mystmd 1.3.23__tar.gz → 1.3.25__tar.gz

{mystmd-1.3.23 → mystmd-1.3.25}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mystmd
-Version: 1.3.23
+Version: 1.3.25
 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-1.3.23 → mystmd-1.3.25}/_package.json

@@ -1,6 +1,6 @@
 {
   "name": "mystmd",
-  "version": "1.3.23",
+  "version": "1.3.25",
   "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": "^1.3.23"
+    "myst-cli": "^1.3.25"
   }
 }

{mystmd-1.3.23 → mystmd-1.3.25}/src/mystmd_py/myst.cjs

@@ -48855,7 +48855,7 @@ var require_input4 = __commonJS({
     var { nanoid: nanoid3 } = require_non_secure();
     var { isAbsolute, resolve: resolve9 } = require("path");
     var { SourceMapConsumer, SourceMapGenerator } = require_source_map();
-    var { fileURLToPath: fileURLToPath5, pathToFileURL } = require("url");
+    var { fileURLToPath: fileURLToPath5, pathToFileURL: pathToFileURL2 } = require("url");
     var CssSyntaxError = require_css_syntax_error();
     var PreviousMap = require_previous_map();
     var terminalHighlight = require_terminal_highlight();
@@ -48944,8 +48944,8 @@ var require_input4 = __commonJS({
         }
         result.input = { column, endColumn, endLine, line: line2, source: this.css };
         if (this.file) {
-          if (pathToFileURL) {
-            result.input.url = pathToFileURL(this.file).toString();
+          if (pathToFileURL2) {
+            result.input.url = pathToFileURL2(this.file).toString();
           }
           result.input.file = this.file;
         }
@@ -49008,11 +49008,11 @@ var require_input4 = __commonJS({
         }
         let fromUrl;
         if (isAbsolute(from4.source)) {
-          fromUrl = pathToFileURL(from4.source);
+          fromUrl = pathToFileURL2(from4.source);
         } else {
           fromUrl = new URL(
             from4.source,
-            this.map.consumer().sourceRoot || pathToFileURL(this.map.mapFile)
+            this.map.consumer().sourceRoot || pathToFileURL2(this.map.mapFile)
           );
         }
         let result = {
@@ -49267,7 +49267,7 @@ var require_map_generator = __commonJS({
     "use strict";
     var { dirname: dirname8, relative: relative6, resolve: resolve9, sep: sep5 } = require("path");
     var { SourceMapConsumer, SourceMapGenerator } = require_source_map();
-    var { pathToFileURL } = require("url");
+    var { pathToFileURL: pathToFileURL2 } = require("url");
     var Input = require_input4();
     var sourceMapAvailable = Boolean(SourceMapConsumer && SourceMapGenerator);
     var pathAvailable = Boolean(dirname8 && resolve9 && relative6 && sep5);
@@ -49565,8 +49565,8 @@ var require_map_generator = __commonJS({
         let cached = this.memoizedFileURLs.get(path44);
         if (cached)
           return cached;
-        if (pathToFileURL) {
-          let fileURL = pathToFileURL(path44).toString();
+        if (pathToFileURL2) {
+          let fileURL = pathToFileURL2(path44).toString();
           this.memoizedFileURLs.set(path44, fileURL);
           return fileURL;
         } else {
@@ -193891,7 +193891,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.3.23";
+var version = "1.3.25";
 var version_default = version;
 
 // ../myst-cli/dist/build/build.js
@@ -194769,10 +194769,10 @@ var doiOrg = {
 };
 var elife = {
   test(url) {
-    return url.hostname.endsWith("elifesciences.org") && url.pathname.startsWith("/articles/");
+    return url.hostname.endsWith("elifesciences.org") && /^\/(?:articles|reviewed-preprints)\/\d+$/.test(url.pathname);
   },
   parse(url) {
-    return `10.7554/eLife.${url.pathname.replace("/articles/", "")}`;
+    return `10.7554/eLife.${url.pathname.replace(/^\/(?:articles|reviewed-preprints)\//, "")}`;
   }
 };
 var zenodo = {
@@ -195602,7 +195602,8 @@ var PAGE_FRONTMATTER_KEYS = [
   "tags",
   "site",
   "enumerator",
-  "content_includes_title"
+  "content_includes_title",
+  "skip_execution"
 ];
 
 // ../myst-frontmatter/dist/exports/types.js
@@ -199691,6 +199692,9 @@ function validatePageFrontmatterKeys(value, opts) {
   if (defined(value.jupytext)) {
     output2.jupytext = validateJupytext(value.jupytext, incrementOptions("jupytext", opts));
   }
+  if (defined(value.skip_execution)) {
+    output2.skip_execution = validateBoolean(value.skip_execution, incrementOptions("skip_execution", opts));
+  }
   if (defined(value.enumerator)) {
     output2.enumerator = validateString(value.enumerator, incrementOptions("enumerator", opts));
   }
@@ -205546,7 +205550,6 @@ var TRANSFORM_SOURCE = "myst-transforms:footnotes";
 function footnotesTransform(mdast2, file) {
   const footnotes = selectAll("footnoteDefinition", mdast2);
   const footnotesLookup = Object.fromEntries(footnotes.map((n) => {
-    delete n.number;
     return [n.identifier, n];
   }));
   const references = selectAll("footnoteReference", mdast2);
@@ -205571,20 +205574,15 @@ function footnotesTransform(mdast2, file) {
       return;
     }
     if (def.enumerator) {
-      node3.number = def.number;
       node3.enumerator = def.enumerator;
       return;
     }
     const identifierNumber = Number(node3.identifier);
     if (!Number.isNaN(identifierNumber) && identifierNumber > 0) {
-      def.number = identifierNumber;
-      node3.number = identifierNumber;
       def.enumerator = String(identifierNumber);
       node3.enumerator = String(identifierNumber);
     } else {
       footnoteCount = nextNumber(footnoteCount, reserved);
-      def.number = footnoteCount;
-      node3.number = footnoteCount;
       def.enumerator = String(footnoteCount);
       node3.enumerator = String(footnoteCount);
     }
@@ -237360,7 +237358,7 @@ var TRANSFORM_SOURCE2 = "BlockTransform:BlockMetadata";
 function blockMetadataTransform(mdast2, file) {
   const blocks2 = selectAll("block", mdast2);
   blocks2.forEach((block5) => {
-    var _a6, _b, _c;
+    var _a6, _b, _c, _d2, _e;
     if (block5.meta) {
       try {
         const data = JSON.parse(block5.meta);
@@ -237374,7 +237372,17 @@ function blockMetadataTransform(mdast2, file) {
         });
       }
     }
-    const label = (_b = (_a6 = block5.data) === null || _a6 === void 0 ? void 0 : _a6.label) !== null && _b !== void 0 ? _b : (_c = block5.data) === null || _c === void 0 ? void 0 : _c.id;
+    const kind = (_a6 = block5.data) === null || _a6 === void 0 ? void 0 : _a6.kind;
+    if (kind) {
+      block5.kind = kind;
+      delete block5.data.kind;
+    }
+    const className = (_b = block5.data) === null || _b === void 0 ? void 0 : _b.class;
+    if (className) {
+      block5.class = className;
+      delete block5.data.class;
+    }
+    const label = (_d2 = (_c = block5.data) === null || _c === void 0 ? void 0 : _c.label) !== null && _d2 !== void 0 ? _d2 : (_e = block5.data) === null || _e === void 0 ? void 0 : _e.id;
     if (typeof label === "string") {
       const normalized = normalizeLabel(label);
       if (normalized) {
@@ -238916,6 +238924,154 @@ async function headingDepthTransform(tree, vfile2, opts) {
   });
 }
 
+// ../myst-transforms/dist/toc.js
+function listFromPages(pages, projectSlug) {
+  if (pages.length === 0)
+    return { type: "list", children: [] };
+  let ignore3 = false;
+  const level = pages[0].level;
+  const children = pages.map((page, index4) => {
+    if (ignore3)
+      return void 0;
+    if (page.level < level)
+      ignore3 = true;
+    if (page.level !== level)
+      return void 0;
+    return listItemFromPages(pages.slice(index4), projectSlug);
+  }).filter((item) => !!item);
+  return { type: "list", children };
+}
+function listItemFromPages(pages, projectSlug) {
+  if (pages.length === 0)
+    return;
+  const { title, slug, enumerator, level } = pages[0];
+  const text7 = {
+    type: "text",
+    value: `${enumerator ? `${enumerator} ` : ""}${title}`
+  };
+  const child = slug != null ? {
+    type: "link",
+    url: `${projectSlug ? `/${projectSlug}` : ""}/${slug}`,
+    internal: true,
+    children: [text7]
+  } : text7;
+  const item = {
+    type: "listItem",
+    children: [child]
+  };
+  if (pages[1] && pages[1].level > level) {
+    item.children.push(listFromPages(pages.slice(1), projectSlug));
+  }
+  return item;
+}
+function listFromHeadings(headings) {
+  if (headings.length === 0)
+    return { type: "list", children: [] };
+  let ignore3 = false;
+  const depth = headings[0].depth;
+  const children = headings.map((heading6, index4) => {
+    if (ignore3)
+      return void 0;
+    if (heading6.depth < depth)
+      ignore3 = true;
+    if (heading6.depth !== depth)
+      return void 0;
+    return listItemFromHeadings(headings.slice(index4));
+  }).filter((item) => !!item);
+  return { type: "list", children };
+}
+function listItemFromHeadings(headings) {
+  if (headings.length === 0)
+    return;
+  const { children, enumerator, depth, identifier } = headings[0];
+  const text7 = {
+    type: "text",
+    value: `${enumerator ? `${enumerator} ` : ""}${toText(children)}`
+  };
+  const child = identifier ? {
+    type: "link",
+    url: `#${identifier}`,
+    internal: true,
+    children: [text7],
+    suppressImplicitWarning: true
+  } : text7;
+  const item = {
+    type: "listItem",
+    children: [child]
+  };
+  if (headings[1] && headings[1].depth > depth) {
+    item.children.push(listFromHeadings(headings.slice(1)));
+  }
+  return item;
+}
+function buildTocTransform(mdast2, vfile2, pages, projectSlug) {
+  const tocHeadings = selectAll("toc > heading", mdast2);
+  const tocsAndHeadings = selectAll("toc,heading", mdast2).filter((item) => {
+    return !tocHeadings.includes(item);
+  });
+  if (!tocsAndHeadings.find((node3) => node3.type === "toc"))
+    return;
+  const projectTocs = tocsAndHeadings.filter((node3) => node3.type === "toc" && node3.kind === "project");
+  const pageTocs = tocsAndHeadings.filter((node3) => node3.type === "toc" && node3.kind === "page");
+  const sectionTocs = tocsAndHeadings.filter((node3) => node3.type === "toc" && node3.kind === "section");
+  if (projectTocs.length) {
+    if (!pages) {
+      fileError(vfile2, `Pages not available to build Table of Contents`);
+    } else {
+      if (pages[0].level !== 1) {
+        fileWarn(vfile2, `First page of Table of Contents must be level 1`);
+      }
+      projectTocs.forEach((toc) => {
+        const filteredPages = toc.depth ? pages.filter((page) => page.level <= toc.depth) : pages;
+        toc.type = "block";
+        delete toc.kind;
+        toc.data = { part: "toc:project" };
+        if (!toc.children)
+          toc.children = [];
+        toc.children.push(listFromPages(filteredPages, projectSlug));
+      });
+    }
+  }
+  if (pageTocs.length) {
+    const headings = tocsAndHeadings.filter((node3) => node3.type === "heading");
+    if (headings.length === 0) {
+      fileWarn(vfile2, `No page headings found for Table of Contents`);
+    } else {
+      if (Math.min(...headings.map((h4) => h4.depth)) !== headings[0].depth) {
+        fileWarn(vfile2, "Page heading levels do not start with highest level");
+      }
+      pageTocs.forEach((toc) => {
+        const filteredHeadings = toc.depth ? headings.filter((heading6) => heading6.depth - headings[0].depth < toc.depth) : headings;
+        toc.type = "block";
+        delete toc.kind;
+        toc.data = { part: "toc:page" };
+        if (!toc.children)
+          toc.children = [];
+        toc.children.push(listFromHeadings(filteredHeadings));
+      });
+    }
+  }
+  if (sectionTocs.length) {
+    tocsAndHeadings.forEach((toc, index4) => {
+      if (toc.type !== "toc" || toc.kind !== "section")
+        return;
+      const headings = tocsAndHeadings.slice(index4 + 1).filter((h4) => h4.type === "heading");
+      if (headings.length === 0) {
+        fileWarn(vfile2, `No section headings found for Table of Contents`);
+      } else {
+        const filteredHeadings = toc.depth ? headings.filter((heading6) => heading6.depth - headings[0].depth < toc.depth) : headings;
+        toc.type = "block";
+        delete toc.kind;
+        toc.data = { part: "toc:section" };
+        if (!toc.children)
+          toc.children = [];
+        const nextSection = filteredHeadings.findIndex((h4) => h4.depth < filteredHeadings[0].depth);
+        toc.children.push(listFromHeadings(nextSection === -1 ? filteredHeadings : filteredHeadings.slice(0, nextSection)));
+      }
+    });
+  }
+}
+
 // ../myst-transforms/dist/enumerate.js
 var TRANSFORM_NAME2 = "myst-transforms:enumerate";
 var DEFAULT_NUMBERING = {
@@ -239378,7 +239534,7 @@ function addContainerCaptionNumbersTransform(tree, file, opts) {
   });
 }
 function implicitTargetWarning(target, node3, opts) {
-  if (target.node.implicit && opts.state.vfile) {
+  if (target.node.implicit && opts.state.vfile && !node3.suppressImplicitWarning) {
     fileWarn(opts.state.vfile, `Linking "${target.node.identifier}" to an implicit ${target.kind} reference, best practice is to create an explicit reference.`, {
       node: node3,
       note: "Explicit references do not break when you update the title to a section, they are preferred over using the implicit HTML ID created for headers.",
@@ -239386,6 +239542,7 @@ function implicitTargetWarning(target, node3, opts) {
       ruleId: RuleId.referenceTargetExplicit
     });
   }
+  delete node3.suppressImplicitWarning;
 }
 var resolveReferenceLinksTransform = (tree, opts) => {
   selectAll("link", tree).forEach((node3) => {
@@ -282455,33 +282612,26 @@ var includeDirective = {
     var _a6, _b, _c, _d2, _e, _f, _g, _h, _j, _k, _l, _m, _o, _p;
     const literal = data.name === "literalinclude" || !!((_a6 = data.options) === null || _a6 === void 0 ? void 0 : _a6.literal) || !!((_b = data.options) === null || _b === void 0 ? void 0 : _b.lang);
     const file = data.arg;
-    if (!literal) {
-      const include4 = {
-        type: "include",
-        file
-      };
-      addCommonDirectiveOptions(data, include4);
-      return [include4];
-    }
     const lang = (_d2 = (_c = data.options) === null || _c === void 0 ? void 0 : _c.lang) !== null && _d2 !== void 0 ? _d2 : extToLanguage(file.split(".").pop());
-    const opts = getCodeBlockOptions(
+    const opts = literal ? getCodeBlockOptions(
       data,
       vfile2,
       // Set the filename in the literal include by default
       file.split(/\/|\\/).pop()
-    );
+    ) : {};
+    const caption3 = literal ? (_e = data.options) === null || _e === void 0 ? void 0 : _e.caption : void 0;
     const filter7 = {};
     ensureOnlyOneOf(data, vfile2, ["start-at", "start-line", "start-after", "lines"]);
     ensureOnlyOneOf(data, vfile2, ["end-at", "end-line", "end-before", "lines"]);
-    filter7.startAt = (_e = data.options) === null || _e === void 0 ? void 0 : _e["start-at"];
-    filter7.startAfter = (_f = data.options) === null || _f === void 0 ? void 0 : _f["start-after"];
-    filter7.endAt = (_g = data.options) === null || _g === void 0 ? void 0 : _g["end-at"];
-    filter7.endBefore = (_h = data.options) === null || _h === void 0 ? void 0 : _h["end-before"];
-    if ((_j = data.options) === null || _j === void 0 ? void 0 : _j.lines) {
-      filter7.lines = parseLinesString(vfile2, (_k = select('mystDirectiveOption[name="lines"]', data.node)) !== null && _k !== void 0 ? _k : void 0, (_l = data.options) === null || _l === void 0 ? void 0 : _l.lines);
+    filter7.startAt = (_f = data.options) === null || _f === void 0 ? void 0 : _f["start-at"];
+    filter7.startAfter = (_g = data.options) === null || _g === void 0 ? void 0 : _g["start-after"];
+    filter7.endAt = (_h = data.options) === null || _h === void 0 ? void 0 : _h["end-at"];
+    filter7.endBefore = (_j = data.options) === null || _j === void 0 ? void 0 : _j["end-before"];
+    if ((_k = data.options) === null || _k === void 0 ? void 0 : _k.lines) {
+      filter7.lines = parseLinesString(vfile2, (_l = select('mystDirectiveOption[name="lines"]', data.node)) !== null && _l !== void 0 ? _l : void 0, (_m = data.options) === null || _m === void 0 ? void 0 : _m.lines);
     } else {
-      const startLine = (_m = data.options) === null || _m === void 0 ? void 0 : _m["start-line"];
-      const endLine = (_o = data.options) === null || _o === void 0 ? void 0 : _o["end-line"];
+      const startLine = (_o = data.options) === null || _o === void 0 ? void 0 : _o["start-line"];
+      const endLine = (_p = data.options) === null || _p === void 0 ? void 0 : _p["end-line"];
       const lines = [];
       if (startLine != null)
         lines.push(startLine);
@@ -282499,13 +282649,14 @@ var includeDirective = {
         ];
       }
     }
+    const usesFilter = Object.values(filter7).some((value) => value !== void 0);
     const include3 = {
       type: "include",
       file,
       literal,
       lang,
-      caption: (_p = data.options) === null || _p === void 0 ? void 0 : _p.caption,
-      filter: Object.keys(filter7).length > 0 ? filter7 : void 0,
+      caption: caption3,
+      filter: usesFilter ? filter7 : void 0,
       ...opts
     };
     addCommonDirectiveOptions(data, include3);
@@ -282658,7 +282809,8 @@ var genIndexDirective = {
       } else {
         children.push({
           type: "heading",
-          depth: 1,
+          depth: 2,
+          enumerated: false,
           children: parsedArg
         });
       }
@@ -286150,6 +286302,61 @@ var divDirective = {
   }
 };
 
+// ../myst-directives/dist/toc.js
+var CONTEXTS = ["project", "page", "section"];
+var tocDirective = {
+  name: "toc",
+  doc: "Inserts table of contents in the page. This may be for the project (each page has an entry), the current page (each heading has an entry), or the current section (only headings in the section have an entry).",
+  alias: ["tableofcontents", "table-of-contents", "toctree", "contents"],
+  arg: {
+    type: "myst",
+    doc: "Heading to be included with table of contents"
+  },
+  options: {
+    context: {
+      type: String,
+      doc: "Table of Contents context; one of project, page, or section",
+      alias: ["kind"]
+    },
+    depth: {
+      type: Number,
+      doc: "Number of levels to include in Table of Contents; by default, all levels will be included",
+      alias: ["maxdepth"]
+    },
+    ...commonDirectiveOptions("toc")
+  },
+  run(data, vfile2) {
+    var _a6, _b, _c;
+    let context = ((_a6 = data.options) === null || _a6 === void 0 ? void 0 : _a6.context) ? data.options.context : data.name === "contents" ? "section" : "project";
+    if (!CONTEXTS.includes(context)) {
+      fileError(vfile2, `Unknown context for ${data.name} directive: ${context}`);
+      context = "project";
+    }
+    let depth = (_b = data.options) === null || _b === void 0 ? void 0 : _b.depth;
+    if (depth != null && depth < 1) {
+      fileError(vfile2, `Table of Contents 'depth' must be a number greater than 0`);
+      depth = void 0;
+    }
+    const children = [];
+    if (data.arg) {
+      const parsedArg = data.arg;
+      if (((_c = parsedArg[0]) === null || _c === void 0 ? void 0 : _c.type) === "heading") {
+        children.push(...parsedArg);
+      } else {
+        children.push({
+          type: "heading",
+          depth: 2,
+          enumerated: false,
+          children: parsedArg
+        });
+      }
+    }
+    const toc = { type: "toc", kind: context, depth, children };
+    addCommonDirectiveOptions(data, toc);
+    return [toc];
+  }
+};
+
 // ../myst-directives/dist/index.js
 var defaultDirectives = [
   admonitionDirective,
@@ -286177,7 +286384,8 @@ var defaultDirectives = [
   rawDirective,
   rawLatexDirective,
   rawTypstDirective,
-  divDirective
+  divDirective,
+  tocDirective
 ];
 
 // ../myst-roles/dist/abbreviation.js
@@ -289547,7 +289755,7 @@ var import_node_path16 = __toESM(require("path"), 1);
 var import_nbtx = __toESM(require_cjs2(), 1);
 
 // ../myst-cli/dist/version.js
-var version2 = "1.3.23";
+var version2 = "1.3.25";
 var version_default2 = version2;
 
 // ../myst-cli/dist/utils/headers.js
@@ -300032,6 +300240,9 @@ var Domains;
 var import_node_fs24 = __toESM(require("fs"), 1);
 var import_node_path29 = __toESM(require("path"), 1);
 
+// ../myst-cli/dist/spec-version.js
+var SPEC_VERSION = 1;
+
 // ../myst-cli/dist/build/site/template.js
 var import_node_fs22 = __toESM(require("fs"), 1);
 var import_node_path26 = require("path");
@@ -301413,6 +301624,71 @@ async function collectExportOptions(session, files, formats, opts) {
   return filterAndMakeUnique(exportOptionsList);
 }
 
+// ../myst-cli/dist/build/utils/projectManifest.js
+async function manifestPagesFromProject(session, projectPath) {
+  const state = session.store.getState();
+  const proj = selectors_exports.selectLocalProject(state, projectPath);
+  if (!proj)
+    return [];
+  const cache = castSession(session);
+  const pages = await Promise.all(proj.pages.map(async (page) => {
+    var _a6, _b, _c, _d2, _e, _f, _g, _h, _j, _k;
+    if ("file" in page) {
+      const fileInfo3 = selectors_exports.selectFileInfo(state, page.file);
+      const title = fileInfo3.title || fileTitle(page.file);
+      const short_title = (_a6 = fileInfo3.short_title) !== null && _a6 !== void 0 ? _a6 : void 0;
+      const description = (_b = fileInfo3.description) !== null && _b !== void 0 ? _b : "";
+      const thumbnail = (_c = fileInfo3.thumbnail) !== null && _c !== void 0 ? _c : "";
+      const thumbnailOptimized = (_d2 = fileInfo3.thumbnailOptimized) !== null && _d2 !== void 0 ? _d2 : "";
+      const banner = (_e = fileInfo3.banner) !== null && _e !== void 0 ? _e : "";
+      const bannerOptimized = (_f = fileInfo3.bannerOptimized) !== null && _f !== void 0 ? _f : "";
+      const date = (_g = fileInfo3.date) !== null && _g !== void 0 ? _g : "";
+      const tags = (_h = fileInfo3.tags) !== null && _h !== void 0 ? _h : [];
+      const { slug, level, file } = page;
+      const { frontmatter } = (_k = (_j = cache.$getMdast(file)) === null || _j === void 0 ? void 0 : _j.post) !== null && _k !== void 0 ? _k : {};
+      const projectPage = {
+        slug,
+        title,
+        short_title,
+        description,
+        date,
+        thumbnail,
+        thumbnailOptimized,
+        banner,
+        bannerOptimized,
+        tags,
+        level,
+        enumerator: frontmatter === null || frontmatter === void 0 ? void 0 : frontmatter.enumerator
+      };
+      return projectPage;
+    }
+    return { ...page };
+  }));
+  return pages;
+}
+function manifestTitleFromProject(session, projectPath) {
+  const state = session.store.getState();
+  const projConfig = selectors_exports.selectLocalProjectConfig(state, projectPath);
+  if (projConfig === null || projConfig === void 0 ? void 0 : projConfig.title)
+    return projConfig.title;
+  const proj = selectors_exports.selectLocalProject(state, projectPath);
+  if (!proj)
+    return "Untitled";
+  const projectFileInfo = selectors_exports.selectFileInfo(session.store.getState(), proj.file);
+  return projectFileInfo.title || proj.index || "Untitled";
+}
+function indexFrontmatterFromProject(session, projectPath) {
+  var _a6, _b;
+  const state = session.store.getState();
+  const cache = castSession(session);
+  const proj = selectors_exports.selectLocalProject(state, projectPath);
+  if (!proj)
+    return {};
+  const { file } = proj;
+  const { frontmatter } = (_b = (_a6 = cache.$getMdast(file)) === null || _a6 === void 0 ? void 0 : _a6.post) !== null && _b !== void 0 ? _b : {};
+  return frontmatter !== null && frontmatter !== void 0 ? frontmatter : {};
+}
+
 // ../myst-cli/dist/build/site/manifest.js
 async function resolvePageExports(session, file) {
   const exports2 = (await collectExportOptions(session, [file], [
@@ -301479,7 +301755,6 @@ async function resolvePageDownloads(session, file, projectPath) {
   return resolvedDownloads;
 }
 async function localToManifestProject(session, projectPath, projectSlug) {
-  var _a6, _b;
   if (!projectPath)
     return null;
   const state = session.store.getState();
@@ -301487,43 +301762,9 @@ async function localToManifestProject(session, projectPath, projectSlug) {
   const proj = selectors_exports.selectLocalProject(state, projectPath);
   if (!proj)
     return null;
-  const { index: index4, file: indexFile } = proj;
+  const { index: index4 } = proj;
   const projectFileInfo = selectors_exports.selectFileInfo(state, proj.file);
-  const projectTitle = (projConfig === null || projConfig === void 0 ? void 0 : projConfig.title) || projectFileInfo.title || proj.index;
-  const cache = castSession(session);
-  const pages = await Promise.all(proj.pages.map(async (page) => {
-    var _a7, _b2, _c, _d2, _e, _f, _g, _h, _j, _k;
-    if ("file" in page) {
-      const fileInfo3 = selectors_exports.selectFileInfo(state, page.file);
-      const title = fileInfo3.title || fileTitle(page.file);
-      const short_title = (_a7 = fileInfo3.short_title) !== null && _a7 !== void 0 ? _a7 : void 0;
-      const description = (_b2 = fileInfo3.description) !== null && _b2 !== void 0 ? _b2 : "";
-      const thumbnail2 = (_c = fileInfo3.thumbnail) !== null && _c !== void 0 ? _c : "";
-      const thumbnailOptimized = (_d2 = fileInfo3.thumbnailOptimized) !== null && _d2 !== void 0 ? _d2 : "";
-      const banner2 = (_e = fileInfo3.banner) !== null && _e !== void 0 ? _e : "";
-      const bannerOptimized = (_f = fileInfo3.bannerOptimized) !== null && _f !== void 0 ? _f : "";
-      const date = (_g = fileInfo3.date) !== null && _g !== void 0 ? _g : "";
-      const tags = (_h = fileInfo3.tags) !== null && _h !== void 0 ? _h : [];
-      const { slug, level, file } = page;
-      const { frontmatter: frontmatter2 } = (_k = (_j = cache.$getMdast(file)) === null || _j === void 0 ? void 0 : _j.post) !== null && _k !== void 0 ? _k : {};
-      const projectPage = {
-        slug,
-        title,
-        short_title,
-        description,
-        date,
-        thumbnail: thumbnail2,
-        thumbnailOptimized,
-        banner: banner2,
-        bannerOptimized,
-        tags,
-        level,
-        enumerator: frontmatter2 === null || frontmatter2 === void 0 ? void 0 : frontmatter2.enumerator
-      };
-      return projectPage;
-    }
-    return { ...page };
-  }));
+  const pages = await manifestPagesFromProject(session, projectPath);
   const projFrontmatter = projConfig ? filterKeys(projConfig, PROJECT_FRONTMATTER_KEYS) : {};
   const projConfigFile = selectors_exports.selectLocalConfigFile(state, projectPath);
   const exports2 = projConfigFile ? await resolvePageExports(session, projConfigFile) : [];
@@ -301531,7 +301772,7 @@ async function localToManifestProject(session, projectPath, projectSlug) {
   const parts = resolveFrontmatterParts(session, projFrontmatter);
   const banner = await transformBanner(session, import_node_path29.default.join(projectPath, "myst.yml"), projFrontmatter, session.publicPath(), { altOutputFolder: "/", webp: true });
   const thumbnail = await transformThumbnail(session, null, import_node_path29.default.join(projectPath, "myst.yml"), projFrontmatter, session.publicPath(), { altOutputFolder: "/", webp: true });
-  const { frontmatter } = (_b = (_a6 = cache.$getMdast(indexFile)) === null || _a6 === void 0 ? void 0 : _a6.post) !== null && _b !== void 0 ? _b : {};
+  const frontmatter = indexFrontmatterFromProject(session, projectPath);
   return {
     ...projFrontmatter,
     // TODO: a null in the project frontmatter should not fall back to index page
@@ -301544,7 +301785,7 @@ async function localToManifestProject(session, projectPath, projectSlug) {
     downloads,
     parts,
     bibliography: projFrontmatter.bibliography || [],
-    title: projectTitle || "Untitled",
+    title: manifestTitleFromProject(session, projectPath),
     slug: projectSlug,
     index: index4,
     enumerator: frontmatter === null || frontmatter === void 0 ? void 0 : frontmatter.enumerator,
@@ -301659,9 +301900,10 @@ async function getSiteManifest(session, opts) {
   validatedFrontmatter.options = resolvedOptions;
   const parts = resolveFrontmatterParts(session, validatedFrontmatter);
   const manifest = {
+    version: SPEC_VERSION,
+    myst: version_default2,
     ...validatedFrontmatter,
     parts,
-    myst: version_default2,
     nav: nav || [],
     actions: actions || [],
     projects: siteProjects
@@ -304300,7 +304542,7 @@ async function transformMdast(session, opts) {
     rendererFiles.push(...localFiles);
   }
   const fileCitationRenderer = combineCitationRenderers(cache, ...rendererFiles);
-  if (execute) {
+  if (execute && !frontmatter.skip_execution) {
     const cachePath2 = import_node_path39.default.join(session.buildPath(), "execute");
     await kernelExecutionTransform(mdast2, vfile2, {
       basePath: session.sourcePath(),
@@ -304360,8 +304602,8 @@ async function transformMdast(session, opts) {
   if (!watchMode)
     log.info(toc(`\u{1F4D6} Built ${file} in %s.`));
 }
-async function postProcessMdast(session, { file, checkLinks, pageReferenceStates, extraLinkTransformers }) {
-  var _a6;
+async function postProcessMdast(session, { file, checkLinks, pageReferenceStates, extraLinkTransformers, site }) {
+  var _a6, _b, _c;
   const toc = tic();
   const { log } = session;
   const cache = castSession(session);
@@ -304373,6 +304615,21 @@ async function postProcessMdast(session, { file, checkLinks, pageReferenceStates
   const { mdast: mdast2, dependencies, frontmatter } = mdastPost;
   const state = new MultiPageReferenceResolver(pageReferenceStates, file, vfile2);
   const externalReferences = Object.values(cache.$externalReferences);
+  const storeState = session.store.getState();
+  const projectPath = selectors_exports.selectCurrentProjectPath(storeState);
+  const siteConfig = selectors_exports.selectCurrentSiteConfig(storeState);
+  const projectSlug = (_b = (_a6 = siteConfig === null || siteConfig === void 0 ? void 0 : siteConfig.projects) === null || _a6 === void 0 ? void 0 : _a6.find((proj) => proj.path === projectPath)) === null || _b === void 0 ? void 0 : _b.slug;
+  if (site) {
+    buildTocTransform(mdast2, vfile2, projectPath ? [
+      {
+        title: manifestTitleFromProject(session, projectPath),
+        level: 1,
+        slug: "",
+        enumerator: indexFrontmatterFromProject(session, projectPath).enumerator
+      },
+      ...await manifestPagesFromProject(session, projectPath)
+    ] : void 0, projectSlug);
+  }
   const transformers = [
     ...extraLinkTransformers || [],
     new WikiTransformer(),
@@ -304396,7 +304653,7 @@ async function postProcessMdast(session, { file, checkLinks, pageReferenceStates
   await transformMystXRefs(session, vfile2, mdast2, frontmatter);
   await embedTransform(session, mdast2, file, dependencies, state);
   const pipe = unified();
-  (_a6 = session.plugins) === null || _a6 === void 0 ? void 0 : _a6.transforms.forEach((t2) => {
+  (_c = session.plugins) === null || _c === void 0 ? void 0 : _c.transforms.forEach((t2) => {
     if (t2.stage !== "project")
       return;
     pipe.use(t2.plugin, void 0, pluginUtils);
@@ -304807,6 +305064,7 @@ async function writeFile(session, { file, pageSlug, projectSlug, projectPath })
   const parts = resolveFrontmatterParts(session, frontmatter);
   const frontmatterWithExports = { ...frontmatter, exports: exports2, downloads, parts };
   const mystData = {
+    version: SPEC_VERSION,
     kind,
     sha256,
     slug,
@@ -304857,7 +305115,8 @@ async function fastProcessFile(session, { file, pageSlug, projectPath, projectSl
     return postProcessMdast(session, {
       file: f3,
       pageReferenceStates,
-      extraLinkTransformers
+      extraLinkTransformers,
+      site: true
     });
   }));
   await Promise.all([...pages.map((p5) => p5.file), ...fileParts].map(async (f3) => {
@@ -304869,7 +305128,7 @@ async function fastProcessFile(session, { file, pageSlug, projectPath, projectSl
         imageAltOutputFolder: imageAltOutputFolder !== null && imageAltOutputFolder !== void 0 ? imageAltOutputFolder : "/",
         imageExtensions: imageExtensions !== null && imageExtensions !== void 0 ? imageExtensions : WEB_IMAGE_EXTENSIONS,
         optimizeWebp: true,
-        processThumbnail: true,
+        processThumbnail: f3 === file,
         maxSizeWebp
       });
     }
@@ -304937,7 +305196,8 @@ async function processProject(session, siteProject, opts) {
     file: page.file,
     checkLinks: checkLinks || strict,
     pageReferenceStates,
-    extraLinkTransformers
+    extraLinkTransformers,
+    site: true
   })));
   if (writeFiles) {
     await Promise.all(pagesToTransform.map(async (page) => {
@@ -309540,7 +309800,7 @@ var caption2 = (state, node3) => {
 };
 function getFootnoteNumber(node3) {
   var _a6;
-  return (_a6 = node3.number) !== null && _a6 !== void 0 ? _a6 : Number(node3.identifier);
+  return (_a6 = Number.parseInt(node3.enumerator, 10)) !== null && _a6 !== void 0 ? _a6 : Number(node3.identifier);
 }
 var footnoteDefinition = (state, node3) => {
   const { children, current: current2 } = state;
@@ -318229,7 +318489,7 @@ function rewriteAssetsFolder(directory, baseurl) {
     if (![".html", ".js", ".json"].includes(import_node_path57.default.extname(file)))
       return;
     const data = import_fs_extra.default.readFileSync(file).toString();
-    const modified = data.replace(new RegExp(`\\/${ASSETS_FOLDER}\\/`, "g"), `${baseurl || ""}/build/`).replace('href="/favicon.ico"', `href="${baseurl || ""}/favicon.ico"`);
+    const modified = data.replace(new RegExp(`\\/${ASSETS_FOLDER}\\/`, "g"), `${baseurl || ""}/build/`).replace('href="/favicon.ico"', `href="${baseurl || ""}/favicon.ico"`).replace('href="/myst-theme.css"', `href="${baseurl || ""}/myst-theme.css"`);
     import_fs_extra.default.writeFileSync(file, modified);
   });
 }
@@ -325347,7 +325607,7 @@ var TOCTreeOptions = z.object({
   caption: z.string(),
   hidden: z.boolean(),
   maxdepth: z.number(),
-  numberted: z.boolean(),
+  numbered: z.boolean(),
   reversed: z.boolean(),
   titlesonly: z.boolean()
 }).partial();
@@ -325802,6 +326062,7 @@ async function upgradeGlossary(documentLines) {
 
 // ../myst-cli/dist/init/jupyter-book/upgrade.js
 async function upgradeJupyterBook(session, configFile) {
+  var _a6, _b;
   const config3 = {
     version: 1,
     project: {}
@@ -325815,14 +326076,19 @@ async function upgradeJupyterBook(session, configFile) {
     session.log.info(`Migrating Jupyter Book configuration to ${source_default.blue("myst.yml")}`);
     ({ site: config3.site, project: config3.project } = upgradeConfig(configData2));
   }
-  if (await fsExists("_toc.yml")) {
-    const tocContent = await import_promises4.default.readFile("_toc.yml", { encoding: "utf-8" });
-    const tocData = validateSphinxExternalTOC(js_yaml_default.load(tocContent));
-    if (defined2(tocData)) {
-      session.log.info(`Migrating TOC to ${source_default.blue("myst.yml")}`);
-      config3.project.toc = upgradeTOC(session, tocData);
-    }
+  if (!await fsExists("_toc.yml")) {
+    throw new Error(`${source_default.blue("_toc.yml")} is a required Jupyter Book configuration file`);
+  }
+  const tocContent = await import_promises4.default.readFile("_toc.yml", { encoding: "utf-8" });
+  const tocData = validateSphinxExternalTOC(js_yaml_default.load(tocContent));
+  if (defined2(tocData)) {
+    session.log.info(`Migrating TOC to ${source_default.blue("myst.yml")}`);
+    config3.project.toc = upgradeTOC(session, tocData);
   }
+  config3.site = (_a6 = config3.site) !== null && _a6 !== void 0 ? _a6 : {};
+  config3.site.options = (_b = config3.site.options) !== null && _b !== void 0 ? _b : {};
+  session.log.debug(source_default.dim(`Setting ${source_default.blue("site.options.folders")} to ${source_default.blue("true")}`));
+  config3.site.options.folders = true;
   await upgradeProjectSyntax(session);
   await import_promises4.default.writeFile(configFile, js_yaml_default.dump(config3));
   await import_promises4.default.rename("_config.yml", "._config.yml.bak");
@@ -326003,6 +326269,7 @@ You can start the ${readableName()} web server later with:`), source_default.bol
 
 // ../myst-cli/dist/plugins.js
 var import_node_fs44 = __toESM(require("fs"), 1);
+var import_node_url3 = require("url");
 
 // ../myst-cli/dist/executablePlugin.js
 var import_node_child_process2 = require("child_process");
@@ -326144,10 +326411,11 @@ async function loadPlugins(session) {
   }
   session.log.debug(`Loading plugins: "${configPlugins.map((info) => `${info.path} (${info.type})`).join('", "')}"`);
   const modules = await Promise.all(configPlugins.map(async (info) => {
+    var _a6, _b;
     const { type: type2, path: path44 } = info;
     switch (type2) {
       case "executable": {
-        if (!import_node_fs44.default.statSync(path44).isFile) {
+        if (!((_a6 = import_node_fs44.default.statSync(path44, { throwIfNoEntry: false })) === null || _a6 === void 0 ? void 0 : _a6.isFile())) {
           addWarningForFile(session, path44, `Unknown plugin "${path44}", it must be an executable file`, "error", {
             ruleId: RuleId.pluginLoads
           });
@@ -326171,15 +326439,16 @@ async function loadPlugins(session) {
         return { path: path44, module: { plugin: plugin5 } };
       }
       case "javascript": {
-        if (!import_node_fs44.default.statSync(path44).isFile || !path44.endsWith(".mjs")) {
+        if (!((_b = import_node_fs44.default.statSync(path44, { throwIfNoEntry: false })) === null || _b === void 0 ? void 0 : _b.isFile()) || !path44.endsWith(".mjs")) {
           addWarningForFile(session, path44, `Unknown plugin "${path44}", it must be an mjs file`, "error", {
             ruleId: RuleId.pluginLoads
           });
           return null;
         }
         let module2;
+        const pathURL = (0, import_node_url3.pathToFileURL)(path44);
         try {
-          module2 = await import(path44);
+          module2 = await import(pathURL.toString());
         } catch (error) {
           session.log.debug(`
 
@@ -326874,7 +327143,7 @@ var AbortError2 = class extends RequestError {
 var import_node_process8 = __toESM(require("process"), 1);
 var import_node_buffer4 = require("buffer");
 var import_node_stream6 = require("stream");
-var import_node_url5 = require("url");
+var import_node_url6 = require("url");
 var import_node_http4 = __toESM(require("http"), 1);
 
 // ../../node_modules/@szmarczak/http-timer/dist/source/index.js
@@ -326984,7 +327253,7 @@ var source_default5 = timer;
 
 // ../../node_modules/cacheable-request/dist/index.js
 var import_node_events2 = __toESM(require("events"), 1);
-var import_node_url3 = __toESM(require("url"), 1);
+var import_node_url4 = __toESM(require("url"), 1);
 var import_node_crypto5 = __toESM(require("crypto"), 1);
 var import_node_stream5 = __toESM(require("stream"), 1);
 
@@ -327313,10 +327582,10 @@ var CacheableRequest = class {
     this.request = () => (options, cb) => {
       let url;
       if (typeof options === "string") {
-        url = normalizeUrlObject(import_node_url3.default.parse(options));
+        url = normalizeUrlObject(import_node_url4.default.parse(options));
         options = {};
-      } else if (options instanceof import_node_url3.default.URL) {
-        url = normalizeUrlObject(import_node_url3.default.parse(options.toString()));
+      } else if (options instanceof import_node_url4.default.URL) {
+        url = normalizeUrlObject(import_node_url4.default.parse(options.toString()));
         options = {};
       } else {
         const [pathname, ...searchParts] = (options.path ?? "").split("?");
@@ -327334,7 +327603,7 @@ var CacheableRequest = class {
       };
       options.headers = Object.fromEntries(entries(options.headers).map(([key3, value]) => [key3.toLowerCase(), value]));
       const ee = new import_node_events2.default();
-      const normalizedUrlString = normalizeUrl(import_node_url3.default.format(url), {
+      const normalizedUrlString = normalizeUrl(import_node_url4.default.format(url), {
         stripWWW: false,
         removeTrailingSlash: false,
         stripAuthentication: false
@@ -328069,7 +328338,7 @@ var calculate_retry_delay_default = calculateRetryDelay;
 // ../../node_modules/got/dist/source/core/options.js
 var import_node_process7 = __toESM(require("process"), 1);
 var import_node_util6 = require("util");
-var import_node_url4 = require("url");
+var import_node_url5 = require("url");
 var import_node_tls = require("tls");
 var import_node_http3 = __toESM(require("http"), 1);
 var import_node_https2 = __toESM(require("https"), 1);
@@ -328614,7 +328883,7 @@ var defaultInternals = {
       const next = parsed.find((entry) => entry.parameters.rel === "next" || entry.parameters.rel === '"next"');
       if (next) {
         return {
-          url: new import_node_url4.URL(next.reference, response.url)
+          url: new import_node_url5.URL(next.reference, response.url)
         };
       }
       return false;
@@ -328655,7 +328924,7 @@ var cloneInternals = (internals) => {
       beforeRetry: [...hooks.beforeRetry],
       afterResponse: [...hooks.afterResponse]
     },
-    searchParams: internals.searchParams ? new import_node_url4.URLSearchParams(internals.searchParams) : void 0,
+    searchParams: internals.searchParams ? new import_node_url5.URLSearchParams(internals.searchParams) : void 0,
     pagination: { ...internals.pagination }
   };
   if (result.url !== void 0) {
@@ -329106,7 +329375,7 @@ var Options2 = class {
       throw new Error("`url` must not start with a slash");
     }
     const urlString = `${this.prefixUrl}${value.toString()}`;
-    const url = new import_node_url4.URL(urlString);
+    const url = new import_node_url5.URL(urlString);
     this._internals.url = url;
     if (url.protocol === "unix:") {
       url.href = `http://unix${url.pathname}${url.search}`;
@@ -329240,7 +329509,7 @@ var Options2 = class {
       return this._internals.url.searchParams;
     }
     if (this._internals.searchParams === void 0) {
-      this._internals.searchParams = new import_node_url4.URLSearchParams();
+      this._internals.searchParams = new import_node_url5.URLSearchParams();
     }
     return this._internals.searchParams;
   }
@@ -329257,12 +329526,12 @@ var Options2 = class {
     const searchParameters = this.searchParams;
     let updated;
     if (dist_default5.string(value)) {
-      updated = new import_node_url4.URLSearchParams(value);
-    } else if (value instanceof import_node_url4.URLSearchParams) {
+      updated = new import_node_url5.URLSearchParams(value);
+    } else if (value instanceof import_node_url5.URLSearchParams) {
       updated = value;
     } else {
       validateSearchParameters(value);
-      updated = new import_node_url4.URLSearchParams();
+      updated = new import_node_url5.URLSearchParams();
       for (const key2 in value) {
         const entry = value[key2];
         if (entry === null) {
@@ -330571,7 +330840,7 @@ var Request3 = class extends import_node_stream6.Duplex {
         }
         const { form } = options;
         options.form = void 0;
-        options.body = new import_node_url5.URLSearchParams(form).toString();
+        options.body = new import_node_url6.URLSearchParams(form).toString();
       } else {
         if (noContentType) {
           headers["content-type"] = "application/json";
@@ -330675,7 +330944,7 @@ var Request3 = class extends import_node_stream6.Duplex {
       }
       try {
         const redirectBuffer = import_node_buffer4.Buffer.from(response.headers.location, "binary").toString();
-        const redirectUrl = new import_node_url5.URL(redirectBuffer, url);
+        const redirectUrl = new import_node_url6.URL(redirectBuffer, url);
         if (!isUnixSocketURL(url) && isUnixSocketURL(redirectUrl)) {
           this._beforeError(new RequestError("Cannot redirect to UNIX socket", {}, this));
           return;