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Repetible-Research Generic Python Project

Manifesto

Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.

Status

Project folder structure

This project has been structured using this rr-init repository as a template. In order to keep an upstream to such project, add it as remote like this:

git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description

 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations

Use a virtual environment (Virtualenv + VirtualenvWrapper)

Virtual-environments are not virtual machines. Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system. Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.

Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:

mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment. The command deactivate is used to exit the virtual environment. Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.

Remember to keep requirements.txt up to date. For more details regarding the usage of the virtual enviroment, please look at the command reference.

Todo

General

  • Add sphinx documentation as project.io website
  • Add paper submodule
  • Add code modules
  • Add travis
  • [ ]

Coding

About

Research project initialization and organization following reproducible research guidelines

Resources

Readme
MIT license
Activity

Stars

0 stars

Watchers

0 watching

Forks

1 fork
Report repository

Releases

Packages

Contributors

, '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
BranchesTags
Repository files navigation
Repetible-Research Generic Python Project
Manifesto
Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.
Status
Project folder structure
This project has been structured using this rr-init repository as a template.
In order to keep an upstream to such project, add it as remote like this:
git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description
 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations
Use a virtual environment (Virtualenv + VirtualenvWrapper)
Virtual-environments are not virtual machines.
Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system.
Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.
Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:
mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment.
The command deactivate is used to exit the virtual environment.
Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.
Remember to keep requirements.txt up to date.
For more details regarding the usage of the virtual enviroment, please look at the command reference.
Todo
General
  •  Add sphinx documentation as project.io website
  •  Add paper submodule
  •  Add code modules
  •  Add travis
  • [ ]
Coding
About
Research project initialization and organization following reproducible research guidelines 
Resources
Readme
MIT license
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors

, '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
Repetible-Research Generic Python Project
Manifesto
Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.
Status
Project folder structure
This project has been structured using this rr-init repository as a template.
In order to keep an upstream to such project, add it as remote like this:
git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description
 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations
Use a virtual environment (Virtualenv + VirtualenvWrapper)
Virtual-environments are not virtual machines.
Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system.
Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.
Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:
mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment.
The command deactivate is used to exit the virtual environment.
Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.
Remember to keep requirements.txt up to date.
For more details regarding the usage of the virtual enviroment, please look at the command reference.
Todo
General
  •  Add sphinx documentation as project.io website
  •  Add paper submodule
  •  Add code modules
  •  Add travis
  • [ ]
Coding
About
Research project initialization and organization following reproducible research guidelines 
Resources
Readme
MIT license
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors

, '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
Repetible-Research Generic Python Project
Manifesto
Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.
Status
Project folder structure
This project has been structured using this rr-init repository as a template.
In order to keep an upstream to such project, add it as remote like this:
git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description
 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations
Use a virtual environment (Virtualenv + VirtualenvWrapper)
Virtual-environments are not virtual machines.
Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system.
Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.
Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:
mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment.
The command deactivate is used to exit the virtual environment.
Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.
Remember to keep requirements.txt up to date.
For more details regarding the usage of the virtual enviroment, please look at the command reference.
Todo
General
  •  Add sphinx documentation as project.io website
  •  Add paper submodule
  •  Add code modules
  •  Add travis
  • [ ]
Coding
About
Research project initialization and organization following reproducible research guidelines 
Resources
Readme
MIT license
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors

, '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
Repetible-Research Generic Python Project
Manifesto
Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.
Status
Project folder structure
This project has been structured using this rr-init repository as a template.
In order to keep an upstream to such project, add it as remote like this:
git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description
 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations
Use a virtual environment (Virtualenv + VirtualenvWrapper)
Virtual-environments are not virtual machines.
Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system.
Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.
Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:
mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment.
The command deactivate is used to exit the virtual environment.
Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.
Remember to keep requirements.txt up to date.
For more details regarding the usage of the virtual enviroment, please look at the command reference.
Todo
General
  •  Add sphinx documentation as project.io website
  •  Add paper submodule
  •  Add code modules
  •  Add travis
  • [ ]
Coding
About
Research project initialization and organization following reproducible research guidelines 
Resources
Readme
MIT license
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors

, '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
Repetible-Research Generic Python Project
Manifesto
Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.
Status
Project folder structure
This project has been structured using this rr-init repository as a template.
In order to keep an upstream to such project, add it as remote like this:
git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description
 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations
Use a virtual environment (Virtualenv + VirtualenvWrapper)
Virtual-environments are not virtual machines.
Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system.
Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.
Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:
mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment.
The command deactivate is used to exit the virtual environment.
Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.
Remember to keep requirements.txt up to date.
For more details regarding the usage of the virtual enviroment, please look at the command reference.
Todo
General
  •  Add sphinx documentation as project.io website
  •  Add paper submodule
  •  Add code modules
  •  Add travis
  • [ ]
Coding
About
Research project initialization and organization following reproducible research guidelines 
Resources
Readme
MIT license
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors

, '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
Repetible-Research Generic Python Project
Manifesto
Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.
Status
Project folder structure
This project has been structured using this rr-init repository as a template.
In order to keep an upstream to such project, add it as remote like this:
git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description
 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations
Use a virtual environment (Virtualenv + VirtualenvWrapper)
Virtual-environments are not virtual machines.
Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system.
Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.
Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:
mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment.
The command deactivate is used to exit the virtual environment.
Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.
Remember to keep requirements.txt up to date.
For more details regarding the usage of the virtual enviroment, please look at the command reference.
Todo
General
  •  Add sphinx documentation as project.io website
  •  Add paper submodule
  •  Add code modules
  •  Add travis
  • [ ]
Coding
About
Research project initialization and organization following reproducible research guidelines 
Resources
Readme
MIT license
Activity
Stars
0 stars
Watchers
0 watching
Forks
1 fork
Report repository
Releases
Packages
Contributors

, '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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Repetible-Research Generic Python Project
Manifesto
Because Human is perfectible and error-prone, because Science should be open and flow and because cogito ergo sum.
Status
Project folder structure
This project has been structured using this rr-init repository as a template.
In order to keep an upstream to such project, add it as remote like this:
git remote add rr-initUPS git@github.com:massich/rr-init.git

Structure Description
 project
|- doc/ # documentation for the study
| |- paper/ # manuscript(s), whether generated or not
| +- source/ # sphinx source
|
|- data # raw and primary data, are not changed once created
| |- raw/ # raw data, will not be altered
| +- clean/ # cleaned data, will not be altered once created
|
|- results # all output from workflows and analyses
| |- figures/ # graphs, likely designated for manuscript figures
| +- pictures/ # diagrams, images, and other non-graph graphics
|
|- scratch/ # temporary files that can be safely deleted or lost
|- src/ # any programmatic code
|
|- datapackage.json # metadata for the (input and output) data files
|- requirements.txt # list of the required packages (see virtualenv)
|
|- LICENSE.md
|- README.md # the top level description of content

Recomendations
Use a virtual environment (Virtualenv + VirtualenvWrapper)
Virtual-environments are not virtual machines.
Virtual-environments are used to avoid library classing between the libraries of a project and those fom the system.
Find more information in this virtual environment post describing how to use virtual environment for a mozilla marketplace testing.
Use the following to create a myPyProject environment based on the ./requirements.txt associated with the source directory ./src:
mkvirtualenv myPyProject -a src -r ../requirements.txt

Notice that mkvirtualenv activates such environment.
The command deactivate is used to exit the virtual environment.
Once the virtual environment exist on the system, the command workon myPyProject is rather convenient since it jumps into the working directory and activates the virtual enviroment.
Remember to keep requirements.txt up to date.
For more details regarding the usage of the virtual enviroment, please look at the command reference.
Todo
General
  •  Add sphinx documentation as project.io website
  •  Add paper submodule
  •  Add code modules
  •  Add travis
  • [ ]
Coding
About
Research project initialization and organization following reproducible research guidelines 
Resources
Readme
MIT license
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