deploy: 4518f22

.buildinfo

@@ -1,4 +1,4 @@
 # 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: 8105fe924271a3bc5ab8ae14db52272c
+config: 13a282ac25bfaccf6dd7d4a5e2b65a6f
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/plugins/tutorials/add-2nd-transformer.md

@@ -23,6 +23,7 @@ Transformers in QIIME 2 are designed to handle converstions between objects behi
 In this section, we'll do a small refactor of the code we wrote in the previous section.
 
 ```{admonition} tl;dr
+:class: tip
 The code that I wrote for this section can be found here: {{ dwq2_add_2nd_transformer_commit_url }}.
 ```
 

_sources/plugins/tutorials/conclusion.md

@@ -2,7 +2,7 @@
 # Conclusion
 
 That's the end of the QIIME 2 plugin development tutorial, for now.
-As of this writing (13 April 2024), this tutorial is still in development, and new content is planned.
+As of this writing (22 August 2024), this tutorial is still in development, and new content is planned.
 You can see a list of content planned for the plugin tutorial on our issue tracker [here](https://github.com/caporaso-lab/developing-with-qiime2/issues?q=is%3Aissue+is%3Aopen+label%3Aplugins+label%3Atutorial), and more general content planned for the *Plugins* part of *Developing with QIIME 2* [here](https://github.com/caporaso-lab/developing-with-qiime2/issues?q=is%3Aissue+is%3Aopen+label%3Aplugins).
 
 A good next step is to create your own plugin.

_static/references.bib

@@ -118,3 +118,29 @@ @BOOK{pragprog20
   year      =  2019,
   language  = "en"
 }
+
+
+@ARTICLE{Altschul1990,
+  title    = "Basic local alignment search tool",
+  author   = "Altschul, S F and Gish, W and Miller, W and Myers, E W and
+              Lipman, D J",
+  journal  = "J. Mol. Biol.",
+  volume   =  215,
+  number   =  3,
+  pages    = "403--410",
+  month    =  oct,
+  year     =  1990
+}
+
+
+@ARTICLE{Smith1981,
+  title    = "Identification of common molecular subsequences",
+  author   = "Smith, T F and Waterman, M S",
+  journal  = "J. Mol. Biol.",
+  volume   =  147,
+  number   =  1,
+  pages    = "195--197",
+  month    =  mar,
+  year     =  1981,
+  language = "en"
+}

back-matter/bibliography.html

@@ -461,8 +461,16 @@ <h1>List of works cited<a class="headerlink" href="#list-of-works-cited" title="
 <span class="label"><span class="fn-bracket">[</span>4<span class="fn-bracket">]</span></span>
 <p>David Thomas and Andrew Hunt. <em>The Pragmatic Programmer: your journey to mastery, 20th Anniversary Edition</em>. Addison-Wesley Professional, September 2019.</p>
 </div>
-<div class="citation" id="id4" role="doc-biblioentry">
+<div class="citation" id="id8" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>5<span class="fn-bracket">]</span></span>
+<p>S F Altschul, W Gish, W Miller, E W Myers, and D J Lipman. Basic local alignment search tool. <em>J. Mol. Biol.</em>, 215(3):403–410, October 1990.</p>
+</div>
+<div class="citation" id="id9" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span>6<span class="fn-bracket">]</span></span>
+<p>T F Smith and M S Waterman. Identification of common molecular subsequences. <em>J. Mol. Biol.</em>, 147(1):195–197, March 1981.</p>
+</div>
+<div class="citation" id="id4" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span>7<span class="fn-bracket">]</span></span>
 <p>Christopher R Keefe, Matthew R Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V Wood, Evan Bolyen, and J Gregory Caporaso. Facilitating bioinformatics reproducibility with QIIME 2 provenance replay. <em>PLoS Comput. Biol.</em>, 19(11):e1011676, November 2023.</p>
 </div>
 </div>

back-matter/glossary.html

@@ -523,7 +523,7 @@ <h1>Glossary<a class="headerlink" href="#glossary" title="Link to this heading">
 Provenance information describes the host system, the computing environment, Actions performed, parameters passed, primary sources cited, and more.</p>
 </dd>
 <dt id="term-Provenance-Replay">Provenance Replay<a class="headerlink" href="#term-Provenance-Replay" title="Link to this term">#</a></dt><dd><p>The QIIME 2 functionality that enables new executable code to be generated from an existing QIIME 2 <a class="reference internal" href="#term-Result"><span class="xref std std-term">result’s</span></a> <a class="reference internal" href="#term-Provenance"><span class="xref std std-term">provenance</span></a>.
-For additional detail, refer to <span id="id3">[<a class="reference internal" href="bibliography.html#id4" title="Christopher R Keefe, Matthew R Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V Wood, Evan Bolyen, and J Gregory Caporaso. Facilitating bioinformatics reproducibility with QIIME 2 provenance replay. PLoS Comput. Biol., 19(11):e1011676, November 2023.">5</a>]</span>.</p>
+For additional detail, refer to <span id="id3">[<a class="reference internal" href="bibliography.html#id4" title="Christopher R Keefe, Matthew R Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V Wood, Evan Bolyen, and J Gregory Caporaso. Facilitating bioinformatics reproducibility with QIIME 2 provenance replay. PLoS Comput. Biol., 19(11):e1011676, November 2023.">7</a>]</span>.</p>
 </dd>
 <dt id="term-Python-3-API">Python 3 API<a class="headerlink" href="#term-Python-3-API" title="Link to this term">#</a></dt><dd><p>When <em>the Python 3 API</em> is referred to in the context of QIIME 2, this refers to the interface that allows users to work with QIIME 2 plugins and actions natively in Python 3 (for example in a Jupyter Notebook environment). This was formerly referred to as the Artifact API.</p>
 </dd>

framework/explanations/provenance.html

@@ -467,7 +467,7 @@ <h2> Contents </h2>
 
   <section class="tex2jax_ignore mathjax_ignore" id="decentralized-retrospective-provenance-tracking">
 <span id="provenance-explanation"></span><h1>Decentralized retrospective provenance tracking<a class="headerlink" href="#decentralized-retrospective-provenance-tracking" title="Link to this heading">#</a></h1>
-<p>QIIME 2 provides automatic, integrated, and decentralized tracking of analysis metadata, including information about the host system, the computing environment, Actions performed, parameters passed, primary sources cited, and more <span id="id1">[<a class="reference internal" href="../../back-matter/bibliography.html#id4" title="Christopher R Keefe, Matthew R Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V Wood, Evan Bolyen, and J Gregory Caporaso. Facilitating bioinformatics reproducibility with QIIME 2 provenance replay. PLoS Comput. Biol., 19(11):e1011676, November 2023.">5</a>]</span>.
+<p>QIIME 2 provides automatic, integrated, and decentralized tracking of analysis metadata, including information about the host system, the computing environment, Actions performed, parameters passed, primary sources cited, and more <span id="id1">[<a class="reference internal" href="../../back-matter/bibliography.html#id4" title="Christopher R Keefe, Matthew R Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V Wood, Evan Bolyen, and J Gregory Caporaso. Facilitating bioinformatics reproducibility with QIIME 2 provenance replay. PLoS Comput. Biol., 19(11):e1011676, November 2023.">7</a>]</span>.
 We describe all of this information about <em>how an analysis was performed to produce a result</em> as the result’s <strong>provenance</strong>.</p>
 <p>The notion of a QIIME 2 <a class="reference internal" href="../../back-matter/glossary.html#term-Result"><span class="xref std std-term">Result</span></a> is central here.
 Whenever an <a class="reference internal" href="../../back-matter/glossary.html#term-Action"><span class="xref std std-term">Action</span></a> is performed on some data with QIIME 2, the framework captures relevant metadata about the action and environment in a <a class="reference internal" href="../../back-matter/glossary.html#term-Result"><span class="xref std std-term">Result</span></a> object, which is backed by an <a class="reference internal" href="../../back-matter/glossary.html#term-Archive"><span class="xref std std-term">Archive</span></a>.
@@ -500,7 +500,7 @@ <h2>Why Capture Provenance Data?<a class="headerlink" href="#why-capture-provena
 For example, q2view produces directed provenance graphs, <a class="reference external" href="https://view.qiime2.org/provenance/?src=https%3A%2F%2Fdocs.qiime2.org%2F2021.4%2Fdata%2Ftutorials%2Fmoving-pictures%2Fcore-metrics-results%2Funweighted_unifrac_emperor.qzv">like this one</a>, that allow any consummer of that result to understand exactly how it was created.</p></li>
 <li><p>QIIME 2 Artifacts bring their citations with them.</p></li>
 <li><p>Methods-section text could theoretically be generated from a collection of QIIME 2 Artifacts. (If you’re interested in contributing that functionality, please feel free to get in touch - large language models (LLMs) should make this easier than ever!)</p></li>
-<li><p>Analyses are automatically replay-able <span id="id2">[<a class="reference internal" href="../../back-matter/bibliography.html#id4" title="Christopher R Keefe, Matthew R Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V Wood, Evan Bolyen, and J Gregory Caporaso. Facilitating bioinformatics reproducibility with QIIME 2 provenance replay. PLoS Comput. Biol., 19(11):e1011676, November 2023.">5</a>]</span>, meaning that you can generate new code from existing results.</p></li>
+<li><p>Analyses are automatically replay-able <span id="id2">[<a class="reference internal" href="../../back-matter/bibliography.html#id4" title="Christopher R Keefe, Matthew R Dillon, Elizabeth Gehret, Chloe Herman, Mary Jewell, Colin V Wood, Evan Bolyen, and J Gregory Caporaso. Facilitating bioinformatics reproducibility with QIIME 2 provenance replay. PLoS Comput. Biol., 19(11):e1011676, November 2023.">7</a>]</span>, meaning that you can generate new code from existing results.</p></li>
 <li><p>In the unlikely event of a data integrity bug, problematic combinations of hardware, environment, <code class="docutils literal notranslate"><span class="pre">Action</span></code>s, and parameters can be investigated effectively by users, developers, or technical support providers.
 Impacted results can be programatically identified, and could be programatically correctable in some cases.</p></li>
 <li><p>By capturing provenance metadata at the level of Actions and Results, QIIME 2 provenance is both host- and interface-agnostic.

genindex.html

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