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         <h1>Introduction</h1>
         <p>Last updated on 2024-01-04 |
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 <hr class="half-width"><p>For example, consider biology.</p>
 <figure><img src="fig/ew-intro.png" alt="This image shows the many different levels of data that biologists might work with. On the highest level, they work with organisms, shown in the image are a wasp, a tree, and a bacteria. On an intermediate level, they may collect raw data from these organisms. Shown in the image are a picture of dividing yeast cells, a western blot, and a floppy disk containing text data. On the final level, they will have visualisations of the raw data. Shown in the image are a picture of dividing cells with fluorescence at the boundary, a bar plot, and a cartoon of gene transcription." class="figure mx-auto d-block"></figure><p>Biologists study organisms, and have to deal with many kinds of data.
 In biology, as in other sciences:</p>
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 understand
 <ul><li>Where do you even start?</li>
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-</h2>
+</ul></section><section><h2 class="section-heading" id="good-news-everyone-has-these-problems">Good news: everyone has these problems!<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a>
+<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a></h2>
 <hr class="half-width"><ul><li>Other people have thought about good practices and created good
 tools.</li>
 <li>You don’t have to reinvent practices and tools.</li>
 <li>You can learn to be “good enough” in scientific computing.</li>
 <li>This is an ongoing process through your career.</li>
-</ul></section><section id="principles-planning-modular-organization-names-documentation"><h2 class="section-heading">Principles: planning, modular organization, names,
+</ul></section><section><h2 class="section-heading" id="principles-planning-modular-organization-names-documentation">Principles: planning, modular organization, names,
 documentation<a class="anchor" aria-label="anchor" href="#principles-planning-modular-organization-names-documentation"></a>
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 <hr class="half-width"><p>This lesson has episodes covering data management, software, project
 organization, collaboration, keeping track of changes, and
 manuscripts.</p>
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         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
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       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Management</h1>
         <p>Last updated on 2024-01-04 |
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         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/02-data_management.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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 <hr class="half-width"><p>Data within a project may need to exist in various forms, ranging
 from what first arrives to what is actually used for the primary
 analyses. Data management is the process of storing, documenting,
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 <figure><img src="fig/ew-data-loss.png" alt="A comic strip titled 'The four stages of data loss' and subtitled 'dealing with accidental deletion of months of hard-earned data' by PhD Comics. It's based on the common theory of five stages of grief. The first panel is labelled 'stage 1: denial' and shows a man sitting behind a computer. A thought bubble above his head reads 'I did not just erase all my data. I surely made a back-up somewhere'. The second panel is labelled 'stage 2: anger' and shows the man shaking his computer. A speech bubble above his head shows he is shouting 'you stupid piece of crap! Where's my data?!'. The third panel is labelled 'stage 3: depression'. It shows the man crying, the broken computer beside him. He thinks 'Why? Why me?'. The fourth and final panel is labelled 'stage 4: acceptance'. It shows the man coming to terms with what has happened. He says 'I'm never going to graduate'." class="figure mx-auto d-block"><div class="figcaption">Source: PHD Comics. <a href="https://phdcomics.com/comics/archive.php/images/archive.php?comicid=382" class="external-link">“Four
 stages of data loss”</a>
 </div>
-</figure></section><section id="save-the-raw-data"><h2 class="section-heading">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
-</h2>
+</figure></section><section><h2 class="section-heading" id="save-the-raw-data">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
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 incremental backup or specialized storage systems, and people in your
 local IT group or library can often provide advice and assistance on
 options at your university or organization as well.</p>
-</section><section id="working-with-sensitive-data"><h2 class="section-heading">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="working-with-sensitive-data">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a></h2>
 <hr class="half-width"><p>Identify whether your project will work with sensitive data - by
 which we might mean:</p>
 <ul><li>Research data including personal data or identifiers (this might
@@ -531,8 +531,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 Regulation, known as the GDPR). These laws vary between countries and
 may affect whether you can share information between collaborators in
 different countries.</p>
-</section><section id="create-the-data-you-wish-to-see-in-the-world"><h2 class="section-heading">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
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+</section><section><h2 class="section-heading" id="create-the-data-you-wish-to-see-in-the-world">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
+<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a></h2>
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 <li>Use unique identifiers for every record in a table, allowing
 linkages between tables (e.g. sample identifiers are recorded in the
 sequencing experiment metadata)</li>
-</ul></section><section id="create-analysis-friendly-data"><h2 class="section-heading">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="create-analysis-friendly-data">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
+<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a></h2>
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 several time points. Be prepared to gather such columns into a variable
 of measurements, plus a new variable for time point. The figure above
 presents an example of such a transformation.</p>
-</section><section id="record-all-the-steps-used-to-process-data"><h2 class="section-heading">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="record-all-the-steps-used-to-process-data">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
+<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a></h2>
 <hr class="half-width"><p>Data manipulation is as integral to your analysis as statistical
 modeling and inference. If you do not document this step thoroughly, it
 is impossible for you, or anyone else, to repeat the analysis.</p>
@@ -646,9 +646,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 </div>
 </div>
 </div>
-</section><section id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"><h2 class="section-heading">Use multiple tables as necessary, and use a unique identifier for
+</section><section><h2 class="section-heading" id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record">Use multiple tables as necessary, and use a unique identifier for
 every record<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a></h2>
 <hr class="half-width"><p>Raw data, even if tidy, is not necessarily complete. For example, the
 primary data table might hold the heart rate for individual subjects at
 rest and after a physical challenge, identified via a subject ID.
@@ -659,9 +659,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 “014025” in another. It is generally wise to give each record or unit a
 unique, persistent key and to use the same names and codes when
 variables in two datasets refer to the same thing.</p>
-</section><section id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"><h2 class="section-heading">Submit data to a reputable DOI-issuing repository so that others can
+</section><section><h2 class="section-heading" id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it">Submit data to a reputable DOI-issuing repository so that others can
 access and cite it<a class="anchor" aria-label="anchor" href="#submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"></a></h2>
 <hr class="half-width"><div id="sharing-your-data-with-the-world-5-minutes" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
@@ -757,8 +757,8 @@ <h3 class="callout-title">Places to share Data, with DOIs<a class="anchor" aria-
 </ul></div>
 </div>
 </div>
-</section><section id="data-management-plans"><h2 class="section-heading">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
-</h2>
+</section><section><h2 class="section-heading" id="data-management-plans">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
+<a class="anchor" aria-label="anchor" href="#data-management-plans"></a></h2>
 <hr class="half-width"><p>Many universities and funders require researchers to complete a data
 management plan (DMP). A DMP is a document which outlines information
 about your research data and how it will be processed. Many funders
@@ -821,8 +821,8 @@ <h3 class="callout-title">What’s your next step in data management?<a class="a
 </ul></div>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-</h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Taken in order, the recommendations above will make it easier to keep
 track of your data and to work with it. Saving the raw data along with
 clear metadata, backed up, is your insurance policy. Creating
@@ -887,7 +887,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Introduction
         </a>
         <a class="chapter-link float-end" href="03-software.html" rel="next">
-          Next: Code and Software... 
+          Next: Code and Software...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -898,18 +898,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/02-data_management.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
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 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -934,7 +934,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/02-data_management.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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               </div><!--div.sidenav-view-selector -->
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         <a href="index.html">Summary and Setup</a>
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@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
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@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="02-data_management.html">2. Data Management</a>
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@@ -220,7 +220,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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       <div class="accordion-body">
         <ul><li><a href="#what-your-future-self-may-think">What your future self may think…</a></li>
@@ -237,7 +237,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#code-can-be-managed-like-data">Code can be managed like data</a></li>
         </ul></div><!--/div.accordion-body-->
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         <a href="04-collaboration.html">4. Collaboration</a>
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@@ -255,7 +255,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
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                     </ul></div>
                 </div>
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             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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           Previous: Data Management
         </a>
         <a class="chapter-link float-end" href="04-collaboration.html" rel="next">
-          Next: Collaboration... 
+          Next: Collaboration...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Code and Software</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/03-software.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
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+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -383,8 +383,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="what-your-future-self-may-think"><h2 class="section-heading">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
-</h2>
+<section><h2 class="section-heading" id="what-your-future-self-may-think">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
+<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a></h2>
 <hr class="half-width"><figure><img src="fig/ew-software-twit.png" alt="A tweet from Neil Ferguson, posted on March 22nd 2020. It reads 'I'm conscious that lots of people would like to see and run the pandemic simulation code we are using to model control measures against COVID-19. To explain the background — I wrote the code (thousands of lines on undocumented C) 13 plus years ago to model flu pandemics…'" class="figure mx-auto d-block"></figure><p>The <a href="https://twitter.com/neil_ferguson/status/1241835454707699713" class="external-link">twitter
 thread illustrates a real example of research software problems</a>,
 from <a href="https://en.wikipedia.org/wiki/Neil_Ferguson_(epidemiologist)" class="external-link">Prof. Neil
@@ -398,8 +398,8 @@ <h3 class="card-title">Objectives</h3>
 adapt your analysis to a new dataset</li>
 <li>you publish a paper, and a masters student from the other side of
 the world emails you to reproduce the results for their project</li>
-</ul></section><section id="what-is-research-code-and-software"><h2 class="section-heading">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="what-is-research-code-and-software">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
+<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a></h2>
 <hr class="half-width"><p>There are many different shapes and sizes of research software:</p>
 <ul><li>Any code that runs in order to process your research data.</li>
 <li>A record of all the steps used to process your data (scripts and
@@ -459,9 +459,9 @@ <h4 class="accordion-header" id="headingSolution1"> Suggestions </h4>
 benefit for you and collaborators.</p>
 <p>Programs themselves are modular, and can be written in scripts that
 run a clearly-defined set of functions on defined inputs.</p>
-</section><section id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"><h2 class="section-heading">Place a brief explanatory comment at the start of every script or
+</section><section><h2 class="section-heading" id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program">Place a brief explanatory comment at the start of every script or
 program<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a></h2>
 <hr class="half-width"><p>Short is fine; always include at least one example of how the program
 is used. Remember, a good example is worth a thousand words. Where
 possible, the comment should also indicate reasonable values for
@@ -530,8 +530,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="decompose-programs-into-functions"><h2 class="section-heading">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
-</h2>
+</section><section><h2 class="section-heading" id="decompose-programs-into-functions">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
+<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a></h2>
 <hr class="half-width"><p>A function is a reusable section of software that can be treated as a
 black box by the rest of the program. This is like the way we combine
 actions in everyday life. Suppose that it is teatime. You could get a
@@ -633,8 +633,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="be-ruthless-about-eliminating-duplication"><h2 class="section-heading">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
-</h2>
+</section><section><h2 class="section-heading" id="be-ruthless-about-eliminating-duplication">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
+<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a></h2>
 <hr class="half-width"><p>Write and re-use functions instead of copying and pasting code, and
 use data structures like lists instead of creating many closely-related
 variables, e.g. create <code>score = (1, 2, 3)</code> rather than
@@ -649,8 +649,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 So <strong><em>always search for well-maintained software libraries that
 do what you need</em></strong> before writing new code yourself, but
 <strong><em>test libraries before relying on them</em></strong>.</p>
-</section><section id="give-functions-and-variables-meaningful-names"><h2 class="section-heading">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
-</h2>
+</section><section><h2 class="section-heading" id="give-functions-and-variables-meaningful-names">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
+<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a></h2>
 <hr class="half-width"><p>Meaningful names for functions and variables document their purpose
 and make the program generally easy to read. As a rule of thumb, the
 greater the scope of a variable, the more informative its name should
@@ -743,16 +743,16 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 </div>
 </div>
 </div>
-</section><section id="make-dependencies-and-requirements-explicit."><h2 class="section-heading">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
-</h2>
+</section><section><h2 class="section-heading" id="make-dependencies-and-requirements-explicit-">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
+<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit-"></a></h2>
 <hr class="half-width"><p>This is usually done on a per-project rather than per-program basis,
 i.e., by adding a file called something like
 <code>requirements.txt</code> to the root directory of the project, or
 by adding a “Getting Started” section to the <code>README</code>
 file.</p>
-</section><section id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"><h2 class="section-heading">Do not comment and uncomment sections of code to control a program’s
+</section><section><h2 class="section-heading" id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior">Do not comment and uncomment sections of code to control a program’s
 behavior<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a></h2>
 <hr class="half-width"><p>This is error prone and makes it difficult or impossible to automate
 analyses. Instead, put if/else statements in the program to control what
 it does, and use input arguments on the command line to select
@@ -760,8 +760,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 <code>--option</code> and corresponding if/else statements to control
 running an optional piece of the program. Remember to use descriptive
 names for input arguments.</p>
-</section><section id="provide-a-simple-example-or-test-data-set"><h2 class="section-heading">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
-</h2>
+</section><section><h2 class="section-heading" id="provide-a-simple-example-or-test-data-set">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
+<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a></h2>
 <hr class="half-width"><p>Users (including yourself) can run your program on this set to
 determine whether it is working and whether it gives a known correct
 output for a simple known input. Such a test is particularly helpful
@@ -769,8 +769,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 it has to run on several different machines, e.g., the developer’s
 laptop and the department’s cluster. This type of test is called an
 integration test.</p>
-</section><section id="code-can-be-managed-like-data"><h2 class="section-heading">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="code-can-be-managed-like-data">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
+<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a></h2>
 <hr class="half-width"><p>Your code is like your data and also needs to be managed, backed up,
 and shared.</p>
 <p>Your software is as much a product of your research as your papers,
@@ -822,7 +822,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Data Management
         </a>
         <a class="chapter-link float-end" href="04-collaboration.html" rel="next">
-          Next: Collaboration... 
+          Next: Collaboration...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -833,18 +833,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/03-software.md" class="external-link">Edit on GitHub</a>
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+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -869,7 +869,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/03-software.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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             </li>
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         <a href="01-introduction.html">1. Introduction</a>
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         <a href="03-software.html">3. Code and Software</a>
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         </span>
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@@ -242,7 +242,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#recommended-resources">Recommended resources</a></li>
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         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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           Previous: Code and Software
         </a>
         <a class="chapter-link float-end" href="05-project_organization.html" rel="next">
-          Next: Project Organization... 
+          Next: Project Organization...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Collaboration</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/04-collaboration.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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         </div>
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 </div>
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 </div>
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-</h2>
+<section><h2 class="section-heading" id="create-an-overview-of-your-project">Create an overview of your project<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
+<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a></h2>
 <hr class="half-width"><p>Written documentation is essential for collaboration. Future you will
 forget things, and your collaborators will not know them in the first
 place. An overview document can collect the most important information
@@ -453,8 +453,8 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <li>Up-to-date contact information</li>
 <li>An example or two of how to run the most important tasks</li>
 <li>Overview of folder structure</li>
-</ul></section><section id="describe-how-to-contribute-to-the-project"><h2 class="section-heading">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="describe-how-to-contribute-to-the-project">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a></h2>
 <hr class="half-width"><p>Because the README is usually the first thing users and collaborators
 on your project will look at, make it explicit how you want people to
 engage with the project. If you are looking for more contributors, make
@@ -514,8 +514,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="create-a-shared-to-do-list"><h2 class="section-heading">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
-</h2>
+</section><section><h2 class="section-heading" id="create-a-shared-to-do-list">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
+<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a></h2>
 <hr class="half-width"><p>This can be a plain text file called something like
 <code>notes.txt</code> or <code>todo.txt</code>, or you can use sites
 such as GitHub or Bitbucket to create a new <em>issue</em> for each
@@ -523,23 +523,23 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 point newcomers at issues that are good starting points.) Whatever you
 choose, describe the items clearly so that they make sense to
 newcomers.</p>
-</section><section id="decide-on-communication-strategies"><h2 class="section-heading">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
-</h2>
+</section><section><h2 class="section-heading" id="decide-on-communication-strategies">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
+<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a></h2>
 <hr class="half-width"><p>Make explicit decisions about (and publicize where appropriate) how
 members of the project will communicate with each other and with
 external users / collaborators. This includes the location and
 technology for email lists, chat channels, voice / video conferencing,
 documentation, and meeting notes, as well as which of these channels
 will be public or private.</p>
-</section><section id="collaborations-with-sensitive-data"><h2 class="section-heading">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="collaborations-with-sensitive-data">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a></h2>
 <hr class="half-width"><p>If you determine that your project will include work with sensitive
 data, it is important to agree with collaborators on how and where the
 data will be stored, as well as what the mechanisms for sharing the data
 will be and who is ultimately responsible for ensuring these are
 followed.</p>
-</section><section id="make-the-license-explicit"><h2 class="section-heading">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
-</h2>
+</section><section><h2 class="section-heading" id="make-the-license-explicit">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a></h2>
 <hr class="half-width"><div id="what-is-a-licence" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
@@ -586,8 +586,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 permissively-licensed software into other projects, see chapter three in
 [<a href="https://www.oreilly.com/library/view/understanding-open-source/0596005814/" class="external-link">laurent2004</a>].</p>
 </blockquote>
-</section><section id="make-the-project-citable"><h2 class="section-heading">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
-</h2>
+</section><section><h2 class="section-heading" id="make-the-project-citable">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a></h2>
 <hr class="half-width"><p>A <code>CITATION</code> file describes how to cite this project as a
 whole, and where to find (and how to cite) any data sets, code, figures,
 and other artifacts that have their own DOIs. The example below shows
@@ -600,8 +600,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 Morris, B.D. and E.P. White. 2013. "The EcoData Retriever:
 improving access to existing ecological data." PLOS ONE 8:e65848.
 http://doi.org/doi:10.1371/journal.pone.0065848</code></pre>
-</section><section id="recommended-resources"><h2 class="section-heading">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
-</h2>
+</section><section><h2 class="section-heading" id="recommended-resources">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
+<a class="anchor" aria-label="anchor" href="#recommended-resources"></a></h2>
 <hr class="half-width"><ul><li><a href="https://the-turing-way.netlify.app/collaboration/collaboration.html" class="external-link">The
 Turing Way Guide for Collaboration</a></li>
 </ul><div id="attribution" class="callout">
@@ -646,7 +646,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Code and Software
         </a>
         <a class="chapter-link float-end" href="05-project_organization.html" rel="next">
-          Next: Project Organization... 
+          Next: Project Organization...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
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       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/04-collaboration.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -693,7 +693,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/04-collaboration.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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         <a href="index.html">Summary and Setup</a>
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@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="01-introduction.html">1. Introduction</a>
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         <a href="03-software.html">3. Code and Software</a>
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         </span>
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         <a href="08-what_next.html">8. What To Do Next</a>
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                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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           Previous: Collaboration
         </a>
         <a class="chapter-link float-end" href="06-track_changes.html" rel="next">
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+          Next: Keeping Track of...
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         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Project Organization</h1>
         <p>Last updated on 2024-01-04 |
-        
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         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/05-project_organization.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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         </div>
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 </div>
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 </div>
-<section id="put-each-project-in-its-own-directory-which-is-named-after-the-project"><h2 class="section-heading">Put each project in its own directory, which is named after the
+<section><h2 class="section-heading" id="put-each-project-in-its-own-directory-which-is-named-after-the-project">Put each project in its own directory, which is named after the
 project<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a></h2>
 <hr class="half-width"><p>Similar to deciding when a chunk of code should be made a function,
 the ultimate goal of dividing research into distinct projects is to help
 you and others best understand your work. Some researchers create a
@@ -441,17 +441,17 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 names help you effectively find and use things later. Your lab or
 organization may have a template to use.</p>
 </blockquote>
-</section><section id="put-text-documents-associated-with-the-project-in-the-doc-directory."><h2 class="section-heading">Put text documents associated with the project in the
+</section><section><h2 class="section-heading" id="put-text-documents-associated-with-the-project-in-the-doc-directory-">Put text documents associated with the project in the
 <code>doc</code> directory.<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory."></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory-"></a></h2>
 <hr class="half-width"><p>This includes files for manuscripts, documentation for source code,
 and/or an electronic lab notebook recording your experiments.
 Subdirectories may be created for these different classes of files in
 large projects.</p>
-</section><section id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"><h2 class="section-heading">Put raw data and metadata in a <code>data</code> directory, and
+</section><section><h2 class="section-heading" id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory">Put raw data and metadata in a <code>data</code> directory, and
 files generated during cleanup and analysis in a <code>results</code>
 directory<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a></h2>
 <hr class="half-width"><p>When we refer to “generated files”, this includes intermediate
 results, such as cleaned data sets or simulated data, as well as final
 results such as figures and tables.</p>
@@ -464,8 +464,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 together. Similarly, the <code>data</code> directory might require
 subdirectories to organize raw data based on time, method of collection,
 or other metadata most relevant to your analysis.</p>
-</section><section id="put-project-source-code-in-the-src-directory"><h2 class="section-heading">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
-</h2>
+</section><section><h2 class="section-heading" id="put-project-source-code-in-the-src-directory">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a></h2>
 <hr class="half-width"><p><code>src</code> contains all of the code written for the project.
 This includes programs written in interpreted languages such as R or
 Python; those written compiled languages like Fortran, C++, or Java; as
@@ -500,8 +500,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 
     echo "Cleaning up..."
     rm -rf $(TEMP_DIR)</code></pre>
-</section><section id="put-compiled-programs-in-the-bin-directory"><h2 class="section-heading">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
-</h2>
+</section><section><h2 class="section-heading" id="put-compiled-programs-in-the-bin-directory">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a></h2>
 <hr class="half-width"><p><code>bin</code> contains executable programs compiled from code in
 the <code>src</code> directory. Projects that do not have any will not
 require <code>bin</code>.</p>
@@ -526,8 +526,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 the same rule. As with many of our other recommendations, consistency
 and predictability are more important than hair-splitting.</p>
 </blockquote>
-</section><section id="name-all-files-to-reflect-their-content-or-function."><h2 class="section-heading">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
-</h2>
+</section><section><h2 class="section-heading" id="name-all-files-to-reflect-their-content-or-function-">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
+<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function-"></a></h2>
 <hr class="half-width"><p>For example, use names such as <code>bird_count_table.csv</code>,
 <code>manuscript.md</code>, or <code>sightings_analysis.py</code>. Do
 <em>not</em> use sequential numbers (e.g., <code>result1.csv</code>,
@@ -542,8 +542,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 <li>Optional: Consistent</li>
 <li>Optional: Play well with default ordering</li>
 </ul></blockquote>
-</section><section id="example"><h2 class="section-heading">Example<a class="anchor" aria-label="anchor" href="#example"></a>
-</h2>
+</section><section><h2 class="section-heading" id="example">Example<a class="anchor" aria-label="anchor" href="#example"></a>
+<a class="anchor" aria-label="anchor" href="#example"></a></h2>
 <hr class="half-width"><p>The diagram below provides a concrete example of how a simple project
 might be organized following these recommendations:</p>
 <pre><code>    .
@@ -601,23 +601,23 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <li>on/off are different media (on sucrose, off sucrose)</li>
 <li>measurement date</li>
 <li>other details are timepoint and raw or normalized data</li>
-</ul><pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv  
-2020-07-14_s1_phyA_on_LD_t05.raw.csv  
-2020-07-14_s2_phyB_on_SD_t11.raw.csv  
-2020-08-12_s03_phyA_on_LD_t03.raw.csv  
-2020-08-12_s12_phyB_on_LD_t01.raw.csv  
-2020-08-13_s01_phyB_on_SD_t02.raw.csv  
-2020-7-12_s2_phyB_on_SD_t01.raw.csv  
-AUG-13_phyB_on_LD_s1_t11.raw.csv  
-JUL-31_phyB_on_LD_s1_t03.raw.csv  
-LD_phyA_off_t04_2020-08-12.norm.csv  
-LD_phyA_on_t04_2020-07-14.norm.csv  
-LD_phyB_off_t04_2020-08-12.norm.csv  
-LD_phyB_on_t04_2020-07-14.norm.csv  
-SD_phyB_off_t04_2020-08-13.norm.csv  
-SD_phyB_on_t04_2020-07-12.norm.csv  
-SD_phya_off_t04_2020-08-13.norm.csv  
-SD_phya_ons_t04_2020-07-12.norm.csv  
+</ul><pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv
+2020-07-14_s1_phyA_on_LD_t05.raw.csv
+2020-07-14_s2_phyB_on_SD_t11.raw.csv
+2020-08-12_s03_phyA_on_LD_t03.raw.csv
+2020-08-12_s12_phyB_on_LD_t01.raw.csv
+2020-08-13_s01_phyB_on_SD_t02.raw.csv
+2020-7-12_s2_phyB_on_SD_t01.raw.csv
+AUG-13_phyB_on_LD_s1_t11.raw.csv
+JUL-31_phyB_on_LD_s1_t03.raw.csv
+LD_phyA_off_t04_2020-08-12.norm.csv
+LD_phyA_on_t04_2020-07-14.norm.csv
+LD_phyB_off_t04_2020-08-12.norm.csv
+LD_phyB_on_t04_2020-07-14.norm.csv
+SD_phyB_off_t04_2020-08-13.norm.csv
+SD_phyB_on_t04_2020-07-12.norm.csv
+SD_phya_off_t04_2020-08-13.norm.csv
+SD_phya_ons_t04_2020-07-12.norm.csv
 ld_phyA_ons_t04_2020-08-12.norm.csv  </code></pre>
 <ul><li>What are the problems with having the date first?</li>
 <li>How do different date formats behave once sorted?</li>
@@ -637,7 +637,7 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul><li>Using dates up front makes it difficult to quickly find data for
 particular conditions or genotypes. It also masks the “logical” order of
@@ -728,7 +728,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Collaboration
         </a>
         <a class="chapter-link float-end" href="06-track_changes.html" rel="next">
-          Next: Keeping Track of... 
+          Next: Keeping Track of...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -739,18 +739,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/05-project_organization.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -775,7 +775,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/05-project_organization.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/06-track_changes.html b/06-track_changes.html
index 06b5d859..67dd29d8 100644
--- a/06-track_changes.html
+++ b/06-track_changes.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -247,7 +247,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       </button>
     </div><!--/div.accordion-header-->
-        
+
     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created">Back up (almost) everything created by a human being as soon as it
@@ -263,7 +263,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#what-not-to-put-under-version-control">What Not to Put Under Version Control</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -272,7 +272,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading8">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -281,7 +281,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading9">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -307,16 +307,16 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -337,18 +337,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Project Organization
         </a>
         <a class="chapter-link float-end" href="07-manuscripts.html" rel="next">
-          Next: Manuscripts... 
+          Next: Manuscripts...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Keeping Track of Changes</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/06-track_changes.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -435,14 +435,14 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 </ol><p>and you can use the first while working towards the second, or just
 jump in to version control.</p>
 <p>Whatever system you chose, we recommend that you:</p>
-<section id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"><h2 class="section-heading">Back up (almost) everything created by a human being as soon as it
+<section><h2 class="section-heading" id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created">Back up (almost) everything created by a human being as soon as it
 is created<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a></h2>
 <hr class="half-width"><p>This includes scripts and programs of all kinds, software packages
 that your project depends on, and documentation. A few exceptions to
 this rule are discussed below.</p>
-</section><section id="keep-changes-small"><h2 class="section-heading">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
-</h2>
+</section><section><h2 class="section-heading" id="keep-changes-small">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
+<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a></h2>
 <hr class="half-width"><p>Each change should not be so large as to make the change tracking
 irrelevant. For example, a single change such as “Revise script file”
 that adds or changes several hundred lines is likely too large, as it
@@ -451,8 +451,8 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 pieces that are too small. As a rule of thumb, a good size for a single
 change is a group of edits that you could imagine wanting to undo in one
 step at some point in the future.</p>
-</section><section id="share-changes-frequently"><h2 class="section-heading">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
-</h2>
+</section><section><h2 class="section-heading" id="share-changes-frequently">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
+<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a></h2>
 <hr class="half-width"><p>Everyone working on the project should share and incorporate changes
 from others on a regular basis. Do not allow individual investigator’s
 versions of the project repository to drift apart, as the effort
@@ -460,17 +460,17 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 difference. This is particularly important for the manual versioning
 procedure described below, which does not provide any assistance for
 merging simultaneous, possibly conflicting, changes.</p>
-</section><section id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"><h2 class="section-heading">Create, maintain, and use a checklist for saving and sharing changes
+</section><section><h2 class="section-heading" id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project">Create, maintain, and use a checklist for saving and sharing changes
 to the project<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a></h2>
 <hr class="half-width"><p>The list should include writing log messages that clearly explain any
 changes, the size and content of individual changes, style guidelines
 for code, updating to-do lists, and bans on committing half-done work or
 broken code. See [<a href="https://books.google.co.uk/books/about/The_Checklist_Manifesto.html?id=qoZCRAAACAAJ&amp;redir_esc=y" class="external-link">gawande2011</a>]
 for more on the proven value of checklists.</p>
-</section><section id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"><h2 class="section-heading">Store each project in a folder that is mirrored off the researcher’s
+</section><section><h2 class="section-heading" id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine">Store each project in a folder that is mirrored off the researcher’s
 working machine<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a></h2>
 <hr class="half-width"><p>This may include:</p>
 <ul><li>using a shared system such as a (institutional) cloud or shared
 drive, or</li>
@@ -518,8 +518,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-</section><section id="manual-versioning"><h2 class="section-heading">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
-</h2>
+</section><section><h2 class="section-heading" id="manual-versioning">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
+<a class="anchor" aria-label="anchor" href="#manual-versioning"></a></h2>
 <hr class="half-width"><p>Our first suggested approach, in which everything is done by hand,
 has two additional parts:</p>
 <ol style="list-style-type: decimal"><li>
@@ -570,8 +570,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 single person is working on specific files at any time. In particular,
 they may wish to create one change log file per contributor, and to
 merge those files whenever a backup copy is made.</p>
-</section><section id="version-control-systems"><h2 class="section-heading">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
-</h2>
+</section><section><h2 class="section-heading" id="version-control-systems">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
+<a class="anchor" aria-label="anchor" href="#version-control-systems"></a></h2>
 <hr class="half-width"><p>What the manual process described above requires most is
 self-discipline. The version control tools that underpin our second
 approach—the one we use in our own projects–don’t just accelerate the
@@ -657,7 +657,7 @@ <h3 class="callout-title">Changelog in action<a class="anchor" aria-label="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Some good things:</p>
 <ul><li>all log entries contain date and author</li>
@@ -684,8 +684,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="what-not-to-put-under-version-control"><h2 class="section-heading">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
-</h2>
+</section><section><h2 class="section-heading" id="what-not-to-put-under-version-control">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a></h2>
 <hr class="half-width"><p>The benefits of version control systems don’t apply equally to all
 file types. In particular, version control can be more or less rewarding
 depending on file size and format. First, file comparison in version
@@ -793,7 +793,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Project Organization
         </a>
         <a class="chapter-link float-end" href="07-manuscripts.html" rel="next">
-          Next: Manuscripts... 
+          Next: Manuscripts...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -804,18 +804,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/06-track_changes.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -840,7 +840,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/06-track_changes.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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index d446c30a..66900c81 100644
--- a/07-manuscripts.html
+++ b/07-manuscripts.html
@@ -46,7 +46,7 @@
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           </ul></li>
       </div>
-      
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         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
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     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
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     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
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@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
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@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
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@@ -242,7 +242,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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@@ -256,7 +256,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
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@@ -267,7 +267,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#supplementary-materials">Supplementary Materials</a></li>
         </ul></div><!--/div.accordion-body-->
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@@ -302,16 +302,16 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
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                 </div>
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             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -332,18 +332,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Keeping Track of
         </a>
         <a class="chapter-link float-end" href="08-what_next.html" rel="next">
-          Next: What To Do Next... 
+          Next: What To Do Next...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Manuscripts</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/07-manuscripts.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -412,8 +412,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 write a manuscript. Then agree on a decision and process, and put the
 outcome in writing. If co-authors are learning new tools, ask someone
 familiar with those tools to support them!</p>
-<section id="making-email-based-workflows-work"><h2 class="section-heading">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
-</h2>
+<section><h2 class="section-heading" id="making-email-based-workflows-work">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
+<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a></h2>
 <hr class="half-width"><p>A common practice in academic writing is for the lead author to email
 successive versions of a manuscript to coauthors to collect feedback,
 which is returned as changes to the document, comments on the document,
@@ -437,8 +437,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 responsible for merging comments and sending out updated manuscripts to
 all other co-authors.</li>
 </ol></blockquote>
-</section><section id="good-practices-beyond-an-email-based-workflow"><h2 class="section-heading">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
-</h2>
+</section><section><h2 class="section-heading" id="good-practices-beyond-an-email-based-workflow">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
+<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a></h2>
 <hr class="half-width"><p>Instead of an email-based workflow, we recommend mirroring good
 practices for managing software and data to make writing scalable,
 collaborative, and reproducible. As with our recommendations for version
@@ -457,8 +457,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 and to tell if it is up to date.</p></li>
 <li><p>Make it easy to share that final version with collaborators and
 to submit it to a journal.</p></li>
-</ul></section><section id="single-master-online"><h2 class="section-heading">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="single-master-online">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
+<a class="anchor" aria-label="anchor" href="#single-master-online"></a></h2>
 <hr class="half-width"><p>Our first alternative will already be familiar to many
 researchers:</p>
 <ol style="list-style-type: decimal"><li>
@@ -477,8 +477,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 do this automatically when switching from a desktop file format to text
 and back (although <a href="https://pandoc.org/" class="external-link">Pandoc</a> can go a
 long way).</p>
-</section><section id="text-based-documents-under-version-control"><h2 class="section-heading">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
-</h2>
+</section><section><h2 class="section-heading" id="text-based-documents-under-version-control">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a></h2>
 <hr class="half-width"><p>The second approach treats papers exactly like software, and has been
 used by researchers in mathematics, astronomy, physics, and related
 disciplines for decades:</p>
@@ -507,8 +507,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 <li>Separate sentences by linebreaks in your plain-text document, to
 make comparisons and merging easier.</li>
 </ol></blockquote>
-</section><section id="benefits-and-drawbacks-of-each-approach"><h2 class="section-heading">Benefits and drawbacks of each approach<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
-</h2>
+</section><section><h2 class="section-heading" id="benefits-and-drawbacks-of-each-approach">Benefits and drawbacks of each approach<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
+<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a></h2>
 <hr class="half-width"><table class="table"><colgroup><col width="37%"><col width="17%"><col width="17%"><col width="27%"></colgroup><thead><tr class="header"><th>Things to consider</th>
 <th>Email based workflow</th>
 <th>Single master online</th>
@@ -574,8 +574,8 @@ <h3 class="callout-title">Getting started writing text-based version control<a c
 </div>
 </div>
 </div>
-</section><section id="supplementary-materials"><h2 class="section-heading">Supplementary Materials<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
-</h2>
+</section><section><h2 class="section-heading" id="supplementary-materials">Supplementary Materials<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
+<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a></h2>
 <hr class="half-width"><p>Supplementary materials often contain much of the work that went into
 the project, such as tables and figures or more elaborate descriptions
 of the algorithms, software, methods, and analyses. In order to make
@@ -634,7 +634,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Keeping Track of
         </a>
         <a class="chapter-link float-end" href="08-what_next.html" rel="next">
-          Next: What To Do Next... 
+          Next: What To Do Next...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -645,18 +645,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/07-manuscripts.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
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-        
+
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         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -681,7 +681,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/07-manuscripts.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
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         <ul><li><a href="#learning-good-practices-is-a-long-term-process">Learning good practices is a long-term process</a></li>
@@ -273,7 +273,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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                       <li>
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                       </li>
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             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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         <h1>What To Do Next</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/08-what_next.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -383,8 +383,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 </div>
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+<section><h2 class="section-heading" id="learning-good-practices-is-a-long-term-process">Learning good practices is a long-term process<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
+<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a></h2>
 <hr class="half-width"><p>We have outlined a series of good enough practices for scientific
 computing. These practices are pragmatic, broadly accessible, and can be
 applied by both individuals and groups. Most importantly, these
@@ -408,8 +408,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 people, including for your future self. Thinking through your work from
 a collaborator’s point of view is helpful, and ultimately kinder to your
 future self.</p>
-</section><section id="what-we-left-out-and-where-to-learn-more"><h2 class="section-heading">What we left out, and where to learn more<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
-</h2>
+</section><section><h2 class="section-heading" id="what-we-left-out-and-where-to-learn-more">What we left out, and where to learn more<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a></h2>
 <hr class="half-width"><p>Learning good practices is a long-term process that never stops. We
 <a href="what-we-left-out.html">left out many good practices</a> that,
 although useful, have more niche applications.</p>
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 </ul></div>
 </div>
 </div>
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+</section><section><h2 class="section-heading" id="different-people-make-different-contributions-to-good-practice">Different people make different contributions to good practice<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
+<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a></h2>
 <hr class="half-width"><p>Progress in computational good practices comes from different places
 in the scientific community:</p>
 <ul><li>Funders can require <a href="https://www.dcc.ac.uk/resources/data-management-plans" class="external-link">data
@@ -525,18 +525,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/08-what_next.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
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         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -561,7 +561,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/08-what_next.html",
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+  "datePublished": "2024-07-09"
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--- a/404.html
+++ b/404.html
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
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     </div>
 <!--/div.accordion-header-->
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                       <li>
                         <a href="https://carpentries-lab.github.io/good-enough-practices/profiles.html" class="external-link">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="https://carpentries-lab.github.io/good-enough-practices/aio.html" class="external-link">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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-</h2>
+<section><h2 class="section-heading" id="our-apologies">Our apologies!<a class="anchor" aria-label="anchor" href="#our-apologies"></a>
+<a class="anchor" aria-label="anchor" href="#our-apologies"></a></h2>
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 <ol style="list-style-type: decimal"><li>try going back to the <a href="javascript:history.back()">previous
@@ -349,18 +349,18 @@ <h1>Page not found</h1>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
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+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
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           </ul></li>
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         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
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@@ -286,16 +286,16 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
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                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
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@@ -323,11 +323,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -366,18 +366,18 @@ <h1>Contributor Code of Conduct</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
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-        
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 			</div>
@@ -402,7 +402,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/CODE_OF_CONDUCT.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
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--- a/LICENSE.html
+++ b/LICENSE.html
@@ -46,7 +46,7 @@
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         <h1>Licenses</h1>
         <p>Last updated on 2024-01-04 |
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         </div>
 
         
 
-<section id="instructional-material"><h2 class="section-heading">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
-</h2>
+<section><h2 class="section-heading" id="instructional-material">Instructional Material<a class="anchor" aria-label="anchor" href="#instructional-material"></a>
+<a class="anchor" aria-label="anchor" href="#instructional-material"></a></h2>
 <hr class="half-width"><p>All Carpentries (Software Carpentry, Data Carpentry, and Library
 Carpentry) instructional material is made available under the <a href="https://creativecommons.org/licenses/by/4.0/" class="external-link">Creative Commons
 Attribution license</a>. The following is a human-readable summary of
@@ -368,8 +368,8 @@ <h1>Licenses</h1>
 permissions necessary for your intended use. For example, other rights
 such as publicity, privacy, or moral rights may limit how you use the
 material.</li>
-</ul></section><section id="software"><h2 class="section-heading">Software<a class="anchor" aria-label="anchor" href="#software"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="software">Software<a class="anchor" aria-label="anchor" href="#software"></a>
+<a class="anchor" aria-label="anchor" href="#software"></a></h2>
 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
 provided by The Carpentries are made available under the <a href="https://opensource.org" class="external-link">OSI</a>-approved <a href="https://opensource.org/licenses/mit-license.html" class="external-link">MIT
 license</a>.</p>
@@ -389,8 +389,8 @@ <h1>Licenses</h1>
 CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
 TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</p>
-</section><section id="trademark"><h2 class="section-heading">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
-</h2>
+</section><section><h2 class="section-heading" id="trademark">Trademark<a class="anchor" aria-label="anchor" href="#trademark"></a>
+<a class="anchor" aria-label="anchor" href="#trademark"></a></h2>
 <hr class="half-width"><p>“The Carpentries”, “Software Carpentry”, “Data Carpentry”, and
 “Library Carpentry” and their respective logos are registered trademarks
 of <a href="https://communityin.org/" class="external-link">Community Initiatives</a>.</p>
@@ -417,18 +417,18 @@ <h1>Licenses</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/LICENSE.md" class="external-link">Edit on GitHub</a>
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+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -453,7 +453,7 @@ <h1>Licenses</h1>
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/LICENSE.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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 <p>Last updated on 2024-01-04 |
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 <div class="text-end">
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-<section id="challenges-in-data-heavy-biology"><h2 class="section-heading">Challenges in data-heavy biology<a class="anchor" aria-label="anchor" href="#challenges-in-data-heavy-biology"></a>
+<section><h2 class="section-heading" id="challenges-in-data-heavy-biology">Challenges in data-heavy biology<a class="anchor" aria-label="anchor" href="#challenges-in-data-heavy-biology"></a>
+<a class="anchor" aria-label="anchor" href="#challenges-in-data-heavy-biology"></a>
 </h2>
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 <p>For example, consider biology.</p>
@@ -500,7 +501,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <li>Where do you even start?</li>
 </ul>
 </li>
-</ul></section><section id="good-news-everyone-has-these-problems"><h2 class="section-heading">Good news: everyone has these problems!<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a>
+</ul></section><section><h2 class="section-heading" id="good-news-everyone-has-these-problems">Good news: everyone has these problems!<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a>
+<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a>
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 <li>You don’t have to reinvent practices and tools.</li>
 <li>You can learn to be “good enough” in scientific computing.</li>
 <li>This is an ongoing process through your career.</li>
-</ul></section><section id="principles-planning-modular-organization-names-documentation"><h2 class="section-heading">Principles: planning, modular organization, names,
+</ul></section><section><h2 class="section-heading" id="principles-planning-modular-organization-names-documentation">Principles: planning, modular organization, names,
 documentation<a class="anchor" aria-label="anchor" href="#principles-planning-modular-organization-names-documentation"></a>
+<a class="anchor" aria-label="anchor" href="#principles-planning-modular-organization-names-documentation"></a>
 </h2>
 <hr class="half-width">
 <p>This lesson has episodes covering data management, software, project
@@ -550,7 +553,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-02-data_management"><p>Content from <a href="02-data_management.html">Data Management</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
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 </div>
 </div>
 </div>
-<section id="data-management"><h2 class="section-heading">Data management<a class="anchor" aria-label="anchor" href="#data-management"></a>
+<section><h2 class="section-heading" id="data-management">Data management<a class="anchor" aria-label="anchor" href="#data-management"></a>
+<a class="anchor" aria-label="anchor" href="#data-management"></a>
 </h2>
 <hr class="half-width">
 <p>Data within a project may need to exist in various forms, ranging
@@ -637,7 +641,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <figure><img src="fig/ew-data-loss.png" alt="A comic strip titled 'The four stages of data loss' and subtitled 'dealing with accidental deletion of months of hard-earned data' by PhD Comics. It's based on the common theory of five stages of grief. The first panel is labelled 'stage 1: denial' and shows a man sitting behind a computer. A thought bubble above his head reads 'I did not just erase all my data. I surely made a back-up somewhere'. The second panel is labelled 'stage 2: anger' and shows the man shaking his computer. A speech bubble above his head shows he is shouting 'you stupid piece of crap! Where's my data?!'. The third panel is labelled 'stage 3: depression'. It shows the man crying, the broken computer beside him. He thinks 'Why? Why me?'. The fourth and final panel is labelled 'stage 4: acceptance'. It shows the man coming to terms with what has happened. He says 'I'm never going to graduate'." class="figure mx-auto d-block"><div class="figcaption">Source: PHD Comics. <a href="https://phdcomics.com/comics/archive.php/images/archive.php?comicid=382" class="external-link">“Four
 stages of data loss”</a>
 </div>
-</figure></section><section id="save-the-raw-data"><h2 class="section-heading">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
+</figure></section><section><h2 class="section-heading" id="save-the-raw-data">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
+<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
 </h2>
 <hr class="half-width">
 <div id="backing-up-your-data-5-minutes" class="callout challenge">
@@ -722,7 +727,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 incremental backup or specialized storage systems, and people in your
 local IT group or library can often provide advice and assistance on
 options at your university or organization as well.</p>
-</section><section id="working-with-sensitive-data"><h2 class="section-heading">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
+</section><section><h2 class="section-heading" id="working-with-sensitive-data">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
 </h2>
 <hr class="half-width">
 <p>Identify whether your project will work with sensitive data - by
@@ -745,7 +751,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 Regulation, known as the GDPR). These laws vary between countries and
 may affect whether you can share information between collaborators in
 different countries.</p>
-</section><section id="create-the-data-you-wish-to-see-in-the-world"><h2 class="section-heading">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
+</section><section><h2 class="section-heading" id="create-the-data-you-wish-to-see-in-the-world">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
+<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
 </h2>
 <hr class="half-width">
 <div id="discussion-2-minutes" class="callout discussion">
@@ -800,7 +807,8 @@ <h3 class="callout-title">Discussion (2 minutes)<a class="anchor" aria-label="an
 <li>Use unique identifiers for every record in a table, allowing
 linkages between tables (e.g. sample identifiers are recorded in the
 sequencing experiment metadata)</li>
-</ul></section><section id="create-analysis-friendly-data"><h2 class="section-heading">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
+</ul></section><section><h2 class="section-heading" id="create-analysis-friendly-data">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
+<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
 </h2>
 <hr class="half-width">
 <div id="discussion-2-minutes-1" class="callout discussion">
@@ -829,7 +837,8 @@ <h3 class="callout-title">Discussion (2 minutes)<a class="anchor" aria-label="an
 several time points. Be prepared to gather such columns into a variable
 of measurements, plus a new variable for time point. The figure above
 presents an example of such a transformation.</p>
-</section><section id="record-all-the-steps-used-to-process-data"><h2 class="section-heading">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
+</section><section><h2 class="section-heading" id="record-all-the-steps-used-to-process-data">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
+<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
 </h2>
 <hr class="half-width">
 <p>Data manipulation is as integral to your analysis as statistical
@@ -864,8 +873,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 </div>
 </div>
 </div>
-</section><section id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"><h2 class="section-heading">Use multiple tables as necessary, and use a unique identifier for
+</section><section><h2 class="section-heading" id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record">Use multiple tables as necessary, and use a unique identifier for
 every record<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a>
+<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a>
 </h2>
 <hr class="half-width">
 <p>Raw data, even if tidy, is not necessarily complete. For example, the
@@ -878,8 +888,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 “014025” in another. It is generally wise to give each record or unit a
 unique, persistent key and to use the same names and codes when
 variables in two datasets refer to the same thing.</p>
-</section><section id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"><h2 class="section-heading">Submit data to a reputable DOI-issuing repository so that others can
+</section><section><h2 class="section-heading" id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it">Submit data to a reputable DOI-issuing repository so that others can
 access and cite it<a class="anchor" aria-label="anchor" href="#submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"></a>
+<a class="anchor" aria-label="anchor" href="#submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"></a>
 </h2>
 <hr class="half-width">
 <div id="sharing-your-data-with-the-world-5-minutes" class="callout challenge">
@@ -985,7 +996,8 @@ <h3 class="callout-title">Places to share Data, with DOIs<a class="anchor" aria-
 </div>
 </div>
 </div>
-</section><section id="data-management-plans"><h2 class="section-heading">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
+</section><section><h2 class="section-heading" id="data-management-plans">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
+<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
 </h2>
 <hr class="half-width">
 <p>Many universities and funders require researchers to complete a data
@@ -1056,7 +1068,8 @@ <h3 class="callout-title">What’s your next step in data management?<a class="a
 </div>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Taken in order, the recommendations above will make it easier to keep
@@ -1116,7 +1129,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-03-software"><p>Content from <a href="03-software.html">Code and Software</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/03-software.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -1152,7 +1165,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="what-your-future-self-may-think"><h2 class="section-heading">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
+<section><h2 class="section-heading" id="what-your-future-self-may-think">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
+<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
 </h2>
 <hr class="half-width">
 <figure><img src="fig/ew-software-twit.png" alt="A tweet from Neil Ferguson, posted on March 22nd 2020. It reads 'I'm conscious that lots of people would like to see and run the pandemic simulation code we are using to model control measures against COVID-19. To explain the background — I wrote the code (thousands of lines on undocumented C) 13 plus years ago to model flu pandemics…'" class="figure mx-auto d-block"></figure><p>The <a href="https://twitter.com/neil_ferguson/status/1241835454707699713" class="external-link">twitter
@@ -1169,7 +1183,8 @@ <h3 class="card-title">Objectives</h3>
 adapt your analysis to a new dataset</li>
 <li>you publish a paper, and a masters student from the other side of
 the world emails you to reproduce the results for their project</li>
-</ul></section><section id="what-is-research-code-and-software"><h2 class="section-heading">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
+</ul></section><section><h2 class="section-heading" id="what-is-research-code-and-software">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
+<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
 </h2>
 <hr class="half-width">
 <p>There are many different shapes and sizes of research software:</p>
@@ -1235,8 +1250,9 @@ <h4 class="accordion-header" id="headingSolution1"> Suggestions </h4>
 benefit for you and collaborators.</p>
 <p>Programs themselves are modular, and can be written in scripts that
 run a clearly-defined set of functions on defined inputs.</p>
-</section><section id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"><h2 class="section-heading">Place a brief explanatory comment at the start of every script or
+</section><section><h2 class="section-heading" id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program">Place a brief explanatory comment at the start of every script or
 program<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a>
+<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a>
 </h2>
 <hr class="half-width">
 <p>Short is fine; always include at least one example of how the program
@@ -1312,7 +1328,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="decompose-programs-into-functions"><h2 class="section-heading">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
+</section><section><h2 class="section-heading" id="decompose-programs-into-functions">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
+<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
 </h2>
 <hr class="half-width">
 <p>A function is a reusable section of software that can be treated as a
@@ -1418,7 +1435,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="be-ruthless-about-eliminating-duplication"><h2 class="section-heading">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
+</section><section><h2 class="section-heading" id="be-ruthless-about-eliminating-duplication">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
+<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
 </h2>
 <hr class="half-width">
 <p>Write and re-use functions instead of copying and pasting code, and
@@ -1435,7 +1453,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 So <strong><em>always search for well-maintained software libraries that
 do what you need</em></strong> before writing new code yourself, but
 <strong><em>test libraries before relying on them</em></strong>.</p>
-</section><section id="give-functions-and-variables-meaningful-names"><h2 class="section-heading">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
+</section><section><h2 class="section-heading" id="give-functions-and-variables-meaningful-names">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
+<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
 </h2>
 <hr class="half-width">
 <p>Meaningful names for functions and variables document their purpose
@@ -1538,7 +1557,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 </div>
 </div>
 </div>
-</section><section id="make-dependencies-and-requirements-explicit."><h2 class="section-heading">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
+</section><section><h2 class="section-heading" id="make-dependencies-and-requirements-explicit-">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
+<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit-"></a>
 </h2>
 <hr class="half-width">
 <p>This is usually done on a per-project rather than per-program basis,
@@ -1546,8 +1566,9 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 <code>requirements.txt</code> to the root directory of the project, or
 by adding a “Getting Started” section to the <code>README</code>
 file.</p>
-</section><section id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"><h2 class="section-heading">Do not comment and uncomment sections of code to control a program’s
+</section><section><h2 class="section-heading" id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior">Do not comment and uncomment sections of code to control a program’s
 behavior<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a>
+<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a>
 </h2>
 <hr class="half-width">
 <p>This is error prone and makes it difficult or impossible to automate
@@ -1557,7 +1578,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 <code>--option</code> and corresponding if/else statements to control
 running an optional piece of the program. Remember to use descriptive
 names for input arguments.</p>
-</section><section id="provide-a-simple-example-or-test-data-set"><h2 class="section-heading">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
+</section><section><h2 class="section-heading" id="provide-a-simple-example-or-test-data-set">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
+<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
 </h2>
 <hr class="half-width">
 <p>Users (including yourself) can run your program on this set to
@@ -1567,7 +1589,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 it has to run on several different machines, e.g., the developer’s
 laptop and the department’s cluster. This type of test is called an
 integration test.</p>
-</section><section id="code-can-be-managed-like-data"><h2 class="section-heading">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
+</section><section><h2 class="section-heading" id="code-can-be-managed-like-data">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
+<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
 </h2>
 <hr class="half-width">
 <p>Your code is like your data and also needs to be managed, backed up,
@@ -1614,7 +1637,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-04-collaboration"><p>Content from <a href="04-collaboration.html">Collaboration</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/04-collaboration.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -1715,7 +1738,8 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 </div>
 </div>
 </div>
-<section id="create-an-overview-of-your-project"><h2 class="section-heading">Create an overview of your project<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
+<section><h2 class="section-heading" id="create-an-overview-of-your-project">Create an overview of your project<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
+<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
 </h2>
 <hr class="half-width">
 <p>Written documentation is essential for collaboration. Future you will
@@ -1734,7 +1758,8 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <li>Up-to-date contact information</li>
 <li>An example or two of how to run the most important tasks</li>
 <li>Overview of folder structure</li>
-</ul></section><section id="describe-how-to-contribute-to-the-project"><h2 class="section-heading">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
+</ul></section><section><h2 class="section-heading" id="describe-how-to-contribute-to-the-project">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
 </h2>
 <hr class="half-width">
 <p>Because the README is usually the first thing users and collaborators
@@ -1802,7 +1827,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="create-a-shared-to-do-list"><h2 class="section-heading">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
+</section><section><h2 class="section-heading" id="create-a-shared-to-do-list">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
+<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
 </h2>
 <hr class="half-width">
 <p>This can be a plain text file called something like
@@ -1812,7 +1838,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 point newcomers at issues that are good starting points.) Whatever you
 choose, describe the items clearly so that they make sense to
 newcomers.</p>
-</section><section id="decide-on-communication-strategies"><h2 class="section-heading">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
+</section><section><h2 class="section-heading" id="decide-on-communication-strategies">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
+<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
 </h2>
 <hr class="half-width">
 <p>Make explicit decisions about (and publicize where appropriate) how
@@ -1821,7 +1848,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 technology for email lists, chat channels, voice / video conferencing,
 documentation, and meeting notes, as well as which of these channels
 will be public or private.</p>
-</section><section id="collaborations-with-sensitive-data"><h2 class="section-heading">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
+</section><section><h2 class="section-heading" id="collaborations-with-sensitive-data">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
 </h2>
 <hr class="half-width">
 <p>If you determine that your project will include work with sensitive
@@ -1829,7 +1857,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 data will be stored, as well as what the mechanisms for sharing the data
 will be and who is ultimately responsible for ensuring these are
 followed.</p>
-</section><section id="make-the-license-explicit"><h2 class="section-heading">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
+</section><section><h2 class="section-heading" id="make-the-license-explicit">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
 </h2>
 <hr class="half-width">
 <div id="what-is-a-licence" class="callout">
@@ -1880,7 +1909,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 permissively-licensed software into other projects, see chapter three in
 [<a href="https://www.oreilly.com/library/view/understanding-open-source/0596005814/" class="external-link">laurent2004</a>].</p>
 </blockquote>
-</section><section id="make-the-project-citable"><h2 class="section-heading">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
+</section><section><h2 class="section-heading" id="make-the-project-citable">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
 </h2>
 <hr class="half-width">
 <p>A <code>CITATION</code> file describes how to cite this project as a
@@ -1895,7 +1925,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 Morris, B.D. and E.P. White. 2013. "The EcoData Retriever:
 improving access to existing ecological data." PLOS ONE 8:e65848.
 http://doi.org/doi:10.1371/journal.pone.0065848</code></pre>
-</section><section id="recommended-resources"><h2 class="section-heading">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
+</section><section><h2 class="section-heading" id="recommended-resources">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
+<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
 </h2>
 <hr class="half-width">
 <ul>
@@ -1937,7 +1968,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-05-project_organization"><p>Content from <a href="05-project_organization.html">Project Organization</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/05-project_organization.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -2003,8 +2034,9 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 </div>
 </div>
 </div>
-<section id="put-each-project-in-its-own-directory-which-is-named-after-the-project"><h2 class="section-heading">Put each project in its own directory, which is named after the
+<section><h2 class="section-heading" id="put-each-project-in-its-own-directory-which-is-named-after-the-project">Put each project in its own directory, which is named after the
 project<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a>
 </h2>
 <hr class="half-width">
 <p>Similar to deciding when a chunk of code should be made a function,
@@ -2037,17 +2069,19 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 names help you effectively find and use things later. Your lab or
 organization may have a template to use.</p>
 </blockquote>
-</section><section id="put-text-documents-associated-with-the-project-in-the-doc-directory."><h2 class="section-heading">Put text documents associated with the project in the
+</section><section><h2 class="section-heading" id="put-text-documents-associated-with-the-project-in-the-doc-directory-">Put text documents associated with the project in the
 <code>doc</code> directory.<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory."></a>
+<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory-"></a>
 </h2>
 <hr class="half-width">
 <p>This includes files for manuscripts, documentation for source code,
 and/or an electronic lab notebook recording your experiments.
 Subdirectories may be created for these different classes of files in
 large projects.</p>
-</section><section id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"><h2 class="section-heading">Put raw data and metadata in a <code>data</code> directory, and
+</section><section><h2 class="section-heading" id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory">Put raw data and metadata in a <code>data</code> directory, and
 files generated during cleanup and analysis in a <code>results</code>
 directory<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a>
 </h2>
 <hr class="half-width">
 <p>When we refer to “generated files”, this includes intermediate
@@ -2062,7 +2096,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 together. Similarly, the <code>data</code> directory might require
 subdirectories to organize raw data based on time, method of collection,
 or other metadata most relevant to your analysis.</p>
-</section><section id="put-project-source-code-in-the-src-directory"><h2 class="section-heading">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
+</section><section><h2 class="section-heading" id="put-project-source-code-in-the-src-directory">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
 </h2>
 <hr class="half-width">
 <p><code>src</code> contains all of the code written for the project.
@@ -2099,7 +2134,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 
     echo "Cleaning up..."
     rm -rf $(TEMP_DIR)</code></pre>
-</section><section id="put-compiled-programs-in-the-bin-directory"><h2 class="section-heading">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
+</section><section><h2 class="section-heading" id="put-compiled-programs-in-the-bin-directory">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
 </h2>
 <hr class="half-width">
 <p><code>bin</code> contains executable programs compiled from code in
@@ -2126,7 +2162,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 the same rule. As with many of our other recommendations, consistency
 and predictability are more important than hair-splitting.</p>
 </blockquote>
-</section><section id="name-all-files-to-reflect-their-content-or-function."><h2 class="section-heading">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
+</section><section><h2 class="section-heading" id="name-all-files-to-reflect-their-content-or-function-">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
+<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function-"></a>
 </h2>
 <hr class="half-width">
 <p>For example, use names such as <code>bird_count_table.csv</code>,
@@ -2145,7 +2182,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 <li>Optional: Play well with default ordering</li>
 </ul>
 </blockquote>
-</section><section id="example"><h2 class="section-heading">Example<a class="anchor" aria-label="anchor" href="#example"></a>
+</section><section><h2 class="section-heading" id="example">Example<a class="anchor" aria-label="anchor" href="#example"></a>
+<a class="anchor" aria-label="anchor" href="#example"></a>
 </h2>
 <hr class="half-width">
 <p>The diagram below provides a concrete example of how a simple project
@@ -2207,23 +2245,23 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <li>measurement date</li>
 <li>other details are timepoint and raw or normalized data</li>
 </ul>
-<pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv  
-2020-07-14_s1_phyA_on_LD_t05.raw.csv  
-2020-07-14_s2_phyB_on_SD_t11.raw.csv  
-2020-08-12_s03_phyA_on_LD_t03.raw.csv  
-2020-08-12_s12_phyB_on_LD_t01.raw.csv  
-2020-08-13_s01_phyB_on_SD_t02.raw.csv  
-2020-7-12_s2_phyB_on_SD_t01.raw.csv  
-AUG-13_phyB_on_LD_s1_t11.raw.csv  
-JUL-31_phyB_on_LD_s1_t03.raw.csv  
-LD_phyA_off_t04_2020-08-12.norm.csv  
-LD_phyA_on_t04_2020-07-14.norm.csv  
-LD_phyB_off_t04_2020-08-12.norm.csv  
-LD_phyB_on_t04_2020-07-14.norm.csv  
-SD_phyB_off_t04_2020-08-13.norm.csv  
-SD_phyB_on_t04_2020-07-12.norm.csv  
-SD_phya_off_t04_2020-08-13.norm.csv  
-SD_phya_ons_t04_2020-07-12.norm.csv  
+<pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv
+2020-07-14_s1_phyA_on_LD_t05.raw.csv
+2020-07-14_s2_phyB_on_SD_t11.raw.csv
+2020-08-12_s03_phyA_on_LD_t03.raw.csv
+2020-08-12_s12_phyB_on_LD_t01.raw.csv
+2020-08-13_s01_phyB_on_SD_t02.raw.csv
+2020-7-12_s2_phyB_on_SD_t01.raw.csv
+AUG-13_phyB_on_LD_s1_t11.raw.csv
+JUL-31_phyB_on_LD_s1_t03.raw.csv
+LD_phyA_off_t04_2020-08-12.norm.csv
+LD_phyA_on_t04_2020-07-14.norm.csv
+LD_phyB_off_t04_2020-08-12.norm.csv
+LD_phyB_on_t04_2020-07-14.norm.csv
+SD_phyB_off_t04_2020-08-13.norm.csv
+SD_phyB_on_t04_2020-07-12.norm.csv
+SD_phya_off_t04_2020-08-13.norm.csv
+SD_phya_ons_t04_2020-07-12.norm.csv
 ld_phyA_ons_t04_2020-08-12.norm.csv  </code></pre>
 <ul>
 <li>What are the problems with having the date first?</li>
@@ -2245,7 +2283,7 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul>
 <li>Using dates up front makes it difficult to quickly find data for
@@ -2337,7 +2375,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-06-track_changes"><p>Content from <a href="06-track_changes.html">Keeping Track of Changes</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/06-track_changes.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -2430,14 +2468,16 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 <p>and you can use the first while working towards the second, or just
 jump in to version control.</p>
 <p>Whatever system you chose, we recommend that you:</p>
-<section id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"><h2 class="section-heading">Back up (almost) everything created by a human being as soon as it
+<section><h2 class="section-heading" id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created">Back up (almost) everything created by a human being as soon as it
 is created<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a>
+<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a>
 </h2>
 <hr class="half-width">
 <p>This includes scripts and programs of all kinds, software packages
 that your project depends on, and documentation. A few exceptions to
 this rule are discussed below.</p>
-</section><section id="keep-changes-small"><h2 class="section-heading">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
+</section><section><h2 class="section-heading" id="keep-changes-small">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
+<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
 </h2>
 <hr class="half-width">
 <p>Each change should not be so large as to make the change tracking
@@ -2448,7 +2488,8 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 pieces that are too small. As a rule of thumb, a good size for a single
 change is a group of edits that you could imagine wanting to undo in one
 step at some point in the future.</p>
-</section><section id="share-changes-frequently"><h2 class="section-heading">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
+</section><section><h2 class="section-heading" id="share-changes-frequently">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
+<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
 </h2>
 <hr class="half-width">
 <p>Everyone working on the project should share and incorporate changes
@@ -2458,8 +2499,9 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 difference. This is particularly important for the manual versioning
 procedure described below, which does not provide any assistance for
 merging simultaneous, possibly conflicting, changes.</p>
-</section><section id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"><h2 class="section-heading">Create, maintain, and use a checklist for saving and sharing changes
+</section><section><h2 class="section-heading" id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project">Create, maintain, and use a checklist for saving and sharing changes
 to the project<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a>
 </h2>
 <hr class="half-width">
 <p>The list should include writing log messages that clearly explain any
@@ -2467,8 +2509,9 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 for code, updating to-do lists, and bans on committing half-done work or
 broken code. See [<a href="https://books.google.co.uk/books/about/The_Checklist_Manifesto.html?id=qoZCRAAACAAJ&amp;redir_esc=y" class="external-link">gawande2011</a>]
 for more on the proven value of checklists.</p>
-</section><section id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"><h2 class="section-heading">Store each project in a folder that is mirrored off the researcher’s
+</section><section><h2 class="section-heading" id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine">Store each project in a folder that is mirrored off the researcher’s
 working machine<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a>
+<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a>
 </h2>
 <hr class="half-width">
 <p>This may include:</p>
@@ -2524,7 +2567,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-</section><section id="manual-versioning"><h2 class="section-heading">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
+</section><section><h2 class="section-heading" id="manual-versioning">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
+<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
 </h2>
 <hr class="half-width">
 <p>Our first suggested approach, in which everything is done by hand,
@@ -2581,7 +2625,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 single person is working on specific files at any time. In particular,
 they may wish to create one change log file per contributor, and to
 merge those files whenever a backup copy is made.</p>
-</section><section id="version-control-systems"><h2 class="section-heading">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
+</section><section><h2 class="section-heading" id="version-control-systems">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
+<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
 </h2>
 <hr class="half-width">
 <p>What the manual process described above requires most is
@@ -2677,7 +2722,7 @@ <h3 class="callout-title">Changelog in action<a class="anchor" aria-label="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Some good things:</p>
 <ul>
@@ -2710,7 +2755,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="what-not-to-put-under-version-control"><h2 class="section-heading">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
+</section><section><h2 class="section-heading" id="what-not-to-put-under-version-control">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
 </h2>
 <hr class="half-width">
 <p>The benefits of version control systems don’t apply equally to all
@@ -2815,7 +2861,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-07-manuscripts"><p>Content from <a href="07-manuscripts.html">Manuscripts</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/07-manuscripts.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -2888,7 +2934,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 write a manuscript. Then agree on a decision and process, and put the
 outcome in writing. If co-authors are learning new tools, ask someone
 familiar with those tools to support them!</p>
-<section id="making-email-based-workflows-work"><h2 class="section-heading">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
+<section><h2 class="section-heading" id="making-email-based-workflows-work">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
+<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
 </h2>
 <hr class="half-width">
 <p>A common practice in academic writing is for the lead author to email
@@ -2916,7 +2963,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 all other co-authors.</li>
 </ol>
 </blockquote>
-</section><section id="good-practices-beyond-an-email-based-workflow"><h2 class="section-heading">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
+</section><section><h2 class="section-heading" id="good-practices-beyond-an-email-based-workflow">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
+<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
 </h2>
 <hr class="half-width">
 <p>Instead of an email-based workflow, we recommend mirroring good
@@ -2938,7 +2986,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 and to tell if it is up to date.</p></li>
 <li><p>Make it easy to share that final version with collaborators and
 to submit it to a journal.</p></li>
-</ul></section><section id="single-master-online"><h2 class="section-heading">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
+</ul></section><section><h2 class="section-heading" id="single-master-online">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
+<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
 </h2>
 <hr class="half-width">
 <p>Our first alternative will already be familiar to many
@@ -2961,7 +3010,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 do this automatically when switching from a desktop file format to text
 and back (although <a href="https://pandoc.org/" class="external-link">Pandoc</a> can go a
 long way).</p>
-</section><section id="text-based-documents-under-version-control"><h2 class="section-heading">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
+</section><section><h2 class="section-heading" id="text-based-documents-under-version-control">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
 </h2>
 <hr class="half-width">
 <p>The second approach treats papers exactly like software, and has been
@@ -2996,7 +3046,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 make comparisons and merging easier.</li>
 </ol>
 </blockquote>
-</section><section id="benefits-and-drawbacks-of-each-approach"><h2 class="section-heading">Benefits and drawbacks of each approach<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
+</section><section><h2 class="section-heading" id="benefits-and-drawbacks-of-each-approach">Benefits and drawbacks of each approach<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
+<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
 </h2>
 <hr class="half-width">
 <table class="table">
@@ -3090,7 +3141,8 @@ <h3 class="callout-title">Getting started writing text-based version control<a c
 </div>
 </div>
 </div>
-</section><section id="supplementary-materials"><h2 class="section-heading">Supplementary Materials<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
+</section><section><h2 class="section-heading" id="supplementary-materials">Supplementary Materials<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
+<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
 </h2>
 <hr class="half-width">
 <p>Supplementary materials often contain much of the work that went into
@@ -3144,7 +3196,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-08-what_next"><p>Content from <a href="08-what_next.html">What To Do Next</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/08-what_next.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
@@ -3189,7 +3241,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 </div>
 </div>
 </div>
-<section id="learning-good-practices-is-a-long-term-process"><h2 class="section-heading">Learning good practices is a long-term process<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
+<section><h2 class="section-heading" id="learning-good-practices-is-a-long-term-process">Learning good practices is a long-term process<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
+<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
 </h2>
 <hr class="half-width">
 <p>We have outlined a series of good enough practices for scientific
@@ -3219,7 +3272,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 people, including for your future self. Thinking through your work from
 a collaborator’s point of view is helpful, and ultimately kinder to your
 future self.</p>
-</section><section id="what-we-left-out-and-where-to-learn-more"><h2 class="section-heading">What we left out, and where to learn more<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
+</section><section><h2 class="section-heading" id="what-we-left-out-and-where-to-learn-more">What we left out, and where to learn more<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
 </h2>
 <hr class="half-width">
 <p>Learning good practices is a long-term process that never stops. We
@@ -3248,7 +3302,8 @@ <h3 class="callout-title">What other resources are available?<a class="anchor" a
 </div>
 </div>
 </div>
-</section><section id="different-people-make-different-contributions-to-good-practice"><h2 class="section-heading">Different people make different contributions to good practice<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
+</section><section><h2 class="section-heading" id="different-people-make-different-contributions-to-good-practice">Different people make different contributions to good practice<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
+<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
 </h2>
 <hr class="half-width">
 <p>Progress in computational good practices comes from different places
@@ -3335,18 +3390,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -3371,8 +3426,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-lab.github.io/good-enough-practices/aio.html",
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/aio.html",
   "dateCreated": "2020-08-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/etherpad_template.html b/etherpad_template.html
index eeea73ea..f79a0c58 100644
--- a/etherpad_template.html
+++ b/etherpad_template.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
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 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
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+
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+
 	
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 			</div>
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/index.md" class="external-link">Edit on GitHub</a>
-        
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 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
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+
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@@ -307,7 +307,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -319,7 +319,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -349,7 +349,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul>
 </div>
                 </div>
@@ -357,11 +357,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
           </div>
 <!-- /div.accordion -->
@@ -380,7 +380,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <h1>Instructor Notes</h1>
         
 
-<section id="expect-varied-audiences"><h2 class="section-heading">Expect varied audiences<a class="anchor" aria-label="anchor" href="#expect-varied-audiences"></a>
+<section><h2 class="section-heading" id="expect-varied-audiences">Expect varied audiences<a class="anchor" aria-label="anchor" href="#expect-varied-audiences"></a>
+<a class="anchor" aria-label="anchor" href="#expect-varied-audiences"></a>
 </h2>
 <hr class="half-width">
 <p>We have run this workshop successfully with PhD students in the UK.
@@ -418,7 +419,8 @@ <h3 id="understand-the-learners-by-discussions">Understand the learners by discu
 learners make this memorable, more than pre-prepared example
 answers.</p>
 </div>
-</section><section id="what-to-skip"><h2 class="section-heading">What to skip<a class="anchor" aria-label="anchor" href="#what-to-skip"></a>
+</section><section><h2 class="section-heading" id="what-to-skip">What to skip<a class="anchor" aria-label="anchor" href="#what-to-skip"></a>
+<a class="anchor" aria-label="anchor" href="#what-to-skip"></a>
 </h2>
 <hr class="half-width">
 <p>The manuscripts episode is skippable for earlier-career audiences
@@ -428,7 +430,8 @@ <h3 id="understand-the-learners-by-discussions">Understand the learners by discu
 non-programmers so can be gone through very quickly or skipped. However,
 people who are already programming and finding it hard to organize their
 code may find it useful to spend more time on.</p>
-</section><section id="discussions-are-the-opportunity-for-peer-to-peer-learning"><h2 class="section-heading">Discussions are the opportunity for peer to peer learning<a class="anchor" aria-label="anchor" href="#discussions-are-the-opportunity-for-peer-to-peer-learning"></a>
+</section><section><h2 class="section-heading" id="discussions-are-the-opportunity-for-peer-to-peer-learning">Discussions are the opportunity for peer to peer learning<a class="anchor" aria-label="anchor" href="#discussions-are-the-opportunity-for-peer-to-peer-learning"></a>
+<a class="anchor" aria-label="anchor" href="#discussions-are-the-opportunity-for-peer-to-peer-learning"></a>
 </h2>
 <hr class="half-width">
 <p>Discussions are the structured opportunity for learners to learn from
@@ -475,8 +478,9 @@ <h3 id="collaborative-document">Collaborative document<a class="anchor" aria-lab
 you use. It includes reminders for a beginning-workshop hello, templates
 for the exercises, and template for evaluation at the end.</p>
 </div>
-</section><section id="this-lesson-prepares-learners-for-version-control-but-does-not-teach-it"><h2 class="section-heading">This lesson prepares learners for version control, but does not
+</section><section><h2 class="section-heading" id="this-lesson-prepares-learners-for-version-control-but-does-not-teach-it">This lesson prepares learners for version control, but does not
 teach it<a class="anchor" aria-label="anchor" href="#this-lesson-prepares-learners-for-version-control-but-does-not-teach-it"></a>
+<a class="anchor" aria-label="anchor" href="#this-lesson-prepares-learners-for-version-control-but-does-not-teach-it"></a>
 </h2>
 <hr class="half-width">
 <p>This lesson helps to develop the motivation for using version
@@ -488,7 +492,8 @@ <h3 id="collaborative-document">Collaborative document<a class="anchor" aria-lab
 git solves all the problems. Be prepared to steer the conversations back
 to the material and suggest that learners take a git workshop in the
 future.</p>
-</section><section id="collect-feedback"><h2 class="section-heading">Collect feedback!<a class="anchor" aria-label="anchor" href="#collect-feedback"></a>
+</section><section><h2 class="section-heading" id="collect-feedback">Collect feedback!<a class="anchor" aria-label="anchor" href="#collect-feedback"></a>
+<a class="anchor" aria-label="anchor" href="#collect-feedback"></a>
 </h2>
 <hr class="half-width">
 <p>If you’re teaching in person you can use <a href="https://swcarpentry.github.io/swc-releases/2017.02/instructor-training/15-practices/" class="external-link">the
@@ -498,7 +503,8 @@ <h3 id="collaborative-document">Collaborative document<a class="anchor" aria-lab
 <p>Please do file an issue on the github site summarizing the feedback,
 and feel free to file issues or pull requests suggesting specific edits
 as well.</p>
-</section><section id="tips"><h2 class="section-heading">Tips<a class="anchor" aria-label="anchor" href="#tips"></a>
+</section><section><h2 class="section-heading" id="tips">Tips<a class="anchor" aria-label="anchor" href="#tips"></a>
+<a class="anchor" aria-label="anchor" href="#tips"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -518,18 +524,18 @@ <h3 id="if-teaching-from-the-website-make-sure-the-font-is-big-enough">If teachi
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -554,8 +560,8 @@ <h3 id="if-teaching-from-the-website-make-sure-the-font-is-big-enough">If teachi
   "url": "https://carpentries-lab.github.io/good-enough-practices/instructor-notes.html",
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor-notes.html",
   "dateCreated": "2020-08-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/01-introduction.html b/instructor/01-introduction.html
index 80d948dc..0e9f4707 100644
--- a/instructor/01-introduction.html
+++ b/instructor/01-introduction.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -202,7 +202,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       </button>
     </div><!--/div.accordion-header-->
-        
+
     <div id="flush-collapsecurrent" class="accordion-collapse collapse show" aria-labelledby="flush-headingcurrent" data-bs-parent="#accordionFlushcurrent">
       <div class="accordion-body">
         <ul><li><a href="#challenges-in-data-heavy-biology">Challenges in data-heavy biology</a></li>
@@ -211,7 +211,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 documentation</a></li>
         </ul></div><!--/div.accordion-body-->
     </div><!--/div.accordion-collapse-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -220,7 +220,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -229,7 +229,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -238,7 +238,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -247,7 +247,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -256,7 +256,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -265,7 +265,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading8">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -274,7 +274,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading9">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -305,10 +305,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -329,20 +329,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Home
         </a>
         <a class="chapter-link float-end" href="../instructor/02-data_management.html" rel="next">
-          Next: Data Management... 
+          Next: Data Management...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/01-introduction.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 15 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -424,8 +424,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-<section id="challenges-in-data-heavy-biology"><h2 class="section-heading">Challenges in data-heavy biology<a class="anchor" aria-label="anchor" href="#challenges-in-data-heavy-biology"></a>
-</h2>
+<section><h2 class="section-heading" id="challenges-in-data-heavy-biology">Challenges in data-heavy biology<a class="anchor" aria-label="anchor" href="#challenges-in-data-heavy-biology"></a>
+<a class="anchor" aria-label="anchor" href="#challenges-in-data-heavy-biology"></a></h2>
 <hr class="half-width"><p>For example, consider biology.</p>
 <figure><img src="../fig/ew-intro.png" alt="This image shows the many different levels of data that biologists might work with. On the highest level, they work with organisms, shown in the image are a wasp, a tree, and a bacteria. On an intermediate level, they may collect raw data from these organisms. Shown in the image are a picture of dividing yeast cells, a western blot, and a floppy disk containing text data. On the final level, they will have visualisations of the raw data. Shown in the image are a picture of dividing cells with fluorescence at the boundary, a bar plot, and a cartoon of gene transcription." class="figure mx-auto d-block"></figure><p>Biologists study organisms, and have to deal with many kinds of data.
 In biology, as in other sciences:</p>
@@ -442,16 +442,16 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 understand
 <ul><li>Where do you even start?</li>
 </ul></li>
-</ul></section><section id="good-news-everyone-has-these-problems"><h2 class="section-heading">Good news: everyone has these problems!<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="good-news-everyone-has-these-problems">Good news: everyone has these problems!<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a>
+<a class="anchor" aria-label="anchor" href="#good-news-everyone-has-these-problems"></a></h2>
 <hr class="half-width"><ul><li>Other people have thought about good practices and created good
 tools.</li>
 <li>You don’t have to reinvent practices and tools.</li>
 <li>You can learn to be “good enough” in scientific computing.</li>
 <li>This is an ongoing process through your career.</li>
-</ul></section><section id="principles-planning-modular-organization-names-documentation"><h2 class="section-heading">Principles: planning, modular organization, names,
+</ul></section><section><h2 class="section-heading" id="principles-planning-modular-organization-names-documentation">Principles: planning, modular organization, names,
 documentation<a class="anchor" aria-label="anchor" href="#principles-planning-modular-organization-names-documentation"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#principles-planning-modular-organization-names-documentation"></a></h2>
 <hr class="half-width"><p>This lesson has episodes covering data management, software, project
 organization, collaboration, keeping track of changes, and
 manuscripts.</p>
@@ -494,7 +494,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Home
         </a>
         <a class="chapter-link float-end" href="../instructor/02-data_management.html" rel="next">
-          Next: Data Management... 
+          Next: Data Management...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -505,18 +505,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/01-introduction.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -541,7 +541,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/01-introduction.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/02-data_management.html b/instructor/02-data_management.html
index cc35248c..5cdb650c 100644
--- a/instructor/02-data_management.html
+++ b/instructor/02-data_management.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
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@@ -211,7 +211,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
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+
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         <ul><li><a href="#data-management">Data management</a></li>
@@ -228,7 +228,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#summary">Summary</a></li>
         </ul></div><!--/div.accordion-body-->
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@@ -237,7 +237,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
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@@ -246,7 +246,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
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         <a href="05-project_organization.html">5. Project Organization</a>
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@@ -264,7 +264,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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           Previous: Introduction
         </a>
         <a class="chapter-link float-end" href="../instructor/03-software.html" rel="next">
-          Next: Code and Software... 
+          Next: Code and Software...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Data Management</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/02-data_management.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
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         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 32 minutes</p>
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -387,8 +387,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="data-management"><h2 class="section-heading">Data management<a class="anchor" aria-label="anchor" href="#data-management"></a>
-</h2>
+<section><h2 class="section-heading" id="data-management">Data management<a class="anchor" aria-label="anchor" href="#data-management"></a>
+<a class="anchor" aria-label="anchor" href="#data-management"></a></h2>
 <hr class="half-width"><p>Data within a project may need to exist in various forms, ranging
 from what first arrives to what is actually used for the primary
 analyses. Data management is the process of storing, documenting,
@@ -432,8 +432,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <figure><img src="../fig/ew-data-loss.png" alt="A comic strip titled 'The four stages of data loss' and subtitled 'dealing with accidental deletion of months of hard-earned data' by PhD Comics. It's based on the common theory of five stages of grief. The first panel is labelled 'stage 1: denial' and shows a man sitting behind a computer. A thought bubble above his head reads 'I did not just erase all my data. I surely made a back-up somewhere'. The second panel is labelled 'stage 2: anger' and shows the man shaking his computer. A speech bubble above his head shows he is shouting 'you stupid piece of crap! Where's my data?!'. The third panel is labelled 'stage 3: depression'. It shows the man crying, the broken computer beside him. He thinks 'Why? Why me?'. The fourth and final panel is labelled 'stage 4: acceptance'. It shows the man coming to terms with what has happened. He says 'I'm never going to graduate'." class="figure mx-auto d-block"><div class="figcaption">Source: PHD Comics. <a href="https://phdcomics.com/comics/archive.php/images/archive.php?comicid=382" class="external-link">“Four
 stages of data loss”</a>
 </div>
-</figure></section><section id="save-the-raw-data"><h2 class="section-heading">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
-</h2>
+</figure></section><section><h2 class="section-heading" id="save-the-raw-data">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
+<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a></h2>
 <hr class="half-width"><div id="backing-up-your-data-5-minutes" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
@@ -512,8 +512,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 incremental backup or specialized storage systems, and people in your
 local IT group or library can often provide advice and assistance on
 options at your university or organization as well.</p>
-</section><section id="working-with-sensitive-data"><h2 class="section-heading">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="working-with-sensitive-data">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a></h2>
 <hr class="half-width"><p>Identify whether your project will work with sensitive data - by
 which we might mean:</p>
 <ul><li>Research data including personal data or identifiers (this might
@@ -532,8 +532,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 Regulation, known as the GDPR). These laws vary between countries and
 may affect whether you can share information between collaborators in
 different countries.</p>
-</section><section id="create-the-data-you-wish-to-see-in-the-world"><h2 class="section-heading">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
-</h2>
+</section><section><h2 class="section-heading" id="create-the-data-you-wish-to-see-in-the-world">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
+<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a></h2>
 <hr class="half-width"><div id="discussion-2-minutes" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
@@ -585,8 +585,8 @@ <h3 class="callout-title">Discussion (2 minutes)<a class="anchor" aria-label="an
 <li>Use unique identifiers for every record in a table, allowing
 linkages between tables (e.g. sample identifiers are recorded in the
 sequencing experiment metadata)</li>
-</ul></section><section id="create-analysis-friendly-data"><h2 class="section-heading">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="create-analysis-friendly-data">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
+<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a></h2>
 <hr class="half-width"><div id="discussion-2-minutes-1" class="callout discussion">
 <div class="callout-square">
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@@ -613,8 +613,8 @@ <h3 class="callout-title">Discussion (2 minutes)<a class="anchor" aria-label="an
 several time points. Be prepared to gather such columns into a variable
 of measurements, plus a new variable for time point. The figure above
 presents an example of such a transformation.</p>
-</section><section id="record-all-the-steps-used-to-process-data"><h2 class="section-heading">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="record-all-the-steps-used-to-process-data">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
+<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a></h2>
 <hr class="half-width"><p>Data manipulation is as integral to your analysis as statistical
 modeling and inference. If you do not document this step thoroughly, it
 is impossible for you, or anyone else, to repeat the analysis.</p>
@@ -647,9 +647,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 </div>
 </div>
 </div>
-</section><section id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"><h2 class="section-heading">Use multiple tables as necessary, and use a unique identifier for
+</section><section><h2 class="section-heading" id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record">Use multiple tables as necessary, and use a unique identifier for
 every record<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a></h2>
 <hr class="half-width"><p>Raw data, even if tidy, is not necessarily complete. For example, the
 primary data table might hold the heart rate for individual subjects at
 rest and after a physical challenge, identified via a subject ID.
@@ -660,9 +660,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 “014025” in another. It is generally wise to give each record or unit a
 unique, persistent key and to use the same names and codes when
 variables in two datasets refer to the same thing.</p>
-</section><section id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"><h2 class="section-heading">Submit data to a reputable DOI-issuing repository so that others can
+</section><section><h2 class="section-heading" id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it">Submit data to a reputable DOI-issuing repository so that others can
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-</h2>
+<a class="anchor" aria-label="anchor" href="#submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"></a></h2>
 <hr class="half-width"><div id="sharing-your-data-with-the-world-5-minutes" class="callout challenge">
 <div class="callout-square">
 <i class="callout-icon" data-feather="zap"></i>
@@ -758,8 +758,8 @@ <h3 class="callout-title">Places to share Data, with DOIs<a class="anchor" aria-
 </ul></div>
 </div>
 </div>
-</section><section id="data-management-plans"><h2 class="section-heading">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
-</h2>
+</section><section><h2 class="section-heading" id="data-management-plans">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
+<a class="anchor" aria-label="anchor" href="#data-management-plans"></a></h2>
 <hr class="half-width"><p>Many universities and funders require researchers to complete a data
 management plan (DMP). A DMP is a document which outlines information
 about your research data and how it will be processed. Many funders
@@ -822,8 +822,8 @@ <h3 class="callout-title">What’s your next step in data management?<a class="a
 </ul></div>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
-</h2>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a></h2>
 <hr class="half-width"><p>Taken in order, the recommendations above will make it easier to keep
 track of your data and to work with it. Saving the raw data along with
 clear metadata, backed up, is your insurance policy. Creating
@@ -888,7 +888,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Introduction
         </a>
         <a class="chapter-link float-end" href="../instructor/03-software.html" rel="next">
-          Next: Code and Software... 
+          Next: Code and Software...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -899,18 +899,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/02-data_management.md" class="external-link">Edit on GitHub</a>
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+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
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+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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@@ -935,7 +935,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/02-data_management.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
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@@ -237,7 +237,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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           Previous: Data Management
         </a>
         <a class="chapter-link float-end" href="../instructor/04-collaboration.html" rel="next">
-          Next: Collaboration... 
+          Next: Collaboration...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Code and Software</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/03-software.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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-        
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -384,8 +384,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="what-your-future-self-may-think"><h2 class="section-heading">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
-</h2>
+<section><h2 class="section-heading" id="what-your-future-self-may-think">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
+<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a></h2>
 <hr class="half-width"><figure><img src="../fig/ew-software-twit.png" alt="A tweet from Neil Ferguson, posted on March 22nd 2020. It reads 'I'm conscious that lots of people would like to see and run the pandemic simulation code we are using to model control measures against COVID-19. To explain the background — I wrote the code (thousands of lines on undocumented C) 13 plus years ago to model flu pandemics…'" class="figure mx-auto d-block"></figure><p>The <a href="https://twitter.com/neil_ferguson/status/1241835454707699713" class="external-link">twitter
 thread illustrates a real example of research software problems</a>,
 from <a href="https://en.wikipedia.org/wiki/Neil_Ferguson_(epidemiologist)" class="external-link">Prof. Neil
@@ -399,8 +399,8 @@ <h3 class="card-title">Objectives</h3>
 adapt your analysis to a new dataset</li>
 <li>you publish a paper, and a masters student from the other side of
 the world emails you to reproduce the results for their project</li>
-</ul></section><section id="what-is-research-code-and-software"><h2 class="section-heading">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="what-is-research-code-and-software">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
+<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a></h2>
 <hr class="half-width"><p>There are many different shapes and sizes of research software:</p>
 <ul><li>Any code that runs in order to process your research data.</li>
 <li>A record of all the steps used to process your data (scripts and
@@ -460,9 +460,9 @@ <h4 class="accordion-header" id="headingSolution1"> Suggestions </h4>
 benefit for you and collaborators.</p>
 <p>Programs themselves are modular, and can be written in scripts that
 run a clearly-defined set of functions on defined inputs.</p>
-</section><section id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"><h2 class="section-heading">Place a brief explanatory comment at the start of every script or
+</section><section><h2 class="section-heading" id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program">Place a brief explanatory comment at the start of every script or
 program<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a></h2>
 <hr class="half-width"><p>Short is fine; always include at least one example of how the program
 is used. Remember, a good example is worth a thousand words. Where
 possible, the comment should also indicate reasonable values for
@@ -531,8 +531,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="decompose-programs-into-functions"><h2 class="section-heading">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
-</h2>
+</section><section><h2 class="section-heading" id="decompose-programs-into-functions">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
+<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a></h2>
 <hr class="half-width"><p>A function is a reusable section of software that can be treated as a
 black box by the rest of the program. This is like the way we combine
 actions in everyday life. Suppose that it is teatime. You could get a
@@ -634,8 +634,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="be-ruthless-about-eliminating-duplication"><h2 class="section-heading">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
-</h2>
+</section><section><h2 class="section-heading" id="be-ruthless-about-eliminating-duplication">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
+<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a></h2>
 <hr class="half-width"><p>Write and re-use functions instead of copying and pasting code, and
 use data structures like lists instead of creating many closely-related
 variables, e.g. create <code>score = (1, 2, 3)</code> rather than
@@ -650,8 +650,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 So <strong><em>always search for well-maintained software libraries that
 do what you need</em></strong> before writing new code yourself, but
 <strong><em>test libraries before relying on them</em></strong>.</p>
-</section><section id="give-functions-and-variables-meaningful-names"><h2 class="section-heading">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
-</h2>
+</section><section><h2 class="section-heading" id="give-functions-and-variables-meaningful-names">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
+<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a></h2>
 <hr class="half-width"><p>Meaningful names for functions and variables document their purpose
 and make the program generally easy to read. As a rule of thumb, the
 greater the scope of a variable, the more informative its name should
@@ -744,16 +744,16 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 </div>
 </div>
 </div>
-</section><section id="make-dependencies-and-requirements-explicit."><h2 class="section-heading">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
-</h2>
+</section><section><h2 class="section-heading" id="make-dependencies-and-requirements-explicit-">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
+<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit-"></a></h2>
 <hr class="half-width"><p>This is usually done on a per-project rather than per-program basis,
 i.e., by adding a file called something like
 <code>requirements.txt</code> to the root directory of the project, or
 by adding a “Getting Started” section to the <code>README</code>
 file.</p>
-</section><section id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"><h2 class="section-heading">Do not comment and uncomment sections of code to control a program’s
+</section><section><h2 class="section-heading" id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior">Do not comment and uncomment sections of code to control a program’s
 behavior<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a></h2>
 <hr class="half-width"><p>This is error prone and makes it difficult or impossible to automate
 analyses. Instead, put if/else statements in the program to control what
 it does, and use input arguments on the command line to select
@@ -761,8 +761,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 <code>--option</code> and corresponding if/else statements to control
 running an optional piece of the program. Remember to use descriptive
 names for input arguments.</p>
-</section><section id="provide-a-simple-example-or-test-data-set"><h2 class="section-heading">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
-</h2>
+</section><section><h2 class="section-heading" id="provide-a-simple-example-or-test-data-set">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
+<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a></h2>
 <hr class="half-width"><p>Users (including yourself) can run your program on this set to
 determine whether it is working and whether it gives a known correct
 output for a simple known input. Such a test is particularly helpful
@@ -770,8 +770,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 it has to run on several different machines, e.g., the developer’s
 laptop and the department’s cluster. This type of test is called an
 integration test.</p>
-</section><section id="code-can-be-managed-like-data"><h2 class="section-heading">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="code-can-be-managed-like-data">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
+<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a></h2>
 <hr class="half-width"><p>Your code is like your data and also needs to be managed, backed up,
 and shared.</p>
 <p>Your software is as much a product of your research as your papers,
@@ -823,7 +823,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Data Management
         </a>
         <a class="chapter-link float-end" href="../instructor/04-collaboration.html" rel="next">
-          Next: Collaboration... 
+          Next: Collaboration...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -834,18 +834,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/03-software.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -870,7 +870,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/03-software.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/04-collaboration.html b/instructor/04-collaboration.html
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--- a/instructor/04-collaboration.html
+++ b/instructor/04-collaboration.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
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         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
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@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
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@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
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@@ -229,7 +229,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         </span>
       </button>
     </div><!--/div.accordion-header-->
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+
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       <div class="accordion-body">
         <ul><li><a href="#create-an-overview-of-your-project">Create an overview of your project</a></li>
@@ -242,7 +242,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#recommended-resources">Recommended resources</a></li>
         </ul></div><!--/div.accordion-body-->
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@@ -251,7 +251,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div><!--/div.accordion-header-->
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@@ -260,7 +260,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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@@ -269,7 +269,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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@@ -278,7 +278,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
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@@ -309,10 +309,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
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           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -333,20 +333,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Code and Software
         </a>
         <a class="chapter-link float-end" href="../instructor/05-project_organization.html" rel="next">
-          Next: Project Organization... 
+          Next: Project Organization...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Collaboration</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/04-collaboration.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 37 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -437,8 +437,8 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 </div>
 </div>
 </div>
-<section id="create-an-overview-of-your-project"><h2 class="section-heading">Create an overview of your project<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
-</h2>
+<section><h2 class="section-heading" id="create-an-overview-of-your-project">Create an overview of your project<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
+<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a></h2>
 <hr class="half-width"><p>Written documentation is essential for collaboration. Future you will
 forget things, and your collaborators will not know them in the first
 place. An overview document can collect the most important information
@@ -454,8 +454,8 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <li>Up-to-date contact information</li>
 <li>An example or two of how to run the most important tasks</li>
 <li>Overview of folder structure</li>
-</ul></section><section id="describe-how-to-contribute-to-the-project"><h2 class="section-heading">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="describe-how-to-contribute-to-the-project">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a></h2>
 <hr class="half-width"><p>Because the README is usually the first thing users and collaborators
 on your project will look at, make it explicit how you want people to
 engage with the project. If you are looking for more contributors, make
@@ -515,8 +515,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="create-a-shared-to-do-list"><h2 class="section-heading">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
-</h2>
+</section><section><h2 class="section-heading" id="create-a-shared-to-do-list">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
+<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a></h2>
 <hr class="half-width"><p>This can be a plain text file called something like
 <code>notes.txt</code> or <code>todo.txt</code>, or you can use sites
 such as GitHub or Bitbucket to create a new <em>issue</em> for each
@@ -524,23 +524,23 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 point newcomers at issues that are good starting points.) Whatever you
 choose, describe the items clearly so that they make sense to
 newcomers.</p>
-</section><section id="decide-on-communication-strategies"><h2 class="section-heading">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
-</h2>
+</section><section><h2 class="section-heading" id="decide-on-communication-strategies">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
+<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a></h2>
 <hr class="half-width"><p>Make explicit decisions about (and publicize where appropriate) how
 members of the project will communicate with each other and with
 external users / collaborators. This includes the location and
 technology for email lists, chat channels, voice / video conferencing,
 documentation, and meeting notes, as well as which of these channels
 will be public or private.</p>
-</section><section id="collaborations-with-sensitive-data"><h2 class="section-heading">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
-</h2>
+</section><section><h2 class="section-heading" id="collaborations-with-sensitive-data">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a></h2>
 <hr class="half-width"><p>If you determine that your project will include work with sensitive
 data, it is important to agree with collaborators on how and where the
 data will be stored, as well as what the mechanisms for sharing the data
 will be and who is ultimately responsible for ensuring these are
 followed.</p>
-</section><section id="make-the-license-explicit"><h2 class="section-heading">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
-</h2>
+</section><section><h2 class="section-heading" id="make-the-license-explicit">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a></h2>
 <hr class="half-width"><div id="what-is-a-licence" class="callout">
 <div class="callout-square">
 <i class="callout-icon" data-feather="bell"></i>
@@ -587,8 +587,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 permissively-licensed software into other projects, see chapter three in
 [<a href="https://www.oreilly.com/library/view/understanding-open-source/0596005814/" class="external-link">laurent2004</a>].</p>
 </blockquote>
-</section><section id="make-the-project-citable"><h2 class="section-heading">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
-</h2>
+</section><section><h2 class="section-heading" id="make-the-project-citable">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a></h2>
 <hr class="half-width"><p>A <code>CITATION</code> file describes how to cite this project as a
 whole, and where to find (and how to cite) any data sets, code, figures,
 and other artifacts that have their own DOIs. The example below shows
@@ -601,8 +601,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 Morris, B.D. and E.P. White. 2013. "The EcoData Retriever:
 improving access to existing ecological data." PLOS ONE 8:e65848.
 http://doi.org/doi:10.1371/journal.pone.0065848</code></pre>
-</section><section id="recommended-resources"><h2 class="section-heading">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
-</h2>
+</section><section><h2 class="section-heading" id="recommended-resources">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
+<a class="anchor" aria-label="anchor" href="#recommended-resources"></a></h2>
 <hr class="half-width"><ul><li><a href="https://the-turing-way.netlify.app/collaboration/collaboration.html" class="external-link">The
 Turing Way Guide for Collaboration</a></li>
 </ul><div id="attribution" class="callout">
@@ -647,7 +647,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Code and Software
         </a>
         <a class="chapter-link float-end" href="../instructor/05-project_organization.html" rel="next">
-          Next: Project Organization... 
+          Next: Project Organization...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -658,18 +658,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/04-collaboration.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
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-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -694,7 +694,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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@@ -46,7 +46,7 @@
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       </div>
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         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
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@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="index.html">Summary and Schedule</a>
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@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
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         <a href="02-data_management.html">2. Data Management</a>
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     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
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       <div class="accordion-body">
         <ul><li><a href="#put-each-project-in-its-own-directory-which-is-named-after-the-project">Put each project in its own directory, which is named after the
@@ -254,7 +254,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#example">Example</a></li>
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         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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         <a href="08-what_next.html">8. What To Do Next</a>
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             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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           Previous: Collaboration
         </a>
         <a class="chapter-link float-end" href="../instructor/06-track_changes.html" rel="next">
-          Next: Keeping Track of... 
+          Next: Keeping Track of...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Project Organization</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/05-project_organization.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
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+
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         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 25 minutes</p>
-        
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         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -411,9 +411,9 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 </div>
 </div>
 </div>
-<section id="put-each-project-in-its-own-directory-which-is-named-after-the-project"><h2 class="section-heading">Put each project in its own directory, which is named after the
+<section><h2 class="section-heading" id="put-each-project-in-its-own-directory-which-is-named-after-the-project">Put each project in its own directory, which is named after the
 project<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a></h2>
 <hr class="half-width"><p>Similar to deciding when a chunk of code should be made a function,
 the ultimate goal of dividing research into distinct projects is to help
 you and others best understand your work. Some researchers create a
@@ -442,17 +442,17 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 names help you effectively find and use things later. Your lab or
 organization may have a template to use.</p>
 </blockquote>
-</section><section id="put-text-documents-associated-with-the-project-in-the-doc-directory."><h2 class="section-heading">Put text documents associated with the project in the
+</section><section><h2 class="section-heading" id="put-text-documents-associated-with-the-project-in-the-doc-directory-">Put text documents associated with the project in the
 <code>doc</code> directory.<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory."></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory-"></a></h2>
 <hr class="half-width"><p>This includes files for manuscripts, documentation for source code,
 and/or an electronic lab notebook recording your experiments.
 Subdirectories may be created for these different classes of files in
 large projects.</p>
-</section><section id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"><h2 class="section-heading">Put raw data and metadata in a <code>data</code> directory, and
+</section><section><h2 class="section-heading" id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory">Put raw data and metadata in a <code>data</code> directory, and
 files generated during cleanup and analysis in a <code>results</code>
 directory<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a></h2>
 <hr class="half-width"><p>When we refer to “generated files”, this includes intermediate
 results, such as cleaned data sets or simulated data, as well as final
 results such as figures and tables.</p>
@@ -465,8 +465,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 together. Similarly, the <code>data</code> directory might require
 subdirectories to organize raw data based on time, method of collection,
 or other metadata most relevant to your analysis.</p>
-</section><section id="put-project-source-code-in-the-src-directory"><h2 class="section-heading">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
-</h2>
+</section><section><h2 class="section-heading" id="put-project-source-code-in-the-src-directory">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a></h2>
 <hr class="half-width"><p><code>src</code> contains all of the code written for the project.
 This includes programs written in interpreted languages such as R or
 Python; those written compiled languages like Fortran, C++, or Java; as
@@ -501,8 +501,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 
     echo "Cleaning up..."
     rm -rf $(TEMP_DIR)</code></pre>
-</section><section id="put-compiled-programs-in-the-bin-directory"><h2 class="section-heading">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
-</h2>
+</section><section><h2 class="section-heading" id="put-compiled-programs-in-the-bin-directory">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a></h2>
 <hr class="half-width"><p><code>bin</code> contains executable programs compiled from code in
 the <code>src</code> directory. Projects that do not have any will not
 require <code>bin</code>.</p>
@@ -527,8 +527,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 the same rule. As with many of our other recommendations, consistency
 and predictability are more important than hair-splitting.</p>
 </blockquote>
-</section><section id="name-all-files-to-reflect-their-content-or-function."><h2 class="section-heading">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
-</h2>
+</section><section><h2 class="section-heading" id="name-all-files-to-reflect-their-content-or-function-">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
+<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function-"></a></h2>
 <hr class="half-width"><p>For example, use names such as <code>bird_count_table.csv</code>,
 <code>manuscript.md</code>, or <code>sightings_analysis.py</code>. Do
 <em>not</em> use sequential numbers (e.g., <code>result1.csv</code>,
@@ -543,8 +543,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 <li>Optional: Consistent</li>
 <li>Optional: Play well with default ordering</li>
 </ul></blockquote>
-</section><section id="example"><h2 class="section-heading">Example<a class="anchor" aria-label="anchor" href="#example"></a>
-</h2>
+</section><section><h2 class="section-heading" id="example">Example<a class="anchor" aria-label="anchor" href="#example"></a>
+<a class="anchor" aria-label="anchor" href="#example"></a></h2>
 <hr class="half-width"><p>The diagram below provides a concrete example of how a simple project
 might be organized following these recommendations:</p>
 <pre><code>    .
@@ -602,23 +602,23 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <li>on/off are different media (on sucrose, off sucrose)</li>
 <li>measurement date</li>
 <li>other details are timepoint and raw or normalized data</li>
-</ul><pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv  
-2020-07-14_s1_phyA_on_LD_t05.raw.csv  
-2020-07-14_s2_phyB_on_SD_t11.raw.csv  
-2020-08-12_s03_phyA_on_LD_t03.raw.csv  
-2020-08-12_s12_phyB_on_LD_t01.raw.csv  
-2020-08-13_s01_phyB_on_SD_t02.raw.csv  
-2020-7-12_s2_phyB_on_SD_t01.raw.csv  
-AUG-13_phyB_on_LD_s1_t11.raw.csv  
-JUL-31_phyB_on_LD_s1_t03.raw.csv  
-LD_phyA_off_t04_2020-08-12.norm.csv  
-LD_phyA_on_t04_2020-07-14.norm.csv  
-LD_phyB_off_t04_2020-08-12.norm.csv  
-LD_phyB_on_t04_2020-07-14.norm.csv  
-SD_phyB_off_t04_2020-08-13.norm.csv  
-SD_phyB_on_t04_2020-07-12.norm.csv  
-SD_phya_off_t04_2020-08-13.norm.csv  
-SD_phya_ons_t04_2020-07-12.norm.csv  
+</ul><pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv
+2020-07-14_s1_phyA_on_LD_t05.raw.csv
+2020-07-14_s2_phyB_on_SD_t11.raw.csv
+2020-08-12_s03_phyA_on_LD_t03.raw.csv
+2020-08-12_s12_phyB_on_LD_t01.raw.csv
+2020-08-13_s01_phyB_on_SD_t02.raw.csv
+2020-7-12_s2_phyB_on_SD_t01.raw.csv
+AUG-13_phyB_on_LD_s1_t11.raw.csv
+JUL-31_phyB_on_LD_s1_t03.raw.csv
+LD_phyA_off_t04_2020-08-12.norm.csv
+LD_phyA_on_t04_2020-07-14.norm.csv
+LD_phyB_off_t04_2020-08-12.norm.csv
+LD_phyB_on_t04_2020-07-14.norm.csv
+SD_phyB_off_t04_2020-08-13.norm.csv
+SD_phyB_on_t04_2020-07-12.norm.csv
+SD_phya_off_t04_2020-08-13.norm.csv
+SD_phya_ons_t04_2020-07-12.norm.csv
 ld_phyA_ons_t04_2020-08-12.norm.csv  </code></pre>
 <ul><li>What are the problems with having the date first?</li>
 <li>How do different date formats behave once sorted?</li>
@@ -638,7 +638,7 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul><li>Using dates up front makes it difficult to quickly find data for
 particular conditions or genotypes. It also masks the “logical” order of
@@ -729,7 +729,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Collaboration
         </a>
         <a class="chapter-link float-end" href="../instructor/06-track_changes.html" rel="next">
-          Next: Keeping Track of... 
+          Next: Keeping Track of...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -740,18 +740,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/05-project_organization.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -776,7 +776,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/05-project_organization.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/06-track_changes.html b/instructor/06-track_changes.html
index d45f9d99..21c4e35a 100644
--- a/instructor/06-track_changes.html
+++ b/instructor/06-track_changes.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
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@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
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@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
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@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
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     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div><!--/div.accordion-header-->
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         <ul><li><a href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created">Back up (almost) everything created by a human being as soon as it
@@ -263,7 +263,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#what-not-to-put-under-version-control">What Not to Put Under Version Control</a></li>
         </ul></div><!--/div.accordion-body-->
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         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
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@@ -312,10 +312,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
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             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -336,20 +336,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Project Organization
         </a>
         <a class="chapter-link float-end" href="../instructor/07-manuscripts.html" rel="next">
-          Next: Manuscripts... 
+          Next: Manuscripts...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Keeping Track of Changes</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/06-track_changes.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 40 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -436,14 +436,14 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 </ol><p>and you can use the first while working towards the second, or just
 jump in to version control.</p>
 <p>Whatever system you chose, we recommend that you:</p>
-<section id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"><h2 class="section-heading">Back up (almost) everything created by a human being as soon as it
+<section><h2 class="section-heading" id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created">Back up (almost) everything created by a human being as soon as it
 is created<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a></h2>
 <hr class="half-width"><p>This includes scripts and programs of all kinds, software packages
 that your project depends on, and documentation. A few exceptions to
 this rule are discussed below.</p>
-</section><section id="keep-changes-small"><h2 class="section-heading">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
-</h2>
+</section><section><h2 class="section-heading" id="keep-changes-small">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
+<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a></h2>
 <hr class="half-width"><p>Each change should not be so large as to make the change tracking
 irrelevant. For example, a single change such as “Revise script file”
 that adds or changes several hundred lines is likely too large, as it
@@ -452,8 +452,8 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 pieces that are too small. As a rule of thumb, a good size for a single
 change is a group of edits that you could imagine wanting to undo in one
 step at some point in the future.</p>
-</section><section id="share-changes-frequently"><h2 class="section-heading">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
-</h2>
+</section><section><h2 class="section-heading" id="share-changes-frequently">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
+<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a></h2>
 <hr class="half-width"><p>Everyone working on the project should share and incorporate changes
 from others on a regular basis. Do not allow individual investigator’s
 versions of the project repository to drift apart, as the effort
@@ -461,17 +461,17 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 difference. This is particularly important for the manual versioning
 procedure described below, which does not provide any assistance for
 merging simultaneous, possibly conflicting, changes.</p>
-</section><section id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"><h2 class="section-heading">Create, maintain, and use a checklist for saving and sharing changes
+</section><section><h2 class="section-heading" id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project">Create, maintain, and use a checklist for saving and sharing changes
 to the project<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a></h2>
 <hr class="half-width"><p>The list should include writing log messages that clearly explain any
 changes, the size and content of individual changes, style guidelines
 for code, updating to-do lists, and bans on committing half-done work or
 broken code. See [<a href="https://books.google.co.uk/books/about/The_Checklist_Manifesto.html?id=qoZCRAAACAAJ&amp;redir_esc=y" class="external-link">gawande2011</a>]
 for more on the proven value of checklists.</p>
-</section><section id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"><h2 class="section-heading">Store each project in a folder that is mirrored off the researcher’s
+</section><section><h2 class="section-heading" id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine">Store each project in a folder that is mirrored off the researcher’s
 working machine<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a></h2>
 <hr class="half-width"><p>This may include:</p>
 <ul><li>using a shared system such as a (institutional) cloud or shared
 drive, or</li>
@@ -519,8 +519,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-</section><section id="manual-versioning"><h2 class="section-heading">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
-</h2>
+</section><section><h2 class="section-heading" id="manual-versioning">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
+<a class="anchor" aria-label="anchor" href="#manual-versioning"></a></h2>
 <hr class="half-width"><p>Our first suggested approach, in which everything is done by hand,
 has two additional parts:</p>
 <ol style="list-style-type: decimal"><li>
@@ -571,8 +571,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 single person is working on specific files at any time. In particular,
 they may wish to create one change log file per contributor, and to
 merge those files whenever a backup copy is made.</p>
-</section><section id="version-control-systems"><h2 class="section-heading">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
-</h2>
+</section><section><h2 class="section-heading" id="version-control-systems">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
+<a class="anchor" aria-label="anchor" href="#version-control-systems"></a></h2>
 <hr class="half-width"><p>What the manual process described above requires most is
 self-discipline. The version control tools that underpin our second
 approach—the one we use in our own projects–don’t just accelerate the
@@ -658,7 +658,7 @@ <h3 class="callout-title">Changelog in action<a class="anchor" aria-label="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Some good things:</p>
 <ul><li>all log entries contain date and author</li>
@@ -685,8 +685,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="what-not-to-put-under-version-control"><h2 class="section-heading">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
-</h2>
+</section><section><h2 class="section-heading" id="what-not-to-put-under-version-control">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a></h2>
 <hr class="half-width"><p>The benefits of version control systems don’t apply equally to all
 file types. In particular, version control can be more or less rewarding
 depending on file size and format. First, file comparison in version
@@ -794,7 +794,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Project Organization
         </a>
         <a class="chapter-link float-end" href="../instructor/07-manuscripts.html" rel="next">
-          Next: Manuscripts... 
+          Next: Manuscripts...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
@@ -805,18 +805,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/06-track_changes.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -841,7 +841,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/06-track_changes.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/07-manuscripts.html b/instructor/07-manuscripts.html
index e66f8c10..64bfb52c 100644
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+++ b/instructor/07-manuscripts.html
@@ -46,7 +46,7 @@
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         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
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@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
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@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="02-data_management.html">2. Data Management</a>
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         <a href="03-software.html">3. Code and Software</a>
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="04-collaboration.html">4. Collaboration</a>
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@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="05-project_organization.html">5. Project Organization</a>
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@@ -242,7 +242,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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@@ -256,7 +256,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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       <div class="accordion-body">
         <ul><li><a href="#making-email-based-workflows-work">Making email-based workflows work</a></li>
@@ -267,7 +267,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
 <li><a href="#supplementary-materials">Supplementary Materials</a></li>
         </ul></div><!--/div.accordion-body-->
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@@ -276,7 +276,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="08-what_next.html">8. What To Do Next</a>
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@@ -307,10 +307,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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@@ -331,20 +331,20 @@ <h2 class="accordion-header" id="flush-headingTwelve">
           Previous: Keeping Track of
         </a>
         <a class="chapter-link float-end" href="../instructor/08-what_next.html" rel="next">
-          Next: What To Do Next... 
+          Next: What To Do Next...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Manuscripts</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/07-manuscripts.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 20 minutes</p>
-        
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -413,8 +413,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 write a manuscript. Then agree on a decision and process, and put the
 outcome in writing. If co-authors are learning new tools, ask someone
 familiar with those tools to support them!</p>
-<section id="making-email-based-workflows-work"><h2 class="section-heading">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
-</h2>
+<section><h2 class="section-heading" id="making-email-based-workflows-work">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
+<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a></h2>
 <hr class="half-width"><p>A common practice in academic writing is for the lead author to email
 successive versions of a manuscript to coauthors to collect feedback,
 which is returned as changes to the document, comments on the document,
@@ -438,8 +438,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 responsible for merging comments and sending out updated manuscripts to
 all other co-authors.</li>
 </ol></blockquote>
-</section><section id="good-practices-beyond-an-email-based-workflow"><h2 class="section-heading">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
-</h2>
+</section><section><h2 class="section-heading" id="good-practices-beyond-an-email-based-workflow">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
+<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a></h2>
 <hr class="half-width"><p>Instead of an email-based workflow, we recommend mirroring good
 practices for managing software and data to make writing scalable,
 collaborative, and reproducible. As with our recommendations for version
@@ -458,8 +458,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 and to tell if it is up to date.</p></li>
 <li><p>Make it easy to share that final version with collaborators and
 to submit it to a journal.</p></li>
-</ul></section><section id="single-master-online"><h2 class="section-heading">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="single-master-online">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
+<a class="anchor" aria-label="anchor" href="#single-master-online"></a></h2>
 <hr class="half-width"><p>Our first alternative will already be familiar to many
 researchers:</p>
 <ol style="list-style-type: decimal"><li>
@@ -478,8 +478,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 do this automatically when switching from a desktop file format to text
 and back (although <a href="https://pandoc.org/" class="external-link">Pandoc</a> can go a
 long way).</p>
-</section><section id="text-based-documents-under-version-control"><h2 class="section-heading">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
-</h2>
+</section><section><h2 class="section-heading" id="text-based-documents-under-version-control">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a></h2>
 <hr class="half-width"><p>The second approach treats papers exactly like software, and has been
 used by researchers in mathematics, astronomy, physics, and related
 disciplines for decades:</p>
@@ -508,8 +508,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 <li>Separate sentences by linebreaks in your plain-text document, to
 make comparisons and merging easier.</li>
 </ol></blockquote>
-</section><section id="benefits-and-drawbacks-of-each-approach"><h2 class="section-heading">Benefits and drawbacks of each approach<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
-</h2>
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+<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a></h2>
 <hr class="half-width"><table class="table"><colgroup><col width="37%"><col width="17%"><col width="17%"><col width="27%"></colgroup><thead><tr class="header"><th>Things to consider</th>
 <th>Email based workflow</th>
 <th>Single master online</th>
@@ -575,8 +575,8 @@ <h3 class="callout-title">Getting started writing text-based version control<a c
 </div>
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 </div>
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+<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a></h2>
 <hr class="half-width"><p>Supplementary materials often contain much of the work that went into
 the project, such as tables and figures or more elaborate descriptions
 of the algorithms, software, methods, and analyses. In order to make
@@ -635,7 +635,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
           Previous: Keeping Track of
         </a>
         <a class="chapter-link float-end" href="../instructor/08-what_next.html" rel="next">
-          Next: What To Do Next... 
+          Next: What To Do Next...
           <i aria-hidden="true" class="small-arrow" data-feather="arrow-right"></i>
         </a>
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@@ -646,18 +646,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
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+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/07-manuscripts.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
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-        
+
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         <h1>What To Do Next</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/08-what_next.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
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+
+
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@@ -384,8 +384,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 </div>
 </div>
 </div>
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-</h2>
+<section><h2 class="section-heading" id="learning-good-practices-is-a-long-term-process">Learning good practices is a long-term process<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
+<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a></h2>
 <hr class="half-width"><p>We have outlined a series of good enough practices for scientific
 computing. These practices are pragmatic, broadly accessible, and can be
 applied by both individuals and groups. Most importantly, these
@@ -409,8 +409,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 people, including for your future self. Thinking through your work from
 a collaborator’s point of view is helpful, and ultimately kinder to your
 future self.</p>
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-</h2>
+</section><section><h2 class="section-heading" id="what-we-left-out-and-where-to-learn-more">What we left out, and where to learn more<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a></h2>
 <hr class="half-width"><p>Learning good practices is a long-term process that never stops. We
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 although useful, have more niche applications.</p>
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 </div>
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-</h2>
+</section><section><h2 class="section-heading" id="different-people-make-different-contributions-to-good-practice">Different people make different contributions to good practice<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
+<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a></h2>
 <hr class="half-width"><p>Progress in computational good practices comes from different places
 in the scientific community:</p>
 <ul><li>Funders can require <a href="https://www.dcc.ac.uk/resources/data-management-plans" class="external-link">data
@@ -526,18 +526,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
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         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/08-what_next.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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+
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@@ -277,7 +277,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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+
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-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
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 			</div>
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         <p>Last updated on 2024-01-04 |
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 <hr class="half-width"><p>Except where otherwise noted, the example programs and other software
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 			</div>
 			<div class="col-md-6">
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+<a class="anchor" aria-label="anchor" href="#principles-planning-modular-organization-names-documentation"></a>
 </h2>
 <hr class="half-width">
 <p>This lesson has episodes covering data management, software, project
@@ -561,7 +564,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-02-data_management"><p>Content from <a href="02-data_management.html">Data Management</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/02-data_management.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 32 minutes</p>
 <div class="text-end">
@@ -601,7 +604,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="data-management"><h2 class="section-heading">Data management<a class="anchor" aria-label="anchor" href="#data-management"></a>
+<section><h2 class="section-heading" id="data-management">Data management<a class="anchor" aria-label="anchor" href="#data-management"></a>
+<a class="anchor" aria-label="anchor" href="#data-management"></a>
 </h2>
 <hr class="half-width">
 <p>Data within a project may need to exist in various forms, ranging
@@ -649,7 +653,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <figure><img src="../fig/ew-data-loss.png" alt="A comic strip titled 'The four stages of data loss' and subtitled 'dealing with accidental deletion of months of hard-earned data' by PhD Comics. It's based on the common theory of five stages of grief. The first panel is labelled 'stage 1: denial' and shows a man sitting behind a computer. A thought bubble above his head reads 'I did not just erase all my data. I surely made a back-up somewhere'. The second panel is labelled 'stage 2: anger' and shows the man shaking his computer. A speech bubble above his head shows he is shouting 'you stupid piece of crap! Where's my data?!'. The third panel is labelled 'stage 3: depression'. It shows the man crying, the broken computer beside him. He thinks 'Why? Why me?'. The fourth and final panel is labelled 'stage 4: acceptance'. It shows the man coming to terms with what has happened. He says 'I'm never going to graduate'." class="figure mx-auto d-block"><div class="figcaption">Source: PHD Comics. <a href="https://phdcomics.com/comics/archive.php/images/archive.php?comicid=382" class="external-link">“Four
 stages of data loss”</a>
 </div>
-</figure></section><section id="save-the-raw-data"><h2 class="section-heading">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
+</figure></section><section><h2 class="section-heading" id="save-the-raw-data">Save the raw data<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
+<a class="anchor" aria-label="anchor" href="#save-the-raw-data"></a>
 </h2>
 <hr class="half-width">
 <div id="backing-up-your-data-5-minutes" class="callout challenge">
@@ -734,7 +739,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 incremental backup or specialized storage systems, and people in your
 local IT group or library can often provide advice and assistance on
 options at your university or organization as well.</p>
-</section><section id="working-with-sensitive-data"><h2 class="section-heading">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
+</section><section><h2 class="section-heading" id="working-with-sensitive-data">Working with sensitive data<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#working-with-sensitive-data"></a>
 </h2>
 <hr class="half-width">
 <p>Identify whether your project will work with sensitive data - by
@@ -757,7 +763,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 Regulation, known as the GDPR). These laws vary between countries and
 may affect whether you can share information between collaborators in
 different countries.</p>
-</section><section id="create-the-data-you-wish-to-see-in-the-world"><h2 class="section-heading">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
+</section><section><h2 class="section-heading" id="create-the-data-you-wish-to-see-in-the-world">Create the data you wish to see in the world<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
+<a class="anchor" aria-label="anchor" href="#create-the-data-you-wish-to-see-in-the-world"></a>
 </h2>
 <hr class="half-width">
 <div id="discussion-2-minutes" class="callout discussion">
@@ -812,7 +819,8 @@ <h3 class="callout-title">Discussion (2 minutes)<a class="anchor" aria-label="an
 <li>Use unique identifiers for every record in a table, allowing
 linkages between tables (e.g. sample identifiers are recorded in the
 sequencing experiment metadata)</li>
-</ul></section><section id="create-analysis-friendly-data"><h2 class="section-heading">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
+</ul></section><section><h2 class="section-heading" id="create-analysis-friendly-data">Create analysis-friendly data<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
+<a class="anchor" aria-label="anchor" href="#create-analysis-friendly-data"></a>
 </h2>
 <hr class="half-width">
 <div id="discussion-2-minutes-1" class="callout discussion">
@@ -841,7 +849,8 @@ <h3 class="callout-title">Discussion (2 minutes)<a class="anchor" aria-label="an
 several time points. Be prepared to gather such columns into a variable
 of measurements, plus a new variable for time point. The figure above
 presents an example of such a transformation.</p>
-</section><section id="record-all-the-steps-used-to-process-data"><h2 class="section-heading">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
+</section><section><h2 class="section-heading" id="record-all-the-steps-used-to-process-data">Record all the steps used to process data<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
+<a class="anchor" aria-label="anchor" href="#record-all-the-steps-used-to-process-data"></a>
 </h2>
 <hr class="half-width">
 <p>Data manipulation is as integral to your analysis as statistical
@@ -876,8 +885,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 </div>
 </div>
 </div>
-</section><section id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"><h2 class="section-heading">Use multiple tables as necessary, and use a unique identifier for
+</section><section><h2 class="section-heading" id="use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record">Use multiple tables as necessary, and use a unique identifier for
 every record<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a>
+<a class="anchor" aria-label="anchor" href="#use-multiple-tables-as-necessary-and-use-a-unique-identifier-for-every-record"></a>
 </h2>
 <hr class="half-width">
 <p>Raw data, even if tidy, is not necessarily complete. For example, the
@@ -890,8 +900,9 @@ <h3 class="callout-title">How, when and why do you document?<a class="anchor" ar
 “014025” in another. It is generally wise to give each record or unit a
 unique, persistent key and to use the same names and codes when
 variables in two datasets refer to the same thing.</p>
-</section><section id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"><h2 class="section-heading">Submit data to a reputable DOI-issuing repository so that others can
+</section><section><h2 class="section-heading" id="submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it">Submit data to a reputable DOI-issuing repository so that others can
 access and cite it<a class="anchor" aria-label="anchor" href="#submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"></a>
+<a class="anchor" aria-label="anchor" href="#submit-data-to-a-reputable-doi-issuing-repository-so-that-others-can-access-and-cite-it"></a>
 </h2>
 <hr class="half-width">
 <div id="sharing-your-data-with-the-world-5-minutes" class="callout challenge">
@@ -997,7 +1008,8 @@ <h3 class="callout-title">Places to share Data, with DOIs<a class="anchor" aria-
 </div>
 </div>
 </div>
-</section><section id="data-management-plans"><h2 class="section-heading">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
+</section><section><h2 class="section-heading" id="data-management-plans">Data management plans<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
+<a class="anchor" aria-label="anchor" href="#data-management-plans"></a>
 </h2>
 <hr class="half-width">
 <p>Many universities and funders require researchers to complete a data
@@ -1068,7 +1080,8 @@ <h3 class="callout-title">What’s your next step in data management?<a class="a
 </div>
 </div>
 </div>
-</section><section id="summary"><h2 class="section-heading">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+</section><section><h2 class="section-heading" id="summary">Summary<a class="anchor" aria-label="anchor" href="#summary"></a>
+<a class="anchor" aria-label="anchor" href="#summary"></a>
 </h2>
 <hr class="half-width">
 <p>Taken in order, the recommendations above will make it easier to keep
@@ -1128,7 +1141,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-03-software"><p>Content from <a href="03-software.html">Code and Software</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/03-software.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 40 minutes</p>
 <div class="text-end">
@@ -1165,7 +1178,8 @@ <h3 class="card-title">Objectives</h3>
 </div>
 </div>
 </div>
-<section id="what-your-future-self-may-think"><h2 class="section-heading">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
+<section><h2 class="section-heading" id="what-your-future-self-may-think">What your future self may think…<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
+<a class="anchor" aria-label="anchor" href="#what-your-future-self-may-think"></a>
 </h2>
 <hr class="half-width">
 <figure><img src="../fig/ew-software-twit.png" alt="A tweet from Neil Ferguson, posted on March 22nd 2020. It reads 'I'm conscious that lots of people would like to see and run the pandemic simulation code we are using to model control measures against COVID-19. To explain the background — I wrote the code (thousands of lines on undocumented C) 13 plus years ago to model flu pandemics…'" class="figure mx-auto d-block"></figure><p>The <a href="https://twitter.com/neil_ferguson/status/1241835454707699713" class="external-link">twitter
@@ -1182,7 +1196,8 @@ <h3 class="card-title">Objectives</h3>
 adapt your analysis to a new dataset</li>
 <li>you publish a paper, and a masters student from the other side of
 the world emails you to reproduce the results for their project</li>
-</ul></section><section id="what-is-research-code-and-software"><h2 class="section-heading">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
+</ul></section><section><h2 class="section-heading" id="what-is-research-code-and-software">What is research code and software?<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
+<a class="anchor" aria-label="anchor" href="#what-is-research-code-and-software"></a>
 </h2>
 <hr class="half-width">
 <p>There are many different shapes and sizes of research software:</p>
@@ -1248,8 +1263,9 @@ <h4 class="accordion-header" id="headingSolution1"> Suggestions </h4>
 benefit for you and collaborators.</p>
 <p>Programs themselves are modular, and can be written in scripts that
 run a clearly-defined set of functions on defined inputs.</p>
-</section><section id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"><h2 class="section-heading">Place a brief explanatory comment at the start of every script or
+</section><section><h2 class="section-heading" id="place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program">Place a brief explanatory comment at the start of every script or
 program<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a>
+<a class="anchor" aria-label="anchor" href="#place-a-brief-explanatory-comment-at-the-start-of-every-script-or-program"></a>
 </h2>
 <hr class="half-width">
 <p>Short is fine; always include at least one example of how the program
@@ -1325,7 +1341,8 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="decompose-programs-into-functions"><h2 class="section-heading">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
+</section><section><h2 class="section-heading" id="decompose-programs-into-functions">Decompose programs into functions<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
+<a class="anchor" aria-label="anchor" href="#decompose-programs-into-functions"></a>
 </h2>
 <hr class="half-width">
 <p>A function is a reusable section of software that can be treated as a
@@ -1431,7 +1448,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="be-ruthless-about-eliminating-duplication"><h2 class="section-heading">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
+</section><section><h2 class="section-heading" id="be-ruthless-about-eliminating-duplication">Be ruthless about eliminating duplication<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
+<a class="anchor" aria-label="anchor" href="#be-ruthless-about-eliminating-duplication"></a>
 </h2>
 <hr class="half-width">
 <p>Write and re-use functions instead of copying and pasting code, and
@@ -1448,7 +1466,8 @@ <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 So <strong><em>always search for well-maintained software libraries that
 do what you need</em></strong> before writing new code yourself, but
 <strong><em>test libraries before relying on them</em></strong>.</p>
-</section><section id="give-functions-and-variables-meaningful-names"><h2 class="section-heading">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
+</section><section><h2 class="section-heading" id="give-functions-and-variables-meaningful-names">Give functions and variables meaningful names<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
+<a class="anchor" aria-label="anchor" href="#give-functions-and-variables-meaningful-names"></a>
 </h2>
 <hr class="half-width">
 <p>Meaningful names for functions and variables document their purpose
@@ -1551,7 +1570,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 </div>
 </div>
 </div>
-</section><section id="make-dependencies-and-requirements-explicit."><h2 class="section-heading">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
+</section><section><h2 class="section-heading" id="make-dependencies-and-requirements-explicit-">Make dependencies and requirements explicit.<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit."></a>
+<a class="anchor" aria-label="anchor" href="#make-dependencies-and-requirements-explicit-"></a>
 </h2>
 <hr class="half-width">
 <p>This is usually done on a per-project rather than per-program basis,
@@ -1559,8 +1579,9 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 <code>requirements.txt</code> to the root directory of the project, or
 by adding a “Getting Started” section to the <code>README</code>
 file.</p>
-</section><section id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"><h2 class="section-heading">Do not comment and uncomment sections of code to control a program’s
+</section><section><h2 class="section-heading" id="do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior">Do not comment and uncomment sections of code to control a program’s
 behavior<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a>
+<a class="anchor" aria-label="anchor" href="#do-not-comment-and-uncomment-sections-of-code-to-control-a-programs-behavior"></a>
 </h2>
 <hr class="half-width">
 <p>This is error prone and makes it difficult or impossible to automate
@@ -1570,7 +1591,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 <code>--option</code> and corresponding if/else statements to control
 running an optional piece of the program. Remember to use descriptive
 names for input arguments.</p>
-</section><section id="provide-a-simple-example-or-test-data-set"><h2 class="section-heading">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
+</section><section><h2 class="section-heading" id="provide-a-simple-example-or-test-data-set">Provide a simple example or test data set<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
+<a class="anchor" aria-label="anchor" href="#provide-a-simple-example-or-test-data-set"></a>
 </h2>
 <hr class="half-width">
 <p>Users (including yourself) can run your program on this set to
@@ -1580,7 +1602,8 @@ <h3 class="callout-title">Callout<a class="anchor" aria-label="anchor" href="#ca
 it has to run on several different machines, e.g., the developer’s
 laptop and the department’s cluster. This type of test is called an
 integration test.</p>
-</section><section id="code-can-be-managed-like-data"><h2 class="section-heading">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
+</section><section><h2 class="section-heading" id="code-can-be-managed-like-data">Code can be managed like data<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
+<a class="anchor" aria-label="anchor" href="#code-can-be-managed-like-data"></a>
 </h2>
 <hr class="half-width">
 <p>Your code is like your data and also needs to be managed, backed up,
@@ -1627,7 +1650,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-04-collaboration"><p>Content from <a href="04-collaboration.html">Collaboration</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/04-collaboration.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 37 minutes</p>
 <div class="text-end">
@@ -1729,7 +1752,8 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 </div>
 </div>
 </div>
-<section id="create-an-overview-of-your-project"><h2 class="section-heading">Create an overview of your project<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
+<section><h2 class="section-heading" id="create-an-overview-of-your-project">Create an overview of your project<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
+<a class="anchor" aria-label="anchor" href="#create-an-overview-of-your-project"></a>
 </h2>
 <hr class="half-width">
 <p>Written documentation is essential for collaboration. Future you will
@@ -1748,7 +1772,8 @@ <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i
 <li>Up-to-date contact information</li>
 <li>An example or two of how to run the most important tasks</li>
 <li>Overview of folder structure</li>
-</ul></section><section id="describe-how-to-contribute-to-the-project"><h2 class="section-heading">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
+</ul></section><section><h2 class="section-heading" id="describe-how-to-contribute-to-the-project">Describe how to contribute to the project<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#describe-how-to-contribute-to-the-project"></a>
 </h2>
 <hr class="half-width">
 <p>Because the README is usually the first thing users and collaborators
@@ -1816,7 +1841,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="create-a-shared-to-do-list"><h2 class="section-heading">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
+</section><section><h2 class="section-heading" id="create-a-shared-to-do-list">Create a shared “to-do” list<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
+<a class="anchor" aria-label="anchor" href="#create-a-shared-to-do-list"></a>
 </h2>
 <hr class="half-width">
 <p>This can be a plain text file called something like
@@ -1826,7 +1852,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 point newcomers at issues that are good starting points.) Whatever you
 choose, describe the items clearly so that they make sense to
 newcomers.</p>
-</section><section id="decide-on-communication-strategies"><h2 class="section-heading">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
+</section><section><h2 class="section-heading" id="decide-on-communication-strategies">Decide on communication strategies<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
+<a class="anchor" aria-label="anchor" href="#decide-on-communication-strategies"></a>
 </h2>
 <hr class="half-width">
 <p>Make explicit decisions about (and publicize where appropriate) how
@@ -1835,7 +1862,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 technology for email lists, chat channels, voice / video conferencing,
 documentation, and meeting notes, as well as which of these channels
 will be public or private.</p>
-</section><section id="collaborations-with-sensitive-data"><h2 class="section-heading">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
+</section><section><h2 class="section-heading" id="collaborations-with-sensitive-data">Collaborations with sensitive data<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
+<a class="anchor" aria-label="anchor" href="#collaborations-with-sensitive-data"></a>
 </h2>
 <hr class="half-width">
 <p>If you determine that your project will include work with sensitive
@@ -1843,7 +1871,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 data will be stored, as well as what the mechanisms for sharing the data
 will be and who is ultimately responsible for ensuring these are
 followed.</p>
-</section><section id="make-the-license-explicit"><h2 class="section-heading">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
+</section><section><h2 class="section-heading" id="make-the-license-explicit">Make the license explicit<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-license-explicit"></a>
 </h2>
 <hr class="half-width">
 <div id="what-is-a-licence" class="callout">
@@ -1894,7 +1923,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 permissively-licensed software into other projects, see chapter three in
 [<a href="https://www.oreilly.com/library/view/understanding-open-source/0596005814/" class="external-link">laurent2004</a>].</p>
 </blockquote>
-</section><section id="make-the-project-citable"><h2 class="section-heading">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
+</section><section><h2 class="section-heading" id="make-the-project-citable">Make the project citable<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
+<a class="anchor" aria-label="anchor" href="#make-the-project-citable"></a>
 </h2>
 <hr class="half-width">
 <p>A <code>CITATION</code> file describes how to cite this project as a
@@ -1909,7 +1939,8 @@ <h3 class="callout-title">What is a licence?<a class="anchor" aria-label="anchor
 Morris, B.D. and E.P. White. 2013. "The EcoData Retriever:
 improving access to existing ecological data." PLOS ONE 8:e65848.
 http://doi.org/doi:10.1371/journal.pone.0065848</code></pre>
-</section><section id="recommended-resources"><h2 class="section-heading">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
+</section><section><h2 class="section-heading" id="recommended-resources">Recommended resources<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
+<a class="anchor" aria-label="anchor" href="#recommended-resources"></a>
 </h2>
 <hr class="half-width">
 <ul>
@@ -1951,7 +1982,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-05-project_organization"><p>Content from <a href="05-project_organization.html">Project Organization</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/05-project_organization.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 25 minutes</p>
 <div class="text-end">
@@ -2018,8 +2049,9 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 </div>
 </div>
 </div>
-<section id="put-each-project-in-its-own-directory-which-is-named-after-the-project"><h2 class="section-heading">Put each project in its own directory, which is named after the
+<section><h2 class="section-heading" id="put-each-project-in-its-own-directory-which-is-named-after-the-project">Put each project in its own directory, which is named after the
 project<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#put-each-project-in-its-own-directory-which-is-named-after-the-project"></a>
 </h2>
 <hr class="half-width">
 <p>Similar to deciding when a chunk of code should be made a function,
@@ -2052,17 +2084,19 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 names help you effectively find and use things later. Your lab or
 organization may have a template to use.</p>
 </blockquote>
-</section><section id="put-text-documents-associated-with-the-project-in-the-doc-directory."><h2 class="section-heading">Put text documents associated with the project in the
+</section><section><h2 class="section-heading" id="put-text-documents-associated-with-the-project-in-the-doc-directory-">Put text documents associated with the project in the
 <code>doc</code> directory.<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory."></a>
+<a class="anchor" aria-label="anchor" href="#put-text-documents-associated-with-the-project-in-the-doc-directory-"></a>
 </h2>
 <hr class="half-width">
 <p>This includes files for manuscripts, documentation for source code,
 and/or an electronic lab notebook recording your experiments.
 Subdirectories may be created for these different classes of files in
 large projects.</p>
-</section><section id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"><h2 class="section-heading">Put raw data and metadata in a <code>data</code> directory, and
+</section><section><h2 class="section-heading" id="put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory">Put raw data and metadata in a <code>data</code> directory, and
 files generated during cleanup and analysis in a <code>results</code>
 directory<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-raw-data-and-metadata-in-a-data-directory-and-files-generated-during-cleanup-and-analysis-in-a-results-directory"></a>
 </h2>
 <hr class="half-width">
 <p>When we refer to “generated files”, this includes intermediate
@@ -2077,7 +2111,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 together. Similarly, the <code>data</code> directory might require
 subdirectories to organize raw data based on time, method of collection,
 or other metadata most relevant to your analysis.</p>
-</section><section id="put-project-source-code-in-the-src-directory"><h2 class="section-heading">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
+</section><section><h2 class="section-heading" id="put-project-source-code-in-the-src-directory">Put project source code in the <code>src</code> directory<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-project-source-code-in-the-src-directory"></a>
 </h2>
 <hr class="half-width">
 <p><code>src</code> contains all of the code written for the project.
@@ -2114,7 +2149,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 
     echo "Cleaning up..."
     rm -rf $(TEMP_DIR)</code></pre>
-</section><section id="put-compiled-programs-in-the-bin-directory"><h2 class="section-heading">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
+</section><section><h2 class="section-heading" id="put-compiled-programs-in-the-bin-directory">Put compiled programs in the <code>bin</code> directory<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
+<a class="anchor" aria-label="anchor" href="#put-compiled-programs-in-the-bin-directory"></a>
 </h2>
 <hr class="half-width">
 <p><code>bin</code> contains executable programs compiled from code in
@@ -2141,7 +2177,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 the same rule. As with many of our other recommendations, consistency
 and predictability are more important than hair-splitting.</p>
 </blockquote>
-</section><section id="name-all-files-to-reflect-their-content-or-function."><h2 class="section-heading">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
+</section><section><h2 class="section-heading" id="name-all-files-to-reflect-their-content-or-function-">Name all files to reflect their content or function.<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function."></a>
+<a class="anchor" aria-label="anchor" href="#name-all-files-to-reflect-their-content-or-function-"></a>
 </h2>
 <hr class="half-width">
 <p>For example, use names such as <code>bird_count_table.csv</code>,
@@ -2160,7 +2197,8 @@ <h3 class="callout-title">README files are magic<a class="anchor" aria-label="an
 <li>Optional: Play well with default ordering</li>
 </ul>
 </blockquote>
-</section><section id="example"><h2 class="section-heading">Example<a class="anchor" aria-label="anchor" href="#example"></a>
+</section><section><h2 class="section-heading" id="example">Example<a class="anchor" aria-label="anchor" href="#example"></a>
+<a class="anchor" aria-label="anchor" href="#example"></a>
 </h2>
 <hr class="half-width">
 <p>The diagram below provides a concrete example of how a simple project
@@ -2222,23 +2260,23 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <li>measurement date</li>
 <li>other details are timepoint and raw or normalized data</li>
 </ul>
-<pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv  
-2020-07-14_s1_phyA_on_LD_t05.raw.csv  
-2020-07-14_s2_phyB_on_SD_t11.raw.csv  
-2020-08-12_s03_phyA_on_LD_t03.raw.csv  
-2020-08-12_s12_phyB_on_LD_t01.raw.csv  
-2020-08-13_s01_phyB_on_SD_t02.raw.csv  
-2020-7-12_s2_phyB_on_SD_t01.raw.csv  
-AUG-13_phyB_on_LD_s1_t11.raw.csv  
-JUL-31_phyB_on_LD_s1_t03.raw.csv  
-LD_phyA_off_t04_2020-08-12.norm.csv  
-LD_phyA_on_t04_2020-07-14.norm.csv  
-LD_phyB_off_t04_2020-08-12.norm.csv  
-LD_phyB_on_t04_2020-07-14.norm.csv  
-SD_phyB_off_t04_2020-08-13.norm.csv  
-SD_phyB_on_t04_2020-07-12.norm.csv  
-SD_phya_off_t04_2020-08-13.norm.csv  
-SD_phya_ons_t04_2020-07-12.norm.csv  
+<pre><code>2020-07-14_s12_phyB_on_SD_t04.raw.csv
+2020-07-14_s1_phyA_on_LD_t05.raw.csv
+2020-07-14_s2_phyB_on_SD_t11.raw.csv
+2020-08-12_s03_phyA_on_LD_t03.raw.csv
+2020-08-12_s12_phyB_on_LD_t01.raw.csv
+2020-08-13_s01_phyB_on_SD_t02.raw.csv
+2020-7-12_s2_phyB_on_SD_t01.raw.csv
+AUG-13_phyB_on_LD_s1_t11.raw.csv
+JUL-31_phyB_on_LD_s1_t03.raw.csv
+LD_phyA_off_t04_2020-08-12.norm.csv
+LD_phyA_on_t04_2020-07-14.norm.csv
+LD_phyB_off_t04_2020-08-12.norm.csv
+LD_phyB_on_t04_2020-07-14.norm.csv
+SD_phyB_off_t04_2020-08-13.norm.csv
+SD_phyB_on_t04_2020-07-12.norm.csv
+SD_phya_off_t04_2020-08-13.norm.csv
+SD_phya_ons_t04_2020-07-12.norm.csv
 ld_phyA_ons_t04_2020-08-12.norm.csv  </code></pre>
 <ul>
 <li>What are the problems with having the date first?</li>
@@ -2260,7 +2298,7 @@ <h3 class="callout-title">Naming and sorting (5 minutes)<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <ul>
 <li>Using dates up front makes it difficult to quickly find data for
@@ -2352,7 +2390,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-06-track_changes"><p>Content from <a href="06-track_changes.html">Keeping Track of Changes</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/06-track_changes.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 40 minutes</p>
 <div class="text-end">
@@ -2446,14 +2484,16 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 <p>and you can use the first while working towards the second, or just
 jump in to version control.</p>
 <p>Whatever system you chose, we recommend that you:</p>
-<section id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"><h2 class="section-heading">Back up (almost) everything created by a human being as soon as it
+<section><h2 class="section-heading" id="back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created">Back up (almost) everything created by a human being as soon as it
 is created<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a>
+<a class="anchor" aria-label="anchor" href="#back-up-almost-everything-created-by-a-human-being-as-soon-as-it-is-created"></a>
 </h2>
 <hr class="half-width">
 <p>This includes scripts and programs of all kinds, software packages
 that your project depends on, and documentation. A few exceptions to
 this rule are discussed below.</p>
-</section><section id="keep-changes-small"><h2 class="section-heading">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
+</section><section><h2 class="section-heading" id="keep-changes-small">Keep changes small<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
+<a class="anchor" aria-label="anchor" href="#keep-changes-small"></a>
 </h2>
 <hr class="half-width">
 <p>Each change should not be so large as to make the change tracking
@@ -2464,7 +2504,8 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 pieces that are too small. As a rule of thumb, a good size for a single
 change is a group of edits that you could imagine wanting to undo in one
 step at some point in the future.</p>
-</section><section id="share-changes-frequently"><h2 class="section-heading">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
+</section><section><h2 class="section-heading" id="share-changes-frequently">Share changes frequently<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
+<a class="anchor" aria-label="anchor" href="#share-changes-frequently"></a>
 </h2>
 <hr class="half-width">
 <p>Everyone working on the project should share and incorporate changes
@@ -2474,8 +2515,9 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 difference. This is particularly important for the manual versioning
 procedure described below, which does not provide any assistance for
 merging simultaneous, possibly conflicting, changes.</p>
-</section><section id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"><h2 class="section-heading">Create, maintain, and use a checklist for saving and sharing changes
+</section><section><h2 class="section-heading" id="create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project">Create, maintain, and use a checklist for saving and sharing changes
 to the project<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a>
+<a class="anchor" aria-label="anchor" href="#create-maintain-and-use-a-checklist-for-saving-and-sharing-changes-to-the-project"></a>
 </h2>
 <hr class="half-width">
 <p>The list should include writing log messages that clearly explain any
@@ -2483,8 +2525,9 @@ <h3 class="callout-title">Problems with change<a class="anchor" aria-label="anch
 for code, updating to-do lists, and bans on committing half-done work or
 broken code. See [<a href="https://books.google.co.uk/books/about/The_Checklist_Manifesto.html?id=qoZCRAAACAAJ&amp;redir_esc=y" class="external-link">gawande2011</a>]
 for more on the proven value of checklists.</p>
-</section><section id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"><h2 class="section-heading">Store each project in a folder that is mirrored off the researcher’s
+</section><section><h2 class="section-heading" id="store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine">Store each project in a folder that is mirrored off the researcher’s
 working machine<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a>
+<a class="anchor" aria-label="anchor" href="#store-each-project-in-a-folder-that-is-mirrored-off-the-researchers-working-machine"></a>
 </h2>
 <hr class="half-width">
 <p>This may include:</p>
@@ -2540,7 +2583,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 </div>
 </div>
 </div>
-</section><section id="manual-versioning"><h2 class="section-heading">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
+</section><section><h2 class="section-heading" id="manual-versioning">Manual Versioning<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
+<a class="anchor" aria-label="anchor" href="#manual-versioning"></a>
 </h2>
 <hr class="half-width">
 <p>Our first suggested approach, in which everything is done by hand,
@@ -2597,7 +2641,8 @@ <h3 class="callout-title">How to document a change<a class="anchor" aria-label="
 single person is working on specific files at any time. In particular,
 they may wish to create one change log file per contributor, and to
 merge those files whenever a backup copy is made.</p>
-</section><section id="version-control-systems"><h2 class="section-heading">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
+</section><section><h2 class="section-heading" id="version-control-systems">Version Control Systems<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
+<a class="anchor" aria-label="anchor" href="#version-control-systems"></a>
 </h2>
 <hr class="half-width">
 <p>What the manual process described above requires most is
@@ -2693,7 +2738,7 @@ <h3 class="callout-title">Changelog in action<a class="anchor" aria-label="ancho
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Some good things:</p>
 <ul>
@@ -2726,7 +2771,8 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </div>
 </div>
 </div>
-</section><section id="what-not-to-put-under-version-control"><h2 class="section-heading">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
+</section><section><h2 class="section-heading" id="what-not-to-put-under-version-control">What Not to Put Under Version Control<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#what-not-to-put-under-version-control"></a>
 </h2>
 <hr class="half-width">
 <p>The benefits of version control systems don’t apply equally to all
@@ -2831,7 +2877,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-07-manuscripts"><p>Content from <a href="07-manuscripts.html">Manuscripts</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/07-manuscripts.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 20 minutes</p>
 <div class="text-end">
@@ -2905,7 +2951,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 write a manuscript. Then agree on a decision and process, and put the
 outcome in writing. If co-authors are learning new tools, ask someone
 familiar with those tools to support them!</p>
-<section id="making-email-based-workflows-work"><h2 class="section-heading">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
+<section><h2 class="section-heading" id="making-email-based-workflows-work">Making email-based workflows work<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
+<a class="anchor" aria-label="anchor" href="#making-email-based-workflows-work"></a>
 </h2>
 <hr class="half-width">
 <p>A common practice in academic writing is for the lead author to email
@@ -2933,7 +2980,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 all other co-authors.</li>
 </ol>
 </blockquote>
-</section><section id="good-practices-beyond-an-email-based-workflow"><h2 class="section-heading">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
+</section><section><h2 class="section-heading" id="good-practices-beyond-an-email-based-workflow">Good practices beyond an email-based workflow<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
+<a class="anchor" aria-label="anchor" href="#good-practices-beyond-an-email-based-workflow"></a>
 </h2>
 <hr class="half-width">
 <p>Instead of an email-based workflow, we recommend mirroring good
@@ -2955,7 +3003,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 and to tell if it is up to date.</p></li>
 <li><p>Make it easy to share that final version with collaborators and
 to submit it to a journal.</p></li>
-</ul></section><section id="single-master-online"><h2 class="section-heading">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
+</ul></section><section><h2 class="section-heading" id="single-master-online">Single Master Online<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
+<a class="anchor" aria-label="anchor" href="#single-master-online"></a>
 </h2>
 <hr class="half-width">
 <p>Our first alternative will already be familiar to many
@@ -2978,7 +3027,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 do this automatically when switching from a desktop file format to text
 and back (although <a href="https://pandoc.org/" class="external-link">Pandoc</a> can go a
 long way).</p>
-</section><section id="text-based-documents-under-version-control"><h2 class="section-heading">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
+</section><section><h2 class="section-heading" id="text-based-documents-under-version-control">Text-based Documents Under Version Control<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
+<a class="anchor" aria-label="anchor" href="#text-based-documents-under-version-control"></a>
 </h2>
 <hr class="half-width">
 <p>The second approach treats papers exactly like software, and has been
@@ -3013,7 +3063,8 @@ <h3 class="callout-title">Discussion (3 mins)<a class="anchor" aria-label="ancho
 make comparisons and merging easier.</li>
 </ol>
 </blockquote>
-</section><section id="benefits-and-drawbacks-of-each-approach"><h2 class="section-heading">Benefits and drawbacks of each approach<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
+</section><section><h2 class="section-heading" id="benefits-and-drawbacks-of-each-approach">Benefits and drawbacks of each approach<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
+<a class="anchor" aria-label="anchor" href="#benefits-and-drawbacks-of-each-approach"></a>
 </h2>
 <hr class="half-width">
 <table class="table">
@@ -3107,7 +3158,8 @@ <h3 class="callout-title">Getting started writing text-based version control<a c
 </div>
 </div>
 </div>
-</section><section id="supplementary-materials"><h2 class="section-heading">Supplementary Materials<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
+</section><section><h2 class="section-heading" id="supplementary-materials">Supplementary Materials<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
+<a class="anchor" aria-label="anchor" href="#supplementary-materials"></a>
 </h2>
 <hr class="half-width">
 <p>Supplementary materials often contain much of the work that went into
@@ -3161,7 +3213,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </section></section><section id="aio-08-what_next"><p>Content from <a href="08-what_next.html">What To Do Next</a></p>
 <hr>
 <p>Last updated on 2024-01-04 |
-        
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         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/episodes/08-what_next.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 10 minutes</p>
 <div class="text-end">
@@ -3207,7 +3259,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 </div>
 </div>
 </div>
-<section id="learning-good-practices-is-a-long-term-process"><h2 class="section-heading">Learning good practices is a long-term process<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
+<section><h2 class="section-heading" id="learning-good-practices-is-a-long-term-process">Learning good practices is a long-term process<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
+<a class="anchor" aria-label="anchor" href="#learning-good-practices-is-a-long-term-process"></a>
 </h2>
 <hr class="half-width">
 <p>We have outlined a series of good enough practices for scientific
@@ -3237,7 +3290,8 @@ <h3 class="callout-title">Heads up<a class="anchor" aria-label="anchor" href="#h
 people, including for your future self. Thinking through your work from
 a collaborator’s point of view is helpful, and ultimately kinder to your
 future self.</p>
-</section><section id="what-we-left-out-and-where-to-learn-more"><h2 class="section-heading">What we left out, and where to learn more<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
+</section><section><h2 class="section-heading" id="what-we-left-out-and-where-to-learn-more">What we left out, and where to learn more<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
+<a class="anchor" aria-label="anchor" href="#what-we-left-out-and-where-to-learn-more"></a>
 </h2>
 <hr class="half-width">
 <p>Learning good practices is a long-term process that never stops. We
@@ -3266,7 +3320,8 @@ <h3 class="callout-title">What other resources are available?<a class="anchor" a
 </div>
 </div>
 </div>
-</section><section id="different-people-make-different-contributions-to-good-practice"><h2 class="section-heading">Different people make different contributions to good practice<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
+</section><section><h2 class="section-heading" id="different-people-make-different-contributions-to-good-practice">Different people make different contributions to good practice<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
+<a class="anchor" aria-label="anchor" href="#different-people-make-different-contributions-to-good-practice"></a>
 </h2>
 <hr class="half-width">
 <p>Progress in computational good practices comes from different places
@@ -3353,18 +3408,18 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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diff --git a/instructor/etherpad_template.html b/instructor/etherpad_template.html
index 4db7083e..2b11989b 100644
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@@ -46,7 +46,7 @@
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+
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           <div class="accordion accordion-flush" id="accordionFlush11">
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         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
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   </div><!--/div.accordion-item-->
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@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
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@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
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   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
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@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div><!--/div.accordion-header-->
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@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div><!--/div.accordion-header-->
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     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -251,7 +251,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading8">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div><!--/div.accordion-header-->
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@@ -260,7 +260,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
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@@ -291,10 +291,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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         <h1>Etherpad template</h1>
         <p>Last updated on 2024-01-04 |
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+
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-        
-        
-        
-        
-        
+
+
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
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@@ -479,18 +479,18 @@ <h4 id="please-list-one-thing-you-liked-or-found-particularly-useful">Please lis
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/etherpad_template.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -515,7 +515,7 @@ <h4 id="please-list-one-thing-you-liked-or-found-particularly-useful">Please lis
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diff --git a/instructor/images.html b/instructor/images.html
index cdc545b7..58d3d8aa 100644
--- a/instructor/images.html
+++ b/instructor/images.html
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       <div class="dropdown" id="instructor-dropdown">
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@@ -207,7 +207,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
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 <!--/div.mobile-row -->
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         <a href="index.html">Summary and Schedule</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
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         <a href="01-introduction.html">1. Introduction</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
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         <a href="02-data_management.html">2. Data Management</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
 </div>
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         <a href="03-software.html">3. Code and Software</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
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         <a href="04-collaboration.html">4. Collaboration</a>
     </div>
 <!--/div.accordion-header-->
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 <!--/div.accordion-item-->
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         <a href="05-project_organization.html">5. Project Organization</a>
     </div>
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         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div>
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         <a href="07-manuscripts.html">7. Manuscripts</a>
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         <a href="08-what_next.html">8. What To Do Next</a>
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@@ -367,11 +367,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
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             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
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@@ -431,18 +431,18 @@ <h3 id="06-track_changes-figure-1">Figure 1</h3>
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
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diff --git a/instructor/index.html b/instructor/index.html
index ea59499f..d028e927 100644
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           </ul></li>
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       <div class="dropdown" id="instructor-dropdown">
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@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
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         </span>
       
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     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
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@@ -246,7 +246,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -255,7 +255,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading8">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -264,7 +264,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading9">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -295,10 +295,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
+
             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -458,18 +458,18 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/index.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -493,8 +493,8 @@ <h3 class="callout-title">Prerequisites<a class="anchor" aria-label="anchor" hre
   "url": "https://carpentries-lab.github.io/good-enough-practices/instructor/index.html",
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/index.html",
   "dateCreated": "2020-08-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index d36d2457..8b24e03a 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -65,7 +65,7 @@
           </ul>
 </li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -207,7 +207,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
-      
+
             <hr>
 </div>
 <!--/div.mobile-row -->
@@ -229,7 +229,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="index.html">Summary and Schedule</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -241,7 +241,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-introduction.html">1. Introduction</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -253,7 +253,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-data_management.html">2. Data Management</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -265,7 +265,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-software.html">3. Code and Software</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -277,7 +277,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -289,7 +289,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -301,7 +301,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -313,7 +313,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -325,7 +325,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -367,11 +367,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
           </div>
 <!-- /div.accordion -->
@@ -390,7 +390,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         <h1>Instructor Notes</h1>
         
 
-<section id="expect-varied-audiences"><h2 class="section-heading">Expect varied audiences<a class="anchor" aria-label="anchor" href="#expect-varied-audiences"></a>
+<section><h2 class="section-heading" id="expect-varied-audiences">Expect varied audiences<a class="anchor" aria-label="anchor" href="#expect-varied-audiences"></a>
+<a class="anchor" aria-label="anchor" href="#expect-varied-audiences"></a>
 </h2>
 <hr class="half-width">
 <p>We have run this workshop successfully with PhD students in the UK.
@@ -428,7 +429,8 @@ <h3 id="understand-the-learners-by-discussions">Understand the learners by discu
 learners make this memorable, more than pre-prepared example
 answers.</p>
 </div>
-</section><section id="what-to-skip"><h2 class="section-heading">What to skip<a class="anchor" aria-label="anchor" href="#what-to-skip"></a>
+</section><section><h2 class="section-heading" id="what-to-skip">What to skip<a class="anchor" aria-label="anchor" href="#what-to-skip"></a>
+<a class="anchor" aria-label="anchor" href="#what-to-skip"></a>
 </h2>
 <hr class="half-width">
 <p>The manuscripts episode is skippable for earlier-career audiences
@@ -438,7 +440,8 @@ <h3 id="understand-the-learners-by-discussions">Understand the learners by discu
 non-programmers so can be gone through very quickly or skipped. However,
 people who are already programming and finding it hard to organize their
 code may find it useful to spend more time on.</p>
-</section><section id="discussions-are-the-opportunity-for-peer-to-peer-learning"><h2 class="section-heading">Discussions are the opportunity for peer to peer learning<a class="anchor" aria-label="anchor" href="#discussions-are-the-opportunity-for-peer-to-peer-learning"></a>
+</section><section><h2 class="section-heading" id="discussions-are-the-opportunity-for-peer-to-peer-learning">Discussions are the opportunity for peer to peer learning<a class="anchor" aria-label="anchor" href="#discussions-are-the-opportunity-for-peer-to-peer-learning"></a>
+<a class="anchor" aria-label="anchor" href="#discussions-are-the-opportunity-for-peer-to-peer-learning"></a>
 </h2>
 <hr class="half-width">
 <p>Discussions are the structured opportunity for learners to learn from
@@ -485,8 +488,9 @@ <h3 id="collaborative-document">Collaborative document<a class="anchor" aria-lab
 you use. It includes reminders for a beginning-workshop hello, templates
 for the exercises, and template for evaluation at the end.</p>
 </div>
-</section><section id="this-lesson-prepares-learners-for-version-control-but-does-not-teach-it"><h2 class="section-heading">This lesson prepares learners for version control, but does not
+</section><section><h2 class="section-heading" id="this-lesson-prepares-learners-for-version-control-but-does-not-teach-it">This lesson prepares learners for version control, but does not
 teach it<a class="anchor" aria-label="anchor" href="#this-lesson-prepares-learners-for-version-control-but-does-not-teach-it"></a>
+<a class="anchor" aria-label="anchor" href="#this-lesson-prepares-learners-for-version-control-but-does-not-teach-it"></a>
 </h2>
 <hr class="half-width">
 <p>This lesson helps to develop the motivation for using version
@@ -498,7 +502,8 @@ <h3 id="collaborative-document">Collaborative document<a class="anchor" aria-lab
 git solves all the problems. Be prepared to steer the conversations back
 to the material and suggest that learners take a git workshop in the
 future.</p>
-</section><section id="collect-feedback"><h2 class="section-heading">Collect feedback!<a class="anchor" aria-label="anchor" href="#collect-feedback"></a>
+</section><section><h2 class="section-heading" id="collect-feedback">Collect feedback!<a class="anchor" aria-label="anchor" href="#collect-feedback"></a>
+<a class="anchor" aria-label="anchor" href="#collect-feedback"></a>
 </h2>
 <hr class="half-width">
 <p>If you’re teaching in person you can use <a href="https://swcarpentry.github.io/swc-releases/2017.02/instructor-training/15-practices/" class="external-link">the
@@ -508,7 +513,8 @@ <h3 id="collaborative-document">Collaborative document<a class="anchor" aria-lab
 <p>Please do file an issue on the github site summarizing the feedback,
 and feel free to file issues or pull requests suggesting specific edits
 as well.</p>
-</section><section id="tips"><h2 class="section-heading">Tips<a class="anchor" aria-label="anchor" href="#tips"></a>
+</section><section><h2 class="section-heading" id="tips">Tips<a class="anchor" aria-label="anchor" href="#tips"></a>
+<a class="anchor" aria-label="anchor" href="#tips"></a>
 </h2>
 <hr class="half-width">
 <div class="section level3">
@@ -536,18 +542,18 @@ <h3 id="if-teaching-from-the-website-make-sure-the-font-is-big-enough">If teachi
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -572,8 +578,8 @@ <h3 id="if-teaching-from-the-website-make-sure-the-font-is-big-enough">If teachi
   "url": "https://carpentries-lab.github.io/good-enough-practices/instructor/instructor-notes.html",
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/instructor-notes.html",
   "dateCreated": "2020-08-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index e331a0f7..c3be19fb 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -65,7 +65,7 @@
           </ul>
 </li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -207,7 +207,7 @@ <h2 class="accordion-header" id="flush-headingNine">
 <!--div.sidenav-view-selector -->
             </div>
 <!--/div.col -->
-      
+
             <hr>
 </div>
 <!--/div.mobile-row -->
@@ -229,7 +229,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="index.html">Summary and Schedule</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -241,7 +241,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="01-introduction.html">1. Introduction</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -253,7 +253,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="02-data_management.html">2. Data Management</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -265,7 +265,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="03-software.html">3. Code and Software</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -277,7 +277,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -289,7 +289,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -301,7 +301,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -313,7 +313,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -325,7 +325,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div>
 <!--/div.accordion-header-->
-        
+
   </div>
 <!--/div.accordion-item-->
 </div>
@@ -367,11 +367,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
             </div>
             <hr class="half-width resources">
 <a href="../instructor/aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none">
 <div class="d-grid gap-1">
-            
+
             </div>
           </div>
 <!-- /div.accordion -->
@@ -465,18 +465,18 @@ <h2 class="accordion-header" id="flush-headingTwelve">
 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -501,8 +501,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://carpentries-lab.github.io/good-enough-practices/instructor/key-points.html",
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/key-points.html",
   "dateCreated": "2020-08-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/instructor/paper.html b/instructor/paper.html
index 1c400e55..b1a3fb0f 100644
--- a/instructor/paper.html
+++ b/instructor/paper.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
-      
+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Schedule</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div><!--/div.accordion-header-->
-        
+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
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         <a href="07-manuscripts.html">7. Manuscripts</a>
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               </div>
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             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
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@@ -322,13 +322,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Good Enough Practices in Scientific Computing: A Learning Module for Researchers</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/paper.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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         </div>
@@ -496,18 +496,18 @@ <h1 id="references">References<a class="anchor" aria-label="anchor" href="#refer
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/paper.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -532,7 +532,7 @@ <h1 id="references">References<a class="anchor" aria-label="anchor" href="#refer
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/paper.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
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@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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               </div>
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@@ -314,8 +314,8 @@ <h1>Learner Profiles</h1>
 material to this lesson, these will help you understand the target
 audience so that we can have a collaboratively developed, but cohesive
 lesson.</p>
-<section id="miriam-microscopist"><h2 class="section-heading">Miriam Microscopist<a class="anchor" aria-label="anchor" href="#miriam-microscopist"></a>
-</h2>
+<section><h2 class="section-heading" id="miriam-microscopist">Miriam Microscopist<a class="anchor" aria-label="anchor" href="#miriam-microscopist"></a>
+<a class="anchor" aria-label="anchor" href="#miriam-microscopist"></a></h2>
 <hr class="half-width"><p>Miriam is a first-year PhD student in Biology, with an undergraduate
 degree in Pharmacology and a Masters in Biochemistry. She has moved to
 the UK from the Egypt for her PhD, and English is her second language.
@@ -330,8 +330,8 @@ <h1>Learner Profiles</h1>
 available to help her solve them. It will introduce the concept of
 scripted data analysis and why that might have benefits over GUI
 applications.</p>
-</section><section id="stuart-simulator"><h2 class="section-heading">Stuart Simulator<a class="anchor" aria-label="anchor" href="#stuart-simulator"></a>
-</h2>
+</section><section><h2 class="section-heading" id="stuart-simulator">Stuart Simulator<a class="anchor" aria-label="anchor" href="#stuart-simulator"></a>
+<a class="anchor" aria-label="anchor" href="#stuart-simulator"></a></h2>
 <hr class="half-width"><p>Stuart is starting his Postdoc in Epidemiology following a PhD in
 Mathematics. During his PhD, he did a mixture of theoretical work and
 simulations written in MATLAB. Although he’s written code in a few
@@ -349,8 +349,8 @@ <h1>Learner Profiles</h1>
 organization, file naming, and scripting, that can immediately help his
 work. It will introduce the concepts of version control and could
 motivate Stuart to learn Git.</p>
-</section><section id="gertrude-group-leader"><h2 class="section-heading">Gertrude Group Leader<a class="anchor" aria-label="anchor" href="#gertrude-group-leader"></a>
-</h2>
+</section><section><h2 class="section-heading" id="gertrude-group-leader">Gertrude Group Leader<a class="anchor" aria-label="anchor" href="#gertrude-group-leader"></a>
+<a class="anchor" aria-label="anchor" href="#gertrude-group-leader"></a></h2>
 <hr class="half-width"><p>Gertrude is a Professor in Biophysics. She has learned Fortran as a
 PhD student and does a lot of scripting in BASH to run Fotran77 code she
 wrote 20 years ago. She has never been taught any formal programming and
@@ -368,8 +368,8 @@ <h1>Learner Profiles</h1>
 the group will help make any code developments outlast a single PhD
 student and help retain knowledge within the group and promote
 reproducibility and transparency.</p>
-</section><section id="linus-the-lab-manager"><h2 class="section-heading">Linus the Lab Manager<a class="anchor" aria-label="anchor" href="#linus-the-lab-manager"></a>
-</h2>
+</section><section><h2 class="section-heading" id="linus-the-lab-manager">Linus the Lab Manager<a class="anchor" aria-label="anchor" href="#linus-the-lab-manager"></a>
+<a class="anchor" aria-label="anchor" href="#linus-the-lab-manager"></a></h2>
 <hr class="half-width"><p>Linus is the Lab Manager of a large lab that combines computational
 and experimental techniques and is in charge of making sure the lab is
 running smoothly. They are responsible for organising lab meetings,
@@ -385,8 +385,8 @@ <h1>Learner Profiles</h1>
 management and project structures are implemented in the group and that
 this information can form part of the research group and will not be
 lost through a Postdoc or PhD student leaving.</p>
-</section><section id="udaya-the-undergraduate"><h2 class="section-heading">Udaya the Undergraduate<a class="anchor" aria-label="anchor" href="#udaya-the-undergraduate"></a>
-</h2>
+</section><section><h2 class="section-heading" id="udaya-the-undergraduate">Udaya the Undergraduate<a class="anchor" aria-label="anchor" href="#udaya-the-undergraduate"></a>
+<a class="anchor" aria-label="anchor" href="#udaya-the-undergraduate"></a></h2>
 <hr class="half-width"><p>Udaya is an undergraduate student from Malaysia, who has been
 enrolled for her entire degree at an English speaking university. She
 has very clear ambitions and wants to become a scientist in Microbiology
@@ -408,18 +408,18 @@ <h1>Learner Profiles</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -443,8 +443,8 @@ <h1>Learner Profiles</h1>
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   "identifier": "https://carpentries-lab.github.io/good-enough-practices/instructor/profiles.html",
   "dateCreated": "2020-08-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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             </li>
           </ul></li>
       </div>
-      
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         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Instructor View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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         <a href="index.html">Summary and Schedule</a>
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@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="01-introduction.html">1. Introduction</a>
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         <a href="05-project_organization.html">5. Project Organization</a>
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@@ -291,10 +291,10 @@ <h2 class="accordion-header" id="flush-headingTwelve">
               </div>
             </div>
             <hr class="half-width resources"><a href="../instructor/aio.html">See all in one page</a>
-            
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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             </div>
           </div><!-- /div.accordion -->
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@@ -322,13 +322,13 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Resources</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/resources.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
-        
-        
+
+
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -337,8 +337,8 @@ <h1>Resources</h1>
 
 <p>This page has a collection of resources on good practices in
 scientific computing. Feel free to refer to them.</p>
-<section id="some-other-lessons-with-different-emphasis"><h2 class="section-heading">Some other lessons with different emphasis<a class="anchor" aria-label="anchor" href="#some-other-lessons-with-different-emphasis"></a>
-</h2>
+<section><h2 class="section-heading" id="some-other-lessons-with-different-emphasis">Some other lessons with different emphasis<a class="anchor" aria-label="anchor" href="#some-other-lessons-with-different-emphasis"></a>
+<a class="anchor" aria-label="anchor" href="#some-other-lessons-with-different-emphasis"></a></h2>
 <hr class="half-width"><p>The FAIR principles describe work that is <strong>F</strong>indable,
 <strong>A</strong>ccessible, <strong>I</strong>nteroperable and
 <strong>R</strong>eusable.</p>
@@ -351,8 +351,8 @@ <h1>Resources</h1>
 for Leaders, 1-day lesson aimed at established PIs and institutional
 leaders who set policy and drive changes</a>. Note, this lesson is under
 construction as of December 2022</li>
-</ul></section><section id="further-carpentries-lessons"><h2 class="section-heading">Further Carpentries lessons<a class="anchor" aria-label="anchor" href="#further-carpentries-lessons"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="further-carpentries-lessons">Further Carpentries lessons<a class="anchor" aria-label="anchor" href="#further-carpentries-lessons"></a>
+<a class="anchor" aria-label="anchor" href="#further-carpentries-lessons"></a></h2>
 <hr class="half-width"><p>Many other Carpentries lessons may help further your learning:</p>
 <ul><li>Data management
 <ul><li>Data Carpentry Ecology lessons on <a href="https://datacarpentry.org/spreadsheet-ecology-lesson/" class="external-link">spreadsheets</a>
@@ -386,8 +386,8 @@ <h1>Resources</h1>
 to GitLab</a></li>
 </ul></li>
 </ul></li>
-</ul></section><section id="papers-and-sites-on-open-and-good-practices"><h2 class="section-heading">Papers and sites on open and good practices<a class="anchor" aria-label="anchor" href="#papers-and-sites-on-open-and-good-practices"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="papers-and-sites-on-open-and-good-practices">Papers and sites on open and good practices<a class="anchor" aria-label="anchor" href="#papers-and-sites-on-open-and-good-practices"></a>
+<a class="anchor" aria-label="anchor" href="#papers-and-sites-on-open-and-good-practices"></a></h2>
 <hr class="half-width"><ul><li><a href="https://doi.org/10.1186/s13059-015-0850-7" class="external-link">Five selfish
 reasons to work reproducibly. Florian Markowetz, Genome Biology</a></li>
 <li><a href="https://doi.org/10.1186/s13059-015-0669-2" class="external-link">When will ‘open
@@ -413,8 +413,8 @@ <h1>Resources</h1>
 careers, writing, and more</li>
 <li><a href="https://collections.plos.org/compbiol-education" class="external-link">PLoS
 Computational Biology Education section</a></li>
-</ul></section><section id="ten-simple-rules-for-reproducible-computational-research"><h2 class="section-heading">Ten simple rules for reproducible computational research<a class="anchor" aria-label="anchor" href="#ten-simple-rules-for-reproducible-computational-research"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="ten-simple-rules-for-reproducible-computational-research">Ten simple rules for reproducible computational research<a class="anchor" aria-label="anchor" href="#ten-simple-rules-for-reproducible-computational-research"></a>
+<a class="anchor" aria-label="anchor" href="#ten-simple-rules-for-reproducible-computational-research"></a></h2>
 <hr class="half-width"><ul><li>Keep Track of How Every Result Was Produced</li>
 <li>Avoid Manual Data Manipulation Steps</li>
 <li>Track Versions of All External Programs Used</li>
@@ -427,16 +427,16 @@ <h1>Resources</h1>
 <li>Share Scripts, Runs, and Results</li>
 </ul><p>After <a href="https://doi.org/10.1371/journal.pcbi.1003285" class="external-link">Geir
 Kjetil Sandve et al (2013)</a></p>
-</section><section id="research-is-changing"><h2 class="section-heading">Research is changing<a class="anchor" aria-label="anchor" href="#research-is-changing"></a>
-</h2>
+</section><section><h2 class="section-heading" id="research-is-changing">Research is changing<a class="anchor" aria-label="anchor" href="#research-is-changing"></a>
+<a class="anchor" aria-label="anchor" href="#research-is-changing"></a></h2>
 <hr class="half-width"><p>For example,“papers” aren’t paper any more</p>
 <ul><li>Executable research articles in eLife: <a href="https://elifesciences.org/for-the-press/eb096af1/elife-launches-executable-research-articles-for-publishing-computationally-reproducible-results" class="external-link">https://elifesciences.org/for-the-press/eb096af1/elife-launches-executable-research-articles-for-publishing-computationally-reproducible-results</a>
 </li>
 <li>Interactive figures in f1000 articles: <a href="https://blog.f1000.com/2017/07/19/so-long-static-we-now-support-interactive-ploty-figures-in-our-articles/" class="external-link">https://blog.f1000.com/2017/07/19/so-long-static-we-now-support-interactive-ploty-figures-in-our-articles/</a>
 </li>
 <li>Preprints: arxiv, biorxiv,…</li>
-</ul></section><section id="resources-external-training"><h2 class="section-heading">Resources: External Training<a class="anchor" aria-label="anchor" href="#resources-external-training"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="resources-external-training">Resources: External Training<a class="anchor" aria-label="anchor" href="#resources-external-training"></a>
+<a class="anchor" aria-label="anchor" href="#resources-external-training"></a></h2>
 <hr class="half-width"><p>Many institutions and societies run training courses, for
 example:</p>
 <ul><li><a href="https://carpentries.org/" class="external-link">The Carpentries teaches
@@ -454,9 +454,9 @@ <h1>Resources</h1>
 <li>talk to the head of your PhD program, postdoctoral fellows office,
 etc.</li>
 <li>google “bioinformatics course”, etc.</li>
-</ul></section><section id="an-example-of-one-institution-resources-at-the-university-of-edinburgh"><h2 class="section-heading">An example of one institution: Resources at the University of
+</ul></section><section><h2 class="section-heading" id="an-example-of-one-institution-resources-at-the-university-of-edinburgh">An example of one institution: Resources at the University of
 Edinburgh<a class="anchor" aria-label="anchor" href="#an-example-of-one-institution-resources-at-the-university-of-edinburgh"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#an-example-of-one-institution-resources-at-the-university-of-edinburgh"></a></h2>
 <hr class="half-width"><ul><li><a href="https://www.ed.ac.uk/information-services/research-support/research-data-service" class="external-link">Research
 Data Service (plans, archiving, skills)</a></li>
 <li><a href="https://www.digitalresearchservices.ed.ac.uk/" class="external-link">Digital
@@ -498,18 +498,18 @@ <h1>Resources</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/resources.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -46,7 +46,7 @@
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         <h1>Etherpad Teaching notes</h1>
         <p>Last updated on 2024-01-04 |
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+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/teaching_guide_for_etherpad.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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@@ -434,18 +434,18 @@ <h2 id="m-keeping-track-of-changes">25m Keeping track of changes<a class="anchor
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/teaching_guide_for_etherpad.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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         <h1>What we left out</h1>
         <p>Last updated on 2024-01-04 |
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+<a class="anchor" aria-label="anchor" href="#what-we-left-out"></a></h2>
 <hr class="half-width"><p>We have deliberately left many good tools and practices off our list,
 including some that we use daily, because they only make sense on top of
 the core practices described above, or because it takes a larger
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-        
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         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
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         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
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             <hr class="half-width resources">
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 <div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
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-  "dateModified": "2024-07-02",
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+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
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diff --git a/paper.html b/paper.html
index c7558675..cbe4e8b2 100644
--- a/paper.html
+++ b/paper.html
@@ -46,7 +46,7 @@
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           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
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         <a href="index.html">Summary and Setup</a>
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     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
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     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
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         <a href="04-collaboration.html">4. Collaboration</a>
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     <div class="accordion-header" id="flush-heading9">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
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@@ -286,16 +286,16 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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           </div><!-- /div.accordion -->
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@@ -323,11 +323,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Good Enough Practices in Scientific Computing: A Learning Module for Researchers</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/paper.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -495,18 +495,18 @@ <h1 id="references">References<a class="anchor" aria-label="anchor" href="#refer
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/paper.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
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@@ -531,7 +531,7 @@ <h1 id="references">References<a class="anchor" aria-label="anchor" href="#refer
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/paper.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 988eadba..407f92f4 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,6 +1,5 @@
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+pkgdown: 2.1.0
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-
+last_built: 2024-07-09T00:13Z
diff --git a/profiles.html b/profiles.html
index 816b5c1e..9ac5d471 100644
--- a/profiles.html
+++ b/profiles.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
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+
             <hr></div><!--/div.mobile-row -->
 
           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
-        
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 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
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     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
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+
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 </div><!--/div.accordion-flush-->
 
@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -242,7 +242,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -251,7 +251,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading8">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -260,7 +260,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading9">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
-        
+
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 </div><!--/div.accordion-flush-->
 
@@ -286,16 +286,16 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
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             </div>
           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -315,8 +315,8 @@ <h1>Learner Profiles</h1>
 material to this lesson, these will help you understand the target
 audience so that we can have a collaboratively developed, but cohesive
 lesson.</p>
-<section id="miriam-microscopist"><h2 class="section-heading">Miriam Microscopist<a class="anchor" aria-label="anchor" href="#miriam-microscopist"></a>
-</h2>
+<section><h2 class="section-heading" id="miriam-microscopist">Miriam Microscopist<a class="anchor" aria-label="anchor" href="#miriam-microscopist"></a>
+<a class="anchor" aria-label="anchor" href="#miriam-microscopist"></a></h2>
 <hr class="half-width"><p>Miriam is a first-year PhD student in Biology, with an undergraduate
 degree in Pharmacology and a Masters in Biochemistry. She has moved to
 the UK from the Egypt for her PhD, and English is her second language.
@@ -331,8 +331,8 @@ <h1>Learner Profiles</h1>
 available to help her solve them. It will introduce the concept of
 scripted data analysis and why that might have benefits over GUI
 applications.</p>
-</section><section id="stuart-simulator"><h2 class="section-heading">Stuart Simulator<a class="anchor" aria-label="anchor" href="#stuart-simulator"></a>
-</h2>
+</section><section><h2 class="section-heading" id="stuart-simulator">Stuart Simulator<a class="anchor" aria-label="anchor" href="#stuart-simulator"></a>
+<a class="anchor" aria-label="anchor" href="#stuart-simulator"></a></h2>
 <hr class="half-width"><p>Stuart is starting his Postdoc in Epidemiology following a PhD in
 Mathematics. During his PhD, he did a mixture of theoretical work and
 simulations written in MATLAB. Although he’s written code in a few
@@ -350,8 +350,8 @@ <h1>Learner Profiles</h1>
 organization, file naming, and scripting, that can immediately help his
 work. It will introduce the concepts of version control and could
 motivate Stuart to learn Git.</p>
-</section><section id="gertrude-group-leader"><h2 class="section-heading">Gertrude Group Leader<a class="anchor" aria-label="anchor" href="#gertrude-group-leader"></a>
-</h2>
+</section><section><h2 class="section-heading" id="gertrude-group-leader">Gertrude Group Leader<a class="anchor" aria-label="anchor" href="#gertrude-group-leader"></a>
+<a class="anchor" aria-label="anchor" href="#gertrude-group-leader"></a></h2>
 <hr class="half-width"><p>Gertrude is a Professor in Biophysics. She has learned Fortran as a
 PhD student and does a lot of scripting in BASH to run Fotran77 code she
 wrote 20 years ago. She has never been taught any formal programming and
@@ -369,8 +369,8 @@ <h1>Learner Profiles</h1>
 the group will help make any code developments outlast a single PhD
 student and help retain knowledge within the group and promote
 reproducibility and transparency.</p>
-</section><section id="linus-the-lab-manager"><h2 class="section-heading">Linus the Lab Manager<a class="anchor" aria-label="anchor" href="#linus-the-lab-manager"></a>
-</h2>
+</section><section><h2 class="section-heading" id="linus-the-lab-manager">Linus the Lab Manager<a class="anchor" aria-label="anchor" href="#linus-the-lab-manager"></a>
+<a class="anchor" aria-label="anchor" href="#linus-the-lab-manager"></a></h2>
 <hr class="half-width"><p>Linus is the Lab Manager of a large lab that combines computational
 and experimental techniques and is in charge of making sure the lab is
 running smoothly. They are responsible for organising lab meetings,
@@ -386,8 +386,8 @@ <h1>Learner Profiles</h1>
 management and project structures are implemented in the group and that
 this information can form part of the research group and will not be
 lost through a Postdoc or PhD student leaving.</p>
-</section><section id="udaya-the-undergraduate"><h2 class="section-heading">Udaya the Undergraduate<a class="anchor" aria-label="anchor" href="#udaya-the-undergraduate"></a>
-</h2>
+</section><section><h2 class="section-heading" id="udaya-the-undergraduate">Udaya the Undergraduate<a class="anchor" aria-label="anchor" href="#udaya-the-undergraduate"></a>
+<a class="anchor" aria-label="anchor" href="#udaya-the-undergraduate"></a></h2>
 <hr class="half-width"><p>Udaya is an undergraduate student from Malaysia, who has been
 enrolled for her entire degree at an English speaking university. She
 has very clear ambitions and wants to become a scientist in Microbiology
@@ -409,18 +409,18 @@ <h1>Learner Profiles</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/README.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -444,8 +444,8 @@ <h1>Learner Profiles</h1>
   "url": "https://carpentries-lab.github.io/good-enough-practices/profiles.html",
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/profiles.html",
   "dateCreated": "2020-08-24",
-  "dateModified": "2024-07-02",
-  "datePublished": "2024-07-02"
+  "dateModified": "2024-07-09",
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/resources.html b/resources.html
index ac5c6fd5..ceb3e605 100644
--- a/resources.html
+++ b/resources.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
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@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="index.html">Summary and Setup</a>
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@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="01-introduction.html">1. Introduction</a>
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 </div><!--/div.accordion-flush-->
 
@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
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@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
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 </div><!--/div.accordion-flush-->
 
@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
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@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="05-project_organization.html">5. Project Organization</a>
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@@ -242,7 +242,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
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@@ -251,7 +251,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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@@ -260,7 +260,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
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         <a href="08-what_next.html">8. What To Do Next</a>
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@@ -286,16 +286,16 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
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             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
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           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -323,11 +323,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Resources</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/resources.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
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           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -336,8 +336,8 @@ <h1>Resources</h1>
 
 <p>This page has a collection of resources on good practices in
 scientific computing. Feel free to refer to them.</p>
-<section id="some-other-lessons-with-different-emphasis"><h2 class="section-heading">Some other lessons with different emphasis<a class="anchor" aria-label="anchor" href="#some-other-lessons-with-different-emphasis"></a>
-</h2>
+<section><h2 class="section-heading" id="some-other-lessons-with-different-emphasis">Some other lessons with different emphasis<a class="anchor" aria-label="anchor" href="#some-other-lessons-with-different-emphasis"></a>
+<a class="anchor" aria-label="anchor" href="#some-other-lessons-with-different-emphasis"></a></h2>
 <hr class="half-width"><p>The FAIR principles describe work that is <strong>F</strong>indable,
 <strong>A</strong>ccessible, <strong>I</strong>nteroperable and
 <strong>R</strong>eusable.</p>
@@ -350,8 +350,8 @@ <h1>Resources</h1>
 for Leaders, 1-day lesson aimed at established PIs and institutional
 leaders who set policy and drive changes</a>. Note, this lesson is under
 construction as of December 2022</li>
-</ul></section><section id="further-carpentries-lessons"><h2 class="section-heading">Further Carpentries lessons<a class="anchor" aria-label="anchor" href="#further-carpentries-lessons"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="further-carpentries-lessons">Further Carpentries lessons<a class="anchor" aria-label="anchor" href="#further-carpentries-lessons"></a>
+<a class="anchor" aria-label="anchor" href="#further-carpentries-lessons"></a></h2>
 <hr class="half-width"><p>Many other Carpentries lessons may help further your learning:</p>
 <ul><li>Data management
 <ul><li>Data Carpentry Ecology lessons on <a href="https://datacarpentry.org/spreadsheet-ecology-lesson/" class="external-link">spreadsheets</a>
@@ -385,8 +385,8 @@ <h1>Resources</h1>
 to GitLab</a></li>
 </ul></li>
 </ul></li>
-</ul></section><section id="papers-and-sites-on-open-and-good-practices"><h2 class="section-heading">Papers and sites on open and good practices<a class="anchor" aria-label="anchor" href="#papers-and-sites-on-open-and-good-practices"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="papers-and-sites-on-open-and-good-practices">Papers and sites on open and good practices<a class="anchor" aria-label="anchor" href="#papers-and-sites-on-open-and-good-practices"></a>
+<a class="anchor" aria-label="anchor" href="#papers-and-sites-on-open-and-good-practices"></a></h2>
 <hr class="half-width"><ul><li><a href="https://doi.org/10.1186/s13059-015-0850-7" class="external-link">Five selfish
 reasons to work reproducibly. Florian Markowetz, Genome Biology</a></li>
 <li><a href="https://doi.org/10.1186/s13059-015-0669-2" class="external-link">When will ‘open
@@ -412,8 +412,8 @@ <h1>Resources</h1>
 careers, writing, and more</li>
 <li><a href="https://collections.plos.org/compbiol-education" class="external-link">PLoS
 Computational Biology Education section</a></li>
-</ul></section><section id="ten-simple-rules-for-reproducible-computational-research"><h2 class="section-heading">Ten simple rules for reproducible computational research<a class="anchor" aria-label="anchor" href="#ten-simple-rules-for-reproducible-computational-research"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="ten-simple-rules-for-reproducible-computational-research">Ten simple rules for reproducible computational research<a class="anchor" aria-label="anchor" href="#ten-simple-rules-for-reproducible-computational-research"></a>
+<a class="anchor" aria-label="anchor" href="#ten-simple-rules-for-reproducible-computational-research"></a></h2>
 <hr class="half-width"><ul><li>Keep Track of How Every Result Was Produced</li>
 <li>Avoid Manual Data Manipulation Steps</li>
 <li>Track Versions of All External Programs Used</li>
@@ -426,16 +426,16 @@ <h1>Resources</h1>
 <li>Share Scripts, Runs, and Results</li>
 </ul><p>After <a href="https://doi.org/10.1371/journal.pcbi.1003285" class="external-link">Geir
 Kjetil Sandve et al (2013)</a></p>
-</section><section id="research-is-changing"><h2 class="section-heading">Research is changing<a class="anchor" aria-label="anchor" href="#research-is-changing"></a>
-</h2>
+</section><section><h2 class="section-heading" id="research-is-changing">Research is changing<a class="anchor" aria-label="anchor" href="#research-is-changing"></a>
+<a class="anchor" aria-label="anchor" href="#research-is-changing"></a></h2>
 <hr class="half-width"><p>For example,“papers” aren’t paper any more</p>
 <ul><li>Executable research articles in eLife: <a href="https://elifesciences.org/for-the-press/eb096af1/elife-launches-executable-research-articles-for-publishing-computationally-reproducible-results" class="external-link">https://elifesciences.org/for-the-press/eb096af1/elife-launches-executable-research-articles-for-publishing-computationally-reproducible-results</a>
 </li>
 <li>Interactive figures in f1000 articles: <a href="https://blog.f1000.com/2017/07/19/so-long-static-we-now-support-interactive-ploty-figures-in-our-articles/" class="external-link">https://blog.f1000.com/2017/07/19/so-long-static-we-now-support-interactive-ploty-figures-in-our-articles/</a>
 </li>
 <li>Preprints: arxiv, biorxiv,…</li>
-</ul></section><section id="resources-external-training"><h2 class="section-heading">Resources: External Training<a class="anchor" aria-label="anchor" href="#resources-external-training"></a>
-</h2>
+</ul></section><section><h2 class="section-heading" id="resources-external-training">Resources: External Training<a class="anchor" aria-label="anchor" href="#resources-external-training"></a>
+<a class="anchor" aria-label="anchor" href="#resources-external-training"></a></h2>
 <hr class="half-width"><p>Many institutions and societies run training courses, for
 example:</p>
 <ul><li><a href="https://carpentries.org/" class="external-link">The Carpentries teaches
@@ -453,9 +453,9 @@ <h1>Resources</h1>
 <li>talk to the head of your PhD program, postdoctoral fellows office,
 etc.</li>
 <li>google “bioinformatics course”, etc.</li>
-</ul></section><section id="an-example-of-one-institution-resources-at-the-university-of-edinburgh"><h2 class="section-heading">An example of one institution: Resources at the University of
+</ul></section><section><h2 class="section-heading" id="an-example-of-one-institution-resources-at-the-university-of-edinburgh">An example of one institution: Resources at the University of
 Edinburgh<a class="anchor" aria-label="anchor" href="#an-example-of-one-institution-resources-at-the-university-of-edinburgh"></a>
-</h2>
+<a class="anchor" aria-label="anchor" href="#an-example-of-one-institution-resources-at-the-university-of-edinburgh"></a></h2>
 <hr class="half-width"><ul><li><a href="https://www.ed.ac.uk/information-services/research-support/research-data-service" class="external-link">Research
 Data Service (plans, archiving, skills)</a></li>
 <li><a href="https://www.digitalresearchservices.ed.ac.uk/" class="external-link">Digital
@@ -497,18 +497,18 @@ <h1>Resources</h1>
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/resources.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -533,7 +533,7 @@ <h1>Resources</h1>
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/resources.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
diff --git a/teaching_guide_for_etherpad.html b/teaching_guide_for_etherpad.html
index 5bfe170f..22d6bd93 100644
--- a/teaching_guide_for_etherpad.html
+++ b/teaching_guide_for_etherpad.html
@@ -46,7 +46,7 @@
             </li>
           </ul></li>
       </div>
-      
+
       <div class="dropdown" id="instructor-dropdown">
         <button class="btn btn-secondary dropdown-toggle bordered-button" type="button" id="dropdownMenu1" data-bs-toggle="dropdown" aria-expanded="false">
           <i aria-hidden="true" class="icon" data-feather="eye"></i> Learner View <i data-feather="chevron-down"></i>
@@ -169,7 +169,7 @@ <h2 class="accordion-header" id="flush-headingNine">
                 </div><!--/div.accordion-flush-->
               </div><!--div.sidenav-view-selector -->
             </div><!--/div.col -->
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           <div class="accordion accordion-flush" id="accordionFlush11">
@@ -188,7 +188,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading1">
         <a href="index.html">Summary and Setup</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -197,7 +197,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading2">
         <a href="01-introduction.html">1. Introduction</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -206,7 +206,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading3">
         <a href="02-data_management.html">2. Data Management</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -215,7 +215,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading4">
         <a href="03-software.html">3. Code and Software</a>
     </div><!--/div.accordion-header-->
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+
   </div><!--/div.accordion-item-->
 </div><!--/div.accordion-flush-->
 
@@ -224,7 +224,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading5">
         <a href="04-collaboration.html">4. Collaboration</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -233,7 +233,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading6">
         <a href="05-project_organization.html">5. Project Organization</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -242,7 +242,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading7">
         <a href="06-track_changes.html">6. Keeping Track of Changes</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -251,7 +251,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading8">
         <a href="07-manuscripts.html">7. Manuscripts</a>
     </div><!--/div.accordion-header-->
-        
+
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 </div><!--/div.accordion-flush-->
 
@@ -260,7 +260,7 @@ <h2 class="accordion-header chapters" id="flush-headingEleven">
     <div class="accordion-header" id="flush-heading9">
         <a href="08-what_next.html">8. What To Do Next</a>
     </div><!--/div.accordion-header-->
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 </div><!--/div.accordion-flush-->
 
@@ -286,16 +286,16 @@ <h2 class="accordion-header" id="flush-headingTwelve">
                       <li>
                         <a href="profiles.html">Learner Profiles</a>
                       </li>
-                      
+
                     </ul></div>
                 </div>
               </div>
             </div>
             <hr class="half-width resources"><a href="aio.html">See all in one page</a>
-            
+
 
             <hr class="d-none d-sm-block d-md-none"><div class="d-grid gap-1">
-            
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           </div><!-- /div.accordion -->
         </div><!-- /div.sidebar-inner -->
@@ -323,11 +323,11 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Etherpad Teaching notes</h1>
         <p>Last updated on 2024-01-04 |
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/teaching_guide_for_etherpad.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
-        
-        
-        
+
+
+
         <div class="text-end">
           <button role="button" aria-pressed="false" tabindex="0" id="expand-code" class="pull-right" data-expand="Expand All Solutions " data-collapse="Collapse All Solutions "> Expand All Solutions <i aria-hidden="true" data-feather="plus"></i></button>
         </div>
@@ -433,18 +433,18 @@ <h2 id="m-keeping-track-of-changes">25m Keeping track of changes<a class="anchor
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
         <p>
-        
+
         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/teaching_guide_for_etherpad.md" class="external-link">Edit on GitHub</a>
-        
+
 	
         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
 			</div>
 			<div class="col-md-6">
-        
+
         <p>Materials licensed under <a href="LICENSE.html">CC-BY 4.0</a> by the authors</p>
-        
+
         <p>Template licensed under <a href="https://creativecommons.org/licenses/by-sa/4.0/" class="external-link">CC-BY 4.0</a> by <a href="https://carpentries.org/" class="external-link">The Carpentries</a></p>
         <p>Built with <a href="https://github.com/carpentries/sandpaper/tree/0.16.5" class="external-link">sandpaper (0.16.5)</a>, <a href="https://github.com/carpentries/pegboard/tree/0.7.6" class="external-link">pegboard (0.7.6)</a>, and <a href="https://github.com/carpentries/varnish/tree/1.0.3" class="external-link">varnish (1.0.3)</a></p>
 			</div>
@@ -469,7 +469,7 @@ <h2 id="m-keeping-track-of-changes">25m Keeping track of changes<a class="anchor
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/teaching_guide_for_etherpad.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
 }
 
   </script><script>
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         <h1>What we left out</h1>
         <p>Last updated on 2024-01-04 |
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         <a href="https://github.com/carpentries-lab/good-enough-practices/edit/main/instructors/what-we-left-out.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
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         </div>
 
         
-<section id="what-we-left-out"><h2 class="section-heading">What We Left Out<a class="anchor" aria-label="anchor" href="#what-we-left-out"></a>
-</h2>
+<section><h2 class="section-heading" id="what-we-left-out">What We Left Out<a class="anchor" aria-label="anchor" href="#what-we-left-out"></a>
+<a class="anchor" aria-label="anchor" href="#what-we-left-out"></a></h2>
 <hr class="half-width"><p>We have deliberately left many good tools and practices off our list,
 including some that we use daily, because they only make sense on top of
 the core practices described above, or because it takes a larger
@@ -479,18 +479,18 @@ <h3 class="callout-title">Attribution<a class="anchor" aria-label="anchor" href=
       		<footer class="row footer mx-md-3"><hr><div class="col-md-6">
         <p>This lesson is subject to the <a href="CODE_OF_CONDUCT.html">Code of Conduct</a></p>
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         | <a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CONTRIBUTING.md" class="external-link">Contributing</a>
         | <a href="https://github.com/carpentries-lab/good-enough-practices/" class="external-link">Source</a></p>
 				<p><a href="https://github.com/carpentries-lab/good-enough-practices/blob/main/CITATION" class="external-link">Cite</a> | <a href="mailto:Edward.Wallace@ed.ac.uk">Contact</a> | <a href="https://carpentries.org/about/" class="external-link">About</a></p>
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@@ -515,7 +515,7 @@ <h3 class="callout-title">Attribution<a class="anchor" aria-label="anchor" href=
   "identifier": "https://carpentries-lab.github.io/good-enough-practices/what-we-left-out.html",
   "dateCreated": "2020-08-24",
   "dateModified": "2024-01-04",
-  "datePublished": "2024-07-02"
+  "datePublished": "2024-07-09"
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