Newsletter février (#85)

* prepare news * prépare le post * Préparation infolettre * retour * mixtral et openai * finalise * image * améliore * to do * retour _quarto * improve stats * spoiler * end * snow * snow * js * new featured * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update infolettre/infolettre_16/index.qmd Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Update index.qmd * Apply suggestions from code review Co-authored-by: Marie-Pierre Joubert - de Bellefon <121847164+mpjoubertdebellefon@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Marie-Pierre Joubert - 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InseeFrLab · Feb 26, 2024 · f83be3a · f83be3a
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diff --git a/_extensions/coatless/webr/_extension.yml b/_extensions/coatless/webr/_extension.yml
@@ -0,0 +1,8 @@
+name: webr
+title: Embedded webr code cells
+author: James Joseph Balamuta
+version: 0.4.0
+quarto-required: ">=1.2.198"
+contributes:
+  filters:
+    - webr.lua
diff --git a/_extensions/coatless/webr/qwebr-cell-elements.js b/_extensions/coatless/webr/qwebr-cell-elements.js
@@ -0,0 +1,245 @@
+// Supported Evaluation Types for Context
+globalThis.EvalTypes = Object.freeze({
+  Interactive: 'interactive',
+  Setup: 'setup',
+  Output: 'output',
+});
+
+// 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;
+}
diff --git a/_extensions/coatless/webr/qwebr-cell-initialization.js b/_extensions/coatless/webr/qwebr-cell-initialization.js
@@ -0,0 +1,110 @@
+// Handle cell initialization initialization
+qwebrCellDetails.map(
+  (entry) => {
+    // Handle the creation of the element
+    qwebrCreateHTMLElement(entry);
+    // In the event of interactive, initialize the monaco editor
+    if (entry.options.context == EvalTypes.Interactive) {
+      qwebrCreateMonacoEditorInstance(entry);
+    }
+  }
+);
+
+// Identify non-interactive cells (in order)
+const filteredEntries = qwebrCellDetails.filter(entry => {
+  const contextOption = entry.options && entry.options.context;
+  return ['output', 'setup'].includes(contextOption) || (contextOption == "interactive" && entry.options && entry.options.autorun === 'true');
+});
+
+// Condition non-interactive cells to only be run after webR finishes its initialization.
+qwebrInstance.then(
+  async () => {
+    const nHiddenCells = filteredEntries.length;
+    var currentHiddenCell = 0;
+
+
+    // Modify button state
+    qwebrSetInteractiveButtonState(`🟡 Running hidden code cells ...`, false);
+
+    // Begin processing non-interactive sections
+    // Due to the iteration policy, we must use a for() loop.
+    // Otherwise, we would need to switch to using reduce with an empty
+    // starting promise
+    for (const entry of filteredEntries) {
+
+      // Determine cell being examined
+      currentHiddenCell = currentHiddenCell + 1;
+      const formattedMessage = `Evaluating hidden cell ${currentHiddenCell} out of ${nHiddenCells}`;
+
+      // Update the document status header
+      if (qwebrShowStartupMessage) {
+        qwebrUpdateStatusHeader(formattedMessage);
+      }
+
+      // Display the update in non-active areas
+      qwebrUpdateStatusMessage(formattedMessage);
+
+      // Extract details on the active cell
+      const evalType = entry.options.context;
+      const cellCode = entry.code;
+      const qwebrCounter = entry.id;
+
+      if (['output', 'setup'].includes(evalType)) {
+        // Disable further global status updates
+        const activeContainer = document.getElementById(`qwebr-non-interactive-loading-container-${qwebrCounter}`);
+        activeContainer.classList.remove('qwebr-cell-needs-evaluation');
+        activeContainer.classList.add('qwebr-cell-evaluated');
+
+        // Update status on the code cell
+        const activeStatus = document.getElementById(`qwebr-status-text-${qwebrCounter}`);
+        activeStatus.innerText = " Evaluating hidden code cell...";
+        activeStatus.classList.remove('qwebr-cell-needs-evaluation');
+        activeStatus.classList.add('qwebr-cell-evaluated');
+      }
+
+      switch (evalType) {
+        case 'interactive':
+          // TODO: Make this more standardized.
+          // At the moment, we're overriding the interactive status update by pretending its
+          // output-like. 
+          const tempOptions = entry.options;
+          tempOptions["context"] = "output"
+          // Run the code in a non-interactive state that is geared to displaying output
+          await qwebrExecuteCode(`${cellCode}`, qwebrCounter, tempOptions);
+          break;
+        case 'output':
+          // Run the code in a non-interactive state that is geared to displaying output
+          await qwebrExecuteCode(`${cellCode}`, qwebrCounter, entry.options);
+          break;
+        case 'setup':
+          const activeDiv = document.getElementById(`qwebr-noninteractive-setup-area-${qwebrCounter}`);
+          // Run the code in a non-interactive state with all output thrown away
+          await mainWebR.evalRVoid(`${cellCode}`);
+          break;
+        default: 
+          break; 
+      }
+
+      if (['output', 'setup'].includes(evalType)) {
+        // Disable further global status updates
+        const activeContainer = document.getElementById(`qwebr-non-interactive-loading-container-${qwebrCounter}`);
+        // Disable visibility
+        activeContainer.style.visibility = 'hidden';
+        activeContainer.style.display = 'none';
+      }
+    }
+  }
+).then(
+  () => {
+    // Release document status as ready
+
+    if (qwebrShowStartupMessage) {
+      qwebrStartupMessage.innerText = "🟢 Ready!"
+    }
+
+    qwebrSetInteractiveButtonState(
+      `<i class="fa-solid fa-play qwebr-icon-run-code"></i> <span>Run Code</span>`, 
+      true
+    );  
+  }
+);