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larsvilhuber · Dec 31, 2023 · 778c312 · 778c312
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diff --git a/01_run_it_again.html b/01_run_it_again.html
diff --git a/01_hands_off_running.html → 02_hands_off_running.html b/01_hands_off_running.html → 02_hands_off_running.html
@@ -61,12 +61,10 @@
 const thebe_selector_output = ".output, .cell_output"
 </script>
     <script async="async" src="_static/sphinx-thebe.js"></script>
-    <script>DOCUMENTATION_OPTIONS.pagename = '01_hands_off_running';</script>
-    <link rel="canonical" href="https://larsvilhuber.github.io/self-checking-reproducibility/01_hands_off_running.html" />
+    <script>DOCUMENTATION_OPTIONS.pagename = '02_hands_off_running';</script>
+    <link rel="canonical" href="https://larsvilhuber.github.io/self-checking-reproducibility/02_hands_off_running.html" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Using environments" href="02_environments.html" />
-    <link rel="prev" title="Introduction" href="index.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -163,12 +161,7 @@
                 </a>
             </li>
         </ul>
-        <p aria-level="2" class="caption" role="heading"><span class="caption-text">Simple ways to test replication packages</span></p>
-<ul class="current nav bd-sidenav">
-<li class="toctree-l1 current active"><a class="current reference internal" href="#">Hands-off running</a></li>
-<li class="toctree-l1"><a class="reference internal" href="02_environments.html">Using environments</a></li>
-</ul>
-<p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
+        <p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="29-new-computer.html">Use a new computer</a></li>
 <li class="toctree-l1"><a class="reference internal" href="30-docker.html">Use of containers</a></li>
@@ -243,7 +236,7 @@
 
 
 
-      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/edit/main/01_hands_off_running.md" target="_blank"
+      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/edit/main/02_hands_off_running.md" target="_blank"
    class="btn btn-sm btn-source-edit-button dropdown-item"
    title="Suggest edit"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -260,7 +253,7 @@
 
 
 
-      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/issues/new?title=Issue%20on%20page%20%2F01_hands_off_running.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/issues/new?title=Issue%20on%20page%20%2F02_hands_off_running.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -290,7 +283,7 @@
 
 
 
-      <li><a href="_sources/01_hands_off_running.md" target="_blank"
+      <li><a href="_sources/02_hands_off_running.md" target="_blank"
    class="btn btn-sm btn-download-source-button dropdown-item"
    title="Download source file"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -382,7 +375,7 @@ <h2> Contents </h2>
             </div>
             <nav aria-label="Page">
                 <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#some-simple-examples-of-main-files">Some simple examples of main files</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#examples">Examples</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#what-this-does">What this does</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#what-this-does-not-do">What this does not do</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#what-to-do-next">What to do next</a></li>
@@ -398,15 +391,15 @@ <h2> Contents </h2>
                 <article class="bd-article" role="main">
 
   <section class="tex2jax_ignore mathjax_ignore" id="hands-off-running">
-<h1>Hands-off running<a class="headerlink" href="#hands-off-running" title="Permalink to this heading">#</a></h1>
+<span id="id1"></span><h1>Hands-off running<a class="headerlink" href="#hands-off-running" title="Permalink to this heading">#</a></h1>
 <p>The very first test is that your code must run, beginning to end, top to bottom, without error, and ideally without any user intervention. This should in principle (re)create all figures, tables, and numbers you include in your paper.</p>
 <p>Many users may not be set up to run in one single top-to-bottom run. It helps to have a <code class="docutils literal notranslate"><span class="pre">main</span> <span class="pre">file</span></code> that runs all the other files, or all code, in the correct order, but is not a pre-requisite.</p>
 <div class="admonition warning">
 <p class="admonition-title">Warning</p>
 <p>We have seen users who appear to highlight code and to run it interactively, in pieces, using the program file as a kind of notepad. This is not reproducible, and should be avoided. It is fine for debugging.</p>
 </div>
-<section id="some-simple-examples-of-main-files">
-<h2>Some simple examples of main files<a class="headerlink" href="#some-simple-examples-of-main-files" title="Permalink to this heading">#</a></h2>
+<section id="examples">
+<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this heading">#</a></h2>
 <div class="sd-tab-set docutils">
 <input checked="checked" id="sd-tab-item-0" name="sd-tab-set-0" type="radio">
 </input><label class="sd-tab-label" for="sd-tab-item-0">
@@ -605,24 +598,6 @@ <h2>What to do next<a class="headerlink" href="#what-to-do-next" title="Permalin
                 <footer class="bd-footer-article">
                   <!-- Previous / next buttons -->
 <div class="prev-next-area">
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-      <div class="prev-next-info">
-        <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Introduction</p>
-      </div>
-    </a>
-    <a class="right-next"
-       href="02_environments.html"
-       title="next page">
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-        <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Using environments</p>
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 </div>
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@@ -638,7 +613,7 @@ <h2>What to do next<a class="headerlink" href="#what-to-do-next" title="Permalin
   </div>
   <nav class="bd-toc-nav page-toc">
     <ul class="visible nav section-nav flex-column">
-<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#some-simple-examples-of-main-files">Some simple examples of main files</a></li>
+<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#examples">Examples</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#what-this-does">What this does</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#what-this-does-not-do">What this does not do</a></li>
 <li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#what-to-do-next">What to do next</a></li>

diff --git a/02_environments.html → 10_environments.html b/02_environments.html → 10_environments.html
@@ -61,12 +61,10 @@
 const thebe_selector_output = ".output, .cell_output"
 </script>
     <script async="async" src="_static/sphinx-thebe.js"></script>
-    <script>DOCUMENTATION_OPTIONS.pagename = '02_environments';</script>
-    <link rel="canonical" href="https://larsvilhuber.github.io/self-checking-reproducibility/02_environments.html" />
+    <script>DOCUMENTATION_OPTIONS.pagename = '10_environments';</script>
+    <link rel="canonical" href="https://larsvilhuber.github.io/self-checking-reproducibility/10_environments.html" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="Use a new computer" href="29-new-computer.html" />
-    <link rel="prev" title="Hands-off running" href="01_hands_off_running.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -163,12 +161,7 @@
                 </a>
             </li>
         </ul>
-        <p aria-level="2" class="caption" role="heading"><span class="caption-text">Simple ways to test replication packages</span></p>
-<ul class="current nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="01_hands_off_running.html">Hands-off running</a></li>
-<li class="toctree-l1 current active"><a class="current reference internal" href="#">Using environments</a></li>
-</ul>
-<p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
+        <p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="29-new-computer.html">Use a new computer</a></li>
 <li class="toctree-l1"><a class="reference internal" href="30-docker.html">Use of containers</a></li>
@@ -243,7 +236,7 @@
 
 
 
-      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/edit/main/02_environments.md" target="_blank"
+      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/edit/main/10_environments.md" target="_blank"
    class="btn btn-sm btn-source-edit-button dropdown-item"
    title="Suggest edit"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -260,7 +253,7 @@
 
 
 
-      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/issues/new?title=Issue%20on%20page%20%2F02_environments.html&body=Your%20issue%20content%20here." target="_blank"
+      <li><a href="https://github.com/larsvilhuber/self-checking-reproducibility/issues/new?title=Issue%20on%20page%20%2F10_environments.html&body=Your%20issue%20content%20here." target="_blank"
    class="btn btn-sm btn-source-issues-button dropdown-item"
    title="Open an issue"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -290,7 +283,7 @@
 
 
 
-      <li><a href="_sources/02_environments.md" target="_blank"
+      <li><a href="_sources/10_environments.md" target="_blank"
    class="btn btn-sm btn-download-source-button dropdown-item"
    title="Download source file"
    data-bs-placement="left" data-bs-toggle="tooltip"
@@ -416,24 +409,6 @@ <h1>Using environments<a class="headerlink" href="#using-environments" title="Pe
                 <footer class="bd-footer-article">
                   <!-- Previous / next buttons -->
 <div class="prev-next-area">
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-      <div class="prev-next-info">
-        <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Hands-off running</p>
-      </div>
-    </a>
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-       href="29-new-computer.html"
-       title="next page">
-      <div class="prev-next-info">
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diff --git a/29-new-computer.html b/29-new-computer.html
@@ -66,7 +66,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Use of containers" href="30-docker.html" />
-    <link rel="prev" title="Using environments" href="02_environments.html" />
+    <link rel="prev" title="Introduction" href="index.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -163,12 +163,7 @@
                 </a>
             </li>
         </ul>
-        <p aria-level="2" class="caption" role="heading"><span class="caption-text">Simple ways to test replication packages</span></p>
-<ul class="nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="01_hands_off_running.html">Hands-off running</a></li>
-<li class="toctree-l1"><a class="reference internal" href="02_environments.html">Using environments</a></li>
-</ul>
-<p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
+        <p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Use a new computer</a></li>
 <li class="toctree-l1"><a class="reference internal" href="30-docker.html">Use of containers</a></li>
@@ -418,12 +413,12 @@ <h1>Use a new computer<a class="headerlink" href="#use-a-new-computer" title="Pe
                   <!-- Previous / next buttons -->
 <div class="prev-next-area">
     <a class="left-prev"
-       href="02_environments.html"
+       href="index.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Using environments</p>
+        <p class="prev-next-title">Introduction</p>
       </div>
     </a>
     <a class="right-next"

diff --git a/30-docker.html b/30-docker.html
@@ -162,12 +162,7 @@
                 </a>
             </li>
         </ul>
-        <p aria-level="2" class="caption" role="heading"><span class="caption-text">Simple ways to test replication packages</span></p>
-<ul class="nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="01_hands_off_running.html">Hands-off running</a></li>
-<li class="toctree-l1"><a class="reference internal" href="02_environments.html">Using environments</a></li>
-</ul>
-<p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
+        <p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="29-new-computer.html">Use a new computer</a></li>
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Use of containers</a></li>

diff --git a/README.html b/README.html
@@ -161,12 +161,7 @@
                 </a>
             </li>
         </ul>
-        <p aria-level="2" class="caption" role="heading"><span class="caption-text">Simple ways to test replication packages</span></p>
-<ul class="nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="01_hands_off_running.html">Hands-off running</a></li>
-<li class="toctree-l1"><a class="reference internal" href="02_environments.html">Using environments</a></li>
-</ul>
-<p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
+        <p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="29-new-computer.html">Use a new computer</a></li>
 <li class="toctree-l1"><a class="reference internal" href="30-docker.html">Use of containers</a></li>

diff --git a/_sources/01_run_it_again.md b/_sources/01_run_it_again.md
@@ -0,0 +1,14 @@
+# Run it all again
+
+The very first test is that your code must run, beginning to end, top to bottom, without error, and ideally without any user intervention. This should in principle (re)create all figures, tables, and numbers you include in your paper. 
+
+
+## Exceptions
+
+### Code runs for a very long time
+
+What happens when some of these re-runs are very long? See later in this chapter for how to handle this.
+
+### Making the code run takes you a very long time
+
+While the code, once set to run, can do so on its own, *you* might need to spend a lot of time getting all the various pieces to run. This should be a warning sign: if it takes you a long time to get it to run, or to manually reproduce the results, it might take others even longer. Furthermore, it may suggest that you haven't been able to re-run your own code very often, which can be correlated with fragility or even lack of reproducibility. We address this partially in the [next section](hands-off-running).
diff --git a/_sources/01_hands_off_running.md → _sources/02_hands_off_running.md b/_sources/01_hands_off_running.md → _sources/02_hands_off_running.md
@@ -1,3 +1,4 @@
+(hands-off-running)=
 # Hands-off running
 
 The very first test is that your code must run, beginning to end, top to bottom, without error, and ideally without any user intervention. This should in principle (re)create all figures, tables, and numbers you include in your paper. 
@@ -8,7 +9,7 @@ Many users may not be set up to run in one single top-to-bottom run. It helps to
 We have seen users who appear to highlight code and to run it interactively, in pieces, using the program file as a kind of notepad. This is not reproducible, and should be avoided. It is fine for debugging.
 ```
 
-## Some simple examples of main files
+## Examples
 
 
 

diff --git a/_sources/02_environments.md → _sources/10_environments.md b/_sources/02_environments.md → _sources/10_environments.md
diff --git a/genindex.html b/genindex.html
@@ -160,12 +160,7 @@
                 </a>
             </li>
         </ul>
-        <p aria-level="2" class="caption" role="heading"><span class="caption-text">Simple ways to test replication packages</span></p>
-<ul class="nav bd-sidenav">
-<li class="toctree-l1"><a class="reference internal" href="01_hands_off_running.html">Hands-off running</a></li>
-<li class="toctree-l1"><a class="reference internal" href="02_environments.html">Using environments</a></li>
-</ul>
-<p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
+        <p aria-level="2" class="caption" role="heading"><span class="caption-text">More complex ways to test replication packages</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="29-new-computer.html">Use a new computer</a></li>
 <li class="toctree-l1"><a class="reference internal" href="30-docker.html">Use of containers</a></li>