Frameworks Python Project Template
GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs
DOI:10.3847/2515-5172/ad4da1
This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.
Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!
Our template works best with Copier v9.1 and above.
For all the information, see the detailed user guide in
readthedocs
Getting started
Choose where you would like to create your new project, and call copier with the template.
copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh
Contributing to the Template
GitHub issue custom search in repo
See full documentation at readthedocs
Citation
If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:
Acknowledgements
This project is supported by Schmidt Sciences.
About
LINCC Frameworks scaffolding for Python project best practices
Resources
Readme
BSD-3-Clause license
Activity
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0 forks
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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
LINCC Frameworks Python Project Template
GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs
DOI:10.3847/2515-5172/ad4da1
This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.
Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!
Our template works best with Copier v9.1 and above.
For all the information, see the detailed user guide in
readthedocs
Getting started
Choose where you would like to create your new project, and call copier with the template.
copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh
Contributing to the Template
GitHub issue custom search in repo
See full documentation at readthedocs
Citation
If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:
Acknowledgements
This project is supported by Schmidt Sciences.
About
LINCC Frameworks scaffolding for Python project best practices
Resources
Readme
BSD-3-Clause license
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
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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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
LINCC Frameworks Python Project Template
GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs
DOI:10.3847/2515-5172/ad4da1
This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.
Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!
Our template works best with Copier v9.1 and above.
For all the information, see the detailed user guide in
readthedocs
Getting started
Choose where you would like to create your new project, and call copier with the template.
copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh
Contributing to the Template
GitHub issue custom search in repo
See full documentation at readthedocs
Citation
If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:
Acknowledgements
This project is supported by Schmidt Sciences.
About
LINCC Frameworks scaffolding for Python project best practices
Resources
Readme
BSD-3-Clause license
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
LINCC Frameworks Python Project Template
GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs
DOI:10.3847/2515-5172/ad4da1
This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.
Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!
Our template works best with Copier v9.1 and above.
For all the information, see the detailed user guide in
readthedocs
Getting started
Choose where you would like to create your new project, and call copier with the template.
copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh
Contributing to the Template
GitHub issue custom search in repo
See full documentation at readthedocs
Citation
If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:
Acknowledgements
This project is supported by Schmidt Sciences.
About
LINCC Frameworks scaffolding for Python project best practices
Resources
Readme
BSD-3-Clause license
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); }
})();
})();

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BranchesTags
Repository files navigation
LINCC Frameworks Python Project Template
GitHub release (latest SemVer)GitHub Workflow StatusRead the Docs
DOI:10.3847/2515-5172/ad4da1
This project template codifies LINCC-Framework's best practices for python code organization, testing, documentation, and automation. It is meant to help new python projects get started quickly, letting the user focus on writing code. The template takes care of the minutia of directory structures, tool configurations, and automated testing until the user is ready to take over. You can read more in the PPT research note.
Copier is required to use this template. Copier is an open source tool that hydrates projects from templates and natively supports updating projects as the original template matures. It's really neat!
Our template works best with Copier v9.1 and above.
For all the information, see the detailed user guide in
readthedocs
Getting started
Choose where you would like to create your new project, and call copier with the template.
copier copy gh:lincc-frameworks/python-project-template <path/to/destination>cd<path/to/destination># Create a virtual environment, feel free to use conda, pyenv or your favorite tool
python3 -mvenv ~/.virtualenvs/<env_name>source~/.virtualenvs/<env_name>/bin/activate
bash .initialize_new_project.sh
Contributing to the Template
GitHub issue custom search in repo
See full documentation at readthedocs
Citation
If you use Python Project Template in your work, we ask the you cite the "A Python Project Template for Healthy Scientific Software" research notefull citation:
Acknowledgements
This project is supported by Schmidt Sciences.
About
LINCC Frameworks scaffolding for Python project best practices
Resources
Readme
BSD-3-Clause license
Activity
Stars
0 stars
Watchers
0 watching
Forks
0 forks
Report repository
Releases
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Contributors
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