mystmd 1.3.7__tar.gz → 1.3.9__tar.gz

{mystmd-1.3.7 → mystmd-1.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mystmd
-Version: 1.3.7
+Version: 1.3.9
 Summary: Command line tools for MyST Markdown
 Project-URL: Homepage, https://github.com/jupyter-book/mystmd
 Project-URL: Bug Tracker, https://github.com/jupyter-book/mystmd/issues

{mystmd-1.3.7 → mystmd-1.3.9}/_package.json

@@ -1,6 +1,6 @@
 {
   "name": "mystmd",
-  "version": "1.3.7",
+  "version": "1.3.9",
   "description": "Command line tools for MyST Markdown",
   "author": "Rowan Cockett <rowan@curvenote.com>",
   "license": "MIT",
@@ -45,6 +45,6 @@
     "commander": "^10.0.1",
     "core-js": "^3.31.1",
     "js-yaml": "^4.1.0",
-    "myst-cli": "^1.3.7"
+    "myst-cli": "^1.3.9"
   }
 }

{mystmd-1.3.7 → mystmd-1.3.9}/src/mystmd_py/myst.cjs

@@ -193562,7 +193562,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.3.7";
+var version = "1.3.9";
 var version_default = version;
 
 // ../myst-cli/dist/build/build.js
@@ -195262,7 +195262,8 @@ var PAGE_FRONTMATTER_KEYS = [
   "kernelspec",
   "jupytext",
   "tags",
-  "content_includes_title"
+  "content_includes_title",
+  "site"
 ];
 
 // ../myst-frontmatter/dist/exports/types.js
@@ -198972,6 +198973,9 @@ function validatePageFrontmatterKeys(value, opts) {
   if (defined(value.content_includes_title)) {
     output2.content_includes_title = validateBoolean(value.content_includes_title, incrementOptions("content_includes_title", opts));
   }
+  if (defined(value.site)) {
+    output2.site = validateObject(value.site, incrementOptions("site", opts));
+  }
   return output2;
 }
 function validatePageFrontmatter(input3, opts) {
@@ -241280,6 +241284,61 @@ function writeJsonLogs(session, name3, logData) {
   writeFileToFolder((0, import_node_path6.join)(session.buildPath(), "logs", name3), JSON.stringify(logData, null, 2));
 }
 
+// ../myst-cli/dist/session/cache.js
+var import_node_fs2 = __toESM(require("fs"), 1);
+var import_node_path7 = __toESM(require("path"), 1);
+function castSession(session) {
+  const cache = session;
+  if (!cache.$citationRenderers)
+    cache.$citationRenderers = {};
+  if (!cache.$doiRenderers)
+    cache.$doiRenderers = {};
+  if (!cache.$internalReferences)
+    cache.$internalReferences = {};
+  if (!cache.$externalReferences)
+    cache.$externalReferences = {};
+  if (!cache.$mdast)
+    cache.$mdast = {};
+  if (!cache.$outputs)
+    cache.$outputs = {};
+  cache.$setMdast = (file, data) => {
+    cache.$mdast[import_node_path7.default.resolve(file)] = data;
+  };
+  cache.$getMdast = (file) => {
+    return cache.$mdast[import_node_path7.default.resolve(file)];
+  };
+  return cache;
+}
+function cachePath(session, filename) {
+  return import_node_path7.default.join(session.buildPath(), "cache", filename);
+}
+function writeToCache(session, filename, data) {
+  const file = cachePath(session, filename);
+  session.log.debug(`Writing cache file: ${file}`);
+  writeFileToFolder(file, data);
+}
+function checkCache(session, filename, opts) {
+  const file = cachePath(session, filename);
+  if (!import_node_fs2.default.existsSync(file)) {
+    session.log.debug(`Cache file not found: ${file}`);
+    return false;
+  }
+  const { ctimeMs } = import_node_fs2.default.lstatSync(file);
+  const age = (Date.now() - ctimeMs) / (1e3 * 60 * 60 * 24);
+  if ((opts === null || opts === void 0 ? void 0 : opts.maxAge) != null && age > opts.maxAge) {
+    session.log.debug(`Cache file has expired (age: ${age.toFixed(3)} days, max: ${opts.maxAge} days): ${file}`);
+    return false;
+  }
+  return true;
+}
+function loadFromCache(session, filename, opts) {
+  if (!checkCache(session, filename, opts))
+    return;
+  const file = cachePath(session, filename);
+  session.log.debug(`Loading cache file: ${file}`);
+  return import_node_fs2.default.readFileSync(file).toString();
+}
+
 // ../myst-cli/dist/frontmatter.js
 function frontmatterValidationOpts(vfile2, opts) {
   var _a6;
@@ -241315,12 +241374,27 @@ function getPageFrontmatter(session, tree, vfile2, preFrontmatter, keepTitleNode
   return { frontmatter: pageFrontmatter, identifiers };
 }
 function processPageFrontmatter(session, pageFrontmatter, validationOpts, path41) {
-  var _a6, _b, _c, _d2, _e;
+  var _a6, _b, _c, _d2, _e, _f;
+  const cache = castSession(session);
   const state = session.store.getState();
   const siteFrontmatter = (_a6 = selectors_exports.selectCurrentSiteConfig(state)) !== null && _a6 !== void 0 ? _a6 : {};
   const projectFrontmatter = path41 ? (_b = selectors_exports.selectLocalProjectConfig(state, path41)) !== null && _b !== void 0 ? _b : {} : {};
   const frontmatter = fillPageFrontmatter(pageFrontmatter, projectFrontmatter, validationOpts);
-  if (((_c = siteFrontmatter === null || siteFrontmatter === void 0 ? void 0 : siteFrontmatter.options) === null || _c === void 0 ? void 0 : _c.hide_authors) || ((_e = (_d2 = siteFrontmatter === null || siteFrontmatter === void 0 ? void 0 : siteFrontmatter.options) === null || _d2 === void 0 ? void 0 : _d2.design) === null || _e === void 0 ? void 0 : _e.hide_authors)) {
+  const siteTemplate = cache.$siteTemplate;
+  if (siteTemplate) {
+    const siteOptions = siteTemplate.validateOptions((_c = pageFrontmatter.site) !== null && _c !== void 0 ? _c : {}, path41, {
+      // The property is different on the page vs the myst.yml
+      property: "site",
+      // Passing in the log files ensures this isn't prefixed with `myst.yml`.
+      warningLogFn: session.log.warn,
+      errorLogFn: session.log.error
+    });
+    if (siteOptions && Object.keys(siteOptions).length > 0)
+      frontmatter.site = siteOptions;
+  } else {
+    session.log.debug(`Site template not available to validate site frontmatter in ${path41}`);
+  }
+  if (((_d2 = siteFrontmatter === null || siteFrontmatter === void 0 ? void 0 : siteFrontmatter.options) === null || _d2 === void 0 ? void 0 : _d2.hide_authors) || ((_f = (_e = siteFrontmatter === null || siteFrontmatter === void 0 ? void 0 : siteFrontmatter.options) === null || _e === void 0 ? void 0 : _e.design) === null || _f === void 0 ? void 0 : _f.hide_authors)) {
     delete frontmatter.authors;
   }
   return frontmatter;
@@ -241358,61 +241432,6 @@ function updateFileInfoFromFrontmatter(session, file, frontmatter, url, dataUrl)
   }));
 }
 
-// ../myst-cli/dist/session/cache.js
-var import_node_fs2 = __toESM(require("fs"), 1);
-var import_node_path7 = __toESM(require("path"), 1);
-function castSession(session) {
-  const cache = session;
-  if (!cache.$citationRenderers)
-    cache.$citationRenderers = {};
-  if (!cache.$doiRenderers)
-    cache.$doiRenderers = {};
-  if (!cache.$internalReferences)
-    cache.$internalReferences = {};
-  if (!cache.$externalReferences)
-    cache.$externalReferences = {};
-  if (!cache.$mdast)
-    cache.$mdast = {};
-  if (!cache.$outputs)
-    cache.$outputs = {};
-  cache.$setMdast = (file, data) => {
-    cache.$mdast[import_node_path7.default.resolve(file)] = data;
-  };
-  cache.$getMdast = (file) => {
-    return cache.$mdast[import_node_path7.default.resolve(file)];
-  };
-  return cache;
-}
-function cachePath(session, filename) {
-  return import_node_path7.default.join(session.buildPath(), "cache", filename);
-}
-function writeToCache(session, filename, data) {
-  const file = cachePath(session, filename);
-  session.log.debug(`Writing cache file: ${file}`);
-  writeFileToFolder(file, data);
-}
-function checkCache(session, filename, opts) {
-  const file = cachePath(session, filename);
-  if (!import_node_fs2.default.existsSync(file)) {
-    session.log.debug(`Cache file not found: ${file}`);
-    return false;
-  }
-  const { ctimeMs } = import_node_fs2.default.lstatSync(file);
-  const age = (Date.now() - ctimeMs) / (1e3 * 60 * 60 * 24);
-  if ((opts === null || opts === void 0 ? void 0 : opts.maxAge) != null && age > opts.maxAge) {
-    session.log.debug(`Cache file has expired (age: ${age.toFixed(3)} days, max: ${opts.maxAge} days): ${file}`);
-    return false;
-  }
-  return true;
-}
-function loadFromCache(session, filename, opts) {
-  if (!checkCache(session, filename, opts))
-    return;
-  const file = cachePath(session, filename);
-  session.log.debug(`Loading cache file: ${file}`);
-  return import_node_fs2.default.readFileSync(file).toString();
-}
-
 // ../myst-cli/dist/config.js
 var VERSION = 1;
 function emptyConfig() {
@@ -242190,7 +242209,9 @@ var phrasingTypes = /* @__PURE__ */ new Set([
   "superscript",
   "smallcaps",
   "link",
-  "span"
+  "span",
+  "delete",
+  "crossReference"
 ]);
 var UNHANDLED_ERROR_TEXT = "Unhandled TEX conversion";
 function originalValue(original, node3) {
@@ -242201,6 +242222,15 @@ function originalValue(original, node3) {
     return "";
   return original.slice(from4, to);
 }
+function hasStar(node3) {
+  var _a6, _b;
+  const first2 = (_a6 = node3.args) === null || _a6 === void 0 ? void 0 : _a6[0];
+  if (!first2)
+    return false;
+  if (((_b = first2.content) === null || _b === void 0 ? void 0 : _b.length) === 1 && first2.content[0].type === "string" && first2.content[0].content === "*" && first2.openMark === "" && first2.closeMark === "")
+    return true;
+  return false;
+}
 function getArguments(node3, type2) {
   var _a6, _b;
   return (_b = (_a6 = node3.args) === null || _a6 === void 0 ? void 0 : _a6.filter((n) => {
@@ -242411,8 +242441,11 @@ var marks = {
   textsc: "smallcaps",
   textsubscript: "subscript",
   textsuperscript: "superscript",
-  hl: "strong"
+  hl: "strong",
   // This needs to be done!
+  cancel: "delete",
+  bcancel: "delete",
+  xcancel: "delete"
 };
 var TEXT_MARKS_HANDLERS = {
   ...Object.fromEntries(Object.entries(marks).map(([macro2, kind]) => {
@@ -242643,6 +242676,12 @@ var LINK_HANDLERS = {
     const url = texToText(urlNode);
     state.renderInline(textNode.content, "link", { url });
   },
+  macro_hyperlink(node3, state) {
+    state.openParagraph();
+    const [urlNode, textNode] = getArguments(node3, "group");
+    const url = texToText(urlNode);
+    state.renderInline(textNode.content, "link", { url });
+  },
   macro_url(node3, state) {
     state.openParagraph();
     const url = texToText(node3);
@@ -242652,8 +242691,14 @@ var LINK_HANDLERS = {
     state.openParagraph();
     const [urlNode] = getArguments(node3, "argument");
     const [textNode] = getArguments(node3, "group");
-    const url = texToText(urlNode);
-    state.renderInline(textNode.content, "link", { url });
+    const label = texToText(urlNode);
+    state.renderInline(textNode.content, "crossReference", { label });
+  },
+  macro_hypertarget(node3, state) {
+    state.openParagraph();
+    const [urlNode, content3] = getArguments(node3, "group");
+    const label = texToText(urlNode);
+    state.renderInline(content3, "span", { label });
   }
 };
 
@@ -242665,25 +242710,31 @@ var REF_HANDLERS = {
     const label = texToText(node3);
     const parent2 = state.top();
     const last = (_a6 = parent2 === null || parent2 === void 0 ? void 0 : parent2.children) === null || _a6 === void 0 ? void 0 : _a6.slice(-1)[0];
-    if ((parent2 === null || parent2 === void 0 ? void 0 : parent2.type) === "container") {
+    const grandparent = state.stack[state.stack.length - 2];
+    if (!(parent2 === null || parent2 === void 0 ? void 0 : parent2.label) && ((parent2 === null || parent2 === void 0 ? void 0 : parent2.type) === "container" || (parent2 === null || parent2 === void 0 ? void 0 : parent2.type) === "proof")) {
       parent2.label = label;
-    } else if ((parent2 === null || parent2 === void 0 ? void 0 : parent2.type) === "caption" && state.stack[state.stack.length - 2].type === "container") {
-      state.stack[state.stack.length - 2].label = label;
+    } else if (!(grandparent === null || grandparent === void 0 ? void 0 : grandparent.label) && ((parent2 === null || parent2 === void 0 ? void 0 : parent2.type) === "caption" && (grandparent === null || grandparent === void 0 ? void 0 : grandparent.type) === "container" || (grandparent === null || grandparent === void 0 ? void 0 : grandparent.type) === "proof")) {
+      grandparent.label = label;
     } else {
       if (!last) {
-        if (parent2)
+        if (parent2 && !parent2.label)
           parent2.label = label;
         return;
       }
       if (!parent2)
         return;
-      last.label = label;
+      if (!(last === null || last === void 0 ? void 0 : last.label))
+        last.label = label;
     }
   },
   macro_ref(node3, state) {
     state.openParagraph();
     const label = texToText(getArguments(node3, "group"));
-    state.pushNode(u2("crossReference", { label }, [u2("text", "%s")]));
+    const xref = u2("crossReference", { label }, [u2("text", "%s")]);
+    if (hasStar(node3)) {
+      xref.noLink = true;
+    }
+    state.pushNode(xref);
   },
   macro_subref(node3, state) {
     state.openParagraph();
@@ -278005,7 +278056,11 @@ var macros17 = {
   AA: 1,
   t: 1,
   u: 1,
-  v: 1
+  v: 1,
+  // Cancel
+  cancel: 1,
+  bcancel: 1,
+  xcancel: 1
 };
 var mixed_arg_macros = ["multirow"];
 function patchOpenArgument(args) {
@@ -278982,7 +279037,10 @@ var MISC_HANDLERS = {
     state.closeParagraph();
     const top = state.top();
     if ((top === null || top === void 0 ? void 0 : top.type) === "container" && (top === null || top === void 0 ? void 0 : top.kind) === "figure" && ((_a6 = top === null || top === void 0 ? void 0 : top.children) === null || _a6 === void 0 ? void 0 : _a6.length)) {
-      const topCopy = { ...top, children: [] };
+      const topCopy = copyNode({ ...top, children: [] });
+      delete topCopy.label;
+      delete topCopy.identifier;
+      delete topCopy.html_id;
       state.closeNode();
       state.openNode("container", topCopy);
     }
@@ -280389,7 +280447,7 @@ function runDirectives(state) {
         directiveOpen.map = map14;
         directiveOpen.meta = {
           arg: arg2,
-          options: simplifyDirectiveOptions(options),
+          options: getDirectiveOptions(options),
           // Tightness is computed for all directives (are they separated by a newline before/after)
           tight: computeBlockTightness(state.src, token.map)
         };
@@ -280471,7 +280529,7 @@ function parseDirectiveContent(content3, info, state) {
         const match3 = COLON_OPTION_REGEX.exec(line2);
         const { option: option3, value } = (_a6 = match3 === null || match3 === void 0 ? void 0 : match3.groups) !== null && _a6 !== void 0 ? _a6 : {};
         if (option3)
-          options.push([option3, value || "true"]);
+          options.push([option3, value || true]);
         bodyOffset++;
       }
     }
@@ -280482,31 +280540,28 @@ function parseDirectiveContent(content3, info, state) {
 function directiveArgToTokens(arg2, lineNumber, state) {
   return nestedPartToTokens("directive_arg", arg2, lineNumber, state, "run_directives", true);
 }
-function simplifyDirectiveOptions(options) {
+function getDirectiveOptions(options) {
   if (!options)
     return void 0;
   const simplified = {};
   options.forEach(([key2, val]) => {
     if (simplified[key2] !== void 0) {
       return;
-    } else if (!isNaN(Number(val))) {
-      simplified[key2] = Number(val);
-    } else if (typeof val === "string" && val.toLowerCase() === "true") {
-      simplified[key2] = true;
-    } else if (typeof val === "string" && val.toLowerCase() === "false") {
-      simplified[key2] = false;
-    } else {
-      simplified[key2] = val;
     }
+    simplified[key2] = val;
   });
   return simplified;
 }
 function directiveOptionsToTokens(options, lineNumber, state) {
   const tokens = options.map(([key2, value], index4) => {
-    const optTokens = nestedPartToTokens("directive_option", `${value}`, lineNumber + index4, state, "run_directives", true);
+    const optTokens = typeof value === "string" ? nestedPartToTokens("directive_option", value, lineNumber + index4, state, "run_directives", true) : [
+      new state.Token("directive_option_open", "", 1),
+      new state.Token("directive_option_close", "", -1)
+    ];
     if (optTokens.length) {
       optTokens[0].info = key2;
-      optTokens[0].content = value;
+      optTokens[0].content = typeof value === "string" ? value : "";
+      optTokens[0].meta = { value };
     }
     return optTokens;
   });
@@ -287928,7 +287983,7 @@ var defaultMdast = {
     getAttrs(t2) {
       return {
         name: t2.info,
-        value: t2.content
+        value: t2.meta.value
       };
     }
   },
@@ -288129,6 +288184,8 @@ function contentFromNode(node3, spec, vfile2, description, ruleId) {
     return void 0;
   }
   if (spec.type === ParseTypesEnum.string || spec.type === String) {
+    if (value === true)
+      return "";
     if (typeof value !== "string" && !(value && typeof value === "number" && !isNaN(value))) {
       fileWarn(vfile2, `value is not a string for ${description}`, { node: node3, ruleId });
     }
@@ -288136,7 +288193,7 @@ function contentFromNode(node3, spec, vfile2, description, ruleId) {
   }
   if (spec.type === ParseTypesEnum.number || spec.type === Number) {
     const valueAsNumber = Number(value);
-    if (isNaN(valueAsNumber)) {
+    if (value === true || isNaN(valueAsNumber)) {
       const fileFn = spec.required ? fileError : fileWarn;
       fileFn(vfile2, `number not provided for ${description}`, { node: node3, ruleId });
       return void 0;
@@ -288471,17 +288528,22 @@ var cardDirective = {
   name: "card",
   alias: ["grid-item-card"],
   arg: {
-    type: "myst"
+    type: "myst",
+    doc: "The title of the card, usually shown as bolded text at the top of the card."
   },
   options: {
-    link: {
-      type: String
+    url: {
+      type: String,
+      alias: ["link"],
+      doc: "Turns the card into a link, can be internal or external."
     },
     header: {
-      type: "myst"
+      type: "myst",
+      doc: "Adds a header to the card."
     },
     footer: {
-      type: "myst"
+      type: "myst",
+      doc: "Adds a footer to the card."
     }
     // // https://sphinx-design.readthedocs.io/en/furo-theme/cards.html#card-options
     // width
@@ -288512,10 +288574,11 @@ var cardDirective = {
   },
   body: {
     type: "myst",
-    required: true
+    required: true,
+    doc: "Main body content of the card."
   },
   run(data) {
-    const { link: link4, header, footer: footer2 } = data.options || {};
+    const { url, header, footer: footer2 } = data.options || {};
     let headerChildren;
     let bodyChildren;
     let footerChildren;
@@ -288552,7 +288615,7 @@ var cardDirective = {
     return [
       {
         type: "card",
-        url: link4,
+        url,
         children
       }
     ];
@@ -289038,7 +289101,7 @@ var import_node_path15 = __toESM(require("path"), 1);
 var import_nbtx = __toESM(require_cjs2(), 1);
 
 // ../myst-cli/dist/version.js
-var version2 = "1.3.7";
+var version2 = "1.3.9";
 var version_default2 = version2;
 
 // ../myst-cli/dist/utils/headers.js
@@ -299862,9 +299925,12 @@ var dist_default2 = template_default;
 // ../myst-cli/dist/build/site/template.js
 var DEFAULT_TEMPLATE = "book-theme";
 var DEFAULT_INSTALL_COMMAND = "npm install";
-async function getMystTemplate(session, opts) {
+async function getSiteTemplate(session, opts) {
   var _a6, _b, _c;
-  const state = session.store.getState();
+  const cache = castSession(session);
+  const state = cache.store.getState();
+  if (cache.$siteTemplate)
+    return cache.$siteTemplate;
   const siteConfig = selectors_exports.selectCurrentSiteConfig(state);
   const file = (_a6 = selectors_exports.selectCurrentSiteFile(state)) !== null && _a6 !== void 0 ? _a6 : session.configFiles[0];
   const mystTemplate = new dist_default2(session, {
@@ -299883,6 +299949,7 @@ async function getMystTemplate(session, opts) {
     }
   });
   await mystTemplate.ensureTemplateExistsOnPath();
+  cache.$siteTemplate = mystTemplate;
   return mystTemplate;
 }
 async function installSiteTemplate(session, mystTemplate) {
@@ -300447,7 +300514,7 @@ async function getSiteManifest(session, opts) {
   const { nav } = siteConfig;
   const actions = (_c = siteConfig.actions) === null || _c === void 0 ? void 0 : _c.map((action) => resolveSiteAction(session, action, siteConfigFile, "actions")).filter((action) => !!action);
   const siteFrontmatter = filterKeys(siteConfig, SITE_FRONTMATTER_KEYS);
-  const mystTemplate = await getMystTemplate(session, opts);
+  const mystTemplate = await getSiteTemplate(session, opts);
   const validatedOptions = mystTemplate.validateOptions((_d2 = siteFrontmatter.options) !== null && _d2 !== void 0 ? _d2 : {}, siteConfigFile, { allowRemote: true });
   const validatedFrontmatter = mystTemplate.validateDoc(siteFrontmatter, validatedOptions, void 0, siteConfigFile);
   const resolvedOptions = await resolveTemplateFileOptions(session, mystTemplate, validatedOptions);
@@ -302239,14 +302306,13 @@ async function evaluateExpression(kernel, expr) {
   return { status: result.status, result };
 }
 function buildCacheKey(kernelSpec, nodes) {
-  var _a6, _b, _c;
   const hashableItems = [];
   for (const node3 of nodes) {
     if (isCellBlock(node3)) {
       hashableItems.push({
         kind: node3.type,
         content: select("code", node3).value,
-        raisesException: !!((_c = (_b = (_a6 = node3.data) === null || _a6 === void 0 ? void 0 : _a6.tags) === null || _b === void 0 ? void 0 : _b.includes) === null || _c === void 0 ? void 0 : _c.call(_b, "raises-exception"))
+        raisesException: codeBlockRaisesException(node3)
       });
     } else {
       (0, import_node_assert.default)(isInlineExpression(node3));
@@ -302262,11 +302328,18 @@ function buildCacheKey(kernelSpec, nodes) {
 function isCellBlock(node3) {
   return node3.type === "block" && select("code", node3) !== null && select("output", node3) !== null;
 }
+function codeBlockRaisesException(node3) {
+  var _a6, _b, _c;
+  return !!((_c = (_b = (_a6 = node3.data) === null || _a6 === void 0 ? void 0 : _a6.tags) === null || _b === void 0 ? void 0 : _b.includes) === null || _c === void 0 ? void 0 : _c.call(_b, "raises-exception"));
+}
+function codeBlockSkipsExecution(node3) {
+  var _a6, _b, _c;
+  return !!((_c = (_b = (_a6 = node3.data) === null || _a6 === void 0 ? void 0 : _a6.tags) === null || _b === void 0 ? void 0 : _b.includes) === null || _c === void 0 ? void 0 : _c.call(_b, "skip-execution"));
+}
 function isInlineExpression(node3) {
   return node3.type === "inlineExpression";
 }
 async function computeExecutableNodes(kernel, nodes, opts) {
-  var _a6, _b, _c;
   let errorOccurred = false;
   const results = [];
   for (const matchedNode of nodes) {
@@ -302274,7 +302347,7 @@ async function computeExecutableNodes(kernel, nodes, opts) {
       const code7 = select("code", matchedNode);
       const { status, outputs } = await executeCode(kernel, code7.value);
       results.push(outputs);
-      const allowErrors = !!((_c = (_b = (_a6 = matchedNode.data) === null || _a6 === void 0 ? void 0 : _a6.tags) === null || _b === void 0 ? void 0 : _b.includes) === null || _c === void 0 ? void 0 : _c.call(_b, "raises-exception"));
+      const allowErrors = codeBlockRaisesException(matchedNode);
       if (status === "error" && !allowErrors) {
         const errorMessage = outputs.map((item) => item.traceback).flat().join("\n");
         fileError(opts.vfile, `An exception occurred during code execution, halting further execution:
@@ -302319,13 +302392,13 @@ function applyComputedOutputsToNodes(nodes, computedResult) {
 async function kernelExecutionTransform(tree, vfile2, opts) {
   var _a6;
   const log = (_a6 = opts.log) !== null && _a6 !== void 0 ? _a6 : console;
-  if (opts.frontmatter.kernelspec === void 0) {
-    return fileError(vfile2, `Notebook does not declare the necessary 'kernelspec' frontmatter key required for execution`);
-  }
-  const executableNodes = selectAll(`block[kind=${NotebookCell.code}],inlineExpression`, tree);
+  const executableNodes = selectAll(`block[kind=${NotebookCell.code}],inlineExpression`, tree).filter((node3) => !(isCellBlock(node3) && codeBlockSkipsExecution(node3)));
   if (executableNodes.length === 0) {
     return;
   }
+  if (opts.frontmatter.kernelspec === void 0) {
+    return fileError(vfile2, `Notebook does not declare the necessary 'kernelspec' frontmatter key required for execution`);
+  }
   const cacheKey = buildCacheKey(opts.frontmatter.kernelspec, executableNodes);
   let cachedResults = opts.cache.get(cacheKey);
   if (opts.ignoreCache || cachedResults === void 0) {
@@ -303790,168 +303863,6 @@ function renderTemplate(template, opts) {
 ${rendered}`);
 }
 
-// ../myst-to-tex/dist/tables.js
-var TOTAL_TABLE_WIDTH = 886;
-function renderPColumn(width) {
-  if (width === 1)
-    return `p{\\dimexpr \\linewidth-2\\tabcolsep}`;
-  return `p{\\dimexpr ${width.toFixed(3)}\\linewidth-2\\tabcolsep}`;
-}
-function getColumnWidths(node3) {
-  var _a6, _b, _c;
-  let bestMaybeWidths = [];
-  let mostNonNulls = 0;
-  for (let i2 = 0; i2 < node3.children.length; i2 += 1) {
-    const row2 = node3.children[i2];
-    const maybeWidths = row2.children.reduce((acc, cell3) => {
-      var _a7, _b2;
-      const colwidth = new Array((_a7 = cell3.colspan) !== null && _a7 !== void 0 ? _a7 : 1).fill(cell3.width ? cell3.width / ((_b2 = cell3.colspan) !== null && _b2 !== void 0 ? _b2 : 1) : null);
-      return [...acc, ...colwidth];
-    }, []);
-    const nonNulls = maybeWidths.filter((maybeWidth) => maybeWidth > 0).length;
-    if (i2 === 0 || nonNulls >= mostNonNulls) {
-      mostNonNulls = nonNulls;
-      bestMaybeWidths = maybeWidths;
-      if (mostNonNulls === maybeWidths.length) {
-        break;
-      }
-    }
-  }
-  let widths;
-  if (mostNonNulls === bestMaybeWidths.length) {
-    widths = bestMaybeWidths;
-  } else {
-    const totalDefinedWidths = bestMaybeWidths.reduce((acc, cur) => cur == null ? acc : acc + cur, 0);
-    const remainingSpace = TOTAL_TABLE_WIDTH - totalDefinedWidths;
-    const nullCells = bestMaybeWidths.length - mostNonNulls;
-    const defaultWidth = Math.floor(remainingSpace / nullCells);
-    widths = bestMaybeWidths.map((w) => w == null || w === 0 ? defaultWidth : w);
-  }
-  const total = widths.reduce((acc, cur) => acc + cur, 0);
-  const fractionalWidths = widths.map((w) => w / total);
-  const columnSpec = fractionalWidths.map((w) => renderPColumn(w)).join("");
-  const numColumns = widths.length > 0 ? widths.length : (_c = (_b = (_a6 = node3 === null || node3 === void 0 ? void 0 : node3.children[0]) === null || _a6 === void 0 ? void 0 : _a6.children) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0;
-  return { widths: fractionalWidths, columnSpec, numColumns };
-}
-function renderTableCell(state, cell3, i2, spanIdx, widths, childCount) {
-  var _a6;
-  let renderedSpan = 1;
-  const colspan = (_a6 = cell3.colspan) !== null && _a6 !== void 0 ? _a6 : 1;
-  if (colspan > 1) {
-    let width = 0;
-    for (let j = 0; j < colspan; j += 1) {
-      width += widths[spanIdx + j];
-    }
-    state.write(`\\multicolumn{${colspan}}{${renderPColumn(width)}}{`);
-    renderedSpan = colspan;
-  }
-  if (cell3.children.length === 1 && cell3.children[0].type === "paragraph") {
-    state.renderChildren(cell3.children[0], true);
-  } else {
-    state.renderChildren(cell3, true);
-  }
-  if (colspan > 1)
-    state.write("}");
-  if (i2 < childCount - 1) {
-    state.write(" & ");
-  }
-  return renderedSpan;
-}
-function renderNodeToLatex(node3, state) {
-  state.usePackages("booktabs");
-  const { widths, columnSpec, numColumns } = getColumnWidths(node3);
-  if (!numColumns) {
-    throw new Error("invalid table format, no columns");
-  }
-  state.data.isInTable = true;
-  if (!state.data.isInContainer) {
-    state.write("\\bigskip\\noindent");
-  }
-  state.ensureNewLine();
-  let numHeaderRowsFound = 0;
-  if (state.data.longFigure) {
-    state.ensureNewLine();
-    state.write("\\hline");
-    state.ensureNewLine();
-    let endHeader = false;
-    node3.children.forEach(({ children: rowContent }) => {
-      var _a6, _b;
-      if (endHeader)
-        return;
-      if ((_a6 = rowContent[0]) === null || _a6 === void 0 ? void 0 : _a6.header) {
-        numHeaderRowsFound += 1;
-        let spanIdx = 0;
-        rowContent.forEach((cell3, i2) => {
-          spanIdx += renderTableCell(state, cell3, i2, spanIdx, widths, rowContent.length);
-        });
-        state.write(" \\\\");
-        state.ensureNewLine();
-      }
-      if (!((_b = rowContent[0]) === null || _b === void 0 ? void 0 : _b.header)) {
-        endHeader = true;
-      }
-    });
-    if (numHeaderRowsFound > 0) {
-      state.ensureNewLine();
-      state.write("\\hline");
-      state.ensureNewLine();
-      state.write("\\endfirsthead");
-      state.ensureNewLine();
-      state.write("\\hline");
-      state.ensureNewLine();
-      state.write(`\\multicolumn{${numColumns}}{c}{\\tablename\\ \\thetable\\ -- \\textit{Continued from previous page}}\\\\`);
-      state.ensureNewLine();
-      node3.children.forEach(({ children: rowContent }, index4) => {
-        if (index4 >= numHeaderRowsFound)
-          return;
-        let spanIdx = 0;
-        rowContent.forEach((cell3, i2) => {
-          spanIdx += renderTableCell(state, cell3, i2, spanIdx, widths, rowContent.length);
-        });
-        state.write(" \\\\");
-        state.ensureNewLine();
-      });
-      state.ensureNewLine();
-      state.write("\\hline");
-      state.ensureNewLine();
-      state.write("\\endhead");
-      state.ensureNewLine();
-    }
-  } else {
-    state.write(`\\begin{tabular}{${columnSpec}}`);
-    state.ensureNewLine();
-    state.write(`\\toprule`);
-    state.ensureNewLine();
-  }
-  node3.children.forEach(({ children: rowContent }, index4) => {
-    var _a6;
-    if (index4 < numHeaderRowsFound)
-      return;
-    let spanIdx = 0;
-    rowContent.forEach((cell3, i2) => {
-      spanIdx += renderTableCell(state, cell3, i2, spanIdx, widths, rowContent.length);
-    });
-    state.write(" \\\\");
-    state.ensureNewLine();
-    if ((_a6 = rowContent[0]) === null || _a6 === void 0 ? void 0 : _a6.header) {
-      state.write("\\hline");
-      state.ensureNewLine();
-    }
-  });
-  if (state.data.longFigure) {
-    state.write("\\hline");
-  } else {
-    state.write("\\bottomrule");
-    state.ensureNewLine();
-    state.write("\\end{tabular}");
-  }
-  state.closeBlock(node3);
-  state.data.isInTable = false;
-  if (!state.data.isInContainer) {
-    state.write("\\bigskip");
-  }
-}
-
 // ../myst-to-tex/dist/types.js
 var DEFAULT_IMAGE_WIDTH = 0.7;
 var DEFAULT_PAGE_WIDTH_PIXELS = 800;
@@ -304249,6 +304160,169 @@ function addIndexEntries(node3, state) {
   });
 }
 
+// ../myst-to-tex/dist/tables.js
+var TOTAL_TABLE_WIDTH = 886;
+function renderPColumn(width) {
+  if (width === 1)
+    return `p{\\dimexpr \\linewidth-2\\tabcolsep}`;
+  return `p{\\dimexpr ${width.toFixed(3)}\\linewidth-2\\tabcolsep}`;
+}
+function getColumnWidths(node3) {
+  var _a6, _b, _c;
+  let bestMaybeWidths = [];
+  let mostNonNulls = 0;
+  for (let i2 = 0; i2 < node3.children.length; i2 += 1) {
+    const row2 = node3.children[i2];
+    const maybeWidths = row2.children.reduce((acc, cell3) => {
+      var _a7, _b2;
+      const colwidth = new Array((_a7 = cell3.colspan) !== null && _a7 !== void 0 ? _a7 : 1).fill(cell3.width ? cell3.width / ((_b2 = cell3.colspan) !== null && _b2 !== void 0 ? _b2 : 1) : null);
+      return [...acc, ...colwidth];
+    }, []);
+    const nonNulls = maybeWidths.filter((maybeWidth) => maybeWidth > 0).length;
+    if (i2 === 0 || nonNulls >= mostNonNulls) {
+      mostNonNulls = nonNulls;
+      bestMaybeWidths = maybeWidths;
+      if (mostNonNulls === maybeWidths.length) {
+        break;
+      }
+    }
+  }
+  let widths;
+  if (mostNonNulls === bestMaybeWidths.length) {
+    widths = bestMaybeWidths;
+  } else {
+    const totalDefinedWidths = bestMaybeWidths.reduce((acc, cur) => cur == null ? acc : acc + cur, 0);
+    const remainingSpace = TOTAL_TABLE_WIDTH - totalDefinedWidths;
+    const nullCells = bestMaybeWidths.length - mostNonNulls;
+    const defaultWidth = Math.floor(remainingSpace / nullCells);
+    widths = bestMaybeWidths.map((w) => w == null || w === 0 ? defaultWidth : w);
+  }
+  const total = widths.reduce((acc, cur) => acc + cur, 0);
+  const fractionalWidths = widths.map((w) => w / total);
+  const columnSpec = fractionalWidths.map((w) => renderPColumn(w)).join("");
+  const numColumns = widths.length > 0 ? widths.length : (_c = (_b = (_a6 = node3 === null || node3 === void 0 ? void 0 : node3.children[0]) === null || _a6 === void 0 ? void 0 : _a6.children) === null || _b === void 0 ? void 0 : _b.length) !== null && _c !== void 0 ? _c : 0;
+  return { widths: fractionalWidths, columnSpec, numColumns };
+}
+function renderTableCell(state, cell3, i2, spanIdx, widths, childCount) {
+  var _a6;
+  let renderedSpan = 1;
+  const colspan = (_a6 = cell3.colspan) !== null && _a6 !== void 0 ? _a6 : 1;
+  if (colspan > 1) {
+    let width = 0;
+    for (let j = 0; j < colspan; j += 1) {
+      width += widths[spanIdx + j];
+    }
+    state.write(`\\multicolumn{${colspan}}{${renderPColumn(width)}}{`);
+    renderedSpan = colspan;
+  }
+  if (cell3.children.length === 1 && cell3.children[0].type === "paragraph") {
+    state.renderChildren(cell3.children[0], true);
+  } else {
+    state.renderChildren(cell3, true);
+  }
+  if (colspan > 1)
+    state.write("}");
+  if (i2 < childCount - 1) {
+    state.write(" & ");
+  }
+  return renderedSpan;
+}
+function renderNodeToLatex(node3, state) {
+  state.usePackages("booktabs");
+  const { widths, columnSpec, numColumns } = getColumnWidths(node3);
+  if (!numColumns) {
+    throw new Error("invalid table format, no columns");
+  }
+  addIndexEntries(node3, state);
+  state.data.isInTable = true;
+  if (!state.data.isInContainer) {
+    state.write("\\bigskip\\noindent");
+  }
+  state.ensureNewLine();
+  let numHeaderRowsFound = 0;
+  if (state.data.longFigure) {
+    state.ensureNewLine();
+    state.write("\\hline");
+    state.ensureNewLine();
+    let endHeader = false;
+    node3.children.forEach(({ children: rowContent }) => {
+      var _a6, _b;
+      if (endHeader)
+        return;
+      if ((_a6 = rowContent[0]) === null || _a6 === void 0 ? void 0 : _a6.header) {
+        numHeaderRowsFound += 1;
+        let spanIdx = 0;
+        rowContent.forEach((cell3, i2) => {
+          spanIdx += renderTableCell(state, cell3, i2, spanIdx, widths, rowContent.length);
+        });
+        state.write(" \\\\");
+        state.ensureNewLine();
+      }
+      if (!((_b = rowContent[0]) === null || _b === void 0 ? void 0 : _b.header)) {
+        endHeader = true;
+      }
+    });
+    if (numHeaderRowsFound > 0) {
+      state.ensureNewLine();
+      state.write("\\hline");
+      state.ensureNewLine();
+      state.write("\\endfirsthead");
+      state.ensureNewLine();
+      state.write("\\hline");
+      state.ensureNewLine();
+      state.write(`\\multicolumn{${numColumns}}{c}{\\tablename\\ \\thetable\\ -- \\textit{Continued from previous page}}\\\\`);
+      state.ensureNewLine();
+      node3.children.forEach(({ children: rowContent }, index4) => {
+        if (index4 >= numHeaderRowsFound)
+          return;
+        let spanIdx = 0;
+        rowContent.forEach((cell3, i2) => {
+          spanIdx += renderTableCell(state, cell3, i2, spanIdx, widths, rowContent.length);
+        });
+        state.write(" \\\\");
+        state.ensureNewLine();
+      });
+      state.ensureNewLine();
+      state.write("\\hline");
+      state.ensureNewLine();
+      state.write("\\endhead");
+      state.ensureNewLine();
+    }
+  } else {
+    state.write(`\\begin{tabular}{${columnSpec}}`);
+    state.ensureNewLine();
+    state.write(`\\toprule`);
+    state.ensureNewLine();
+  }
+  node3.children.forEach(({ children: rowContent }, index4) => {
+    var _a6;
+    if (index4 < numHeaderRowsFound)
+      return;
+    let spanIdx = 0;
+    rowContent.forEach((cell3, i2) => {
+      spanIdx += renderTableCell(state, cell3, i2, spanIdx, widths, rowContent.length);
+    });
+    state.write(" \\\\");
+    state.ensureNewLine();
+    if ((_a6 = rowContent[0]) === null || _a6 === void 0 ? void 0 : _a6.header) {
+      state.write("\\hline");
+      state.ensureNewLine();
+    }
+  });
+  if (state.data.longFigure) {
+    state.write("\\hline");
+  } else {
+    state.write("\\bottomrule");
+    state.ensureNewLine();
+    state.write("\\end{tabular}");
+  }
+  state.closeBlock(node3);
+  state.data.isInTable = false;
+  if (!state.data.isInContainer) {
+    state.write("\\bigskip");
+  }
+}
+
 // ../myst-to-tex/dist/container.js
 var CaptionKind;
 (function(CaptionKind3) {
@@ -304383,23 +304457,17 @@ var captionHandler = (node3, state) => {
 };
 
 // ../myst-to-tex/dist/math.js
-var ENVIRONMENTS2 = [
+var TOP_LEVEL_ENVIRONMENTS = [
   "equation",
   "multline",
   "gather",
   "align",
   "alignat",
   "flalign",
-  "matrix",
-  "pmatrix",
-  "bmatrix",
-  "Bmatrix",
-  "vmatrix",
-  "Vmatrix",
   "eqnarray"
 ];
-var RE_OPEN2 = new RegExp(`^\\\\begin{(${ENVIRONMENTS2.join("|")})([*]?)}`);
-function isAmsmathEnvironment(value) {
+var RE_OPEN2 = new RegExp(`^\\\\begin{(${TOP_LEVEL_ENVIRONMENTS.join("|")})([*]?)}`);
+function isTopLevelAmsmathEnvironment(value) {
   const matchOpen = value.trim().match(RE_OPEN2);
   if (!matchOpen)
     return false;
@@ -304445,12 +304513,13 @@ var math4 = (node3, state) => {
   }
   state.usePackages("amsmath");
   addMacrosToState(node3.value, state);
+  addIndexEntries(node3, state);
   if (state.data.isInTable) {
     state.write("\\(\\displaystyle ");
     state.write(node3.value);
     state.write(" \\)");
   } else {
-    const isAmsMath = isAmsmathEnvironment(node3.value);
+    const isAmsMath = isTopLevelAmsmathEnvironment(node3.value);
     if (isAmsMath) {
       state.ensureNewLine();
       state.write(node3.value);
@@ -304554,6 +304623,7 @@ var proofHandler = (node3, state) => {
     t2.type = "__delete__";
   }
   const newNode = remove(node3, "__delete__");
+  addIndexEntries(node3, state);
   state.write("\\begin{");
   state.write(env7);
   state.write("}");
@@ -304776,6 +304846,7 @@ var handlers3 = {
     state.text(node3.value);
   },
   paragraph(node3, state) {
+    addIndexEntries(node3, state);
     state.renderChildren(node3);
   },
   heading(node3, state) {
@@ -304844,9 +304915,11 @@ var handlers3 = {
       state.write("\\printindex\n");
       return;
     }
+    addIndexEntries(node3, state);
     state.renderChildren(node3, false);
   },
   blockquote(node3, state) {
+    addIndexEntries(node3, state);
     state.renderEnvironment(node3, "quote");
   },
   definitionList(node3, state) {
@@ -304870,6 +304943,7 @@ var handlers3 = {
     if (node3.visibility === "remove") {
       return;
     }
+    addIndexEntries(node3, state);
     let start = "\\begin{verbatim}\n";
     let end = "\n\\end{verbatim}";
     if (state.options.codeStyle === "listings" || getClasses(node3.class).includes("listings") && node3.lang !== void 0) {
@@ -304889,6 +304963,7 @@ var handlers3 = {
     state.closeBlock(node3);
   },
   list(node3, state) {
+    addIndexEntries(node3, state);
     if (state.data.isInTable) {
       node3.children.forEach((child, i2) => {
         state.write(node3.ordered ? `${i2}.~~` : "\\textbullet~~");
@@ -304919,6 +304994,7 @@ var handlers3 = {
     state.renderChildren(node3, false);
   },
   div(node3, state) {
+    addIndexEntries(node3, state);
     state.renderChildren(node3, false);
   },
   span(node3, state) {
@@ -305001,6 +305077,7 @@ var handlers3 = {
     state.write("}");
   },
   admonition(node3, state) {
+    addIndexEntries(node3, state);
     state.usePackages("framed");
     state.renderEnvironment(node3, "framed");
   },
@@ -305010,6 +305087,7 @@ var handlers3 = {
   },
   table: renderNodeToLatex,
   image(node3, state) {
+    addIndexEntries(node3, state);
     state.usePackages("graphicx");
     const { width: nodeWidth, url: nodeSrc, align: nodeAlign } = node3;
     const src = nodeSrc;
@@ -316098,7 +316176,7 @@ async function startServer(session, opts) {
   var _a6;
   await session.reload();
   warnOnHostEnvironmentVariable(session, opts);
-  const mystTemplate = await getMystTemplate(session, opts);
+  const mystTemplate = await getSiteTemplate(session, opts);
   if (!opts.headless)
     await installSiteTemplate(session, mystTemplate);
   await buildSite(session, opts);
@@ -316227,7 +316305,7 @@ function get_baseurl(session) {
 }
 async function buildHtml(session, opts) {
   var _a6;
-  const template = await getMystTemplate(session, opts);
+  const template = await getSiteTemplate(session, opts);
   const baseurl = get_baseurl(session);
   const htmlDir = import_node_path54.default.join(session.buildPath(), "html");
   import_fs_extra.default.rmSync(htmlDir, { recursive: true, force: true });