use pkgsite with math rendering

Author: pachadotdev

.github/workflows/test-coverage.yaml

@@ -82,12 +82,27 @@ jobs:
         run: |
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Action"
+          
+          # Save the badge file before switching branches
+          cp badges/coverage.svg /tmp/coverage.svg
+          
+          # Create or switch to coverage branch
+          git checkout -B coverage
+          
+          # Remove everything except .git
+          git rm -rf . || true
+          
+          # Restore just the badge
+          mkdir -p badges
+          cp /tmp/coverage.svg badges/coverage.svg
           git add badges/coverage.svg
+          
           if ! git diff --staged --quiet; then
-            # Amend the last commit to include the updated badge, preserving its message
-            git commit --amend --no-edit
-            # Safely update the remote with force-with-lease to avoid clobbering concurrent changes
-            git push --force-with-lease origin main
+            git commit -m "Update coverage badge"
+            git push --force origin coverage
           else
             echo "No changes to commit"
           fi
+          
+          # Switch back to main
+          git checkout main

R/unvendor.R

@@ -9,8 +9,8 @@
 #' @export
 #' @examples
 #' # create a new directory
-#' dir <- tempfile()
-#' dir.create(dir)
+#' dir <- paste0(tempdir(), "/", gsub("\\s+|[[:punct:]]", "", Sys.time()))
+#' dir.create(dir, recursive = TRUE)
 #'
 #' # vendor the cpp4r headers into the directory
 #' vendor(dir)
@@ -22,22 +22,24 @@
 #' unlink(dir, recursive = TRUE)
 unvendor <- function(path = NULL) {
   stopifnot(!is.null(path), dir.exists(path))
-  
+
   # Check if the cpp4r directory exists
   cpp4r_dir <- file.path(path, "cpp4r")
   cpp4r_hpp_path <- file.path(path, "cpp4r.hpp")
   info_file_path <- file.path(path, "00-cpp4r-vendoring-info.txt")
-  
+
   # Check if vendored files exist
   has_cpp4r_dir <- dir.exists(cpp4r_dir)
   has_cpp4r_hpp <- file.exists(cpp4r_hpp_path)
   has_info_file <- file.exists(info_file_path)
-  
+
   if (!has_cpp4r_dir && !has_cpp4r_hpp && !has_info_file) {
-    if (is_interactive()) { message("Could not find vendored headers") }
+    if (is_interactive()) {
+      message("Could not find vendored headers")
+    }
     return(invisible(NULL))
   }
-  
+
   # Remove the cpp4r directory if it exists
   if (has_cpp4r_dir) {
     unlink(cpp4r_dir, recursive = TRUE)
@@ -47,7 +49,7 @@ unvendor <- function(path = NULL) {
   if (has_cpp4r_hpp) {
     unlink(cpp4r_hpp_path)
   }
-  
+
   # Remove the info file if it exists
   if (has_info_file) {
     unlink(info_file_path)

R/vendor.R

@@ -23,7 +23,7 @@
 #' # vendor the cpp4r headers into the directory
 #' vendor(dir)
 #'
-#' list.files(file.path(dir, "src", "vendor"))
+#' list.files(dir, recursive = TRUE)
 #'
 #' # cleanup
 #' unlink(dir, recursive = TRUE)

README.Rmd

@@ -21,7 +21,7 @@ knitr::opts_chunk$set(
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![R-CMD-check](https://github.com/pachadotdev/cpp4r/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pachadotdev/cpp4r/actions/workflows/R-CMD-check.yaml)
 [![CRAN status](https://www.r-pkg.org/badges/version/cpp4r)](https://CRAN.R-project.org/package=cpp4r)
-[![Test coverage](https://raw.githubusercontent.com/pachadotdev/cpp4r/main/badges/coverage.svg)](https://github.com/pachadotdev/cpp4r/actions/workflows/test-coverage.yaml)
+[![Test coverage](https://raw.githubusercontent.com/pachadotdev/cpp4r/coverage/badges/coverage.svg)](https://github.com/pachadotdev/cpp4r/actions/workflows/test-coverage.yaml)
 [![BuyMeACoffee](https://raw.githubusercontent.com/pachadotdev/buymeacoffee-badges/main/bmc-yellow.svg)](https://buymeacoffee.com/pacha)
 <!-- badges: end -->
 

README.md

@@ -13,7 +13,7 @@ stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://
 [![CRAN
 status](https://www.r-pkg.org/badges/version/cpp4r)](https://CRAN.R-project.org/package=cpp4r)
 [![Test
-coverage](https://raw.githubusercontent.com/pachadotdev/cpp4r/main/badges/coverage.svg)](https://github.com/pachadotdev/cpp4r/actions/workflows/test-coverage.yaml)
+coverage](https://raw.githubusercontent.com/pachadotdev/cpp4r/coverage/badges/coverage.svg)](https://github.com/pachadotdev/cpp4r/actions/workflows/test-coverage.yaml)
 [![BuyMeACoffee](https://raw.githubusercontent.com/pachadotdev/buymeacoffee-badges/main/bmc-yellow.svg)](https://buymeacoffee.com/pacha)
 <!-- badges: end -->
 

docs/content.css

@@ -360,15 +360,21 @@ mjx-container[jax="SVG"][display="false"] {
   display: inline-block !important;
   vertical-align: baseline !important;
   margin: 0 0.1em;
-  transform: translateY(-0.3em) !important;
+  transform: translateY(-0.2em) !important;
   position: relative !important;
 }
 
 /* Target the SVG elements directly for better alignment */
 mjx-container[jax="SVG"][display="false"] svg {
   vertical-align: baseline !important;
   position: relative !important;
-  top: -0.1em !important;
+  top: -0.2em !important;
+}
+
+/* Alternative alignment approach if the above doesn't work well */
+mjx-container[jax="SVG"]:not([display="true"]) {
+  vertical-align: middle !important;
+  line-height: 1 !important;
 }
 
 /* SVG elements should inherit text color for dark mode */
@@ -383,3 +389,43 @@ mjx-container[jax="SVG"][display="false"] svg {
     /* overflow-x: auto; */
   }
 }
+
+/* Styling for executed R examples */
+.sourceCode {
+  margin-bottom: 0.5em;
+}
+
+.sourceCode pre {
+  background-color: var(--code-bg);
+  border: 1px solid var(--border-color);
+  border-radius: 4px;
+  padding: 0.8em;
+  margin: 0;
+}
+
+.output {
+  margin-bottom: 1em;
+}
+
+.output pre {
+  background-color: rgba(0, 0, 0, 0.05);
+  border: none;
+  border-radius: 4px;
+  padding: 0.8em;
+  margin: 0;
+  color: #666;
+}
+
+[data-theme="dark"] .output pre {
+  background-color: rgba(255, 255, 255, 0.05);
+  color: #ccc;
+}
+
+.error pre {
+  background-color: rgba(220, 53, 69, 0.1);
+  border: 1px solid rgba(220, 53, 69, 0.3);
+  border-radius: 4px;
+  padding: 0.8em;
+  margin: 0;
+  color: #dc3545;
+}

docs/index.html

@@ -22,7 +22,7 @@
         processHtmlClass: 'tex2jax_process'
       }
     };
-  </script><script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script><script id="MathJax-script" async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js"></script></head><body>
+  </script><script id="MathJax-script" async src="js/tex-svg.js"></script></head><body>
 <div class="main-container">
 <div id="menu">
   <div>
@@ -39,9 +39,8 @@ <h1>cpp4r Documentation</h1>
 
   <div class="submenu">
     <label>Functions</label>
-    <a href="reference/cpp4r-package.html">cpp4r-package</a>
-    <a href="reference/pkg_template.html">pkg_template</a>
     <a href="reference/register.html">register</a>
+    <a href="reference/pkg_template.html">pkg_template</a>
     <a href="reference/unvendor.html">unvendor</a>
     <a href="reference/vendor.html">vendor</a>
   </div>
@@ -75,7 +74,7 @@ <h1>cpp4r Documentation</h1>
 <div id="content">
 <div class="content-wrapper">
 <div class="content-main">
-<h1>cpp4r</h1>
+<p># cpp4r</p>
 
 <p><img src="man/figures/logo.svg" height="139" alt=""></p>
 
@@ -84,7 +83,7 @@ <h1>cpp4r</h1>
 <a href="https://github.com/pachadotdev/cpp4r/actions/workflows/R-CMD-check.yaml"><img src="https://github.com/pachadotdev/cpp4r/actions/workflows/R-CMD-check.yaml/badge.svg" alt="R-CMD-check"></a>
 <a href="https://CRAN.R-project.org/package=cpp4r"><img src="https://www.r-pkg.org/badges/version/cpp4r" alt="CRAN
 status"></a>
-<a href="https://github.com/pachadotdev/cpp4r/actions/workflows/test-coverage.yaml"><img src="https://raw.githubusercontent.com/pachadotdev/cpp4r/main/badges/coverage.svg" alt="Test
+<a href="https://github.com/pachadotdev/cpp4r/actions/workflows/test-coverage.yaml"><img src="https://raw.githubusercontent.com/pachadotdev/cpp4r/coverage/badges/coverage.svg" alt="Test
 coverage"></a>
 <a href="https://buymeacoffee.com/pacha"><img src="https://raw.githubusercontent.com/pachadotdev/buymeacoffee-badges/main/bmc-yellow.svg" alt="BuyMeACoffee"></a>
 <!-- badges: end --></p>
@@ -113,12 +112,13 @@ <h1>cpp4r</h1>
 <li><input type="checkbox" checked disabled> Support bidirectional passing of complex numbers/vectors.</li>
 <li><input type="checkbox" checked disabled> Provide flexibility with data types (e.g., cpp4r’s <code>as_integers()</code> and <code>as_doubles()</code> accept logical inputs while cpp11’s do not).</li>
 <li><input type="checkbox" checked disabled> Some internal optimizations for better speed (e.g., <a href="https://github.com/r-lib/cpp11/pull/463">https://github.com/r-lib/cpp11/pull/463</a> and <a href="https://github.com/r-lib/cpp11/pull/430">https://github.com/r-lib/cpp11/pull/430</a>).</li>
-</ul><h2>Getting started</h2>
+</ul>
+## Getting started
 
 <p>Check the <a href="https://cpp4r.org/">documentation</a> to get started using cpp4r
 in your scripts, particularly if you are new to C++ programming.</p>
 
-<h2>Using cpp4r in a package</h2>
+<p>## Using cpp4r in a package</p>
 
 <p>Create a new package with <code>cpp4r::pkg_template("~/path/to/mypkg")</code> and
 then edit the generated files.</p>
@@ -132,8 +132,7 @@ <h2>Using cpp4r in a package</h2>
 
 <pre><code>#' @useDynLib mypkg, .registration = TRUE
 #' @keywords internal
-"_PACKAGE"
-</code></pre>
+"_PACKAGE"</code></pre>
 
 <p>Then decorate C++ functions you want to expose to R with
 <code>[[cpp4r::register]]</code>.</p>
@@ -142,7 +141,7 @@ <h2>Using cpp4r in a package</h2>
 use a shared library. It is straightforward and reliable to use in
 packages without fear of compile-time and run-time mismatches.</p>
 
-<h2>Vendoring</h2>
+<p>## Vendoring</p>
 
 <p>You can <a href="https://cpp4r.org/articles/01-motivations.html">vendor</a> the
 current installed version of cpp4r headers into your package with
@@ -158,24 +157,24 @@ <h2>Vendoring</h2>
 that you will not get bug fixes and new features unless you update the
 vendored headers.</p>
 
-<h2>Getting help</h2>
+<p>## Getting help</p>
 
 <p>Please open an issue or email me. I will do my best to respond before 48
 hours.</p>
 
-<h2>Contributing</h2>
+<p>## Contributing</p>
 
 <p>Contributions are welcome! Please see the <a href="https://cpp4r.org/articles/15-internals.html">internals
 vignette</a> for details
 about design choices and coding style.</p>
 
-<h2>Code of Conduct</h2>
+<p>## Code of Conduct</p>
 
 <p>Please note that the cpp4r project is released with a <a href="https://cpp4r.org/CODE_OF_CONDUCT.html">Contributor Code
 of Conduct</a>. By contributing to
 this project, you agree to abide by its terms.</p>
 </div>
-<footer><p>Last updated: 2025-10-12 11:32:38</p>
+<footer><p>Last updated: 2025-10-12 17:59:33</p>
 </footer><script>
 document.addEventListener('DOMContentLoaded', function() {
   // Theme toggle functionality

docs/js/tex-svg.js

@@ -22,7 +22,7 @@
         processHtmlClass: 'tex2jax_process'
       }
     };
-  </script><script src="https://polyfill.io/v3/polyfill.min.js?features=es6"></script><script id="MathJax-script" async src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js"></script></head><body>
+  </script><script id="MathJax-script" async src="../js/tex-svg.js"></script></head><body>
 <div class="main-container">
 <div id="menu">
   <div>
@@ -39,9 +39,8 @@ <h1>cpp4r Documentation</h1>
 
   <div class="submenu">
     <label>Functions</label>
-    <a href="../reference/cpp4r-package.html">cpp4r-package</a>
-    <a href="../reference/pkg_template.html">pkg_template</a>
     <a href="../reference/register.html">register</a>
+    <a href="../reference/pkg_template.html">pkg_template</a>
     <a href="../reference/unvendor.html">unvendor</a>
     <a href="../reference/vendor.html">vendor</a>
   </div>
@@ -76,21 +75,23 @@ <h1>cpp4r Documentation</h1>
 <div class="content-wrapper">
 <div class="content-main">
 <h1>Changelog</h1>
-<h1>cpp4r 0.3.0</h1>
+<p># cpp4r 0.3.0</p>
 
 <ul><li>Added <code>as_logicals()</code> and <code>as_strings()</code> in the same style of <code>as_doubles()</code> and <code>as_integers()</code></li>
 <li>Improved memory management for <code>r_vector</code> iterators</li>
 <li>Slightly faster than <code>cpp11</code></li>
 <li><code>vendor()</code> and <code>unvendor()</code> use <code>path = NULL</code> as default to adhere to CRAN policies.</li>
-</ul><h1>cpp4r 0.2.0</h1>
+</ul>
+# cpp4r 0.2.0
 
 <ul><li>Reduced dependencies on R side</li>
 <li>The vignettes are rendered only for the package site to keep the CRAN build minimal</li>
-</ul><h1>cpp4r 0.1.0</h1>
+</ul>
+# cpp4r 0.1.0
 
 <ul><li>Initial release</li>
 </ul></div>
-<footer><p>Last updated: 2025-10-12 11:32:44</p>
+<footer><p>Last updated: 2025-10-12 17:59:40</p>
 </footer><script>
 document.addEventListener('DOMContentLoaded', function() {
   // Theme toggle functionality