Use Quarto mechanism for unfreezing index.qmd

danielvartan · Nov 10, 2023 · 32487fc · 32487fc
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diff --git a/R/_dev.R b/R/_dev.R
@@ -85,3 +85,4 @@
 # * Fix the dark theme SCSS.
 # * Finish translating `english-abnt-author-date.csl`.
 # * Add DOI field into ABNT CSL files.
+# * Create `check_quarto_urls()` based on `urlchecker::url_check()`.
diff --git a/R/quarto-pre-render-common.R b/R/quarto-pre-render-common.R
@@ -5,21 +5,6 @@
 # lybrary(stringr)
 # lybrary(yaml)
 
-# Unfreeze documents -----
-
-quarto_yml_path <- here::here("_quarto.yml")
-quarto_yml_vars <- yaml::read_yaml(quarto_yml_path)
-
-unfreeze_files <- c(
-  here::here("index.qmd")
-)
-
-if (!is.null(quarto_yml_vars$execute$freeze)) {
-  if (as.character(quarto_yml_vars$execute$freeze) %in% c("TRUE", "auto")) {
-    for (i in unfreeze_files) rutils:::unfreeze_quarto_file(i)
-  }
-}
-
 # Create environment variables -----
 
 quarto_yml_path <- here::here("_quarto.yml")

diff --git a/R/quarto-setup.R b/R/quarto-setup.R
@@ -1,9 +1,7 @@
 ## Based on <https://github.com/hadley/r4ds/blob/main/_common.R>.
 
-# library(checkmate, quietly = TRUE)
 # library(extrafont)
 # library(here, quietly = TRUE)
-# library(kableExtra, quietly = TRUE)
 # library(knitr, quietly = TRUE)
 # library(ggplot2, quietly = TRUE)
 # lybrary(yaml)
@@ -48,38 +46,24 @@ knitr::opts_chunk$set(
 # Set general options -----
 
 options(
+  scipen = 10,
+  digits = 3,
   dplyr.print_min = 6,
   dplyr.print_max = 6,
   pillar.max_footer_lines = 2,
   pillar.min_chars = 15,
   stringr.view_n = 6,
-  # Temporarily deactivate cli output for quarto
-  # cli.num_colors = 0,
-  # cli.hyperlink = FALSE,
   pillar.bold = TRUE,
   width = 77 # 80 - 3 for #> comment
 )
 
 # Set `ggplot2` -----
 
-if (env_vars$format == "pdf") {
-  ggplot2::theme_set(
-    ggplot2::theme_gray(
-      base_size = base_size,
-      base_family = env_vars$sansfont,
-      base_line_size = base_size / 22, # `ggplot2::theme_gray` default
-      base_rect_size = base_size / 22 # `ggplot2::theme_gray` default
-    )
+ggplot2::theme_set(
+  ggplot2::theme_gray(
+    base_size = base_size,
+    base_family = env_vars$sansfont,
+    base_line_size = base_size / 22, # `ggplot2::theme_gray` default
+    base_rect_size = base_size / 22 # `ggplot2::theme_gray` default
   )
-}
-
-if (env_vars$format == "html") {
-  ggplot2::theme_set(
-    ggplot2::theme_gray(
-      base_size = base_size,
-      base_family = env_vars$sansfont,
-      base_line_size = base_size/22, # `ggplot2::theme_gray` default
-      base_rect_size = base_size/22 # `ggplot2::theme_gray` default
-    )
-  )
-}
+)
diff --git a/_extensions/abnt/scss/theme-dark.scss b/_extensions/abnt/scss/theme-dark.scss
@@ -14,8 +14,7 @@ $font-size-root: 18px !default;
 
 // Code
 
-$code-block-bg: #373A3C;
-$code-block-bg-alpha: 1;
+$code-block-bg-alpha: -.8;
 
 /*-- scss:rules --*/
 
@@ -49,9 +48,9 @@ h2 {
 }
 
 h3 {
-  margin-top: 1.5em; 
-  font-size: 1.2rem; 
-  font-weight: 500; 
+  margin-top: 1.5em;
+  font-size: 1.2rem;
+  font-weight: 500;
 }
 
 h4 {
@@ -80,6 +79,9 @@ code a:any-link {
   text-decoration-color: #ccc;
 }
 
-pre {
-  background-image: linear-gradient(160deg,#f8f8f8 0,#f1f1f1 100%);
+/* Captions ---------- */
+
+legend {
+    font-size: .9rem;
+    color: #bfbfbf;
 }
diff --git a/_extensions/abnt/scss/theme-light.scss b/_extensions/abnt/scss/theme-light.scss
@@ -37,9 +37,9 @@ h2 {
 }
 
 h3 {
-  margin-top: 1.5em; 
-  font-size: 1.2rem; 
-  font-weight: 500; 
+  margin-top: 1.5em;
+  font-size: 1.2rem;
+  font-weight: 500;
 }
 
 h4 {
@@ -71,3 +71,10 @@ code a:any-link {
 pre {
   background-image: linear-gradient(160deg,#f8f8f8 0,#f1f1f1 100%);
 }
+
+/* Captions ---------- */
+
+legend {
+    font-size: .9rem;
+    color: #747a7f;
+}
diff --git a/docs/index.pdf b/docs/index.pdf
diff --git a/docs/qmd/pdf-settings.html b/docs/qmd/pdf-settings.html
@@ -326,14 +326,16 @@
   <li><a href="#redenring-pdf-after-rendering-html-and-vice-versa" id="toc-redenring-pdf-after-rendering-html-and-vice-versa" class="nav-link" data-scroll-target="#redenring-pdf-after-rendering-html-and-vice-versa"><span class="header-section-number">B.6</span> Redenring PDF after rendering HTML (and vice-versa)</a></li>
   <li><a href="#crossreferenceable-elements" id="toc-crossreferenceable-elements" class="nav-link" data-scroll-target="#crossreferenceable-elements"><span class="header-section-number">B.7</span> Crossreferenceable elements</a></li>
   <li><a href="#freezing-and-cache" id="toc-freezing-and-cache" class="nav-link" data-scroll-target="#freezing-and-cache"><span class="header-section-number">B.8</span> Freezing and cache</a></li>
+  <li><a href="#spelling-check" id="toc-spelling-check" class="nav-link" data-scroll-target="#spelling-check"><span class="header-section-number">B.9</span> Spelling check</a></li>
+  <li><a href="#url-check" id="toc-url-check" class="nav-link" data-scroll-target="#url-check"><span class="header-section-number">B.10</span> URL check</a></li>
   <li>
-<a href="#how-to-customize-this-quarto-format" id="toc-how-to-customize-this-quarto-format" class="nav-link" data-scroll-target="#how-to-customize-this-quarto-format"><span class="header-section-number">B.9</span> How to customize this Quarto format</a>
+<a href="#how-to-customize-this-quarto-format" id="toc-how-to-customize-this-quarto-format" class="nav-link" data-scroll-target="#how-to-customize-this-quarto-format"><span class="header-section-number">B.11</span> How to customize this Quarto format</a>
   <ul class="collapse">
-<li><a href="#quarto-system" id="toc-quarto-system" class="nav-link" data-scroll-target="#quarto-system"><span class="header-section-number">B.9.1</span> Quarto system</a></li>
-  <li><a href="#template-and-template-partials" id="toc-template-and-template-partials" class="nav-link" data-scroll-target="#template-and-template-partials"><span class="header-section-number">B.9.2</span> Template and template partials</a></li>
-  <li><a href="#spacing-rules" id="toc-spacing-rules" class="nav-link" data-scroll-target="#spacing-rules"><span class="header-section-number">B.9.3</span> Spacing rules</a></li>
-  <li><a href="#how-to-add-new-citation-styles" id="toc-how-to-add-new-citation-styles" class="nav-link" data-scroll-target="#how-to-add-new-citation-styles"><span class="header-section-number">B.9.4</span> How to add new citation styles</a></li>
-  <li><a href="#must-see-references" id="toc-must-see-references" class="nav-link" data-scroll-target="#must-see-references"><span class="header-section-number">B.9.5</span> Must see references</a></li>
+<li><a href="#quarto-system" id="toc-quarto-system" class="nav-link" data-scroll-target="#quarto-system"><span class="header-section-number">B.11.1</span> Quarto system</a></li>
+  <li><a href="#template-and-template-partials" id="toc-template-and-template-partials" class="nav-link" data-scroll-target="#template-and-template-partials"><span class="header-section-number">B.11.2</span> Template and template partials</a></li>
+  <li><a href="#spacing-rules" id="toc-spacing-rules" class="nav-link" data-scroll-target="#spacing-rules"><span class="header-section-number">B.11.3</span> Spacing rules</a></li>
+  <li><a href="#how-to-add-new-citation-styles" id="toc-how-to-add-new-citation-styles" class="nav-link" data-scroll-target="#how-to-add-new-citation-styles"><span class="header-section-number">B.11.4</span> How to add new citation styles</a></li>
+  <li><a href="#must-see-references" id="toc-must-see-references" class="nav-link" data-scroll-target="#must-see-references"><span class="header-section-number">B.11.5</span> Must see references</a></li>
   </ul>
 </li>
   </ul></nav>
@@ -546,16 +548,23 @@ <h1 class="title"><span id="sec-settings" class="quarto-section-identifier">Appe
 </section><section id="freezing-and-cache" class="level2" data-number="B.8"><h2 data-number="B.8" class="anchored" data-anchor-id="freezing-and-cache">
 <span class="header-section-number">B.8</span> Freezing and cache</h2>
 <p>See <a href="https://quarto.org/docs/projects/code-execution.html#freeze">Freeze</a>.</p>
-</section><section id="how-to-customize-this-quarto-format" class="level2" data-number="B.9"><h2 data-number="B.9" class="anchored" data-anchor-id="how-to-customize-this-quarto-format">
-<span class="header-section-number">B.9</span> How to customize this Quarto format</h2>
-<section id="quarto-system" class="level3" data-number="B.9.1"><h3 data-number="B.9.1" class="anchored" data-anchor-id="quarto-system">
-<span class="header-section-number">B.9.1</span> Quarto system</h3>
+</section><section id="spelling-check" class="level2" data-number="B.9"><h2 data-number="B.9" class="anchored" data-anchor-id="spelling-check">
+<span class="header-section-number">B.9</span> Spelling check</h2>
+<p>See <code>rutils:::spell_check_quarto()</code></p>
+</section><section id="url-check" class="level2" data-number="B.10"><h2 data-number="B.10" class="anchored" data-anchor-id="url-check">
+<span class="header-section-number">B.10</span> URL check</h2>
+<p>Soon.</p>
+<p>(Based on <code><a href="https://rdrr.io/pkg/urlchecker/man/url_check.html">urlchecker::url_check()</a></code>).</p>
+</section><section id="how-to-customize-this-quarto-format" class="level2" data-number="B.11"><h2 data-number="B.11" class="anchored" data-anchor-id="how-to-customize-this-quarto-format">
+<span class="header-section-number">B.11</span> How to customize this Quarto format</h2>
+<section id="quarto-system" class="level3" data-number="B.11.1"><h3 data-number="B.11.1" class="anchored" data-anchor-id="quarto-system">
+<span class="header-section-number">B.11.1</span> Quarto system</h3>
 <p>See <a href="https://quarto.org/docs/guide/">Quarto’s guide</a>.</p>
-</section><section id="template-and-template-partials" class="level3" data-number="B.9.2"><h3 data-number="B.9.2" class="anchored" data-anchor-id="template-and-template-partials">
-<span class="header-section-number">B.9.2</span> Template and template partials</h3>
+</section><section id="template-and-template-partials" class="level3" data-number="B.11.2"><h3 data-number="B.11.2" class="anchored" data-anchor-id="template-and-template-partials">
+<span class="header-section-number">B.11.2</span> Template and template partials</h3>
 <p>See <a href="https://quarto.org/docs/journals/templates.html#template-partials">Tempalte partials</a>.</p>
-</section><section id="spacing-rules" class="level3" data-number="B.9.3"><h3 data-number="B.9.3" class="anchored" data-anchor-id="spacing-rules">
-<span class="header-section-number">B.9.3</span> Spacing rules</h3>
+</section><section id="spacing-rules" class="level3" data-number="B.11.3"><h3 data-number="B.11.3" class="anchored" data-anchor-id="spacing-rules">
+<span class="header-section-number">B.11.3</span> Spacing rules</h3>
 <ul>
 <li>Set fixed dimensions (e.g., page dimensions) in <code>cm</code> or <code>pt</code>. <code>cm</code> is the prefer unit for margins.</li>
 <li>Set line spacing as a proportion of <code>\baselineskip</code> (e.g., <code>1.5\baselineskip</code>).</li>
@@ -564,14 +573,14 @@ <h1 class="title"><span id="sec-settings" class="quarto-section-identifier">Appe
 <li>For relative horizontal spacing, use the <code>em</code> unit.</li>
 </ul>
 <p>See <span class="citation" data-cites="oetiker2023">OETIKER et al. (<a href="references.html#ref-oetiker2023" role="doc-biblioref">2023, sec. 7.5</a>)</span> to learn more about LaTeX spacing features. The articles on <a href="https://www.overleaf.com">Overleaf</a> are also a great source of information. Check <a href="https://www.overleaf.com/learn/latex/Lengths_in_LaTeX">Lengths in LaTeX</a> and <a href="https://www.overleaf.com/learn/latex/Articles/How_to_change_paragraph_spacing_in_LaTeX">How to change paragraph spacing in LaTeX</a> to get a sense of the subject.</p>
-<section id="unit-equivalences" class="level4" data-number="B.9.3.1"><h4 data-number="B.9.3.1" class="anchored" data-anchor-id="unit-equivalences">
-<span class="header-section-number">B.9.3.1</span> Unit equivalences</h4>
+<section id="unit-equivalences" class="level4" data-number="B.11.3.1"><h4 data-number="B.11.3.1" class="anchored" data-anchor-id="unit-equivalences">
+<span class="header-section-number">B.11.3.1</span> Unit equivalences</h4>
 <ul>
 <li>1<code>em</code> <span class="math inline">\(==\)</span> 12<code>pt</code> or <span class="math inline">\(\approx\)</span> 0.423333<code>cm</code>.</li>
 <li>1<code>ex</code> <span class="math inline">\(==\)</span> <span class="math inline">\(\approx\)</span> 6.22266<code>pt</code> or <span class="math inline">\(\approx\)</span> 0.219521<code>cm</code>.</li>
 </ul>
-<section id="baselineskip" class="level5" data-number="B.9.3.1.1"><h5 data-number="B.9.3.1.1" class="anchored" data-anchor-id="baselineskip">
-<span class="header-section-number">B.9.3.1.1</span> <code>\baselineskip</code>
+<section id="baselineskip" class="level5" data-number="B.11.3.1.1"><h5 data-number="B.11.3.1.1" class="anchored" data-anchor-id="baselineskip">
+<span class="header-section-number">B.11.3.1.1</span> <code>\baselineskip</code>
 </h5>
 <p>These are the equivalences for a Arial typeface with size 12<code>pt</code>:</p>
 <p>Use <code>\the\baselineskip</code> and <code>\gevalue{}</code> to figure out the exact value. Note that <code>\gevalue{}</code> will return the value in <code>pt</code>.</p>
@@ -609,13 +618,13 @@ <h1 class="title"><span id="sec-settings" class="quarto-section-identifier">Appe
 <code>3\baselineskip</code> <span class="math inline">\(==\)</span> 65.25<code>pt</code> or <span class="math inline">\(\approx\)</span> 2.301875<code>cm</code>.</li>
 </ul>
 </li>
-</ul></section></section></section><section id="how-to-add-new-citation-styles" class="level3" data-number="B.9.4"><h3 data-number="B.9.4" class="anchored" data-anchor-id="how-to-add-new-citation-styles">
-<span class="header-section-number">B.9.4</span> How to add new citation styles</h3>
-</section><section id="must-see-references" class="level3" data-number="B.9.5"><h3 data-number="B.9.5" class="anchored" data-anchor-id="must-see-references">
-<span class="header-section-number">B.9.5</span> Must see references</h3>
+</ul></section></section></section><section id="how-to-add-new-citation-styles" class="level3" data-number="B.11.4"><h3 data-number="B.11.4" class="anchored" data-anchor-id="how-to-add-new-citation-styles">
+<span class="header-section-number">B.11.4</span> How to add new citation styles</h3>
+</section><section id="must-see-references" class="level3" data-number="B.11.5"><h3 data-number="B.11.5" class="anchored" data-anchor-id="must-see-references">
+<span class="header-section-number">B.11.5</span> Must see references</h3>
 <p>To learn the basics about LaTeX, see <span class="citation" data-cites="oetiker2023">OETIKER et al. (<a href="references.html#ref-oetiker2023" role="doc-biblioref">2023</a>)</span>. To delve deeper into the LaTeX system, see <span class="citation" data-cites="lamport1994">LAMPORT (<a href="references.html#ref-lamport1994" role="doc-biblioref">1994</a>)</span> and <span class="citation" data-cites="knuth1986">KNUTH (<a href="references.html#ref-knuth1986" role="doc-biblioref">1986</a>)</span>.</p>
-<section id="manuals" class="level4" data-number="B.9.5.1"><h4 data-number="B.9.5.1" class="anchored" data-anchor-id="manuals">
-<span class="header-section-number">B.9.5.1</span> Manuals</h4>
+<section id="manuals" class="level4" data-number="B.11.5.1"><h4 data-number="B.11.5.1" class="anchored" data-anchor-id="manuals">
+<span class="header-section-number">B.11.5.1</span> Manuals</h4>
 <div>
 
 </div>
@@ -640,8 +649,8 @@ <h1 class="title"><span id="sec-settings" class="quarto-section-identifier">Appe
 </div>
 </div>
 </div>
-</section><section id="r-packages" class="level4" data-number="B.9.5.2"><h4 data-number="B.9.5.2" class="anchored" data-anchor-id="r-packages">
-<span class="header-section-number">B.9.5.2</span> R packages</h4>
+</section><section id="r-packages" class="level4" data-number="B.11.5.2"><h4 data-number="B.11.5.2" class="anchored" data-anchor-id="r-packages">
+<span class="header-section-number">B.11.5.2</span> R packages</h4>
 <div>
 
 </div>

diff --git a/docs/qmd/references.html b/docs/qmd/references.html
@@ -312,7 +312,7 @@ <h1 class="title">References</h1>
 <div id="ref-kuhlman2018" class="csl-entry" role="listitem">
 KUHLMAN, S. J.; CRAIG, L. M.; DUFFY, J. F. <a href="https://doi.org/10.1101/cshperspect.a033613">Introduction to
 chronobiology</a>. <strong>Cold Spring Harbor Perspectives in
-Biology</strong>, v. 10, n. 9, p. a033613, set. 2018.
+Biology</strong>, v. 10, n. 9, p. a033613, Sep. 2018.
 </div>
 <div id="ref-lamport1994" class="csl-entry" role="listitem">
 LAMPORT, L. <strong><span>LaTeX</span>: a document preparation system:
@@ -321,7 +321,7 @@ <h1 class="title">References</h1>
 </div>
 <div id="ref-latinitium" class="csl-entry" role="listitem">
 LATINITIUM. <strong>Latin dictionaries</strong>. Disponível em: &lt;<a href="https://latinitium.com/latin-dictionaries/">https://latinitium.com/latin-dictionaries/</a>&gt;.
-Acesso em: 21 set. 2023.
+Acesso em: 21 sep. 2023.
 </div>
 <div id="ref-marques2012" class="csl-entry" role="listitem">
 MARQUES, M. D.; ODA, G. <a href="https://www.revistas.usp.br/revbiologia/article/view/114816">Glossário</a>.
@@ -330,7 +330,7 @@ <h1 class="title">References</h1>
 <div id="ref-mitchell2013" class="csl-entry" role="listitem">
 MITCHELL, M. <strong>Introduction to complexity</strong>. Online course.
 Disponível em: &lt;<a href="https://www.complexityexplorer.org/courses/1-https://www.complexityexplorer.org/courses/1">https://www.complexityexplorer.org/courses/1-https://www.complexityexplorer.org/courses/1</a>&gt;.
-Acesso em: 21 set. 2023.
+Acesso em: 21 sep. 2023.
 </div>
 <div id="ref-oetiker2023" class="csl-entry" role="listitem">
 OETIKER, T. et al. <strong><a href="https://tobi.oetiker.ch/lshort">The
@@ -347,7 +347,7 @@ <h1 class="title">References</h1>
 PITTENDRIGH, C. S. <a href="https://doi.org/10.1146/annurev.ph.55.030193.000313">Temporal
 organization: reflections of a darwinian clock-watcher</a>.
 <strong>Annual Review of Physiology</strong>, v. 55, n. 1, p. 17–54,
-out. 1993.
+Oct. 1993.
 </div>
 <div id="ref-popper1979" class="csl-entry" role="listitem">
 POPPER, K. R. <strong>Objective knowledge: an evolutionary
@@ -356,12 +356,12 @@ <h1 class="title">References</h1>
 <div id="ref-roenneberg2012a" class="csl-entry" role="listitem">
 ROENNEBERG, T. et al. <a href="https://doi.org/10.1016/j.cub.2012.03.038">Social jetlag and
 obesity</a>. <strong>Current Biology</strong>, v. 22, n. 10, p. 939–943,
-maio 2012.
+May 2012.
 </div>
 <div id="ref-roenneberg2003" class="csl-entry" role="listitem">
 ROENNEBERG, T.; WIRZ-JUSTICE, A.; MERROW, M. <a href="https://doi.org/10.1177/0748730402239679">Life between clocks:
 daily temporal patterns of human chronotypes</a>. <strong>Journal of
-Biological Rhythms</strong>, v. 18, n. 1, p. 80–90, fev. 2003.
+Biological Rhythms</strong>, v. 18, n. 1, p. 80–90, Feb. 2003.
 </div>
 <div id="ref-wickham2016a" class="csl-entry" role="listitem">
 WICKHAM, H. <strong><a href="https://doi.org/10.1007/978-3-319-24277-4">ggplot2: elegant