deploy: f6ba94d

_sources/back-matter/glossary.md

@@ -124,6 +124,9 @@ Semantic Type
   When associated with a {term}`directory format`, the combination defines an {term}`artifact class`.
   These types may be extended by {term}`plugins<Plugin>`.
 
+Single-Use Plugin (SUP)
+  A plugin that is intended for one specific use case, such as generating figures for a single manuscript, as opposed to a plugin that is intended for general widespread usage.
+
 tl;dr
   "Too long; didn't read."
   In other words, a quick summary of the content that follows.

back-matter/glossary.html

@@ -517,6 +517,8 @@ <h1>Glossary<a class="headerlink" href="#glossary" title="Link to this heading">
 When associated with a <a class="reference internal" href="#term-Directory-Format"><span class="xref std std-term">directory format</span></a>, the combination defines an <a class="reference internal" href="#term-Artifact-class"><span class="xref std std-term">artifact class</span></a>.
 These types may be extended by <a class="reference internal" href="#term-Plugin"><span class="xref std std-term">plugins</span></a>.</p>
 </dd>
+<dt id="term-Single-Use-Plugin-SUP">Single-Use Plugin (SUP)<a class="headerlink" href="#term-Single-Use-Plugin-SUP" title="Link to this term">#</a></dt><dd><p>A plugin that is intended for one specific use case, such as generating figures for a single manuscript, as opposed to a plugin that is intended for general widespread usage.</p>
+</dd>
 <dt id="term-tl-dr">tl;dr<a class="headerlink" href="#term-tl-dr" title="Link to this term">#</a></dt><dd><p>“Too long; didn’t read.”
 In other words, a quick summary of the content that follows.</p>
 </dd>

genindex.html

@@ -831,6 +831,8 @@ <h2 id="S">S</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="plugins/references/api/testing.html#qiime2.plugin.testing.TestPluginBase.setUp">setUp() (qiime2.plugin.testing.TestPluginBase method)</a>
+</li>
+      <li><a href="back-matter/glossary.html#term-Single-Use-Plugin-SUP"><strong>Single-Use Plugin (SUP)</strong></a>
 </li>
       <li><a href="plugins/references/api/formats.html#qiime2.plugin.SingleFileDirectoryFormat">SingleFileDirectoryFormat() (in module qiime2.plugin)</a>
 </li>

plugins/references/api/citations.html

@@ -447,12 +447,12 @@ <h2> Contents </h2>
 (<a class="reference external" href="https://docs.python.org/3.9/library/stdtypes.html#list" title="Python 3.9"><code class="docutils literal notranslate"><span class="pre">list</span></code></a> and <a class="reference internal" href="#qiime2.plugin.Citations" title="qiime2.plugin.Citations"><code class="xref myst py py-class docutils literal notranslate"><span class="pre">Citations</span></code></a>).</p>
 <dl class="py class">
 <dt class="sig sig-object py" id="qiime2.plugin.Citations">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">qiime2.plugin.</span></span><span class="sig-name descname"><span class="pre">Citations</span></span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/5fb10c4/qiime2/core/cite.py#L39"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">qiime2.plugin.</span></span><span class="sig-name descname"><span class="pre">Citations</span></span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/2024.10.0/qiime2/core/cite.py#L39"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations" title="Link to this definition">#</a></dt>
 <dd><p>A simple subclass of <a class="reference external" href="https://docs.python.org/3.9/library/collections.html#collections.OrderedDict" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">collections.OrderedDict</span></code></a>
 but iterates over values instead of keys by default.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="qiime2.plugin.Citations.load">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">package</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/5fb10c4/qiime2/core/cite.py#L42"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations.load" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">load</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">package</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/2024.10.0/qiime2/core/cite.py#L42"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations.load" title="Link to this definition">#</a></dt>
 <dd><p>Load a bibtex file from a path (or relative package path)</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -470,13 +470,13 @@ <h2> Contents </h2>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="qiime2.plugin.Citations.__iter__">
-<span class="sig-name descname"><span class="pre">__iter__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/5fb10c4/qiime2/core/cite.py#L86"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations.__iter__" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">__iter__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/2024.10.0/qiime2/core/cite.py#L86"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations.__iter__" title="Link to this definition">#</a></dt>
 <dd><p>Iterates over the contained <a class="reference internal" href="#qiime2.plugin.CitationRecord" title="qiime2.plugin.CitationRecord"><code class="xref py py-class docutils literal notranslate"><span class="pre">CitationRecord</span></code></a>’s</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="qiime2.plugin.Citations.save">
-<span class="sig-name descname"><span class="pre">save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/5fb10c4/qiime2/core/cite.py#L90"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations.save" title="Link to this definition">#</a></dt>
+<span class="sig-name descname"><span class="pre">save</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">f</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/2024.10.0/qiime2/core/cite.py#L90"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.Citations.save" title="Link to this definition">#</a></dt>
 <dd><p>Save object as bibtex to a filepath or filehandle</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -492,7 +492,7 @@ <h2> Contents </h2>
 
 <dl class="py class">
 <dt class="sig sig-object py" id="qiime2.plugin.CitationRecord">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">qiime2.plugin.</span></span><span class="sig-name descname"><span class="pre">CitationRecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fields</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/5fb10c4/qiime2/core/cite.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.CitationRecord" title="Link to this definition">#</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">qiime2.plugin.</span></span><span class="sig-name descname"><span class="pre">CitationRecord</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fields</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/2024.10.0/qiime2/core/cite.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.plugin.CitationRecord" title="Link to this definition">#</a></dt>
 <dd><p>A <a class="reference external" href="https://docs.python.org/3.9/library/collections.html#collections.namedtuple" title="(in Python v3.9)"><code class="xref py py-func docutils literal notranslate"><span class="pre">collections.namedtuple()</span></code></a> of bibtex entry type and entry fields.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>

plugins/references/api/context.html

@@ -441,7 +441,7 @@ <h1>Pipeline Context Object<a class="headerlink" href="#pipeline-context-object"
 Plugins may use these methods to invoke other registered actions or create artifacts.</p>
 <dl class="py method">
 <dt class="sig sig-object py" id="qiime2.sdk.Context.get_action">
-<span class="sig-prename descclassname"><span class="pre">Context.</span></span><span class="sig-name descname"><span class="pre">get_action</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plugin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">action</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/5fb10c4/qiime2/sdk/context.py#L44"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.sdk.Context.get_action" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Context.</span></span><span class="sig-name descname"><span class="pre">get_action</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">plugin</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">action</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/2024.10.0/qiime2/sdk/context.py#L43"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.sdk.Context.get_action" title="Link to this definition">#</a></dt>
 <dd><p>Return a function matching the callable API of an action.
 This function is aware of the pipeline context and manages its own
 cleanup as appropriate.</p>
@@ -451,7 +451,7 @@ <h1>Pipeline Context Object<a class="headerlink" href="#pipeline-context-object"
 
 <dl class="py method">
 <dt class="sig sig-object py" id="qiime2.sdk.Context.make_artifact">
-<span class="sig-prename descclassname"><span class="pre">Context.</span></span><span class="sig-name descname"><span class="pre">make_artifact</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">view</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">view_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/5fb10c4/qiime2/sdk/context.py#L180"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.sdk.Context.make_artifact" title="Link to this definition">#</a></dt>
+<span class="sig-prename descclassname"><span class="pre">Context.</span></span><span class="sig-name descname"><span class="pre">make_artifact</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">type</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">view</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">view_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/qiime2/qiime2/tree/2024.10.0/qiime2/sdk/context.py#L179"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#qiime2.sdk.Context.make_artifact" title="Link to this definition">#</a></dt>
 <dd><p>Return a new artifact from a given view.</p>
 <p>This artifact is automatically tracked and cleaned by the pipeline
 context.</p>