add files for first complete example book

This includes:
- parts/chapters in _quarto.yml
- a DESCRIPTION file
- a GitHub Action
- a WebR example page

DESCRIPTION

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+# [A] SET PACKAGE NAME, BOOK TITLE AND VERSION
+Package: PACKAGE_NAME
+Title: BOOK_TITLE
+Version: 0.1
+
+# [B] SET AUTHOR NAMES AND EMAILS
+Authors@R: c(
+    person("FORENAME1", "SURNAME1", , "[email protected]", role = c("aut", "cre")),
+    person("FORENAME2", "SURNAME2", , "[email protected]", role = c("aut", "cre"))
+  )
+
+# [C] SET REPOSITORY URL
+URL: https://github.com/sipbs-compbiol/REPOSITORY
+
+# [D] SET REQUIRED PACKAGES IN R
+Depends: 
+    R (>= 3.1.0)
+Imports:
+    tidyverse (>= 2.0.0),
+    ggplot2,
+    flextable,
+    kableExtra
+Suggests:
+    knitr,
+    sessioninfo
+Remotes: tidyverse/dplyr
+Encoding: UTF-8
+
+# [E] SET LICENCING INFORMATION
+License: CC NC ND 4.0

README.md

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+# README.md sipbs-compbiol-book-template
+
+This repository is a template, intended as a convenience to take some manual work out of setting the style for Quarto books used by SIPBS Computational Biology.
+
+This version of the template includes:
+
+- a GitHub Action (`.github/workflows/publish.yml`) that should update the GitHub Pages version of the book on each push to the `main` branch.
+- an example WebR page
+
+## How to use this template
+
+### Setting Up
+
+1. Click on the `Use This Template` button to create a new repository/project based on this template
+2. Clone or download the project to your local development environment
+3. Open the project folder and modify `_variables.yml` to change:
+  - `[A]` academic year
+  - `[B]` administrator name and contact information
+  - `[C]` GitHub URLs for the repository
+4. Modify `_quarto.yml` to change:
+  - `[A]` book title
+  - `[B]` footer text
+  - `[C]` GitHub repository URL
+  - `[D]` author name and publication/presentation date
+  - `[E]` chapters and sections
+5. Modify `DESCRIPTION` to change:
+  - `[A]` package name and book title
+  - `[B]` author names and emails
+  - `[C]` repository URL
+  - `[D]` required R packages
+  - `[E]` licensing information
+6. Change or update the licence, if required
+7. Add the `quarto-webr` extension (if necessary) using the command `quarto add coatless/quarto-webr`
+8. Generate the book by issuing `quarto render` in the terminal, or using the `Render` button in `RStudio`
+9. Commit your updates in the local development environment
+10. Publish your book to GitHub Pages by issuing `quarto publish gh-pages` in the terminal
+
+### General Usage
+
+1. Make changes to the `.qmd` files, updating chapter information in `_quarto.yml`, as needed for your material
+2. Commit your changes locally to the git repository
+3. Push your changes to the GitHub repository

_extensions/coatless/webr/_extension.yml

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+name: webr
+title: Embedded webr code cells
+author: James Joseph Balamuta
+version: 0.4.2-dev.4
+quarto-required: ">=1.2.198"
+contributes:
+  filters:
+    - webr.lua

_extensions/coatless/webr/qwebr-cell-elements.js

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+// Supported Evaluation Types for Context
+globalThis.EvalTypes = Object.freeze({
+  Interactive: 'interactive',
+  Setup: 'setup',
+  Output: 'output',
+});
+
+// Function that obtains the font size for a given element 
+globalThis.qwebrCurrentFontSizeOnElement = function(element, cssProperty = 'font-size') {
+
+  const currentFontSize = parseFloat(
+    window
+    .getComputedStyle(element)
+    .getPropertyValue(cssProperty)
+  );
+
+  return currentFontSize;
+}
+
+// Function to determine font scaling
+globalThis.qwebrScaledFontSize = function(div, qwebrOptions) {
+  // Determine if we should compute font-size using RevealJS's `--r-main-font-size` 
+  // or if we can directly use the document's `font-size`.
+  const cssProperty = document.body.classList.contains('reveal') ? 
+    "--r-main-font-size" : "font-size";
+
+  // Get the current font size on the div element
+  const elementFontSize = qwebrCurrentFontSizeOnElement(div, cssProperty);
+
+  // Determine the scaled font size value
+  const scaledFontSize = ((qwebrOptions['editor-font-scale'] ?? 1) * elementFontSize) ?? 17.5;
+
+  return scaledFontSize;
+}
+
+
+// Function that dispatches the creation request
+globalThis.qwebrCreateHTMLElement = function (
+  cellData
+) {
+
+  // Extract key components
+  const evalType = cellData.options.context;
+  const qwebrCounter = cellData.id;
+
+  // We make an assumption that insertion points are defined by the Lua filter as:
+  // qwebr-insertion-location-{qwebrCounter} 
+  const elementLocator = document.getElementById(`qwebr-insertion-location-${qwebrCounter}`);
+
+  // Figure out the routine to use to insert the element.
+  let qwebrElement;
+  switch ( evalType ) {
+    case EvalTypes.Interactive:
+      qwebrElement = qwebrCreateInteractiveElement(qwebrCounter, cellData.options);
+      break;
+    case EvalTypes.Output: 
+      qwebrElement = qwebrCreateNonInteractiveOutputElement(qwebrCounter, cellData.options);
+      break;
+    case EvalTypes.Setup: 
+      qwebrElement = qwebrCreateNonInteractiveSetupElement(qwebrCounter, cellData.options);
+      break;
+    default: 
+      qwebrElement = document.createElement('div');
+      qwebrElement.textContent = 'Error creating `quarto-webr` element';
+  }
+
+  // Insert the dynamically generated object at the document location.
+  elementLocator.appendChild(qwebrElement);
+};
+
+// Function that setups the interactive element creation
+globalThis.qwebrCreateInteractiveElement = function (qwebrCounter, qwebrOptions) {
+
+  // Create main div element
+  var mainDiv = document.createElement('div');
+  mainDiv.id = 'qwebr-interactive-area-' + qwebrCounter;
+  mainDiv.className = `qwebr-interactive-area`;
+  if (qwebrOptions.classes) {
+    mainDiv.className += " " + qwebrOptions.classes
+  }
+
+  // Add a unique cell identifier that users can customize
+  if (qwebrOptions.label) {
+    mainDiv.setAttribute('data-id', qwebrOptions.label);
+  }
+
+  // Create toolbar div
+  var toolbarDiv = document.createElement('div');
+  toolbarDiv.className = 'qwebr-editor-toolbar';
+  toolbarDiv.id = 'qwebr-editor-toolbar-' + qwebrCounter;
+
+  // Create a div to hold the left buttons
+  var leftButtonsDiv = document.createElement('div');
+  leftButtonsDiv.className = 'qwebr-editor-toolbar-left-buttons';
+
+  // Create a div to hold the right buttons
+  var rightButtonsDiv = document.createElement('div');
+  rightButtonsDiv.className = 'qwebr-editor-toolbar-right-buttons';
+
+  // Create Run Code button
+  var runCodeButton = document.createElement('button');
+  runCodeButton.className = 'btn btn-default qwebr-button qwebr-button-run';
+  runCodeButton.disabled = true;
+  runCodeButton.type = 'button';
+  runCodeButton.id = 'qwebr-button-run-' + qwebrCounter;
+  runCodeButton.textContent = '🟡 Loading webR...';
+  runCodeButton.title = `Run code (Shift + Enter)`;
+
+  // Append buttons to the leftButtonsDiv
+  leftButtonsDiv.appendChild(runCodeButton);
+
+  // Create Reset button
+  var resetButton = document.createElement('button');
+  resetButton.className = 'btn btn-light btn-xs qwebr-button qwebr-button-reset';
+  resetButton.type = 'button';
+  resetButton.id = 'qwebr-button-reset-' + qwebrCounter;
+  resetButton.title = 'Start over';
+  resetButton.innerHTML = '<i class="fa-solid fa-arrows-rotate"></i>';
+
+  // Create Copy button
+  var copyButton = document.createElement('button');
+  copyButton.className = 'btn btn-light btn-xs qwebr-button qwebr-button-copy';
+  copyButton.type = 'button';
+  copyButton.id = 'qwebr-button-copy-' + qwebrCounter;
+  copyButton.title = 'Copy code';
+  copyButton.innerHTML = '<i class="fa-regular fa-copy"></i>';
+
+  // Append buttons to the rightButtonsDiv
+  rightButtonsDiv.appendChild(resetButton);
+  rightButtonsDiv.appendChild(copyButton);
+
+  // Create console area div
+  var consoleAreaDiv = document.createElement('div');
+  consoleAreaDiv.id = 'qwebr-console-area-' + qwebrCounter;
+  consoleAreaDiv.className = 'qwebr-console-area';
+
+  // Create editor div
+  var editorDiv = document.createElement('div');
+  editorDiv.id = 'qwebr-editor-' + qwebrCounter;
+  editorDiv.className = 'qwebr-editor';
+
+  // Create output code area div
+  var outputCodeAreaDiv = document.createElement('div');
+  outputCodeAreaDiv.id = 'qwebr-output-code-area-' + qwebrCounter;
+  outputCodeAreaDiv.className = 'qwebr-output-code-area';
+  outputCodeAreaDiv.setAttribute('aria-live', 'assertive');
+
+  // Create pre element inside output code area
+  var preElement = document.createElement('pre');
+  preElement.style.visibility = 'hidden';
+  outputCodeAreaDiv.appendChild(preElement);
+
+  // Create output graph area div
+  var outputGraphAreaDiv = document.createElement('div');
+  outputGraphAreaDiv.id = 'qwebr-output-graph-area-' + qwebrCounter;
+  outputGraphAreaDiv.className = 'qwebr-output-graph-area';
+
+  // Append buttons to the toolbar
+  toolbarDiv.appendChild(leftButtonsDiv);
+  toolbarDiv.appendChild(rightButtonsDiv);
+
+  // Append all elements to the main div
+  mainDiv.appendChild(toolbarDiv);
+  consoleAreaDiv.appendChild(editorDiv);
+  consoleAreaDiv.appendChild(outputCodeAreaDiv);
+  mainDiv.appendChild(consoleAreaDiv);
+  mainDiv.appendChild(outputGraphAreaDiv);
+
+  return mainDiv;
+}
+
+// Function that adds output structure for non-interactive output
+globalThis.qwebrCreateNonInteractiveOutputElement = function(qwebrCounter, qwebrOptions) {
+  // Create main div element
+  var mainDiv = document.createElement('div');
+  mainDiv.id = 'qwebr-noninteractive-area-' + qwebrCounter;
+  mainDiv.className = `qwebr-noninteractive-area`;
+  if (qwebrOptions.classes) {
+    mainDiv.className += " " + qwebrOptions.classes
+  }
+
+  // Add a unique cell identifier that users can customize
+  if (qwebrOptions.label) {
+    mainDiv.setAttribute('data-id', qwebrOptions.label);
+  }
+
+  // Create a status container div
+  var statusContainer = createLoadingContainer(qwebrCounter);
+
+  // Create output code area div
+  var outputCodeAreaDiv = document.createElement('div');
+  outputCodeAreaDiv.id = 'qwebr-output-code-area-' + qwebrCounter;
+  outputCodeAreaDiv.className = 'qwebr-output-code-area';
+  outputCodeAreaDiv.setAttribute('aria-live', 'assertive');
+
+  // Create pre element inside output code area
+  var preElement = document.createElement('pre');
+  preElement.style.visibility = 'hidden';
+  outputCodeAreaDiv.appendChild(preElement);
+
+  // Create output graph area div
+  var outputGraphAreaDiv = document.createElement('div');
+  outputGraphAreaDiv.id = 'qwebr-output-graph-area-' + qwebrCounter;
+  outputGraphAreaDiv.className = 'qwebr-output-graph-area';
+
+  // Append all elements to the main div
+  mainDiv.appendChild(statusContainer);
+  mainDiv.appendChild(outputCodeAreaDiv);
+  mainDiv.appendChild(outputGraphAreaDiv);
+
+  return mainDiv;
+};
+
+// Function that adds a stub in the page to indicate a setup cell was used.
+globalThis.qwebrCreateNonInteractiveSetupElement = function(qwebrCounter, qwebrOptions) {
+  // Create main div element
+  var mainDiv = document.createElement('div');
+  mainDiv.id = `qwebr-noninteractive-setup-area-${qwebrCounter}`;
+  mainDiv.className = `qwebr-noninteractive-setup-area`;
+  if (qwebrOptions.classes) {
+    mainDiv.className += " " + qwebrOptions.classes
+  }
+
+
+  // Add a unique cell identifier that users can customize
+  if (qwebrOptions.label) {
+    mainDiv.setAttribute('data-id', qwebrOptions.label);
+  }
+
+  // Create a status container div
+  var statusContainer = createLoadingContainer(qwebrCounter);
+
+  // Append status onto the main div
+  mainDiv.appendChild(statusContainer);
+
+  return mainDiv;
+}
+
+
+// Function to create loading container with specified ID
+globalThis.createLoadingContainer = function(qwebrCounter) {
+
+  // Create a status container
+  const container = document.createElement('div');
+  container.id = `qwebr-non-interactive-loading-container-${qwebrCounter}`;
+  container.className = 'qwebr-non-interactive-loading-container qwebr-cell-needs-evaluation';
+
+  // Create an R project logo to indicate its a code space
+  const rProjectIcon = document.createElement('i');
+  rProjectIcon.className = 'fa-brands fa-r-project fa-3x qwebr-r-project-logo';
+
+  // Setup a loading icon from font awesome
+  const spinnerIcon = document.createElement('i');
+  spinnerIcon.className = 'fa-solid fa-spinner fa-spin fa-1x qwebr-icon-status-spinner';
+
+  // Add a section for status text
+  const statusText = document.createElement('p');
+  statusText.id = `qwebr-status-text-${qwebrCounter}`;
+  statusText.className = `qwebr-status-text qwebr-cell-needs-evaluation`;
+  statusText.innerText = 'Loading webR...';
+
+  // Incorporate an inner container
+  const innerContainer = document.createElement('div');
+
+  // Append elements to the inner container
+  innerContainer.appendChild(spinnerIcon);
+  innerContainer.appendChild(statusText);
+
+  // Append elements to the main container
+  container.appendChild(rProjectIcon);
+  container.appendChild(innerContainer);
+
+  return container;
+}