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pythonhealthdatascience · Sep 20, 2024 · a8b062c · a8b062c
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-29e6dbc4
+c609ae87
diff --git a/evaluation/badges.html b/evaluation/badges.html
@@ -256,7 +256,7 @@ <h1 class="title">Journal badges</h1>
 <p><em>Caveat: Please note that these criteria are based on available information about each badge online, and that we have likely differences in our procedure (e.g.&nbsp;allowed troubleshooting for execution and reproduction, not under tight time pressure to complete). Moreover, we focus only on reproduction of the discrete-event simulation, and not on other aspects of the article. We cannot guarantee that the badges below would have been awarded in practice by these journals.</em></p>
 <section id="criteria" class="level2">
 <h2 class="anchored" data-anchor-id="criteria">Criteria</h2>
-<div id="887dcc5f" class="cell" data-execution_count="1">
+<div id="42eb46c2" class="cell" data-execution_count="1">
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> IPython.display <span class="im">import</span> display, Markdown</span>
@@ -389,7 +389,7 @@ <h2 class="anchored" data-anchor-id="criteria">Criteria</h2>
 </section>
 <section id="badges" class="level2">
 <h2 class="anchored" data-anchor-id="badges">Badges</h2>
-<div id="d935363d" class="cell" data-execution_count="2">
+<div id="a101749a" class="cell" data-execution_count="2">
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Full badge names</span></span>

diff --git a/evaluation/reproduction_report.html b/evaluation/reproduction_report.html
diff --git a/evaluation/reproduction_success.html b/evaluation/reproduction_success.html
diff --git a/index.html b/index.html
@@ -259,7 +259,7 @@ <h2 class="anchored" data-anchor-id="protocol">Protocol</h2>
 <section id="citation" class="level2">
 <h2 class="anchored" data-anchor-id="citation">Citation</h2>
 <p><strong>APA:</strong></p>
-<p>Heather A., Monks T., Harper A., Mustafee N., Mayne A. (2024). Template for computational reproducibility assessments on STARS (version 1.0.4). URL: https://github.com/pythonhealthdatascience/stars_reproduction_template</p>
+<p>Heather A., Monks T., Harper A. (2024). STARS: Computational reproducibility of Hernandez et al.&nbsp;2015 (version 0.1.0). URL: https://github.com/pythonhealthdatascience/stars-reproduce-hernandez-2015</p>
 <p>See <code>CITATION.cff</code> and <code>citation_bibtex.bib</code> for alternative formats.</p>
 </section>
 <section id="license" class="level2">

diff --git a/logbook/logbook.html b/logbook/logbook.html
@@ -256,7 +256,7 @@ <h5 class="quarto-listing-category-title">Categories</h5><div class="quarto-list
 
 <div class="quarto-listing quarto-listing-container-default" id="listing-listing">
 <div class="list quarto-listing-default">
-<div class="quarto-post image-right" data-index="0" data-categories="setup" data-listing-date-sort="1726790400000" data-listing-file-modified-sort="1726840654462" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="96">
+<div class="quarto-post image-right" data-index="0" data-categories="setup" data-listing-date-sort="1726790400000" data-listing-file-modified-sort="1726840826450" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="108">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_09_20/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_09_20/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>

diff --git a/logbook/posts/2024_09_20/index.html b/logbook/posts/2024_09_20/index.html
@@ -237,7 +237,7 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#previously-contacted-the-authors" id="toc-previously-contacted-the-authors" class="nav-link active" data-scroll-target="#previously-contacted-the-authors">Previously: Contacted the authors</a></li>
   <li><a href="#set-up-repository" id="toc-set-up-repository" class="nav-link" data-scroll-target="#set-up-repository">14.38-14.52: Set-up repository</a></li>
-  <li><a href="#x-upload-code-to-repository" id="toc-x-upload-code-to-repository" class="nav-link" data-scroll-target="#x-upload-code-to-repository">14.57-X: Upload code to repository</a></li>
+  <li><a href="#upload-code-to-repository" id="toc-upload-code-to-repository" class="nav-link" data-scroll-target="#upload-code-to-repository">14.57-14.58: Upload code to repository</a></li>
   <li><a href="#timings" id="toc-timings" class="nav-link" data-scroll-target="#timings">Timings</a></li>
   </ul>
 <div class="toc-actions"><ul><li><a href="https://github.com/pythonhealthdatascience/stars-reproduce-hernandez-2015/edit/main/logbook/posts/2024_09_20/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/pythonhealthdatascience/stars-reproduce-hernandez-2015/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
@@ -281,12 +281,13 @@ <h2 class="anchored" data-anchor-id="set-up-repository">14.38-14.52: Set-up repo
 <li>Set up site on GitHub pages (<code>quarto publish gh-pages</code>)</li>
 </ul>
 </section>
-<section id="x-upload-code-to-repository" class="level2">
-<h2 class="anchored" data-anchor-id="x-upload-code-to-repository">14.57-X: Upload code to repository</h2>
+<section id="upload-code-to-repository" class="level2">
+<h2 class="anchored" data-anchor-id="upload-code-to-repository">14.57-14.58: Upload code to repository</h2>
+<p>The code is available at <a href="https://github.com/ivihernandez/staff-allocation/tree/master" class="uri">https://github.com/ivihernandez/staff-allocation/tree/master</a>. It is licensed under an MIT license.</p>
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="4b1c7a74" class="cell" data-execution_count="1">
+<div id="8ac8a7cc" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

diff --git a/search.json b/search.json
@@ -186,7 +186,7 @@
     "href": "index.html#citation",
     "title": "Reproducing Hernandez et al. 2015",
     "section": "Citation",
-    "text": "Citation\nAPA:\nHeather A., Monks T., Harper A., Mustafee N., Mayne A. (2024). Template for computational reproducibility assessments on STARS (version 1.0.4). URL: https://github.com/pythonhealthdatascience/stars_reproduction_template\nSee CITATION.cff and citation_bibtex.bib for alternative formats."
+    "text": "Citation\nAPA:\nHeather A., Monks T., Harper A. (2024). STARS: Computational reproducibility of Hernandez et al. 2015 (version 0.1.0). URL: https://github.com/pythonhealthdatascience/stars-reproduce-hernandez-2015\nSee CITATION.cff and citation_bibtex.bib for alternative formats."
   },
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     "objectID": "index.html#license",
@@ -217,11 +217,11 @@
     "text": "14.38-14.52: Set-up repository\n\nCreated repository from template\nSet up environment\nModified template files:\n\nREADME.md\nquarto site index.qmd\nCITATION.cff\n_quarto.yml\n\nSet up site on GitHub pages (quarto publish gh-pages)"
   },
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-    "href": "logbook/posts/2024_09_20/index.html#x-upload-code-to-repository",
+    "objectID": "logbook/posts/2024_09_20/index.html#upload-code-to-repository",
+    "href": "logbook/posts/2024_09_20/index.html#upload-code-to-repository",
     "title": "Day 1",
-    "section": "14.57-X: Upload code to repository",
-    "text": "14.57-X: Upload code to repository"
+    "section": "14.57-14.58: Upload code to repository",
+    "text": "14.57-14.58: Upload code to repository\nThe code is available at https://github.com/ivihernandez/staff-allocation/tree/master. It is licensed under an MIT license."
   },
   {
     "objectID": "logbook/posts/2024_09_20/index.html#timings",

diff --git a/sitemap.xml b/sitemap.xml
@@ -2,62 +2,62 @@
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-    <lastmod>2024-09-20T13:57:34.460Z</lastmod>
+    <lastmod>2024-09-20T14:00:26.450Z</lastmod>
   </url>
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-    <lastmod>2024-09-20T13:57:34.463Z</lastmod>
+    <lastmod>2024-09-20T14:00:26.491Z</lastmod>
   </url>
   <url>
     <loc>https://pythonhealthdatascience.github.io/stars-reproduce-hernandez-2015/quarto_site/license.html</loc>
-    <lastmod>2024-09-20T13:57:34.462Z</lastmod>
+    <lastmod>2024-09-20T14:00:26.490Z</lastmod>
   </url>
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     <loc>https://pythonhealthdatascience.github.io/stars-reproduce-hernandez-2015/evaluation/reporting.html</loc>
-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
+    <lastmod>2024-09-20T14:00:26.450Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.462Z</lastmod>
+    <lastmod>2024-09-20T14:00:26.450Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
+    <lastmod>2024-09-20T14:00:26.450Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
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-    <lastmod>2024-09-20T13:57:34.461Z</lastmod>
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