fix: use Quarto 1.6

Fixes #188
mcanouil · Dec 30, 2024 · e991c83 · e991c83
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diff --git a/_site/blog.html b/_site/blog.html
diff --git a/_site/index.html b/_site/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.7.5">
+<meta name="generator" content="quarto-99.9.9">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
@@ -35,10 +35,10 @@
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
 <link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="site_libs/quarto-html/quarto-syntax-highlighting-dark-356f70157ff813ec4d6c5f6934bf6a09.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<link href="site_libs/quarto-html/quarto-syntax-highlighting-dark-56b67755cebbfb78539c873898544994.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <script src="site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="site_libs/bootstrap/bootstrap-1255f90ac73abe9cb20281312d59c5bb.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="dark">
+<link href="site_libs/bootstrap/bootstrap-57499b4f46d5837da520b93964ea9a35.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="dark">
 <script src="site_libs/quarto-contrib/iconify-2.1.0/iconify-icon.min.js"></script>
 <script src="site_libs/quarto-contrib/glightbox/glightbox.min.js"></script>
 <link href="site_libs/quarto-contrib/glightbox/glightbox.min.css" rel="stylesheet">

diff --git a/_site/listings.json b/_site/listings.json
@@ -1,16 +1,4 @@
 [
-  {
-    "listing": "/talks.html",
-    "items": [
-      "/talks/2021-04-15-rlille-reproducibility/index.html",
-      "/talks/2021-04-14-min2rien-reproducibility/index.html",
-      "/talks/2020-10-07-rlille-rstartup/index.html",
-      "/talks/2019-09-06-lausanne-switzerland/index.html",
-      "/talks/2019-01-21-lund-sweden/index.html",
-      "/talks/2017-09-29-phd/index.html",
-      "/talks/2016-02-11-smpgd/index.html"
-    ]
-  },
   {
     "listing": "/blog.html",
     "items": [
@@ -23,6 +11,18 @@
       "/posts/2020-05-06-ggpacman/index.html"
     ]
   },
+  {
+    "listing": "/talks.html",
+    "items": [
+      "/talks/2021-04-15-rlille-reproducibility/index.html",
+      "/talks/2021-04-14-min2rien-reproducibility/index.html",
+      "/talks/2020-10-07-rlille-rstartup/index.html",
+      "/talks/2019-09-06-lausanne-switzerland/index.html",
+      "/talks/2019-01-21-lund-sweden/index.html",
+      "/talks/2017-09-29-phd/index.html",
+      "/talks/2016-02-11-smpgd/index.html"
+    ]
+  },
   {
     "listing": "/projects.html",
     "items": []

diff --git a/_site/posts/2020-05-06-ggpacman/index.html b/_site/posts/2020-05-06-ggpacman/index.html
diff --git a/_site/posts/2021-05-06-floating-toc-in-blogdown/index.html b/_site/posts/2021-05-06-floating-toc-in-blogdown/index.html
diff --git a/_site/posts/2023-03-05-quarto-auto-table-crossref/index.html b/_site/posts/2023-03-05-quarto-auto-table-crossref/index.html
@@ -2,7 +2,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.7.5">
+<meta name="generator" content="quarto-99.9.9">
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 <meta name="author" content="Mickaël CANOUIL">
 <meta name="description" content="A small example of how to automatically have labels and captions for an unknown number of tables in Quarto, using knitr and R.">
@@ -68,10 +68,10 @@
 <script src="../../site_libs/quarto-html/tippy.umd.min.js"></script>
 <script src="../../site_libs/quarto-html/anchor.min.js"></script>
 <link href="../../site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="../../site_libs/quarto-html/quarto-syntax-highlighting-dark-356f70157ff813ec4d6c5f6934bf6a09.css" rel="stylesheet" id="quarto-text-highlighting-styles">
+<link href="../../site_libs/quarto-html/quarto-syntax-highlighting-dark-56b67755cebbfb78539c873898544994.css" rel="stylesheet" id="quarto-text-highlighting-styles">
 <script src="../../site_libs/bootstrap/bootstrap.min.js"></script>
 <link href="../../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="../../site_libs/bootstrap/bootstrap-1255f90ac73abe9cb20281312d59c5bb.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="dark">
+<link href="../../site_libs/bootstrap/bootstrap-57499b4f46d5837da520b93964ea9a35.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="dark">
 <script src="../../site_libs/quarto-contrib/iconify-2.1.0/iconify-icon.min.js"></script>
 <script src="../../site_libs/quarto-contrib/glightbox/glightbox.min.js"></script>
 <link href="../../site_libs/quarto-contrib/glightbox/glightbox.min.css" rel="stylesheet">
@@ -266,45 +266,45 @@ <h1 class="title">Quarto Q&amp;A: How to have labels and captions for an unknown
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">---</span></span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#| include: false</span></span>
-<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (ipkg <span class="cf">in</span> <span class="fu">c</span>(<span class="st">"palmerpenguins"</span>, <span class="st">"gt"</span>, <span class="st">"dplyr"</span>)) {</span>
-<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>  <span class="cf">if</span> (<span class="sc">!</span><span class="fu">require</span>(ipkg, <span class="at">character.only =</span> <span class="cn">TRUE</span>)) {</span>
-<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>    <span class="fu">install.packages</span>(ipkg)</span>
-<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>    <span class="fu">library</span>(ipkg, <span class="at">character.only =</span> <span class="cn">TRUE</span>)</span>
-<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>  }</span>
-<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a>}</span>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="in">#| include: false</span></span>
+<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="in">for (ipkg in c("palmerpenguins", "gt", "dplyr")) {</span></span>
+<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="in">  if (!require(ipkg, character.only = TRUE)) {</span></span>
+<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="in">    install.packages(ipkg)</span></span>
+<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="in">    library(ipkg, character.only = TRUE)</span></span>
+<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="in">  }</span></span>
+<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="in">}</span></span>
 <span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span>
 <span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a>Below are tables of the first six rows of the Palmer penguins dataset by species:</span>
 <span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="in">```{r}</span></span>
-<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="co">#| echo: false</span></span>
-<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="co">#| output: asis</span></span>
-<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="fu">cat</span>(</span>
-<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a>  <span class="fu">sprintf</span>(</span>
-<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a>    <span class="st">"- `%s` (@tbl-%s)"</span>,</span>
-<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a>    <span class="fu">levels</span>(penguins[[<span class="st">"species"</span>]]),</span>
-<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a>    <span class="fu">levels</span>(penguins[[<span class="st">"species"</span>]])</span>
-<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a>  ),</span>
-<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a>  <span class="at">sep =</span> <span class="st">"</span><span class="sc">\n</span><span class="st">"</span></span>
-<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a>)</span>
+<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="in">#| echo: false</span></span>
+<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="in">#| output: asis</span></span>
+<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="in">cat(</span></span>
+<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="in">  sprintf(</span></span>
+<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a><span class="in">    "- `%s` (@tbl-%s)",</span></span>
+<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="in">    levels(penguins[["species"]]),</span></span>
+<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="in">    levels(penguins[["species"]])</span></span>
+<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a><span class="in">  ),</span></span>
+<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="in">  sep = "\n"</span></span>
+<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a><span class="in">)</span></span>
 <span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> (ispecies <span class="cf">in</span> <span class="fu">levels</span>(penguins[[<span class="st">"species"</span>]])) {</span>
-<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a>  tab <span class="ot">&lt;-</span> penguins <span class="sc">|&gt;</span></span>
-<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a>    <span class="fu">filter</span>(species <span class="sc">%in%</span> ispecies) <span class="sc">|&gt;</span></span>
-<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a>    <span class="fu">select</span>(<span class="sc">-</span>species) <span class="sc">|&gt;</span></span>
-<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a>    <span class="fu">head</span>() <span class="sc">|&gt;</span></span>
-<span id="cb1-34"><a href="#cb1-34" aria-hidden="true" tabindex="-1"></a>    <span class="fu">gt</span>() <span class="sc">|&gt;</span></span>
-<span id="cb1-35"><a href="#cb1-35" aria-hidden="true" tabindex="-1"></a>    <span class="fu">tab_header</span>(<span class="at">title =</span> ispecies)</span>
-<span id="cb1-36"><a href="#cb1-36" aria-hidden="true" tabindex="-1"></a>  <span class="fu">cat</span>(<span class="at">sep =</span> <span class="st">"</span><span class="sc">\n</span><span class="st">"</span>, knitr<span class="sc">::</span><span class="fu">knit_child</span>(<span class="at">quiet =</span> <span class="cn">TRUE</span>, <span class="at">text =</span> <span class="fu">c</span>(</span>
-<span id="cb1-37"><a href="#cb1-37" aria-hidden="true" tabindex="-1"></a>    <span class="st">"```{r}"</span>,</span>
-<span id="cb1-38"><a href="#cb1-38" aria-hidden="true" tabindex="-1"></a>    <span class="st">"#| echo: false"</span>,</span>
-<span id="cb1-39"><a href="#cb1-39" aria-hidden="true" tabindex="-1"></a>    <span class="fu">sprintf</span>(<span class="st">"#| tbl-cap: %s"</span>, ispecies),</span>
-<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a>    <span class="fu">sprintf</span>(<span class="st">"#| label: tbl-%s"</span>, ispecies),</span>
-<span id="cb1-41"><a href="#cb1-41" aria-hidden="true" tabindex="-1"></a>    <span class="st">"tab"</span>,</span>
-<span id="cb1-42"><a href="#cb1-42" aria-hidden="true" tabindex="-1"></a>    <span class="st">"```"</span></span>
-<span id="cb1-43"><a href="#cb1-43" aria-hidden="true" tabindex="-1"></a>  )))</span>
-<span id="cb1-44"><a href="#cb1-44" aria-hidden="true" tabindex="-1"></a>}</span>
+<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a><span class="in">for (ispecies in levels(penguins[["species"]])) {</span></span>
+<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a><span class="in">  tab &lt;- penguins |&gt;</span></span>
+<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a><span class="in">    filter(species %in% ispecies) |&gt;</span></span>
+<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a><span class="in">    select(-species) |&gt;</span></span>
+<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a><span class="in">    head() |&gt;</span></span>
+<span id="cb1-34"><a href="#cb1-34" aria-hidden="true" tabindex="-1"></a><span class="in">    gt() |&gt;</span></span>
+<span id="cb1-35"><a href="#cb1-35" aria-hidden="true" tabindex="-1"></a><span class="in">    tab_header(title = ispecies)</span></span>
+<span id="cb1-36"><a href="#cb1-36" aria-hidden="true" tabindex="-1"></a><span class="in">  cat(sep = "\n", knitr::knit_child(quiet = TRUE, text = c(</span></span>
+<span id="cb1-37"><a href="#cb1-37" aria-hidden="true" tabindex="-1"></a><span class="in">    "```{r}",</span></span>
+<span id="cb1-38"><a href="#cb1-38" aria-hidden="true" tabindex="-1"></a><span class="in">    "#| echo: false",</span></span>
+<span id="cb1-39"><a href="#cb1-39" aria-hidden="true" tabindex="-1"></a><span class="in">    sprintf("#| tbl-cap: %s", ispecies),</span></span>
+<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a><span class="in">    sprintf("#| label: tbl-%s", ispecies),</span></span>
+<span id="cb1-41"><a href="#cb1-41" aria-hidden="true" tabindex="-1"></a><span class="in">    "tab",</span></span>
+<span id="cb1-42"><a href="#cb1-42" aria-hidden="true" tabindex="-1"></a><span class="in">    "```"</span></span>
+<span id="cb1-43"><a href="#cb1-43" aria-hidden="true" tabindex="-1"></a><span class="in">  )))</span></span>
+<span id="cb1-44"><a href="#cb1-44" aria-hidden="true" tabindex="-1"></a><span class="in">}</span></span>
 <span id="cb1-45"><a href="#cb1-45" aria-hidden="true" tabindex="-1"></a><span class="in">```</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </div>
 <div id="tabset-1-2" class="tab-pane" role="tabpanel" aria-labelledby="tabset-1-2-tab">
@@ -798,53 +798,8 @@ <h1 class="title">Quarto Q&amp;A: How to have labels and captions for an unknown
     }
   }
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-    return document.body.classList.contains('quarto-dark') ? altTheme : baseTheme;
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