From 928a5e262599afd6e3cbf4cc7682d09f0b884b3a Mon Sep 17 00:00:00 2001
From: Quarto GHA Workflow Runner <quarto-github-actions-publish@example.com>
Date: Thu, 1 Aug 2024 14:16:10 +0000
Subject: [PATCH] Built site for gh-pages

---
 .nojekyll                            |  2 +-
 evaluation/badges.html               |  4 ++--
 evaluation/reproduction_report.html  |  6 ++---
 evaluation/reproduction_success.html | 10 ++++----
 logbook/logbook.html                 |  2 +-
 logbook/posts/2024_08_01/index.html  |  2 +-
 quarto_site/license.html             | 25 ++++++++++++--------
 search.json                          |  2 +-
 sitemap.xml                          | 34 ++++++++++++++--------------
 9 files changed, 46 insertions(+), 41 deletions(-)

diff --git a/.nojekyll b/.nojekyll
index fc16b68..dc329b0 100644
--- a/.nojekyll
+++ b/.nojekyll
@@ -1 +1 @@
-87510a9c
\ No newline at end of file
+bba72b2a
\ No newline at end of file
diff --git a/evaluation/badges.html b/evaluation/badges.html
index c74ff62..519253f 100644
--- 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="be271c20" class="cell" data-execution_count="1">
+<div id="5a21646d" 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="a45b9747" class="cell" data-execution_count="2">
+<div id="a1e13579" 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
index 315d9f0..9e62f2d 100644
--- a/evaluation/reproduction_report.html
+++ b/evaluation/reproduction_report.html
@@ -253,11 +253,11 @@ <h2 class="anchored" data-anchor-id="computational-reproducibility">Computationa
 </section>
 <section id="evaluation-against-guidelines" class="level2">
 <h2 class="anchored" data-anchor-id="evaluation-against-guidelines">Evaluation against guidelines</h2>
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+<div id="4ae9befc" class="cell" data-execution_count="1">
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diff --git a/logbook/logbook.html b/logbook/logbook.html
index 64d22d5..ada0f7b 100644
--- 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="1722470400000" data-listing-file-modified-sort="1722521326532" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="531">
+<div class="quarto-post image-right" data-index="0" data-categories="setup" data-listing-date-sort="1722470400000" data-listing-file-modified-sort="1722521702830" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="531">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_08_01/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_08_01/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
diff --git a/logbook/posts/2024_08_01/index.html b/logbook/posts/2024_08_01/index.html
index 82e31f0..fa79696 100644
--- a/logbook/posts/2024_08_01/index.html
+++ b/logbook/posts/2024_08_01/index.html
@@ -314,7 +314,7 @@ <h2 class="anchored" data-anchor-id="read-article-and-consensus-on-scope.">14.53
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="da93fc9d" class="cell" data-execution_count="1">
+<div id="fcdaac8c" 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/quarto_site/license.html b/quarto_site/license.html
index caa4915..680ee3c 100644
--- a/quarto_site/license.html
+++ b/quarto_site/license.html
@@ -188,8 +188,7 @@ <h1 class="title">Open Source License</h1>
 </header>
 
 
-<!-- TODO: Update with appropriate license -->
-<p>This repository is licensed under the [license].</p>
+<p>This repository is licensed under the BSD 3-Clause License.</p>
 <div class="callout callout-style-simple callout-note no-icon callout-titled">
 <div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-1-contents" aria-controls="callout-1" aria-expanded="false" aria-label="Toggle callout">
 <div class="callout-icon-container">
@@ -214,8 +213,7 @@ <h1 class="title">Open Source License</h1>
 </div>
 </div>
 </div>
-<!-- TODO: Update with appropriate license -->
-<p>This is aligned with the original study, who shared their code under [license].</p>
+<p>This is aligned with the original study, who shared their code under BSD 3-Clause License.</p>
 <div class="callout callout-style-simple callout-note no-icon callout-titled">
 <div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-2-contents" aria-controls="callout-2" aria-expanded="false" aria-label="Toggle callout">
 <div class="callout-icon-container">
@@ -228,26 +226,33 @@ <h1 class="title">Open Source License</h1>
 </div>
 <div id="callout-2" class="callout-2-contents callout-collapse collapse">
 <div class="callout-body-container callout-body">
-<!-- TODO: Provide relative path to embed license from the original study, as done above for the main repository license -->
-<p>[Embedded license]</p>
+<p>BSD 3-Clause License</p>
+<p>Copyright (c) 2022, Anastasia Anagnostou All rights reserved.</p>
+<p>Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:</p>
+<ol type="1">
+<li><p>Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.</p></li>
+<li><p>Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.</p></li>
+<li><p>Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.</p></li>
+</ol>
+<p>THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</p>
 </div>
 </div>
 </div>
-<!-- TODO: Add info about the article license -->
-<p>The original study was published in the journal “[Journal name]”. They distributed the article under [Add more details about license]</p>
+<p>The original study was published in the journal “IEEE Xplore”. The copyright is retained by this journal. Open access versions are available with <a href="https://bura.brunel.ac.uk/handle/2438/25912">Brunel University Research Archive</a> and <a href="https://discovery.ucl.ac.uk/id/eprint/10187277/">UCL Discovery</a>, but these are just for personal use, as in the statement below:</p>
 <div class="callout callout-style-simple callout-note no-icon callout-titled">
 <div class="callout-header d-flex align-content-center" data-bs-toggle="collapse" data-bs-target=".callout-3-contents" aria-controls="callout-3" aria-expanded="false" aria-label="Toggle callout">
 <div class="callout-icon-container">
 <i class="callout-icon no-icon"></i>
 </div>
 <div class="callout-title-container flex-fill">
-View copyright statement from journal
+View copyright statement
 </div>
 <div class="callout-btn-toggle d-inline-block border-0 py-1 ps-1 pe-0 float-end"><i class="callout-toggle"></i></div>
 </div>
 <div id="callout-3" class="callout-3-contents callout-collapse collapse">
 <div class="callout-body-container callout-body">
-<!-- TODO: Add copyright statement -->
+<p>“Copyright © 2022 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.”</p>
+<p><a href="https://bura.brunel.ac.uk/handle/2438/25912" class="uri">https://bura.brunel.ac.uk/handle/2438/25912</a></p>
 </div>
 </div>
 </div>
diff --git a/search.json b/search.json
index a713937..54f953c 100644
--- a/search.json
+++ b/search.json
@@ -186,7 +186,7 @@
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     "section": "",
-    "text": "This repository is licensed under the [license].\n\n\n\n\n\n\nView license\n\n\n\n\n\nBSD 3-Clause License\nCopyright (c) 2024, STARS Project Team, using code from 2022, Anastasia Anagnostou. All rights reserved.\nRedistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:\n\nRedistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.\nRedistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.\nNeither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n\n\n\n\nThis is aligned with the original study, who shared their code under [license].\n\n\n\n\n\n\nView license\n\n\n\n\n\n\n[Embedded license]\n\n\n\n\nThe original study was published in the journal “[Journal name]”. They distributed the article under [Add more details about license]\n\n\n\n\n\n\nView copyright statement from journal"
+    "text": "This repository is licensed under the BSD 3-Clause License.\n\n\n\n\n\n\nView license\n\n\n\n\n\nBSD 3-Clause License\nCopyright (c) 2024, STARS Project Team, using code from 2022, Anastasia Anagnostou. All rights reserved.\nRedistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:\n\nRedistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.\nRedistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.\nNeither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n\n\n\nThis is aligned with the original study, who shared their code under BSD 3-Clause License.\n\n\n\n\n\n\nView license\n\n\n\n\n\nBSD 3-Clause License\nCopyright (c) 2022, Anastasia Anagnostou All rights reserved.\nRedistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:\n\nRedistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.\nRedistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.\nNeither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n\n\n\nThe original study was published in the journal “IEEE Xplore”. The copyright is retained by this journal. Open access versions are available with Brunel University Research Archive and UCL Discovery, but these are just for personal use, as in the statement below:\n\n\n\n\n\n\nView copyright statement\n\n\n\n\n\n“Copyright © 2022 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.”\nhttps://bura.brunel.ac.uk/handle/2438/25912"
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diff --git a/sitemap.xml b/sitemap.xml
index 60d92af..1d84a9f 100644
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-    <lastmod>2024-08-01T14:08:46.532Z</lastmod>
+    <lastmod>2024-08-01T14:15:02.830Z</lastmod>
   </url>
   <url>
     <loc>https://pythonhealthdatascience.github.io/stars-reproduce-anagnostou-2022/original_study/charm/CHARM_INFO.html</loc>
-    <lastmod>2024-08-01T14:08:46.532Z</lastmod>
+    <lastmod>2024-08-01T14:15:02.830Z</lastmod>
   </url>
   <url>
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-    <lastmod>2024-08-01T14:08:46.532Z</lastmod>
+    <lastmod>2024-08-01T14:15:02.830Z</lastmod>
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-    <lastmod>2024-08-01T14:08:46.532Z</lastmod>
+    <lastmod>2024-08-01T14:15:02.830Z</lastmod>
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   <url>
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+    <lastmod>2024-08-01T14:15:02.830Z</lastmod>
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