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index.html

@@ -9,7 +9,7 @@
 <meta name="author" content="Julien Brun">
 <meta name="author" content="Renata Curty">
 <meta name="author" content="Greg Janée">
-<meta name="dcterms.date" content="2024-06-27">
+<meta name="dcterms.date" content="2024-06-28">
 
 <title>Designing a Reproducible and Collaborative Lab (RCL)</title>
 <style>
@@ -412,7 +412,7 @@ <h1 class="title">Designing a Reproducible and Collaborative Lab (RCL)</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">June 27, 2024</p>
+      <p class="date">June 28, 2024</p>
     </div>
   </div>
 
@@ -476,13 +476,13 @@ <h3 class="anchored" data-anchor-id="want-to-know-more">Want to know more?</h3>
 <div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" id="quarto-citation"><h2 class="anchored quarto-appendix-heading">Citation</h2><div><div class="quarto-appendix-secondary-label">BibTeX citation:</div><pre class="sourceCode code-with-copy quarto-appendix-bibtex"><code class="sourceCode bibtex">@online{brun2024,
   author = {Brun, Julien and Curty, Renata and Janée, Greg},
   title = {Designing a {Reproducible} and {Collaborative} {Lab} {(RCL)}},
-  date = {2024-06-27},
+  date = {2024-06-28},
   url = {https://ucsb-library-research-data-services.github.io/reproducible-lab/},
   langid = {en}
 }
 </code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre><div class="quarto-appendix-secondary-label">For attribution, please cite this work as:</div><div id="ref-brun2024" class="csl-entry quarto-appendix-citeas" role="listitem">
 Brun, Julien, Renata Curty, and Greg Janée. 2024. <span>“Designing a
-Reproducible and Collaborative Lab (RCL).”</span> June 27, 2024. <a href="https://ucsb-library-research-data-services.github.io/reproducible-lab/">https://ucsb-library-research-data-services.github.io/reproducible-lab/</a>.
+Reproducible and Collaborative Lab (RCL).”</span> June 28, 2024. <a href="https://ucsb-library-research-data-services.github.io/reproducible-lab/">https://ucsb-library-research-data-services.github.io/reproducible-lab/</a>.
 </div></div></section></div></main> <!-- /main -->
 <div>
   <p></p><hr><p></p>

preserve_computing-env.html

@@ -406,7 +406,11 @@
     <h2 id="toc-title">On this page</h2>
 
   <ul>
-  <li><a href="#virtual-environments" id="toc-virtual-environments" class="nav-link active" data-scroll-target="#virtual-environments">Virtual environments</a></li>
+  <li><a href="#virtual-environments" id="toc-virtual-environments" class="nav-link active" data-scroll-target="#virtual-environments">Virtual environments</a>
+  <ul class="collapse">
+  <li><a href="#r" id="toc-r" class="nav-link" data-scroll-target="#r">R</a></li>
+  <li><a href="#python" id="toc-python" class="nav-link" data-scroll-target="#python">Python</a></li>
+  </ul></li>
   </ul>
 </nav>
     </div>
@@ -437,12 +441,12 @@ <h1 class="title">Preserve your computing environment</h1>
 <p><code>sessionInfo()</code> or <code>devtools::session_info()</code> are great ways to capture this information. You should save it into a session_info.txt file to include in your GitHub repository</p>
 <p>In Python:</p>
 <p><code>pip freeze &gt; requirements.txt</code> will capture all the python modules installed in your current environment</p>
-<section id="virtual-environments" class="level3">
-<h3 class="anchored" data-anchor-id="virtual-environments">Virtual environments</h3>
+<section id="virtual-environments" class="level2">
+<h2 class="anchored" data-anchor-id="virtual-environments">Virtual environments</h2>
 <p>You can even go a step further and help others to recreate the same computing environment that you used independently of what versions you have installed on your machine.</p>
 <p><a href="https://media.giphy.com/media/v1.Y2lkPTc5MGI3NjExemkwd3RnMzA4a3FocHZ2bWJscHgxNG9yaW4yeGZ6YzZpaXgzNHJhciZlcD12MV9pbnRlcm5hbF9naWZfYnlfaWQmY3Q9Zw/x2woMnCz4W0Vy/giphy.gif">Level up!</a></p>
-<section id="r" class="level4">
-<h4 class="anchored" data-anchor-id="r">R</h4>
+<section id="r" class="level3">
+<h3 class="anchored" data-anchor-id="r">R</h3>
 <p>Here is a short introduction to <code>renv</code>, an R package that creates virtual environment to encapsulate your R work. <img src="../../img/renv.png" class="img-fluid" alt="source: https://rstudio.github.io/renv/articles/renv.html"></p>
 <p>We are going to add renv to our shorebird data cleaning project. Make sure you have the renv package installed:</p>
 <div class="sourceCode" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"renv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -468,8 +472,8 @@ <h4 class="anchored" data-anchor-id="r">R</h4>
 <p>Use <code>.libPaths()</code> to confirm where package installations are located!</p>
 <p>Want to know more? here is a good resource to get started: <a href="https://rstudio.github.io/renv/articles/renv.html" class="uri">https://rstudio.github.io/renv/articles/renv.html</a></p>
 </section>
-<section id="python" class="level4">
-<h4 class="anchored" data-anchor-id="python">Python</h4>
+<section id="python" class="level3">
+<h3 class="anchored" data-anchor-id="python">Python</h3>
 <p><a href="https://docs.python-guide.org/dev/virtualenvs/#lower-level-virtualenv"><code>virtualenv</code></a> is a tool to create Python virtual environments. In a nutsheel here are the steps to follow:</p>
 <p>Create a new folder, your project folder. I will use EDS213. Make sure you set the path to this folder.</p>
 <ul>
@@ -529,7 +533,6 @@ <h4 class="anchored" data-anchor-id="python">Python</h4>
 <li><p>The environment should be something you should throw away and be able to rebuild easily.</p></li>
 <li><p>Make sure to deactivate when done using it.</p></li>
 </ul>
-</section>
 <section id="if-you-are-using-conda" class="level4">
 <h4 class="anchored" data-anchor-id="if-you-are-using-conda">If you are using Conda</h4>
 <p><strong>Checking what is in the system:</strong></p>
@@ -585,6 +588,7 @@ <h4 class="anchored" data-anchor-id="if-you-are-using-conda">If you are using Co
 <p>More info: <a href="https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html"><u>https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html</u></a></p>
 
 
+</section>
 </section>
 </section>