Migrate content from API to UG - modules 1, 2, 3, 4 #417

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Migrate content from API to UG - modules 1, 2, 3, 4#417
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SDG23work on Small Development Grant 2023

Description

@namiroues
namiroues
opened on Mar 29, 2025

Description:

As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).

Steps:

Review API documentation.
Create a document that categorizes content into
Content to retain in the API docs
Content to migrate to the User Guide
Begin content migration and cleanup accordingly.

Activity

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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" + '

    Skip to content
    Migrate content from API to UG - modules 1, 2, 3, 4 #417
    Open
    Open
    Migrate content from API to UG - modules 1, 2, 3, 4#417
    Labels
    SDG23work on Small Development Grant 2023
    Description
    @namiroues
    namiroues
    opened on Mar 29, 2025
    Description:
    As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).
    Steps:
    Review API documentation.
    
Create a document that categorizes content into
    
Content to retain in the API docs
    
Content to migrate to the User Guide
    
Begin content migration and cleanup accordingly.
    Activity
    Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
    Metadata
    Metadata
    Assignees
    No one assigned
      Labels
      SDG23work on Small Development Grant 2023
      Type
      No type
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      No milestone
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      None yet
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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
      Migrate content from API to UG - modules 1, 2, 3, 4 #417
      Open
      Open
      Migrate content from API to UG - modules 1, 2, 3, 4#417
      Labels
      SDG23work on Small Development Grant 2023
      Description
      @namiroues
      namiroues
      opened on Mar 29, 2025
      Description:
      As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).
      Steps:
      Review API documentation.
      
Create a document that categorizes content into
      
Content to retain in the API docs
      
Content to migrate to the User Guide
      
Begin content migration and cleanup accordingly.
      Activity
      Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
      Metadata
      Metadata
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      No one assigned
        Labels
        SDG23work on Small Development Grant 2023
        Type
        No type
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        Milestone
        No milestone
        Relationships
        None yet
        Development
        No branches or pull requests
        Issue actions
        
, '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
        Migrate content from API to UG - modules 1, 2, 3, 4 #417
        Open
        Open
        Migrate content from API to UG - modules 1, 2, 3, 4#417
        Labels
        SDG23work on Small Development Grant 2023
        Description
        @namiroues
        namiroues
        opened on Mar 29, 2025
        Description:
        As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).
        Steps:
        Review API documentation.
        
Create a document that categorizes content into
        
Content to retain in the API docs
        
Content to migrate to the User Guide
        
Begin content migration and cleanup accordingly.
        Activity
        Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
        Metadata
        Metadata
        Assignees
        No one assigned
          Labels
          SDG23work on Small Development Grant 2023
          Type
          No type
          Projects
          Milestone
          No milestone
          Relationships
          None yet
          Development
          No branches or pull requests
          Issue actions
          
, '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
          Migrate content from API to UG - modules 1, 2, 3, 4 #417
          Open
          Open
          Migrate content from API to UG - modules 1, 2, 3, 4#417
          Labels
          SDG23work on Small Development Grant 2023
          Description
          @namiroues
          namiroues
          opened on Mar 29, 2025
          Description:
          As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).
          Steps:
          Review API documentation.
          
Create a document that categorizes content into
          
Content to retain in the API docs
          
Content to migrate to the User Guide
          
Begin content migration and cleanup accordingly.
          Activity
          Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
          Metadata
          Metadata
          Assignees
          No one assigned
            Labels
            SDG23work on Small Development Grant 2023
            Type
            No type
            Projects
            Milestone
            No milestone
            Relationships
            None yet
            Development
            No branches or pull requests
            Issue actions
            
, '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
            Migrate content from API to UG - modules 1, 2, 3, 4 #417
            Open
            Open
            Migrate content from API to UG - modules 1, 2, 3, 4#417
            Labels
            SDG23work on Small Development Grant 2023
            Description
            @namiroues
            namiroues
            opened on Mar 29, 2025
            Description:
            As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).
            Steps:
            Review API documentation.
            
Create a document that categorizes content into
            
Content to retain in the API docs
            
Content to migrate to the User Guide
            
Begin content migration and cleanup accordingly.
            Activity
            Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
            Metadata
            Metadata
            Assignees
            No one assigned
              Labels
              SDG23work on Small Development Grant 2023
              Type
              No type
              Projects
              Milestone
              No milestone
              Relationships
              None yet
              Development
              No branches or pull requests
              Issue actions
              
, '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
              Migrate content from API to UG - modules 1, 2, 3, 4 #417
              Open
              Open
              Migrate content from API to UG - modules 1, 2, 3, 4#417
              Labels
              SDG23work on Small Development Grant 2023
              Description
              @namiroues
              namiroues
              opened on Mar 29, 2025
              Description:
              As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).
              Steps:
              Review API documentation.
              
Create a document that categorizes content into
              
Content to retain in the API docs
              
Content to migrate to the User Guide
              
Begin content migration and cleanup accordingly.
              Activity
              Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
              Metadata
              Metadata
              Assignees
              No one assigned
                Labels
                SDG23work on Small Development Grant 2023
                Type
                No type
                Projects
                Milestone
                No milestone
                Relationships
                None yet
                Development
                No branches or pull requests
                Issue actions
                
, '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
                Migrate content from API to UG - modules 1, 2, 3, 4 #417
                Open
                Open
                Migrate content from API to UG - modules 1, 2, 3, 4#417
                Labels
                SDG23work on Small Development Grant 2023
                Description
                @namiroues
                namiroues
                opened on Mar 29, 2025
                Description:
                As part of the MDAnalysis SDG23 project, we are performing a cleanup and integration of content within the API documentation. The goal is to differentiate between the API Guide (auto-generated references) and the User Guide (narrative, how-to, and conceptual documentation).
                Steps:
                Review API documentation.
                
Create a document that categorizes content into
                
Content to retain in the API docs
                
Content to migrate to the User Guide
                
Begin content migration and cleanup accordingly.
                Activity
                Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
                Metadata
                Metadata
                Assignees
                No one assigned
                  Labels
                  SDG23work on Small Development Grant 2023
                  Type
                  No type
                  Projects
                  Milestone
                  No milestone
                  Relationships
                  None yet
                  Development
                  No branches or pull requests
                  Issue actions