Quarto html and updated introduction.

pyproject.toml

@@ -7,10 +7,10 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.12"
-ontoweaver = "^0.2.4"
+ontoweaver = "^0.2.5"
 pandas = "^2.0.1"
 notebook = "^7.4.3"
-biocypher = "^0.9.6"
+biocypher = "^0.10.1"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.3.4"

vignette_jobim_files/libs/bootstrap/bootstrap-icons.css

@@ -1,14 +1,14 @@
 /*!
- * Bootstrap Icons v1.11.1 (https://icons.getbootstrap.com/)
- * Copyright 2019-2023 The Bootstrap Authors
+ * Bootstrap Icons v1.13.1 (https://icons.getbootstrap.com/)
+ * Copyright 2019-2024 The Bootstrap Authors
  * Licensed under MIT (https://github.com/twbs/icons/blob/main/LICENSE)
  */
 
 @font-face {
   font-display: block;
   font-family: "bootstrap-icons";
   src: 
-url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff");
+url("./bootstrap-icons.woff?e34853135f9e39acf64315236852cd5a") format("woff");
 }
 
 .bi::before,
@@ -2076,3 +2076,31 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff");
 .bi-suitcase2-fill::before { content: "\f901"; }
 .bi-suitcase2::before { content: "\f902"; }
 .bi-vignette::before { content: "\f903"; }
+.bi-bluesky::before { content: "\f7f9"; }
+.bi-tux::before { content: "\f904"; }
+.bi-beaker-fill::before { content: "\f905"; }
+.bi-beaker::before { content: "\f906"; }
+.bi-flask-fill::before { content: "\f907"; }
+.bi-flask-florence-fill::before { content: "\f908"; }
+.bi-flask-florence::before { content: "\f909"; }
+.bi-flask::before { content: "\f90a"; }
+.bi-leaf-fill::before { content: "\f90b"; }
+.bi-leaf::before { content: "\f90c"; }
+.bi-measuring-cup-fill::before { content: "\f90d"; }
+.bi-measuring-cup::before { content: "\f90e"; }
+.bi-unlock2-fill::before { content: "\f90f"; }
+.bi-unlock2::before { content: "\f910"; }
+.bi-battery-low::before { content: "\f911"; }
+.bi-anthropic::before { content: "\f912"; }
+.bi-apple-music::before { content: "\f913"; }
+.bi-claude::before { content: "\f914"; }
+.bi-openai::before { content: "\f915"; }
+.bi-perplexity::before { content: "\f916"; }
+.bi-css::before { content: "\f917"; }
+.bi-javascript::before { content: "\f918"; }
+.bi-typescript::before { content: "\f919"; }
+.bi-fork-knife::before { content: "\f91a"; }
+.bi-globe-americas-fill::before { content: "\f91b"; }
+.bi-globe-asia-australia-fill::before { content: "\f91c"; }
+.bi-globe-central-south-asia-fill::before { content: "\f91d"; }
+.bi-globe-europe-africa-fill::before { content: "\f91e"; }

vignette_jobim_files/libs/quarto-html/axe/axe-check.js

@@ -0,0 +1,145 @@
+class QuartoAxeReporter {
+  constructor(axeResult, options) {
+    this.axeResult = axeResult;
+    this.options = options;
+  }
+
+  report() {
+    throw new Error("report() is an abstract method");
+  }
+}
+
+class QuartoAxeJsonReporter extends QuartoAxeReporter {
+  constructor(axeResult, options) {
+    super(axeResult, options);
+  }
+
+  report() {
+    console.log(JSON.stringify(this.axeResult, null, 2));
+  }
+}
+
+class QuartoAxeConsoleReporter extends QuartoAxeReporter {
+  constructor(axeResult, options) {
+    super(axeResult, options);
+  }
+
+  report() {
+    for (const violation of this.axeResult.violations) {
+      console.log(violation.description);
+      for (const node of violation.nodes) {
+        for (const target of node.target) {
+          console.log(target);
+          console.log(document.querySelector(target));
+        }
+      }
+    }
+  }
+}
+
+class QuartoAxeDocumentReporter extends QuartoAxeReporter {
+  constructor(axeResult, options) {
+    super(axeResult, options);
+  }
+
+  createViolationElement(violation) {
+    const violationElement = document.createElement("div");
+
+    const descriptionElement = document.createElement("div");
+    descriptionElement.className = "quarto-axe-violation-description";
+    descriptionElement.innerText = `${violation.impact.replace(/^[a-z]/, match => match.toLocaleUpperCase())}: ${violation.description}`;
+    violationElement.appendChild(descriptionElement);
+
+    const helpElement = document.createElement("div");
+    helpElement.className = "quarto-axe-violation-help";
+    helpElement.innerText = violation.help;
+    violationElement.appendChild(helpElement);
+
+    const nodesElement = document.createElement("div");
+    nodesElement.className = "quarto-axe-violation-nodes";
+    violationElement.appendChild(nodesElement);
+    const nodeElement = document.createElement("div");
+    nodeElement.className = "quarto-axe-violation-selector";
+    for (const node of violation.nodes) {
+      for (const target of node.target) {
+        const targetElement = document.createElement("span");
+        targetElement.className = "quarto-axe-violation-target";
+        targetElement.innerText = target;
+        nodeElement.appendChild(targetElement);
+        nodeElement.addEventListener("mouseenter", () => {
+          const element = document.querySelector(target);
+          if (element) {
+            element.scrollIntoView({ behavior: "smooth", block: "center" });
+            element.classList.add("quarto-axe-hover-highlight");
+            setTimeout(() => {
+              element.style.border = "";
+            }, 2000);
+          }
+        });
+        nodeElement.addEventListener("mouseleave", () => {
+          const element = document.querySelector(target);
+          if (element) {
+            element.classList.remove("quarto-axe-hover-highlight");
+          }
+        });
+        nodeElement.addEventListener("click", () => {
+          console.log(document.querySelector(target));
+        });
+        nodeElement.appendChild(targetElement);
+      }
+      nodesElement.appendChild(nodeElement);
+    }
+    return violationElement;
+  }
+
+  report() {
+    const violations = this.axeResult.violations;
+    const reportElement = document.createElement("div");
+    reportElement.className = "quarto-axe-report";
+    if (violations.length === 0) {
+      const noViolationsElement = document.createElement("div");
+      noViolationsElement.className = "quarto-axe-no-violations";
+      noViolationsElement.innerText = "No axe-core violations found.";
+      reportElement.appendChild(noViolationsElement);
+    }
+    violations.forEach((violation) => {
+      reportElement.appendChild(this.createViolationElement(violation));
+    });
+    document.querySelector("main").appendChild(reportElement);
+  }
+}
+
+const reporters = {
+  json: QuartoAxeJsonReporter,
+  console: QuartoAxeConsoleReporter,
+  document: QuartoAxeDocumentReporter,
+};
+
+class QuartoAxeChecker {
+  constructor(opts) {
+    this.options = opts;
+  }
+  async init() {
+    const axe = (await import("https://cdn.skypack.dev/pin/[email protected]/mode=imports,min/optimized/axe-core.js")).default;
+    const result = await axe.run({
+      exclude: [
+       // https://github.com/microsoft/tabster/issues/288
+       // MS has claimed they won't fix this, so we need to add an exclusion to
+       // all tabster elements
+       "[data-tabster-dummy]"
+      ],
+      preload: { assets: ['cssom'], timeout: 50000 }    
+    });
+    const reporter = this.options === true ? new QuartoAxeConsoleReporter(result) : new reporters[this.options.output](result, this.options);
+    reporter.report();
+  }
+}
+
+export async function init() {
+  const opts = document.querySelector("#quarto-axe-checker-options");
+  if (opts) {
+    const jsonOptions = JSON.parse(atob(opts.textContent));
+    const checker = new QuartoAxeChecker(jsonOptions);
+    await checker.init();
+  }
+}