Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107

Closed
#121
Closed
Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
#121
Assignees
drewoldag
Labels
bugSomething isn't workingdocumentationImprovements or additions to documentation
Milestone
Release tag 1.3

Description

@drewoldag
drewoldag
opened on Mar 13, 2023

The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:

This is after repeating the build 3 times:

reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.

If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.

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    , 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

    Skip to content
    Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107
    Closed
    #121
    Closed
    Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
    #121
    Assignees
    drewoldag
    Labels
    bugSomething isn't workingdocumentationImprovements or additions to documentation
    Milestone
    Release tag 1.3
    Description
    @drewoldag
    drewoldag
    opened on Mar 13, 2023
    The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:
    This is after repeating the build 3 times:
    reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

    Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.
    If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.
    Metadata
    Metadata
    Assignees
    Labels
    bugSomething isn't workingdocumentationImprovements or additions to documentation
    Type
    No type
    Projects
    No projects
      Milestone
      Relationships
      None yet
      Development
      No branches or pull requests
      Issue actions
      
, '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");
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

      Skip to content
      Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107
      Closed
      #121
      Closed
      Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
      #121
      Assignees
      drewoldag
      Labels
      bugSomething isn't workingdocumentationImprovements or additions to documentation
      Milestone
      Release tag 1.3
      Description
      @drewoldag
      drewoldag
      opened on Mar 13, 2023
      The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:
      This is after repeating the build 3 times:
      reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

      Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.
      If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.
      Metadata
      Metadata
      Assignees
      Labels
      bugSomething isn't workingdocumentationImprovements or additions to documentation
      Type
      No type
      Projects
      No projects
        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");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

        Skip to content
        Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107
        Closed
        #121
        Closed
        Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
        #121
        Assignees
        drewoldag
        Labels
        bugSomething isn't workingdocumentationImprovements or additions to documentation
        Milestone
        Release tag 1.3
        Description
        @drewoldag
        drewoldag
        opened on Mar 13, 2023
        The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:
        This is after repeating the build 3 times:
        reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

        Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.
        If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.
        Metadata
        Metadata
        Assignees
        Labels
        bugSomething isn't workingdocumentationImprovements or additions to documentation
        Type
        No type
        Projects
        No projects
          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");
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(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

          Skip to content
          Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107
          Closed
          #121
          Closed
          Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
          #121
          Assignees
          drewoldag
          Labels
          bugSomething isn't workingdocumentationImprovements or additions to documentation
          Milestone
          Release tag 1.3
          Description
          @drewoldag
          drewoldag
          opened on Mar 13, 2023
          The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:
          This is after repeating the build 3 times:
          reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

          Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.
          If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.
          Metadata
          Metadata
          Assignees
          Labels
          bugSomething isn't workingdocumentationImprovements or additions to documentation
          Type
          No type
          Projects
          No projects
            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
            Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107
            Closed
            #121
            Closed
            Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
            #121
            Assignees
            drewoldag
            Labels
            bugSomething isn't workingdocumentationImprovements or additions to documentation
            Milestone
            Release tag 1.3
            Description
            @drewoldag
            drewoldag
            opened on Mar 13, 2023
            The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:
            This is after repeating the build 3 times:
            reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

            Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.
            If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.
            Metadata
            Metadata
            Assignees
            Labels
            bugSomething isn't workingdocumentationImprovements or additions to documentation
            Type
            No type
            Projects
            No projects
              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");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

              Skip to content
              Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107
              Closed
              #121
              Closed
              Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
              #121
              Assignees
              drewoldag
              Labels
              bugSomething isn't workingdocumentationImprovements or additions to documentation
              Milestone
              Release tag 1.3
              Description
              @drewoldag
              drewoldag
              opened on Mar 13, 2023
              The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:
              This is after repeating the build 3 times:
              reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

              Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.
              If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.
              Metadata
              Metadata
              Assignees
              Labels
              bugSomething isn't workingdocumentationImprovements or additions to documentation
              Type
              No type
              Projects
              No projects
                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); }
})();
})();

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                Multiple rebuilds of the documentation result in unexpected warnings about notebooks #107
                Closed
                #121
                Closed
                Multiple rebuilds of the documentation result in unexpected warnings about notebooks#107
                #121
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                drewoldag
                Labels
                bugSomething isn't workingdocumentationImprovements or additions to documentation
                Milestone
                Release tag 1.3
                Description
                @drewoldag
                drewoldag
                opened on Mar 13, 2023
                The first time the user builds the documentation locally, everything will work smoothly. However subsequent builds (without first removing the _build directory) will result in errors like the following:
                This is after repeating the build 3 times:
                reading sources... [ 9%] _build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intrreading sources... [100%] notebooks/intro_notebook
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
/home/drew/code/new_science/docs/_build/doctrees/nbsphinx/notebooks/intro_notebook.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done

                Note that the warning after "checking consistency" produce deeper and deeper copies of the same directory structure.
                If there's a way to instruct Sphinx to first delete all of the _build and output directories before starting, I think that would be the easiest approach.
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