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fix(repo): Rename all references to data and output dir

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Marty Oehme 2024-07-15 21:38:05 +02:00
parent f384515737
commit b4730f6ea8
Signed by: Marty
GPG key ID: EDBF2ED917B2EF6A
22 changed files with 67 additions and 69 deletions
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@ -5125,7 +5125,7 @@ window.document.addEventListener("DOMContentLoaded", function (event) {
});
</script><div class="modal fade" id="quarto-embedded-source-code-modal" tabindex="-1" aria-labelledby="quarto-embedded-source-code-modal-label" aria-hidden="true"><div class="modal-dialog modal-dialog-scrollable"><div class="modal-content"><div class="modal-header"><h5 class="modal-title" id="quarto-embedded-source-code-modal-label">Source Code</h5><button class="btn-close" data-bs-dismiss="modal"></button></div><div class="modal-body"><div class>
<div class="sourceCode" id="cb2" data-shortcodes="false"><pre class="sourceCode markdown code-with-copy"><code class="sourceCode markdown"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="an">bibliography:</span><span class="co"> 02-data/intermediate/zotero-library.bib</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="an">bibliography:</span><span class="co"> data/intermediate/zotero-library.bib</span></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="an">csl:</span><span class="co"> /home/marty/documents/library/utilities/styles/APA-7.csl</span></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a><span class="an">papersize:</span><span class="co"> A4</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a><span class="an">linestretch:</span><span class="co"> 1.5</span></span>
@ -5148,7 +5148,7 @@ window.document.addEventListener("DOMContentLoaded", function (event) {
<span id="cb2-24"><a href="#cb2-24" aria-hidden="true" tabindex="-1"></a><span class="in">```{python}</span></span>
<span id="cb2-25"><a href="#cb2-25" aria-hidden="true" tabindex="-1"></a><span class="co">#| echo: false</span></span>
<span id="cb2-26"><a href="#cb2-26" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> pathlib <span class="im">import</span> Path</span>
<span id="cb2-27"><a href="#cb2-27" aria-hidden="true" tabindex="-1"></a>DATA_DIR<span class="op">=</span>Path(<span class="st">&quot;./02-data&quot;</span>)</span>
<span id="cb2-27"><a href="#cb2-27" aria-hidden="true" tabindex="-1"></a>DATA_DIR<span class="op">=</span>Path(<span class="st">&quot;./data&quot;</span>)</span>
<span id="cb2-28"><a href="#cb2-28" aria-hidden="true" tabindex="-1"></a>RAW_DATA<span class="op">=</span>DATA_DIR.joinpath(<span class="st">&quot;raw&quot;</span>)</span>
<span id="cb2-29"><a href="#cb2-29" aria-hidden="true" tabindex="-1"></a>WORKING_DATA<span class="op">=</span>DATA_DIR.joinpath(<span class="st">&quot;intermediate&quot;</span>)</span>
<span id="cb2-30"><a href="#cb2-30" aria-hidden="true" tabindex="-1"></a>PROCESSED_DATA<span class="op">=</span>DATA_DIR.joinpath(<span class="st">&quot;processed&quot;</span>)</span>
@ -5522,7 +5522,7 @@ window.document.addEventListener("DOMContentLoaded", function (event) {
<span id="cb2-400"><a href="#cb2-400" aria-hidden="true" tabindex="-1"></a><span class="co">#| label: tbl-inclusion-criteria</span></span>
<span id="cb2-401"><a href="#cb2-401" aria-hidden="true" tabindex="-1"></a><span class="co">#| tbl-cap: Study inclusion and exclusion scoping criteria {#tbl-inclusion-criteria}</span></span>
<span id="cb2-402"><a href="#cb2-402" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-403"><a href="#cb2-403" aria-hidden="true" tabindex="-1"></a>inclusion_criteria <span class="op">=</span> pd.read_csv(<span class="st">&quot;02-data/supplementary/inclusion-criteria.tsv&quot;</span>, sep<span class="op">=</span><span class="st">&quot;</span><span class="ch">\t</span><span class="st">&quot;</span>)</span>
<span id="cb2-403"><a href="#cb2-403" aria-hidden="true" tabindex="-1"></a>inclusion_criteria <span class="op">=</span> pd.read_csv(<span class="st">&quot;data/supplementary/inclusion-criteria.tsv&quot;</span>, sep<span class="op">=</span><span class="st">&quot;</span><span class="ch">\t</span><span class="st">&quot;</span>)</span>
<span id="cb2-404"><a href="#cb2-404" aria-hidden="true" tabindex="-1"></a>md(tabulate(inclusion_criteria, showindex<span class="op">=</span><span class="va">False</span>, headers<span class="op">=</span><span class="st">&quot;keys&quot;</span>, tablefmt<span class="op">=</span><span class="st">&quot;grid&quot;</span>))</span>
<span id="cb2-405"><a href="#cb2-405" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
<span id="cb2-406"><a href="#cb2-406" aria-hidden="true" tabindex="-1"></a></span>