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crosenth committed Jul 24, 2024
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2 changes: 1 addition & 1 deletion .buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 5d1623759bef96d488dc1ef9dd005e04
config: dba13f05062c34c6f8696dc88c7ff38e
tags: 645f666f9bcd5a90fca523b33c5a78b7
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8 changes: 4 additions & 4 deletions _modules/index.html
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<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand All @@ -39,7 +39,7 @@ <h1>All modules for which code is available</h1>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<search id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
Expand All @@ -55,7 +55,7 @@ <h3 id="searchlabel">Quick search</h3>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
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Expand All @@ -67,7 +67,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions _modules/taxtastic/refpkg.html
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<link rel="index" title="Index" href="../../genindex.html" />
<link rel="search" title="Search" href="../../search.html" />
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
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<li class="right" style="margin-right: 10px">
Expand Down Expand Up @@ -949,7 +949,7 @@ <h1>Source code for taxtastic.refpkg</h1><div class="highlight"><pre>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<search id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
Expand All @@ -965,7 +965,7 @@ <h3 id="searchlabel">Quick search</h3>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="related navigation">
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<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand All @@ -978,7 +978,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
7 changes: 4 additions & 3 deletions _static/searchtools.js
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Expand Up @@ -178,7 +178,7 @@ const Search = {

htmlToText: (htmlString, anchor) => {
const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
for (const removalQuery of [".headerlinks", "script", "style"]) {
for (const removalQuery of [".headerlink", "script", "style"]) {
htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
}
if (anchor) {
Expand Down Expand Up @@ -328,13 +328,14 @@ const Search = {
for (const [title, foundTitles] of Object.entries(allTitles)) {
if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
for (const [file, id] of foundTitles) {
let score = Math.round(100 * queryLower.length / title.length)
const score = Math.round(Scorer.title * queryLower.length / title.length);
const boost = titles[file] === title ? 1 : 0; // add a boost for document titles
normalResults.push([
docNames[file],
titles[file] !== title ? `${titles[file]} > ${title}` : title,
id !== null ? "#" + id : "",
null,
score,
score + boost,
filenames[file],
]);
}
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8 changes: 4 additions & 4 deletions commands.html
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<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="The Python Refpkg API" href="refpkg_api.html" />
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand Down Expand Up @@ -976,7 +976,7 @@ <h2>update_taxids<a class="headerlink" href="#update-taxids" title="Link to this
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<div>
<h3><a href="index.html">Table of Contents</a></h3>
Expand Down Expand Up @@ -1033,7 +1033,7 @@ <h3 id="searchlabel">Quick search</h3>
</div>
<div class="clearer"></div>
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<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand All @@ -1048,7 +1048,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions genindex.html
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<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
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<li class="right" style="margin-right: 10px">
Expand Down Expand Up @@ -154,7 +154,7 @@ <h2 id="U">U</h2>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<search id="searchbox" style="display: none" role="search">
<h3 id="searchlabel">Quick search</h3>
Expand All @@ -170,7 +170,7 @@ <h3 id="searchlabel">Quick search</h3>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand All @@ -182,7 +182,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions index.html
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<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Installation" href="installation.html" />
</head><body>
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<h3>Navigation</h3>
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Expand Down Expand Up @@ -102,7 +102,7 @@ <h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Li
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<div>
<h3><a href="#">Table of Contents</a></h3>
Expand Down Expand Up @@ -138,7 +138,7 @@ <h3 id="searchlabel">Quick search</h3>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand All @@ -153,7 +153,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions installation.html
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Expand Up @@ -18,7 +18,7 @@
<link rel="next" title="Quickstart" href="quickstart.html" />
<link rel="prev" title="taxtastic" href="index.html" />
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand Down Expand Up @@ -87,7 +87,7 @@ <h1>Installation<a class="headerlink" href="#installation" title="Link to this h
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<div>
<h4>Previous topic</h4>
Expand Down Expand Up @@ -120,7 +120,7 @@ <h3 id="searchlabel">Quick search</h3>
</div>
<div class="clearer"></div>
</div>
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<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand All @@ -138,7 +138,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions quickstart.html
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<link rel="next" title="Manipulating the NCBI taxonomy" href="taxonomy.html" />
<link rel="prev" title="Installation" href="installation.html" />
</head><body>
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Expand Down Expand Up @@ -104,7 +104,7 @@ <h2>Taxonomically equipped reference package example<a class="headerlink" href="
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<div>
<h3><a href="index.html">Table of Contents</a></h3>
Expand Down Expand Up @@ -148,7 +148,7 @@ <h3 id="searchlabel">Quick search</h3>
</div>
<div class="clearer"></div>
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<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand All @@ -166,7 +166,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions refpkg.html
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<link rel="next" title="The Python Refpkg API" href="refpkg_api.html" />
<link rel="prev" title="Manipulating the NCBI taxonomy" href="taxonomy.html" />
</head><body>
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<div class="related" role="navigation" aria-label="Related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
Expand Down Expand Up @@ -145,7 +145,7 @@ <h2>The Refpkg format<a class="headerlink" href="#the-refpkg-format" title="Link
</div>
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</div>
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<div class="sphinxsidebar" role="navigation" aria-label="Main">
<div class="sphinxsidebarwrapper">
<div>
<h3><a href="index.html">Table of Contents</a></h3>
Expand Down Expand Up @@ -189,7 +189,7 @@ <h3 id="searchlabel">Quick search</h3>
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Expand All @@ -207,7 +207,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions refpkg_api.html
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<link rel="next" title="Detailed taxit documentation" href="commands.html" />
<link rel="prev" title="Creating and manipulating refpkgs" href="refpkg.html" />
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Expand Down Expand Up @@ -282,7 +282,7 @@ <h2><code class="docutils literal notranslate"><span class="pre">pplacer</span><
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<div class="sphinxsidebarwrapper">
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<h3><a href="index.html">Table of Contents</a></h3>
Expand Down Expand Up @@ -358,7 +358,7 @@ <h3 id="searchlabel">Quick search</h3>
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Expand All @@ -376,7 +376,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
8 changes: 4 additions & 4 deletions search.html
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Expand Up @@ -22,7 +22,7 @@


</head><body>
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<h3>Navigation</h3>
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Expand Down Expand Up @@ -70,13 +70,13 @@ <h1 id="search-documentation">Search</h1>
</div>
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<h3>Navigation</h3>
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Expand All @@ -88,7 +88,7 @@ <h3>Navigation</h3>
</div>
<div class="footer" role="contentinfo">
&#169; Copyright 2011-2024, Noah Hoffman, Erick Matsen, Brian Hodges, Connor McCoy, Chris Rosenthal.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.3.7.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
</div>
</body>
</html>
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