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index 781da10..64a1fa4 100644
--- a/.nojekyll
+++ b/.nojekyll
@@ -1 +1 @@
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+6f19479b
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diff --git a/evaluation/badges.html b/evaluation/badges.html
index e02fa92..b492268 100644
--- a/evaluation/badges.html
+++ b/evaluation/badges.html
@@ -266,7 +266,7 @@ <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="eb9a649f" class="cell" data-execution_count="1">
+<div id="32a1f936" 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>
@@ -399,7 +399,7 @@ <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="29512df6" class="cell" data-execution_count="2">
+<div id="93c9fea6" 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/reporting.html b/evaluation/reporting.html
index f1fff42..8ad30b2 100644
--- a/evaluation/reporting.html
+++ b/evaluation/reporting.html
@@ -1064,7 +1064,7 @@ <h2 class="anchored" data-anchor-id="des-checklist-derived-from-ispor-sdm">DES c
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","loop":false,"descPosition":"bottom","selector":".lightbox","openEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"openEffect":"zoom","closeEffect":"zoom","descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
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diff --git a/evaluation/reproduction_report.html b/evaluation/reproduction_report.html
index ce8a027..1bac987 100644
--- a/evaluation/reproduction_report.html
+++ b/evaluation/reproduction_report.html
@@ -265,11 +265,11 @@ <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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index 4c746b1..327b561 100644
--- a/evaluation/reproduction_success.html
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+var gd = document.getElementById('66af8e6b-5b94-425e-94d2-9991b5379f52');
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@@ -391,7 +391,7 @@ <h3 class="anchored" data-anchor-id="in-text-result-1">In-text result 1</h3>
 <p><strong>Consensus: Successfully reproduced</strong></p>
 <p>“Exclusive-Use Scenario. In this scenario, the overall wait time probability at angioINR was reduced compared to baseline (red line in Figure 2B compared to Figure 2A). This represents a <strong>decrease in ECR patient wait time for angioINR by an average of 6 min</strong>.” <span class="citation" data-cites="huang_optimizing_2019">Huang et al. (<a href="#ref-huang_optimizing_2019" role="doc-biblioref">2019</a>)</span></p>
 <p>Reproduction:</p>
-<div id="52ee34f7" class="cell" data-execution_count="4">
+<div id="e699ed6e" class="cell" data-execution_count="4">
 <div class="cell-output cell-output-display" data-execution_count="4">
 <div>
 <div>
@@ -432,7 +432,7 @@ <h3 class="anchored" data-anchor-id="in-text-result-2">In-text result 2</h3>
 <p><strong>Consensus: Successfully reproduced</strong></p>
 <p>“Two angioINRs Scenario. This scenario simulates the effect a facility upgrade to two biplane angiographic suites, but without additional staff changes. The wait time probability at angioINR was reduced compared to baseline (Figure 2C). The reduction represents an <strong>average of 4 min less in queue for angioINR</strong>.” <span class="citation" data-cites="huang_optimizing_2019">Huang et al. (<a href="#ref-huang_optimizing_2019" role="doc-biblioref">2019</a>)</span></p>
 <p>Reproduction:</p>
-<div id="c76d29e3" class="cell" data-execution_count="5">
+<div id="8e76d498" class="cell" data-execution_count="5">
 <div class="cell-output cell-output-display" data-execution_count="5">
 <div>
 <div>
@@ -473,7 +473,7 @@ <h3 class="anchored" data-anchor-id="in-text-result-3">In-text result 3</h3>
 <p><strong>Consensus: Not reproduced</strong></p>
 <p>“Extended Schedule Scenario. The wait time probability at angioINR in the exclusive- use scenario was further reduced by extended work hours (Figure 3B). In contrast, work extension did not affect baseline or the 2 angioINRs scenario (Figures 3A,C). For the baseline scenario, 1 and 2 h of extra work resulted in an <strong>average wait time of 1.7 and 0.9 min reduction, respectively</strong>. For the 2 angioINRs scenario, 1 and 2 h of extra work resulted in an <strong>average wait time gain of 1 and 0.3 min, respectively</strong>.” <span class="citation" data-cites="huang_optimizing_2019">Huang et al. (<a href="#ref-huang_optimizing_2019" role="doc-biblioref">2019</a>)</span></p>
 <p>Reproduction:</p>
-<div id="d8ea6b4c" class="cell" data-execution_count="6">
+<div id="21b0367a" class="cell" data-execution_count="6">
 <div class="cell-output cell-output-display" data-execution_count="6">
 <div>
 <div>
@@ -996,7 +996,7 @@ <h3 class="anchored" data-anchor-id="in-text-result-3">In-text result 3</h3>
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","closeEffect":"zoom","selector":".lightbox","loop":false});
+<script>var lightboxQuarto = GLightbox({"openEffect":"zoom","descPosition":"bottom","selector":".lightbox","closeEffect":"zoom","loop":false});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;
diff --git a/evaluation/scope.html b/evaluation/scope.html
index 626240a..b2cd875 100644
--- a/evaluation/scope.html
+++ b/evaluation/scope.html
@@ -899,7 +899,7 @@ <h2 class="anchored" data-anchor-id="outside-scope">Outside scope</h2>
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"loop":false,"selector":".lightbox","openEffect":"zoom","closeEffect":"zoom","descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"openEffect":"zoom","closeEffect":"zoom","descPosition":"bottom"});
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diff --git a/logbook/logbook.html b/logbook/logbook.html
index 6867a77..19c73ed 100644
--- a/logbook/logbook.html
+++ b/logbook/logbook.html
@@ -268,7 +268,7 @@ <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="compendium" data-listing-date-sort="1721343600000" data-listing-file-modified-sort="1721376393118" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="2" data-listing-word-count-sort="280">
+<div class="quarto-post image-right" data-index="0" data-categories="compendium" data-listing-date-sort="1721343600000" data-listing-file-modified-sort="1721389945630" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="6" data-listing-word-count-sort="1066">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_07_19/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_07_19/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
@@ -287,7 +287,7 @@ <h3 class="no-anchor listing-title">
 </div>
 </div>
 <div class="listing-description">
-<a href="../logbook/posts/2024_07_19/index.html" class="no-external">Finishing up research compendium: final bit of troubleshooting docker.</a>
+<a href="../logbook/posts/2024_07_19/index.html" class="no-external">Finishing up research compendium: final bit of troubleshooting docker, then GHCR.</a>
 </div>
 </div>
 <div class="metadata">
diff --git a/logbook/posts/2024_07_03/index.html b/logbook/posts/2024_07_03/index.html
index d737b78..8d8b906 100644
--- a/logbook/posts/2024_07_03/index.html
+++ b/logbook/posts/2024_07_03/index.html
@@ -310,7 +310,7 @@ <h2 class="anchored" data-anchor-id="check-journal-article-license-and-upload">1
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="2a40fb74" class="cell" data-execution_count="1">
+<div id="a36b1551" 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/logbook/posts/2024_07_04/index.html b/logbook/posts/2024_07_04/index.html
index 2b7bfcf..5d307b3 100644
--- a/logbook/posts/2024_07_04/index.html
+++ b/logbook/posts/2024_07_04/index.html
@@ -553,7 +553,7 @@ <h2 class="anchored" data-anchor-id="look-over-code-and-set-up-environment">16.0
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="e3c966e0" class="cell" data-execution_count="1">
+<div id="df812257" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb8"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>
diff --git a/logbook/posts/2024_07_05/index.html b/logbook/posts/2024_07_05/index.html
index ffd19ea..792169a 100644
--- a/logbook/posts/2024_07_05/index.html
+++ b/logbook/posts/2024_07_05/index.html
@@ -629,7 +629,7 @@ <h2 class="anchored" data-anchor-id="continuing-to-troubleshoot-in-text-results-
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="56f12725" class="cell" data-execution_count="1">
+<div id="3714bdb4" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb10"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>
diff --git a/logbook/posts/2024_07_08/index.html b/logbook/posts/2024_07_08/index.html
index 601ef08..a3156de 100644
--- a/logbook/posts/2024_07_08/index.html
+++ b/logbook/posts/2024_07_08/index.html
@@ -386,7 +386,7 @@ <h2 class="anchored" data-anchor-id="adding-seeds">09.50-10.49, 11.02-11.05, 11.
 <li>Difference: 5.84 minutes</li>
 </ul>
 <p>Hence, I feel we can mark in-text result 1 as reproduced at this time (11.14), with starter seed of 200.</p>
-<div id="e110f60a" class="cell" data-execution_count="1">
+<div id="730b56f7" class="cell" data-execution_count="1">
 <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="im">import</span> sys</span>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>
@@ -622,7 +622,7 @@ <h2 class="anchored" data-anchor-id="returning-to-figure-2">15.31-16.55: Returni
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="d97bf994" class="cell" data-execution_count="2">
+<div id="a2d6441e" class="cell" data-execution_count="2">
 <div class="sourceCode cell-code" id="cb12"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Minutes used prior to today</span></span>
 <span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a>used_to_date <span class="op">=</span> <span class="dv">443</span></span>
 <span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a></span>
diff --git a/logbook/posts/2024_07_09/index.html b/logbook/posts/2024_07_09/index.html
index f81e973..0c14984 100644
--- a/logbook/posts/2024_07_09/index.html
+++ b/logbook/posts/2024_07_09/index.html
@@ -412,7 +412,7 @@ <h2 class="anchored" data-anchor-id="starting-on-figure-3-and-in-text-result-3">
 <p>For this scenario analysis, the “day time working hours of all human resources are extended by up to 2h, extending resource access to all patients” (<span class="citation" data-cites="huang_optimizing_2019">Huang et al. (<a href="#ref-huang_optimizing_2019" role="doc-biblioref">2019</a>)</span>). Given how the model scheduling is set-up, it is assumed that this means we simply adjust the schedule to end at 5, 6 or 7pm (and that that would simply shortern the night staff time).</p>
 <p>I ran these scenarios, processing and saving the relevant model results.</p>
 <p>For in-text result 3, I can see that the results do not match up to the paper. I am not surprised by this though - as the model had no seed control, as it is not mentioned in the paper, we can assume that it might not have been used by the original study, and so variation between the scenarios could (in part) reflect model stochasticity.</p>
-<div id="bdce6319" class="cell" data-execution_count="1">
+<div id="4a66d3f3" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
 <span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>pd.read_csv(<span class="st">"txt3.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -503,7 +503,7 @@ <h2 class="anchored" data-anchor-id="starting-on-figure-3-and-in-text-result-3">
 </div>
 </div>
 <p>To test this assumption, I ran the model again for baseline with two further seeds. We can see the importance of seed control here. For example, with seed 700, we see a broader range of results, with the result for 6pm (13.32) is much higher than for the other two seeds and, compared with their 5pm results, we would’ve seen less of a reduction. Similarly, if we compared the 5pm seed 700 result with the 6pm seed 500 result, we would see a much greater reduction.</p>
-<div id="701023c1" class="cell" data-execution_count="2">
+<div id="ca9b0e8c" class="cell" data-execution_count="2">
 <div class="sourceCode cell-code" id="cb5"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>pd.read_csv(<span class="st">"txt3_seeds.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="2">
 <div>
@@ -559,7 +559,7 @@ <h2 class="anchored" data-anchor-id="starting-on-figure-3-and-in-text-result-3">
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="d578fdcd" class="cell" data-execution_count="3">
+<div id="35a6da8f" class="cell" data-execution_count="3">
 <div class="sourceCode cell-code" id="cb6"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>
diff --git a/logbook/posts/2024_07_11/index.html b/logbook/posts/2024_07_11/index.html
index 5dedc4a..e355e44 100644
--- a/logbook/posts/2024_07_11/index.html
+++ b/logbook/posts/2024_07_11/index.html
@@ -411,7 +411,7 @@ <h2 class="anchored" data-anchor-id="figure-5">15.32-16.31, 16.35-17.00: Figure
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="285fdf0d" class="cell" data-execution_count="1">
+<div id="d6051252" 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/logbook/posts/2024_07_12/index.html b/logbook/posts/2024_07_12/index.html
index f36499d..c525bff 100644
--- a/logbook/posts/2024_07_12/index.html
+++ b/logbook/posts/2024_07_12/index.html
@@ -330,7 +330,7 @@ <h2 class="anchored" data-anchor-id="tidy-and-email-author">10.30-10.50: Tidy an
 </section>
 <section id="timings-for-reproduction" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-reproduction">Timings for reproduction</h2>
-<div id="b6dbc5e6" class="cell" data-execution_count="1">
+<div id="efabf4a9" 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>
@@ -419,7 +419,7 @@ <h2 class="anchored" data-anchor-id="des-checklist-derived-from-ispor-sdm">13.19
 </section>
 <section id="timings-for-evaluation" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-evaluation">Timings for evaluation</h2>
-<div id="46f70fb7" class="cell" data-execution_count="2">
+<div id="ade1fe27" class="cell" data-execution_count="2">
 <div class="sourceCode cell-code" id="cb3"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>
diff --git a/logbook/posts/2024_07_15/index.html b/logbook/posts/2024_07_15/index.html
index db2a167..9b81fb9 100644
--- a/logbook/posts/2024_07_15/index.html
+++ b/logbook/posts/2024_07_15/index.html
@@ -362,7 +362,7 @@ <h2 class="anchored" data-anchor-id="consensus-on-evaluation">08.22-08.30, 08.37
 </section>
 <section id="timings-for-evaluation" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-evaluation">Timings for evaluation</h2>
-<div id="d142d66b" class="cell" data-execution_count="1">
+<div id="ebb95fe0" 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/logbook/posts/2024_07_19/index.html b/logbook/posts/2024_07_19/index.html
index 1d25828..f40078e 100644
--- a/logbook/posts/2024_07_19/index.html
+++ b/logbook/posts/2024_07_19/index.html
@@ -216,6 +216,7 @@ <h2 id="toc-title">On this page</h2>
   <li><a href="#untimed-research-compendium" id="toc-untimed-research-compendium" class="nav-link active" data-scroll-target="#untimed-research-compendium">Untimed: Research compendium</a>
   <ul class="collapse">
   <li><a href="#docker" id="toc-docker" class="nav-link" data-scroll-target="#docker">Docker</a></li>
+  <li><a href="#github-container-registry" id="toc-github-container-registry" class="nav-link" data-scroll-target="#github-container-registry">GitHub Container Registry</a></li>
   </ul></li>
   </ul>
 <div class="toc-actions"><ul><li><a href="https://github.com/pythonhealthdatascience/stars-reproduce-huang-2019/edit/main/logbook/posts/2024_07_19/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-huang-2019/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
@@ -237,21 +238,27 @@ <h2 id="toc-title">On this page</h2>
 </div>
 </div>
 <div class="callout-body-container callout-body">
-<p>Finishing up research compendium: final bit of troubleshooting docker.</p>
+<p>Finishing up research compendium: final bit of troubleshooting docker, then GHCR.</p>
 </div>
 </div>
 <section id="untimed-research-compendium" class="level2">
 <h2 class="anchored" data-anchor-id="untimed-research-compendium">Untimed: Research compendium</h2>
 <section id="docker" class="level3">
 <h3 class="anchored" data-anchor-id="docker">Docker</h3>
-<p>Resuming where I left off yesterday. Reminder of key commands:</p>
+<p>Resuming where I left off yesterday.</p>
+<p>Current challenge is to try and install <code>stringi</code> and <code>openssl</code> into the <code>renv</code>, so the later <code>renv::restore()</code> doesn’t fail.</p>
+<section id="important-commands-when-troubleshooting" class="level4">
+<h4 class="anchored" data-anchor-id="important-commands-when-troubleshooting">Important commands when troubleshooting</h4>
+<p>Reminder of key commands:</p>
 <ul>
 <li><strong>Build image</strong>: <code>sudo docker build --tag huang2019 . -f ./docker/Dockerfile</code></li>
 <li><strong>Delete image</strong>: <code>sudo docker image rm huang2019</code></li>
 <li><strong>Create container and open RStudio</strong>: <code>(sleep 2 &amp;&amp; xdg-open http://localhost:8888) &amp; sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name  huang2019_docker huang2019</code></li>
 <li><strong>Delete container</strong>: <code>sudo docker rm huang2019_docker</code></li>
 </ul>
-<p>Current challenge is to try and install <code>stringi</code> and <code>openssl</code> into the <code>renv</code>, so the later <code>renv::restore()</code> doesn’t fail.</p>
+</section>
+<section id="unsuccessful-attempts" class="level4">
+<h4 class="anchored" data-anchor-id="unsuccessful-attempts">Unsuccessful attempts</h4>
 <p>I tried variants of:</p>
 <ul>
 <li>Permissions (<code>USER root</code>, <code>USER rstudio</code>)</li>
@@ -275,10 +282,17 @@ <h3 class="anchored" data-anchor-id="docker">Docker</h3>
 <li><code>renv appears to be unable to access the requested library path: /home/rstudio/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu. Check that the 'rstudio' user has read / write access to this directory.</code></li>
 <li><code>Error: error downloading 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz' [cannot open URL 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz']</code></li>
 </ul>
-<p>I tried temporarily replacing my lockfile with a simple one:</p>
+</section>
+<section id="minimal-example-small-.lock-and-specific-files-succeeds" class="level4">
+<h4 class="anchored" data-anchor-id="minimal-example-small-.lock-and-specific-files-succeeds">Minimal example (small .lock and specific files) succeeds</h4>
+<p>I tried temporarily replacing my lockfile with a simple one with only my packages markdown and mime, and <code>renv::restore()</code> under user <code>rstudio</code> (similar to the <a href="https://github.com/rstudio/renv/issues/1602">GitHub issue from yesterday</a>).</p>
+<ul>
+<li>When running <code>renv::restore()</code>, it seemed to install its own copy of <code>renv</code> (and didn’t use the one I’d installed above) - and indeed, I found I could remove that from the Dockerfile with no impact on the outcome</li>
+<li>The library was successfully installed and accessible when I opened the container!</li>
+</ul>
 <pre><code>{
   "R": {
-    "Version": "4.2.3",
+    "Version": "4.4.1",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -289,20 +303,71 @@ <h3 class="anchored" data-anchor-id="docker">Docker</h3>
   "Packages": {
     "markdown": {
       "Package": "markdown",
-      "Version": "1.0",
+      "Version": "1.13",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "4584a57f565dd7987d59dda3a02cfb41"
+      "Requirements": [
+        "R",
+        "commonmark",
+        "utils",
+        "xfun"
+      ],
+      "Hash": "074efab766a9d6360865ad39512f2a7e"
     },
-    "mime": {
-      "Package": "mime",
-      "Version": "0.7",
+    "markdown": {
+      "Package": "markdown",
+      "Version": "1.13",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "908d95ccbfd1dd274073ef07a7c93934"
+      "Requirements": [
+        "R",
+        "commonmark",
+        "utils",
+        "xfun"
+      ],
+      "Hash": "074efab766a9d6360865ad39512f2a7e"
     }
   }
 }</code></pre>
+<p>When I did that successful run, I’d only copied over a few essential / example files</p>
+<pre><code>COPY renv.lock renv.lock
+COPY reproduction.Rproj reproduction.Rproj
+COPY scripts scripts</code></pre>
+<p>Instead of</p>
+<pre><code>COPY . .</code></pre>
+<p>However, when I switched back to just copying everything, I get issues that it cannot copy and move files and that permission is denied.</p>
+<p>I tried manually specifying everything from the folder (exc. .Rhistory and .Rproj.user)…</p>
+<pre><code>COPY DESCRIPTION DESCRIPTION
+COPY docker docker
+COPY outputs outputs
+COPY README.md README.md
+COPY renv.lock renv.lock
+COPY reproduction.Rproj reproduction.Rproj
+COPY scripts scripts
+COPY tests tests</code></pre>
+<p>…And that built fine.</p>
+<p>So I tried again with <code>COPY . .</code>, but adding <code>.Rhistory</code> and <code>.Rproj.user</code> to the <code>.dockerignore</code> - but this failed like before. Hence, I decided to stick with specifying the files being copied (and regardless, I guess that has the benefit of being specific about what we include). It appears I must be copying over something undesirable when running <code>COPY . .</code> which is causing us issues, although I can’t spot what this might be.</p>
+</section>
+<section id="troubleshooting-stringi" class="level4">
+<h4 class="anchored" data-anchor-id="troubleshooting-stringi">Troubleshooting stringi</h4>
+<p>I ran <code>renv::snapshot()</code> to restore the lock file back to being complete, and then tried to build the image again. This failed with the <code>libicui18n.so.66</code> error from before. I reverted the lockfile back to the simple version (so the various test runs are quicker), but adding stringi, getting the same error.</p>
+<p>Tried adding install before restore - <code>RUN R -e "renv::install('stringi')"</code> (which automatically installs <code>renv</code> for us before running)…. and it was successfull….! The library contained stringi and the other packages from the lockfile.</p>
+<p>So, I then, again, restored the full lockfile, add an install for openssl, and tried once more.</p>
+<p>This was successful!</p>
+</section>
+<section id="giving-read-write-and-save-access-to-folders" class="level4">
+<h4 class="anchored" data-anchor-id="giving-read-write-and-save-access-to-folders">Giving read, write and save access to folders</h4>
+<p>All the files are present and can be run, and the renv is active with all the required files. However, if we want to save anything (e.g.&nbsp;modifying <code>qmd</code>, or saving output from model with <code>ggsave</code>), we don’t currently have permissions.</p>
+<p>Based on the <a href="https://docs.docker.com/reference/dockerfile/#copy---chown---chmod">docker documentation</a>, I tried using <code>--chown</code> with the COPY statements to specifically give permissions to the user <code>rstudio</code>. I also modified <code>stringi</code> and <code>openssl</code> so they have the specific versions.</p>
+<p>This worked!</p>
+</section>
+</section>
+<section id="github-container-registry" class="level3">
+<h3 class="anchored" data-anchor-id="github-container-registry">GitHub Container Registry</h3>
+<p>Activated and ran but hit issue on <code>COPY renv/activate.R renv/activate.R</code>. It cannot find the file - although the previous commands with relative file paths all ran without issue.</p>
+<pre><code>ERROR: failed to solve: failed to compute cache key: failed to calculate checksum of ref 70b54bab-f7c4-4333-a94b-def3ee959db6::iqqrpwic0590fua1x3sv0utsd: "/renv/activate.R": not found</code></pre>
+<p>Checking on GitHub, the <code>activate.R</code> file is included. However, in my prior example of this (Shoaib et al.&nbsp;2022), I ran the dockerfile from the main folder rather than the reproduction folder. Hence, I tried updating the Dockerfile so that the file paths are relative to reproduction’s parent, which fixed the issue.</p>
+<p>I then tested downloading the image from GHCR and ran one of the scripts within that, and it all worked fine. Add instructions for this to the README.</p>
 
 
 </section>
diff --git a/quarto_site/reproduction_readme.html b/quarto_site/reproduction_readme.html
index 631c4ac..982abda 100644
--- a/quarto_site/reproduction_readme.html
+++ b/quarto_site/reproduction_readme.html
@@ -281,10 +281,25 @@ <h4 class="anchored" data-anchor-id="option-a.-renv">Option A. Renv</h4>
 <p>An <code>renv</code> environment has been provided. To create this environment locally on your machine, you should open the R project with the R environment loaded, and then run <code>renv::restore()</code>.</p>
 <p>In <code>renv.lock</code>, you will see the version of R listed. However, <code>renv</code> will not install this for you, so you will need to switch to this yourself if you wish to also use the same version of R.</p>
 </section>
-<section id="option-b.-docker" class="level4">
-<h4 class="anchored" data-anchor-id="option-b.-docker">Option B. Docker</h4>
-<p>First, you’ll need to ensure that <code>docker</code> is installed on your machine. You then have two options for obtaining the image.</p>
-<!-- TODO: Finished adding instructions! -->
+<section id="option-b.-build-local-docker-image" class="level4">
+<h4 class="anchored" data-anchor-id="option-b.-build-local-docker-image">Option B. Build local docker image</h4>
+<p>A Dockerfile is provided, which you can use to build the Docker image. For this option and option C, you’ll need to ensure that <code>docker</code> is installed on your machine.</p>
+<p>To create the docker image and then open up RStudio, you’ll need to:</p>
+<ol type="1">
+<li>In ther terminal, navigate to the parent directory of your <code>reproduction/</code> folder</li>
+<li>Build the image: <code>docker build --tag huang2019 . -f ./reproduction/docker/Dockerfile</code></li>
+<li>Create container and open RStudio: <code>(sleep 2 &amp;&amp; xdg-open http://localhost:8888) &amp; sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name huang2019_docker huang2019</code></li>
+</ol>
+</section>
+<section id="option-c.-pull-pre-built-docker-image" class="level4">
+<h4 class="anchored" data-anchor-id="option-c.-pull-pre-built-docker-image">Option C. Pull pre-built docker image</h4>
+<p>A pre-built image is available on the GitHub container registry. To use it:</p>
+<ol type="1">
+<li>Create a Personal Access Token (Classic) for your GitHub account with <code>write:packages</code> and <code>delete:packages</code> access</li>
+<li>On terminal, run <code>sudo docker login ghcr.io -u githubusername</code> and enter your sudo password (if prompted), followed by the token just generated (which acts as your GitHub password)</li>
+<li>Download the image: <code>sudo docker pull ghcr.io/pythonhealthdatascience/huang2019</code></li>
+<li>Create container and open RStudio: <code>(sleep 2 &amp;&amp; xdg-open http://localhost:8888) &amp; sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name huang2019_docker ghcr.io/pythonhealthdatascience/huang2019:latest</code></li>
+</ol>
 </section>
 </section>
 <section id="step-2.-running-the-model" class="level3">
diff --git a/search.json b/search.json
index f308c06..43ea628 100644
--- a/search.json
+++ b/search.json
@@ -536,7 +536,7 @@
     "href": "quarto_site/reproduction_readme.html",
     "title": "README for reproduction",
     "section": "",
-    "text": "Huang S, Maingard J, Kok HK, Barras CD, Thijs V, Chandra RV, Brooks DM and Asadi H. Optimizing Resources for Endovascular Clot Retrieval for Acute Ischemic Stroke, a Discrete Event Simulation. Frontiers in Neurology 10, 653 (2019). https://doi.org/10.3389/fneur.2019.00653.\n\nThis is a discrete-event simulation model of an endovascular clot retrieval (ECR) service. ECR is a treatment for acute ischaemic stroke. The model includes the stroke pathway, as well as three other pathways that share resources with the stroke pathway: an elective non-stroke interventional neuroradiology pathway, an emergency interventional radiology pathway, and an elective interventional radiology pathway.\nThe model is created using R Simmer.\nThe paper explores waiting times and resource utilisation - particularly focussing on the biplane angiographic suite (angioINR). A few scenarios are tried to help examine why the wait times are so high for the angioINR.\nModel structure from Huang et al. 2019:\n\n\n\nProcess flow diagram from Huang et al. 2019\n\n\n\n\n\nIn this assessment, we attempted to reproduce 8 items: 5 figures and 3 in-text results.\n\n\n\n\n\n├── docker\n│   └──  ...\n├── outputs\n│   └──  ...\n├── renv\n│   └──  ...\n├── scripts\n│   └──  ...\n├── tests\n│   └──  ...\n├── .Rprofile\n├── DESCRIPTION\n├── README.md\n├── renv.lock\n└── reproduction.Rproj\n\ndocker/ - Instructions for creation of docker container.\noutputs/ - Outputs files from the scripts (e.g. .csv.gz, .png)\nrenv/ - Instructions for creation of R environment\nscripts/ - Code for the model and for reproducing items from the scope\ntests/ - Test to check that the model produces consistent results with our reproduction\n.Rprofile - Activates R environment\nDESCRIPTION - Lists packages that we installed into environment (their dependencies will have also been installed)\nREADME.md - This file!\nrenv.lock - Lists R version and all packages in the R environment\nreproduction.Rproj - Project settings, which specify the Python virtual environment to use when building pages from the Quarto site that include Python. If you choose to build the Quarto site (and not just run the reproduction files in this folder), you will want to update this to a path on your machine (which you can do easily by opening this file in RStudio)\n\n\n\n\n\n\nAn renv environment has been provided. To create this environment locally on your machine, you should open the R project with the R environment loaded, and then run renv::restore().\nIn renv.lock, you will see the version of R listed. However, renv will not install this for you, so you will need to switch to this yourself if you wish to also use the same version of R.\n\n\n\nFirst, you’ll need to ensure that docker is installed on your machine. You then have two options for obtaining the image.\n\n\n\n\n\n\n\nTo run all the model scenarios, open and execute the provided .qmd files in scripts/. You can do so within your preferred IDE (e.g. RStudio).\n\n\n\nThree of the model scenarios have been included as tests within tests/testthat. You can run these tests by running the following command from your R console whilst in the reproduction/ directory:\ntestthat::test_dir(\"tests/testthat\")\nThis will run the three scenarios, save the results as temporary files, and compare the results against those we have saved. Although this will not produce any figures from the paper, and will not run all the scenarios, it will allow you to check if you are getting results consistent with our reproduction, on your own machine.\nAs the tests run, you will see the counter increments on your screen (with the column indicating whether the test is successful). For example, if tests are successul, you will see it increment in the “OK” column:\n✔ | F W  S  OK | Context\n⠏ |          0 | model                                               [1] \"\"\n⠋ |          1 | model                                               [1] \"\"\nEach test will take about 2 minutes (for the machine specs given below). Once all three tests are complete, the run time and results will display:\n══ Results ══════════════════════════════════════════════════════════\nDuration: 371.9 s\n\n[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]\n\n\n\n\n\nThis reproduction was conducted on an Intel Core i7-12700H with 32GB RAM running Ubuntu 22.04.4 Linux.\nOn this machine, the reproduction run time was 29 minutes 10 seconds. This was the total time from executing all the .qmd files that run the model and attempt to produce the figures/results (18.024 + 6.165 + 4.975 minutes).\nThe run time for the tests (which only include a few model scenarios) was 6 minutes 12 seconds.\n\n\n\nTo cite the original study, please refer to the reference above. To cite this reproduction, please refer to the CITATION.cff file in the parent folder.\n\n\n\nThis repository is licensed under the GNU GPL-3.0 license."
+    "text": "Huang S, Maingard J, Kok HK, Barras CD, Thijs V, Chandra RV, Brooks DM and Asadi H. Optimizing Resources for Endovascular Clot Retrieval for Acute Ischemic Stroke, a Discrete Event Simulation. Frontiers in Neurology 10, 653 (2019). https://doi.org/10.3389/fneur.2019.00653.\n\nThis is a discrete-event simulation model of an endovascular clot retrieval (ECR) service. ECR is a treatment for acute ischaemic stroke. The model includes the stroke pathway, as well as three other pathways that share resources with the stroke pathway: an elective non-stroke interventional neuroradiology pathway, an emergency interventional radiology pathway, and an elective interventional radiology pathway.\nThe model is created using R Simmer.\nThe paper explores waiting times and resource utilisation - particularly focussing on the biplane angiographic suite (angioINR). A few scenarios are tried to help examine why the wait times are so high for the angioINR.\nModel structure from Huang et al. 2019:\n\n\n\nProcess flow diagram from Huang et al. 2019\n\n\n\n\n\nIn this assessment, we attempted to reproduce 8 items: 5 figures and 3 in-text results.\n\n\n\n\n\n├── docker\n│   └──  ...\n├── outputs\n│   └──  ...\n├── renv\n│   └──  ...\n├── scripts\n│   └──  ...\n├── tests\n│   └──  ...\n├── .Rprofile\n├── DESCRIPTION\n├── README.md\n├── renv.lock\n└── reproduction.Rproj\n\ndocker/ - Instructions for creation of docker container.\noutputs/ - Outputs files from the scripts (e.g. .csv.gz, .png)\nrenv/ - Instructions for creation of R environment\nscripts/ - Code for the model and for reproducing items from the scope\ntests/ - Test to check that the model produces consistent results with our reproduction\n.Rprofile - Activates R environment\nDESCRIPTION - Lists packages that we installed into environment (their dependencies will have also been installed)\nREADME.md - This file!\nrenv.lock - Lists R version and all packages in the R environment\nreproduction.Rproj - Project settings, which specify the Python virtual environment to use when building pages from the Quarto site that include Python. If you choose to build the Quarto site (and not just run the reproduction files in this folder), you will want to update this to a path on your machine (which you can do easily by opening this file in RStudio)\n\n\n\n\n\n\nAn renv environment has been provided. To create this environment locally on your machine, you should open the R project with the R environment loaded, and then run renv::restore().\nIn renv.lock, you will see the version of R listed. However, renv will not install this for you, so you will need to switch to this yourself if you wish to also use the same version of R.\n\n\n\nA Dockerfile is provided, which you can use to build the Docker image. For this option and option C, you’ll need to ensure that docker is installed on your machine.\nTo create the docker image and then open up RStudio, you’ll need to:\n\nIn ther terminal, navigate to the parent directory of your reproduction/ folder\nBuild the image: docker build --tag huang2019 . -f ./reproduction/docker/Dockerfile\nCreate container and open RStudio: (sleep 2 && xdg-open http://localhost:8888) & sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name huang2019_docker huang2019\n\n\n\n\nA pre-built image is available on the GitHub container registry. To use it:\n\nCreate a Personal Access Token (Classic) for your GitHub account with write:packages and delete:packages access\nOn terminal, run sudo docker login ghcr.io -u githubusername and enter your sudo password (if prompted), followed by the token just generated (which acts as your GitHub password)\nDownload the image: sudo docker pull ghcr.io/pythonhealthdatascience/huang2019\nCreate container and open RStudio: (sleep 2 && xdg-open http://localhost:8888) & sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name huang2019_docker ghcr.io/pythonhealthdatascience/huang2019:latest\n\n\n\n\n\n\n\nTo run all the model scenarios, open and execute the provided .qmd files in scripts/. You can do so within your preferred IDE (e.g. RStudio).\n\n\n\nThree of the model scenarios have been included as tests within tests/testthat. You can run these tests by running the following command from your R console whilst in the reproduction/ directory:\ntestthat::test_dir(\"tests/testthat\")\nThis will run the three scenarios, save the results as temporary files, and compare the results against those we have saved. Although this will not produce any figures from the paper, and will not run all the scenarios, it will allow you to check if you are getting results consistent with our reproduction, on your own machine.\nAs the tests run, you will see the counter increments on your screen (with the column indicating whether the test is successful). For example, if tests are successul, you will see it increment in the “OK” column:\n✔ | F W  S  OK | Context\n⠏ |          0 | model                                               [1] \"\"\n⠋ |          1 | model                                               [1] \"\"\nEach test will take about 2 minutes (for the machine specs given below). Once all three tests are complete, the run time and results will display:\n══ Results ══════════════════════════════════════════════════════════\nDuration: 371.9 s\n\n[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]\n\n\n\n\n\nThis reproduction was conducted on an Intel Core i7-12700H with 32GB RAM running Ubuntu 22.04.4 Linux.\nOn this machine, the reproduction run time was 29 minutes 10 seconds. This was the total time from executing all the .qmd files that run the model and attempt to produce the figures/results (18.024 + 6.165 + 4.975 minutes).\nThe run time for the tests (which only include a few model scenarios) was 6 minutes 12 seconds.\n\n\n\nTo cite the original study, please refer to the reference above. To cite this reproduction, please refer to the CITATION.cff file in the parent folder.\n\n\n\nThis repository is licensed under the GNU GPL-3.0 license."
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@@ -557,7 +557,7 @@
     "href": "quarto_site/reproduction_readme.html#reproducing-these-results",
     "title": "README for reproduction",
     "section": "",
-    "text": "├── docker\n│   └──  ...\n├── outputs\n│   └──  ...\n├── renv\n│   └──  ...\n├── scripts\n│   └──  ...\n├── tests\n│   └──  ...\n├── .Rprofile\n├── DESCRIPTION\n├── README.md\n├── renv.lock\n└── reproduction.Rproj\n\ndocker/ - Instructions for creation of docker container.\noutputs/ - Outputs files from the scripts (e.g. .csv.gz, .png)\nrenv/ - Instructions for creation of R environment\nscripts/ - Code for the model and for reproducing items from the scope\ntests/ - Test to check that the model produces consistent results with our reproduction\n.Rprofile - Activates R environment\nDESCRIPTION - Lists packages that we installed into environment (their dependencies will have also been installed)\nREADME.md - This file!\nrenv.lock - Lists R version and all packages in the R environment\nreproduction.Rproj - Project settings, which specify the Python virtual environment to use when building pages from the Quarto site that include Python. If you choose to build the Quarto site (and not just run the reproduction files in this folder), you will want to update this to a path on your machine (which you can do easily by opening this file in RStudio)\n\n\n\n\n\n\nAn renv environment has been provided. To create this environment locally on your machine, you should open the R project with the R environment loaded, and then run renv::restore().\nIn renv.lock, you will see the version of R listed. However, renv will not install this for you, so you will need to switch to this yourself if you wish to also use the same version of R.\n\n\n\nFirst, you’ll need to ensure that docker is installed on your machine. You then have two options for obtaining the image.\n\n\n\n\n\n\n\nTo run all the model scenarios, open and execute the provided .qmd files in scripts/. You can do so within your preferred IDE (e.g. RStudio).\n\n\n\nThree of the model scenarios have been included as tests within tests/testthat. You can run these tests by running the following command from your R console whilst in the reproduction/ directory:\ntestthat::test_dir(\"tests/testthat\")\nThis will run the three scenarios, save the results as temporary files, and compare the results against those we have saved. Although this will not produce any figures from the paper, and will not run all the scenarios, it will allow you to check if you are getting results consistent with our reproduction, on your own machine.\nAs the tests run, you will see the counter increments on your screen (with the column indicating whether the test is successful). For example, if tests are successul, you will see it increment in the “OK” column:\n✔ | F W  S  OK | Context\n⠏ |          0 | model                                               [1] \"\"\n⠋ |          1 | model                                               [1] \"\"\nEach test will take about 2 minutes (for the machine specs given below). Once all three tests are complete, the run time and results will display:\n══ Results ══════════════════════════════════════════════════════════\nDuration: 371.9 s\n\n[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]"
+    "text": "├── docker\n│   └──  ...\n├── outputs\n│   └──  ...\n├── renv\n│   └──  ...\n├── scripts\n│   └──  ...\n├── tests\n│   └──  ...\n├── .Rprofile\n├── DESCRIPTION\n├── README.md\n├── renv.lock\n└── reproduction.Rproj\n\ndocker/ - Instructions for creation of docker container.\noutputs/ - Outputs files from the scripts (e.g. .csv.gz, .png)\nrenv/ - Instructions for creation of R environment\nscripts/ - Code for the model and for reproducing items from the scope\ntests/ - Test to check that the model produces consistent results with our reproduction\n.Rprofile - Activates R environment\nDESCRIPTION - Lists packages that we installed into environment (their dependencies will have also been installed)\nREADME.md - This file!\nrenv.lock - Lists R version and all packages in the R environment\nreproduction.Rproj - Project settings, which specify the Python virtual environment to use when building pages from the Quarto site that include Python. If you choose to build the Quarto site (and not just run the reproduction files in this folder), you will want to update this to a path on your machine (which you can do easily by opening this file in RStudio)\n\n\n\n\n\n\nAn renv environment has been provided. To create this environment locally on your machine, you should open the R project with the R environment loaded, and then run renv::restore().\nIn renv.lock, you will see the version of R listed. However, renv will not install this for you, so you will need to switch to this yourself if you wish to also use the same version of R.\n\n\n\nA Dockerfile is provided, which you can use to build the Docker image. For this option and option C, you’ll need to ensure that docker is installed on your machine.\nTo create the docker image and then open up RStudio, you’ll need to:\n\nIn ther terminal, navigate to the parent directory of your reproduction/ folder\nBuild the image: docker build --tag huang2019 . -f ./reproduction/docker/Dockerfile\nCreate container and open RStudio: (sleep 2 && xdg-open http://localhost:8888) & sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name huang2019_docker huang2019\n\n\n\n\nA pre-built image is available on the GitHub container registry. To use it:\n\nCreate a Personal Access Token (Classic) for your GitHub account with write:packages and delete:packages access\nOn terminal, run sudo docker login ghcr.io -u githubusername and enter your sudo password (if prompted), followed by the token just generated (which acts as your GitHub password)\nDownload the image: sudo docker pull ghcr.io/pythonhealthdatascience/huang2019\nCreate container and open RStudio: (sleep 2 && xdg-open http://localhost:8888) & sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name huang2019_docker ghcr.io/pythonhealthdatascience/huang2019:latest\n\n\n\n\n\n\n\nTo run all the model scenarios, open and execute the provided .qmd files in scripts/. You can do so within your preferred IDE (e.g. RStudio).\n\n\n\nThree of the model scenarios have been included as tests within tests/testthat. You can run these tests by running the following command from your R console whilst in the reproduction/ directory:\ntestthat::test_dir(\"tests/testthat\")\nThis will run the three scenarios, save the results as temporary files, and compare the results against those we have saved. Although this will not produce any figures from the paper, and will not run all the scenarios, it will allow you to check if you are getting results consistent with our reproduction, on your own machine.\nAs the tests run, you will see the counter increments on your screen (with the column indicating whether the test is successful). For example, if tests are successul, you will see it increment in the “OK” column:\n✔ | F W  S  OK | Context\n⠏ |          0 | model                                               [1] \"\"\n⠋ |          1 | model                                               [1] \"\"\nEach test will take about 2 minutes (for the machine specs given below). Once all three tests are complete, the run time and results will display:\n══ Results ══════════════════════════════════════════════════════════\nDuration: 371.9 s\n\n[ FAIL 0 | WARN 0 | SKIP 0 | PASS 3 ]"
   },
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     "objectID": "quarto_site/reproduction_readme.html#reproduction-specs-and-runtime",
@@ -956,14 +956,14 @@
     "href": "logbook/posts/2024_07_19/index.html",
     "title": "Day 12",
     "section": "",
-    "text": "Note\n\n\n\nFinishing up research compendium: final bit of troubleshooting docker."
+    "text": "Note\n\n\n\nFinishing up research compendium: final bit of troubleshooting docker, then GHCR."
   },
   {
     "objectID": "logbook/posts/2024_07_19/index.html#untimed-research-compendium",
     "href": "logbook/posts/2024_07_19/index.html#untimed-research-compendium",
     "title": "Day 12",
     "section": "Untimed: Research compendium",
-    "text": "Untimed: Research compendium\n\nDocker\nResuming where I left off yesterday. Reminder of key commands:\n\nBuild image: sudo docker build --tag huang2019 . -f ./docker/Dockerfile\nDelete image: sudo docker image rm huang2019\nCreate container and open RStudio: (sleep 2 && xdg-open http://localhost:8888) & sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name  huang2019_docker huang2019\nDelete container: sudo docker rm huang2019_docker\n\nCurrent challenge is to try and install stringi and openssl into the renv, so the later renv::restore() doesn’t fail.\nI tried variants of:\n\nPermissions (USER root, USER rstudio)\nInstallation instructions (remotes, renv, install.packages).\n\nI seemed to be getting success with:\nRUN R -e \"renv::activate()\"\nUSER root\nRUN R -e \"renv::install('stringi@${STRINGI_VERSION}')\"\nRUN R -e \"renv::install('openssl@${OPENSSL_VERSION}')\"\nUSER rstudio\n#RUN R -e \"remotes::install_version('openssl', version='${OPENSSL_VERSION}')\"\nRUN R -e \"renv::restore(lockfile=\\\"${PROJDIRECTORY}/renv.lock\\\", repos = c(CRAN = \\\"https://packagemanager.rstudio.com/all/__linux__/focal/latest\\\"))\"\nThis installed stringi and openssl into the renv successfully, although I seemed to need to have USER root permissions. For renv::restore(), it installed fine without needing to be USER root, but it then failed when installing stringi, so it appears to not have resolved the issue.\nError in dyn.load(file, DLLpath = DLLpath, ...) : \n    unable to load shared object '/tmp/Rtmp8ogTfT/renv-staging-7b6bc3cd/stringi/libs/stringi.so':\n  libicui18n.so.66: cannot open shared object file: No such file or directory\nI tried running all the renv installation whilst being the USER root. The image built successfully, but it did not open as an active project, and the renv/ folder only contained renv.\nI tried just running renv::install() (and not specific installs or restore), but this had errors of:\n\nrenv appears to be unable to access the requested library path: /home/rstudio/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu. Check that the 'rstudio' user has read / write access to this directory.\nError: error downloading 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz' [cannot open URL 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz']\n\nI tried temporarily replacing my lockfile with a simple one:\n{\n  \"R\": {\n    \"Version\": \"4.2.3\",\n    \"Repositories\": [\n      {\n        \"Name\": \"CRAN\",\n        \"URL\": \"https://cloud.r-project.org\"\n      }\n    ]\n  },\n  \"Packages\": {\n    \"markdown\": {\n      \"Package\": \"markdown\",\n      \"Version\": \"1.0\",\n      \"Source\": \"Repository\",\n      \"Repository\": \"CRAN\",\n      \"Hash\": \"4584a57f565dd7987d59dda3a02cfb41\"\n    },\n    \"mime\": {\n      \"Package\": \"mime\",\n      \"Version\": \"0.7\",\n      \"Source\": \"Repository\",\n      \"Repository\": \"CRAN\",\n      \"Hash\": \"908d95ccbfd1dd274073ef07a7c93934\"\n    }\n  }\n}"
+    "text": "Untimed: Research compendium\n\nDocker\nResuming where I left off yesterday.\nCurrent challenge is to try and install stringi and openssl into the renv, so the later renv::restore() doesn’t fail.\n\nImportant commands when troubleshooting\nReminder of key commands:\n\nBuild image: sudo docker build --tag huang2019 . -f ./docker/Dockerfile\nDelete image: sudo docker image rm huang2019\nCreate container and open RStudio: (sleep 2 && xdg-open http://localhost:8888) & sudo docker run -it -p 8888:8787 -e DISABLE_AUTH=true --name  huang2019_docker huang2019\nDelete container: sudo docker rm huang2019_docker\n\n\n\nUnsuccessful attempts\nI tried variants of:\n\nPermissions (USER root, USER rstudio)\nInstallation instructions (remotes, renv, install.packages).\n\nI seemed to be getting success with:\nRUN R -e \"renv::activate()\"\nUSER root\nRUN R -e \"renv::install('stringi@${STRINGI_VERSION}')\"\nRUN R -e \"renv::install('openssl@${OPENSSL_VERSION}')\"\nUSER rstudio\n#RUN R -e \"remotes::install_version('openssl', version='${OPENSSL_VERSION}')\"\nRUN R -e \"renv::restore(lockfile=\\\"${PROJDIRECTORY}/renv.lock\\\", repos = c(CRAN = \\\"https://packagemanager.rstudio.com/all/__linux__/focal/latest\\\"))\"\nThis installed stringi and openssl into the renv successfully, although I seemed to need to have USER root permissions. For renv::restore(), it installed fine without needing to be USER root, but it then failed when installing stringi, so it appears to not have resolved the issue.\nError in dyn.load(file, DLLpath = DLLpath, ...) : \n    unable to load shared object '/tmp/Rtmp8ogTfT/renv-staging-7b6bc3cd/stringi/libs/stringi.so':\n  libicui18n.so.66: cannot open shared object file: No such file or directory\nI tried running all the renv installation whilst being the USER root. The image built successfully, but it did not open as an active project, and the renv/ folder only contained renv.\nI tried just running renv::install() (and not specific installs or restore), but this had errors of:\n\nrenv appears to be unable to access the requested library path: /home/rstudio/renv/library/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu. Check that the 'rstudio' user has read / write access to this directory.\nError: error downloading 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz' [cannot open URL 'https://cloud.r-project.org/src/contrib/mime_0.12.tar.gz']\n\n\n\nMinimal example (small .lock and specific files) succeeds\nI tried temporarily replacing my lockfile with a simple one with only my packages markdown and mime, and renv::restore() under user rstudio (similar to the GitHub issue from yesterday).\n\nWhen running renv::restore(), it seemed to install its own copy of renv (and didn’t use the one I’d installed above) - and indeed, I found I could remove that from the Dockerfile with no impact on the outcome\nThe library was successfully installed and accessible when I opened the container!\n\n{\n  \"R\": {\n    \"Version\": \"4.4.1\",\n    \"Repositories\": [\n      {\n        \"Name\": \"CRAN\",\n        \"URL\": \"https://cloud.r-project.org\"\n      }\n    ]\n  },\n  \"Packages\": {\n    \"markdown\": {\n      \"Package\": \"markdown\",\n      \"Version\": \"1.13\",\n      \"Source\": \"Repository\",\n      \"Repository\": \"CRAN\",\n      \"Requirements\": [\n        \"R\",\n        \"commonmark\",\n        \"utils\",\n        \"xfun\"\n      ],\n      \"Hash\": \"074efab766a9d6360865ad39512f2a7e\"\n    },\n    \"markdown\": {\n      \"Package\": \"markdown\",\n      \"Version\": \"1.13\",\n      \"Source\": \"Repository\",\n      \"Repository\": \"CRAN\",\n      \"Requirements\": [\n        \"R\",\n        \"commonmark\",\n        \"utils\",\n        \"xfun\"\n      ],\n      \"Hash\": \"074efab766a9d6360865ad39512f2a7e\"\n    }\n  }\n}\nWhen I did that successful run, I’d only copied over a few essential / example files\nCOPY renv.lock renv.lock\nCOPY reproduction.Rproj reproduction.Rproj\nCOPY scripts scripts\nInstead of\nCOPY . .\nHowever, when I switched back to just copying everything, I get issues that it cannot copy and move files and that permission is denied.\nI tried manually specifying everything from the folder (exc. .Rhistory and .Rproj.user)…\nCOPY DESCRIPTION DESCRIPTION\nCOPY docker docker\nCOPY outputs outputs\nCOPY README.md README.md\nCOPY renv.lock renv.lock\nCOPY reproduction.Rproj reproduction.Rproj\nCOPY scripts scripts\nCOPY tests tests\n…And that built fine.\nSo I tried again with COPY . ., but adding .Rhistory and .Rproj.user to the .dockerignore - but this failed like before. Hence, I decided to stick with specifying the files being copied (and regardless, I guess that has the benefit of being specific about what we include). It appears I must be copying over something undesirable when running COPY . . which is causing us issues, although I can’t spot what this might be.\n\n\nTroubleshooting stringi\nI ran renv::snapshot() to restore the lock file back to being complete, and then tried to build the image again. This failed with the libicui18n.so.66 error from before. I reverted the lockfile back to the simple version (so the various test runs are quicker), but adding stringi, getting the same error.\nTried adding install before restore - RUN R -e \"renv::install('stringi')\" (which automatically installs renv for us before running)…. and it was successfull….! The library contained stringi and the other packages from the lockfile.\nSo, I then, again, restored the full lockfile, add an install for openssl, and tried once more.\nThis was successful!\n\n\nGiving read, write and save access to folders\nAll the files are present and can be run, and the renv is active with all the required files. However, if we want to save anything (e.g. modifying qmd, or saving output from model with ggsave), we don’t currently have permissions.\nBased on the docker documentation, I tried using --chown with the COPY statements to specifically give permissions to the user rstudio. I also modified stringi and openssl so they have the specific versions.\nThis worked!\n\n\n\nGitHub Container Registry\nActivated and ran but hit issue on COPY renv/activate.R renv/activate.R. It cannot find the file - although the previous commands with relative file paths all ran without issue.\nERROR: failed to solve: failed to compute cache key: failed to calculate checksum of ref 70b54bab-f7c4-4333-a94b-def3ee959db6::iqqrpwic0590fua1x3sv0utsd: \"/renv/activate.R\": not found\nChecking on GitHub, the activate.R file is included. However, in my prior example of this (Shoaib et al. 2022), I ran the dockerfile from the main folder rather than the reproduction folder. Hence, I tried updating the Dockerfile so that the file paths are relative to reproduction’s parent, which fixed the issue.\nI then tested downloading the image from GHCR and ran one of the scripts within that, and it all worked fine. Add instructions for this to the README."
   },
   {
     "objectID": "logbook/posts/2024_07_09/index.html",
diff --git a/sitemap.xml b/sitemap.xml
index 835b336..89c722e 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -110,7 +110,7 @@
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   <url>
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-    <lastmod>2024-07-19T08:08:13.996Z</lastmod>
+    <lastmod>2024-07-19T11:52:25.630Z</lastmod>
   </url>
   <url>
     <loc>https://pythonhealthdatascience.github.io/stars-reproduce-huang-2019/logbook/posts/2024_07_09/index.html</loc>