mystmd 1.1.52__py3-none-any.whl → 1.1.53__py3-none-any.whl

mystmd_py/myst.cjs

@@ -100662,14 +100662,14 @@ var require_node_domexception = __commonJS({
 });
 
 // ../../node_modules/fetch-blob/from.js
-var import_node_fs20, import_node_domexception, stat, _path2, _start, _BlobDataItem, BlobDataItem;
+var import_node_fs19, import_node_domexception, stat, _path2, _start, _BlobDataItem, BlobDataItem;
 var init_from = __esm({
   "../../node_modules/fetch-blob/from.js"() {
-    import_node_fs20 = require("fs");
+    import_node_fs19 = require("fs");
     import_node_domexception = __toESM(require_node_domexception(), 1);
     init_file();
     init_fetch_blob();
-    ({ stat } = import_node_fs20.promises);
+    ({ stat } = import_node_fs19.promises);
     _BlobDataItem = class {
       constructor(options) {
         __privateAdd(this, _path2, void 0);
@@ -100696,7 +100696,7 @@ var init_from = __esm({
         if (mtimeMs > this.lastModified) {
           throw new import_node_domexception.default("The requested file could not be read, typically due to permission problems that have occurred after a reference to a file was acquired.", "NotReadableError");
         }
-        yield* (0, import_node_fs20.createReadStream)(__privateGet(this, _path2), {
+        yield* (0, import_node_fs19.createReadStream)(__privateGet(this, _path2), {
           start: __privateGet(this, _start),
           end: __privateGet(this, _start) + this.size - 1
         });
@@ -193279,7 +193279,7 @@ var {
 } = import_index.default;
 
 // src/version.ts
-var version = "1.1.52";
+var version = "1.1.53";
 var version_default = version;
 
 // ../myst-cli/dist/build/build.js
@@ -198434,8 +198434,8 @@ function unnestKernelSpec(pageFrontmatter) {
 }
 
 // ../myst-cli/dist/project/load.js
-var import_node_fs16 = __toESM(require("fs"), 1);
-var import_node_path23 = require("path");
+var import_node_fs15 = __toESM(require("fs"), 1);
+var import_node_path22 = require("path");
 
 // ../myst-cli-utils/node_modules/chalk/source/vendor/ansi-styles/index.js
 var ANSI_BACKGROUND_OFFSET2 = 10;
@@ -235593,6 +235593,9 @@ function codeTransform(mdast2, file, opts) {
     if (node3.lang.toLowerCase().includes("python") && (opts === null || opts === void 0 ? void 0 : opts.transformPython) !== false) {
       node3.lang = "python";
     }
+    if (node3.lang.toLowerCase() === "r" && (opts === null || opts === void 0 ? void 0 : opts.transformR) !== false) {
+      node3.lang = "r";
+    }
   });
 }
 var codePlugin = (opts) => (tree, file) => {
@@ -236255,10 +236258,23 @@ async function includeDirectiveTransform(tree, vfile2, opts) {
   const includeNodes = selectAll("include", tree);
   if (includeNodes.length === 0)
     return;
+  if (!(opts === null || opts === void 0 ? void 0 : opts.stack))
+    opts.stack = [opts.sourceFile];
   await Promise.all(includeNodes.map(async (node3) => {
+    var _a6, _b, _c;
     if (node3.children && node3.children.length > 0)
       return;
-    const rawContent = await opts.loadFile(node3.file);
+    const fullFile = opts.resolveFile(node3.file, opts.sourceFile, vfile2);
+    if (!fullFile)
+      return;
+    if ((_a6 = opts.stack) === null || _a6 === void 0 ? void 0 : _a6.includes(fullFile)) {
+      fileError(vfile2, `Include Directive: "${fullFile}" depends on itself`, {
+        ruleId: RuleId.includeContentLoads,
+        note: [...opts.stack, fullFile].join(" > ")
+      });
+      return;
+    }
+    const rawContent = await opts.loadFile(fullFile);
     if (rawContent == null)
       return;
     const { content: content3, startingLineNumber } = filterIncludedContent(vfile2, node3.filter, rawContent);
@@ -236310,9 +236326,16 @@ async function includeDirectiveTransform(tree, vfile2, opts) {
         children = [container4];
       }
     } else {
-      children = await opts.parseContent(node3.file, content3);
+      children = await opts.parseContent(fullFile, content3, vfile2);
     }
     node3.children = children;
+    if (!((_b = node3.children) === null || _b === void 0 ? void 0 : _b.length))
+      return;
+    await includeDirectiveTransform(node3, vfile2, {
+      ...opts,
+      stack: [...(_c = opts.stack) !== null && _c !== void 0 ? _c : [], fullFile],
+      sourceFile: fullFile
+    });
   }));
 }
 function index3(n, total) {
@@ -240014,6 +240037,7 @@ var import_node_fs3 = __toESM(require("fs"), 1);
 
 // ../citation-js-utils/dist/index.js
 var import_core4 = __toESM(require_lib6(), 1);
+var import_csl = __toESM(require_csl(), 1);
 var import_sanitize_html = __toESM(require_sanitize_html(), 1);
 
 // ../citation-js-utils/node_modules/@citation-js/plugin-bibtex/lib/index.js
@@ -240077,12 +240101,6 @@ var InlineCite;
   InlineCite2["p"] = "p";
   InlineCite2["t"] = "t";
 })(InlineCite || (InlineCite = {}));
-var defaultString = {
-  format: "string",
-  lang: "en-US",
-  type: "html",
-  style: CitationJSStyles.apa
-};
 function yearFromCitation(data) {
   var _a6, _b, _c, _d2, _e, _f;
   let year = (_c = (_b = (_a6 = data.issued) === null || _a6 === void 0 ? void 0 : _a6["date-parts"]) === null || _b === void 0 ? void 0 : _b[0]) === null || _c === void 0 ? void 0 : _c[0];
@@ -240094,6 +240112,7 @@ function yearFromCitation(data) {
   return "n.d.";
 }
 function getInlineCitation(data, kind, opts) {
+  var _a6;
   let authors = data.author;
   if (!authors || authors.length === 0) {
     authors = data.editor;
@@ -240122,7 +240141,7 @@ function getInlineCitation(data, kind, opts) {
   }
   if (authors.length > 2) {
     return [
-      { type: "text", value: `${prefix2}${authors[0].family} ` },
+      { type: "text", value: `${prefix2}${(_a6 = authors[0].family) !== null && _a6 !== void 0 ? _a6 : authors[0].literal} ` },
       { type: "emphasis", children: [{ type: "text", value: "et al." }] },
       { type: "text", value: `${yearPart}` }
     ];
@@ -240164,10 +240183,22 @@ function firstNonDoiUrl(str2, doi2) {
   const matches4 = [...str2.matchAll(URL_REGEX)];
   return matches4.map((match3) => match3[0]).find((match3) => !doi2 || !match3.includes(doi2));
 }
-async function getCitations(bibtex) {
+function parseCitationStyle(style3) {
+  const [styleType, styleFormat] = style3.split("-");
+  if (styleType !== "citation") {
+    throw new Error(`unexpected citation style: ${style3}`);
+  }
+  return styleFormat;
+}
+function parseBibTeX(source2) {
+  return new import_core4.Cite(source2).data;
+}
+function parseCSLJSON(source2) {
+  return (0, import_csl.clean)(source2);
+}
+async function getCitationRenderers(data) {
   const cite3 = new import_core4.Cite();
-  const p5 = await import_core4.Cite.async(bibtex);
-  return Object.fromEntries(p5.data.map((c) => {
+  return Object.fromEntries(data.map((c) => {
     var _a6, _b, _c;
     const matchDoi = (_b = (_a6 = c.URL) === null || _a6 === void 0 ? void 0 : _a6.match(DOI_IN_TEXT)) !== null && _b !== void 0 ? _b : (_c = c.note) === null || _c === void 0 ? void 0 : _c.match(DOI_IN_TEXT);
     if (!c.DOI && matchDoi) {
@@ -240180,16 +240211,32 @@ async function getCitations(bibtex) {
           return getInlineCitation(c, kind, opts);
         },
         render(style3) {
-          return replaceUrlsWithAnchorElement(cleanRef(cite3.set(c).get({ ...defaultString, style: style3 !== null && style3 !== void 0 ? style3 : CitationJSStyles.apa })), c.DOI);
+          return replaceUrlsWithAnchorElement(cleanRef(cite3.set(c).format("bibliography", {
+            template: parseCitationStyle(style3 !== null && style3 !== void 0 ? style3 : CitationJSStyles.apa),
+            format: "html",
+            lang: "en-US"
+          })), c.DOI);
         },
         getDOI() {
           return c.DOI || void 0;
         },
         getURL() {
           var _a7;
-          return (_a7 = firstNonDoiUrl(cleanRef(cite3.set(c).get(defaultString)), c.DOI)) !== null && _a7 !== void 0 ? _a7 : doiUrl(c.DOI);
+          return (_a7 = firstNonDoiUrl(cleanRef(cite3.set(c).format("bibliography", {
+            template: parseCitationStyle(CitationJSStyles.apa),
+            format: "html",
+            lang: "en-US"
+          })), c.DOI)) !== null && _a7 !== void 0 ? _a7 : doiUrl(c.DOI);
+        },
+        cite: c,
+        getLabel() {
+          var _a7;
+          const bibtexObjects = cite3.set(c).format("bibtex", { format: "object" });
+          return (_a7 = bibtexObjects[0]) === null || _a7 === void 0 ? void 0 : _a7.label;
         },
-        cite: c
+        exportBibTeX() {
+          return cite3.set(c).format("bibtex", { format: "text" });
+        }
       }
     ];
   }));
@@ -240221,7 +240268,7 @@ function castSession(session) {
 }
 
 // ../myst-cli/dist/process/citations.js
-async function loadCitations(session, path42) {
+async function loadBibTeXCitationRenderers(session, path42) {
   const toc = tic();
   let data;
   if (isUrl(path42)) {
@@ -240236,7 +240283,8 @@ async function loadCitations(session, path42) {
     session.log.debug(`Loading citations at "${path42}"`);
     data = import_node_fs3.default.readFileSync(path42).toString();
   }
-  const renderer = await getCitations(data);
+  const csl = parseBibTeX(data);
+  const renderer = await getCitationRenderers(csl);
   session.log.debug(toc(`Read ${plural("%s citations(s)", renderer)} from ${path42} in %s.`));
   return renderer;
 }
@@ -240265,8 +240313,8 @@ function combineProjectCitationRenderers(session, projectPath) {
 }
 
 // ../myst-cli/dist/process/file.js
-var import_node_fs12 = __toESM(require("fs"), 1);
-var import_node_path19 = __toESM(require("path"), 1);
+var import_node_fs11 = __toESM(require("fs"), 1);
+var import_node_path18 = __toESM(require("path"), 1);
 var import_node_crypto2 = require("crypto");
 
 // ../tex-to-myst/dist/utils.js
@@ -283620,7 +283668,7 @@ var import_node_path17 = __toESM(require("path"), 1);
 var import_nbtx = __toESM(require_cjs2(), 1);
 
 // ../myst-cli/dist/version.js
-var version2 = "1.1.52";
+var version2 = "1.1.53";
 var version_default2 = version2;
 
 // ../myst-cli/dist/utils/headers.js
@@ -284765,35 +284813,6 @@ async function processNotebook(session, file, content3) {
   return { type: "root", children: items };
 }
 
-// ../myst-cli/dist/transforms/include.js
-var import_node_path18 = __toESM(require("path"), 1);
-var import_node_fs11 = __toESM(require("fs"), 1);
-var makeFileLoader = (session, vfile2, baseFile) => (filename) => {
-  const dir = import_node_path18.default.dirname(baseFile);
-  const fullFile = import_node_path18.default.join(dir, filename);
-  if (!import_node_fs11.default.existsSync(fullFile)) {
-    fileError(vfile2, `Include Directive: Could not find "${fullFile}" in "${baseFile}"`, {
-      ruleId: RuleId.includeContentLoads
-    });
-    return;
-  }
-  session.store.dispatch(watch.actions.addLocalDependency({
-    path: baseFile,
-    dependency: fullFile
-  }));
-  return import_node_fs11.default.readFileSync(fullFile).toString();
-};
-async function includeFilesTransform(session, baseFile, tree, vfile2) {
-  const parseContent = (filename, content3) => {
-    if (filename.toLowerCase().endsWith(".html")) {
-      return [{ type: "html", value: content3 }];
-    }
-    return parseMyst(session, content3, filename).children;
-  };
-  const loadFile2 = makeFileLoader(session, vfile2, baseFile);
-  await includeDirectiveTransform(tree, vfile2, { loadFile: loadFile2, parseContent });
-}
-
 // ../myst-cli/dist/process/file.js
 function checkCache(cache, content3, file) {
   const sha256 = (0, import_node_crypto2.createHash)("sha256").update(content3).digest("hex");
@@ -284811,16 +284830,16 @@ async function loadFile(session, file, projectPath, extension, opts) {
   let success = true;
   let location4 = file;
   if (projectPath) {
-    location4 = `/${import_node_path19.default.relative(projectPath, file)}`;
+    location4 = `/${import_node_path18.default.relative(projectPath, file)}`;
   }
   location4 = location4.replaceAll("\\", "/");
   const vfile2 = new VFile();
   vfile2.path = file;
   try {
-    const ext2 = extension || import_node_path19.default.extname(file).toLowerCase();
+    const ext2 = extension || import_node_path18.default.extname(file).toLowerCase();
     switch (ext2) {
       case ".md": {
-        const content3 = import_node_fs12.default.readFileSync(file).toString();
+        const content3 = import_node_fs11.default.readFileSync(file).toString();
         const { sha256, useCache } = checkCache(cache, content3, file);
         if (useCache)
           break;
@@ -284833,7 +284852,7 @@ async function loadFile(session, file, projectPath, extension, opts) {
         break;
       }
       case ".ipynb": {
-        const content3 = import_node_fs12.default.readFileSync(file).toString();
+        const content3 = import_node_fs11.default.readFileSync(file).toString();
         const { sha256, useCache } = checkCache(cache, content3, file);
         if (useCache)
           break;
@@ -284846,24 +284865,16 @@ async function loadFile(session, file, projectPath, extension, opts) {
         break;
       }
       case ".bib": {
-        const renderer = await loadCitations(session, file);
+        const renderer = await loadBibTeXCitationRenderers(session, file);
         cache.$citationRenderers[file] = renderer;
         break;
       }
       case ".tex": {
-        const content3 = import_node_fs12.default.readFileSync(file).toString();
+        const content3 = import_node_fs11.default.readFileSync(file).toString();
         const { sha256, useCache } = checkCache(cache, content3, file);
         if (useCache)
           break;
         const tex = new TexParser(content3, vfile2);
-        await includeDirectiveTransform(tex.ast, vfile2, {
-          loadFile: makeFileLoader(session, vfile2, file),
-          parseContent: (filename, input3) => {
-            var _a7;
-            const subTex = new TexParser(input3, vfile2);
-            return (_a7 = subTex.ast.children) !== null && _a7 !== void 0 ? _a7 : [];
-          }
-        });
         const frontmatter = validatePageFrontmatter({
           title: toText(tex.data.frontmatter.title),
           short_title: toText(tex.data.frontmatter.short_title),
@@ -284910,9 +284921,9 @@ ${error === null || error === void 0 ? void 0 : error.stack}
   return (_b = cache.$getMdast(file)) === null || _b === void 0 ? void 0 : _b.pre;
 }
 async function bibFilesInDir(session, dir, load2 = true) {
-  const bibFiles = await Promise.all(import_node_fs12.default.readdirSync(dir).map(async (f3) => {
-    if (import_node_path19.default.extname(f3).toLowerCase() === ".bib") {
-      const bibFile = import_node_path19.default.join(dir, f3);
+  const bibFiles = await Promise.all(import_node_fs11.default.readdirSync(dir).map(async (f3) => {
+    if (import_node_path18.default.extname(f3).toLowerCase() === ".bib") {
+      const bibFile = import_node_path18.default.join(dir, f3);
       if (load2)
         await loadFile(session, bibFile);
       return bibFile;
@@ -284940,7 +284951,7 @@ function selectFile(session, file) {
 }
 async function getRawFrontmatterFromFile(session, file, projectPath) {
   const state = session.store.getState();
-  if (projectPath && import_node_path19.default.resolve(file) === selectors_exports.selectLocalConfigFile(state, projectPath)) {
+  if (projectPath && import_node_path18.default.resolve(file) === selectors_exports.selectLocalConfigFile(state, projectPath)) {
     return selectors_exports.selectLocalProjectConfig(state, projectPath);
   }
   const cache = castSession(session);
@@ -284953,8 +284964,8 @@ async function getRawFrontmatterFromFile(session, file, projectPath) {
 }
 
 // ../myst-cli/dist/project/fromPath.js
-var import_node_fs14 = __toESM(require("fs"), 1);
-var import_node_path21 = require("path");
+var import_node_fs13 = __toESM(require("fs"), 1);
+var import_node_path20 = require("path");
 
 // ../../node_modules/glob/node_modules/minimatch/dist/mjs/index.js
 var import_brace_expansion = __toESM(require_brace_expansion(), 1);
@@ -285653,11 +285664,11 @@ var qmarksTestNoExtDot = ([$0]) => {
   return (f3) => f3.length === len && f3 !== "." && f3 !== "..";
 };
 var defaultPlatform = typeof process === "object" && process ? typeof process.env === "object" && process.env && process.env.__MINIMATCH_TESTING_PLATFORM__ || process.platform : "posix";
-var path15 = {
+var path14 = {
   win32: { sep: "\\" },
   posix: { sep: "/" }
 };
-var sep2 = defaultPlatform === "win32" ? path15.win32.sep : path15.posix.sep;
+var sep2 = defaultPlatform === "win32" ? path14.win32.sep : path14.posix.sep;
 minimatch.sep = sep2;
 var GLOBSTAR = Symbol("globstar **");
 minimatch.GLOBSTAR = GLOBSTAR;
@@ -291338,13 +291349,13 @@ var glob = Object.assign(glob_, {
 glob.glob = glob;
 
 // ../myst-cli/dist/project/fromToc.js
-var import_node_fs13 = __toESM(require("fs"), 1);
-var import_node_path20 = require("path");
+var import_node_fs12 = __toESM(require("fs"), 1);
+var import_node_path19 = require("path");
 function pagesFromChapters(session, path42, chapters, pages = [], level = 1, pageSlugs) {
   const filename = tocFile(path42);
-  const { dir } = (0, import_node_path20.parse)(filename);
+  const { dir } = (0, import_node_path19.parse)(filename);
   chapters.forEach((chapter) => {
-    const file = chapter.file ? resolveExtension((0, import_node_path20.join)(dir, chapter.file)) : void 0;
+    const file = chapter.file ? resolveExtension((0, import_node_path19.join)(dir, chapter.file)) : void 0;
     if (file) {
       const { slug } = fileInfo2(file, pageSlugs);
       pages.push({ file, level, slug });
@@ -291363,16 +291374,16 @@ function pagesFromChapters(session, path42, chapters, pages = [], level = 1, pag
 }
 function projectFromToc(session, path42, level = 1) {
   const filename = tocFile(path42);
-  if (!import_node_fs13.default.existsSync(filename)) {
+  if (!import_node_fs12.default.existsSync(filename)) {
     throw new Error(`Could not find TOC "${filename}". Please create a '_toc.yml'.`);
   }
-  const { dir, base: base5 } = (0, import_node_path20.parse)(filename);
+  const { dir, base: base5 } = (0, import_node_path19.parse)(filename);
   const toc = readTOC(session.log, { filename: base5, path: dir });
   const pageSlugs = {};
-  const indexFile = resolveExtension((0, import_node_path20.join)(dir, toc.root));
+  const indexFile = resolveExtension((0, import_node_path19.join)(dir, toc.root));
   if (!indexFile) {
     throw Error(`The table of contents defined in "${tocFile(path42)}" could not find file "${toc.root}" defined as the "root:" page. Please ensure that one of these files is defined:
-- ${VALID_FILE_EXTENSIONS.map((ext2) => (0, import_node_path20.join)(dir, `${toc.root}${ext2}`)).join("\n- ")}
+- ${VALID_FILE_EXTENSIONS.map((ext2) => (0, import_node_path19.join)(dir, `${toc.root}${ext2}`)).join("\n- ")}
 `);
   }
   const { slug } = fileInfo2(indexFile, pageSlugs);
@@ -291415,18 +291426,18 @@ function sortByNumber(a2, b) {
 }
 function projectPagesFromPath(session, path42, level, pageSlugs, opts) {
   const { ignore: ignore3, suppressWarnings } = opts || {};
-  const contents = import_node_fs14.default.readdirSync(path42).filter((file) => !shouldIgnoreFile(session, file)).map((file) => (0, import_node_path21.join)(path42, file)).filter((file) => !ignore3 || !ignore3.includes(file)).sort(sortByNumber);
-  if (session.configFiles.filter((file) => contents.includes((0, import_node_path21.join)(path42, file))).length) {
+  const contents = import_node_fs13.default.readdirSync(path42).filter((file) => !shouldIgnoreFile(session, file)).map((file) => (0, import_node_path20.join)(path42, file)).filter((file) => !ignore3 || !ignore3.includes(file)).sort(sortByNumber);
+  if (session.configFiles.filter((file) => contents.includes((0, import_node_path20.join)(path42, file))).length) {
     session.log.debug(`\u{1F50D} Found config file, ignoring subdirectory: ${path42}`);
     return [];
   }
-  if (contents.includes((0, import_node_path21.join)(path42, "_toc.yml"))) {
+  if (contents.includes((0, import_node_path20.join)(path42, "_toc.yml"))) {
     const prevLevel = level < 2 ? 1 : level - 1;
     try {
       return pagesFromToc(session, path42, prevLevel);
     } catch {
       if (!suppressWarnings) {
-        addWarningForFile(session, (0, import_node_path21.join)(path42, "_toc.yml"), `Invalid table of contents ignored`, "warn", { ruleId: RuleId.validToc });
+        addWarningForFile(session, (0, import_node_path20.join)(path42, "_toc.yml"), `Invalid table of contents ignored`, "warn", { ruleId: RuleId.validToc });
       }
     }
   }
@@ -291455,7 +291466,7 @@ function indexFileFromPages(pages, path42) {
   const files = pages.filter((page) => "file" in page).map((page) => page.file);
   const matcher = (ext2) => {
     let match3;
-    DEFAULT_INDEX_FILENAMES.map((index4) => `${index4}${ext2}`).map((index4) => (0, import_node_path21.join)(path42, index4).toLowerCase()).forEach((index4) => {
+    DEFAULT_INDEX_FILENAMES.map((index4) => `${index4}${ext2}`).map((index4) => (0, import_node_path20.join)(path42, index4).toLowerCase()).forEach((index4) => {
       if (match3)
         return;
       files.forEach((file) => {
@@ -291468,7 +291479,7 @@ function indexFileFromPages(pages, path42) {
   if (!indexFile)
     indexFile = matcher(".md");
   if (!indexFile)
-    [indexFile] = files.filter((file) => (0, import_node_path21.extname)(file) === ".md");
+    [indexFile] = files.filter((file) => (0, import_node_path20.extname)(file) === ".md");
   if (!indexFile)
     indexFile = matcher(".ipynb");
   if (!indexFile)
@@ -291481,15 +291492,15 @@ async function projectFromPath(session, path42, indexFile) {
   if (indexFile) {
     if (!isValidFile(indexFile))
       throw Error(`Index file ${indexFile} has invalid extension; must be ${ext_string}}`);
-    if (!import_node_fs14.default.existsSync(indexFile))
+    if (!import_node_fs13.default.existsSync(indexFile))
       throw Error(`Index file ${indexFile} not found`);
   }
-  const rootConfigYamls = session.configFiles.map((file) => (0, import_node_path21.join)(path42, file));
+  const rootConfigYamls = session.configFiles.map((file) => (0, import_node_path20.join)(path42, file));
   const projectConfig = selectors_exports.selectLocalProjectConfig(session.store.getState(), path42);
   const excludePatterns = (_a6 = projectConfig === null || projectConfig === void 0 ? void 0 : projectConfig.exclude) !== null && _a6 !== void 0 ? _a6 : [];
   const excludeFiles = (await Promise.all(excludePatterns.map(async (pattern) => {
-    const matches4 = await glob(pattern.split(import_node_path21.sep).join("/"));
-    return matches4.map((match3) => match3.split("/").join(import_node_path21.sep)).filter((match3) => isValidFile(match3));
+    const matches4 = await glob(pattern.split(import_node_path20.sep).join("/"));
+    return matches4.map((match3) => match3.split("/").join(import_node_path20.sep)).filter((match3) => isValidFile(match3));
   }))).flat();
   const ignoreFiles = [...rootConfigYamls, ...excludeFiles];
   let implicitIndex = false;
@@ -291512,12 +291523,12 @@ async function projectFromPath(session, path42, indexFile) {
 }
 
 // ../myst-cli/dist/project/toToc.js
-var import_node_fs15 = __toESM(require("fs"), 1);
-var import_node_path22 = require("path");
+var import_node_fs14 = __toESM(require("fs"), 1);
+var import_node_path21 = require("path");
 function getRelativeDocumentLink(file, path42) {
   if (path42 === ".")
     return removeExtension(file);
-  return removeExtension((0, import_node_path22.relative)(path42, file));
+  return removeExtension((0, import_node_path21.relative)(path42, file));
 }
 var GENERATED_TOC_HEADER = `# Table of Contents
 #
@@ -291577,21 +291588,21 @@ function tocFromProject(project, path42 = ".") {
   return toc;
 }
 function writeTocFromProject(project, path42) {
-  const filename = (0, import_node_path22.join)(path42, "_toc.yml");
+  const filename = (0, import_node_path21.join)(path42, "_toc.yml");
   const content3 = `${GENERATED_TOC_HEADER}${js_yaml_default.dump(tocFromProject(project, path42))}`;
-  import_node_fs15.default.writeFileSync(filename, content3);
+  import_node_fs14.default.writeFileSync(filename, content3);
 }
 
 // ../myst-cli/dist/project/load.js
 async function loadProjectFromDisk(session, path42, opts) {
-  path42 = path42 || (0, import_node_path23.resolve)(".");
+  path42 = path42 || (0, import_node_path22.resolve)(".");
   if (!(opts === null || opts === void 0 ? void 0 : opts.reloadProject)) {
     const cachedProject = selectors_exports.selectLocalProject(session.store.getState(), path42);
     if (cachedProject)
       return cachedProject;
   }
   const projectConfig = selectors_exports.selectLocalProjectConfig(session.store.getState(), path42);
-  const file = (0, import_node_path23.join)(path42, session.configFiles[0]);
+  const file = (0, import_node_path22.join)(path42, session.configFiles[0]);
   if (!projectConfig && (opts === null || opts === void 0 ? void 0 : opts.warnOnNoConfig)) {
     addWarningForFile(session, file, `Loading project from path with no config file: ${path42}
 Consider running "myst init --project" in that directory`, "warn", { ruleId: RuleId.projectConfigExists });
@@ -291632,7 +291643,7 @@ Consider running "myst init --project" in that directory`, "warn", { ruleId: Rul
         return true;
       if (isUrl(bib))
         return true;
-      if (import_node_fs16.default.existsSync(bib)) {
+      if (import_node_fs15.default.existsSync(bib)) {
         allBibFiles.push(bib);
         return true;
       }
@@ -291668,20 +291679,20 @@ var import_fs_extra = __toESM(require_lib16(), 1);
 var import_node_path42 = __toESM(require("path"), 1);
 
 // ../myst-cli/dist/build/site/manifest.js
-var import_node_fs23 = __toESM(require("fs"), 1);
-var import_node_path30 = __toESM(require("path"), 1);
+var import_node_fs22 = __toESM(require("fs"), 1);
+var import_node_path29 = __toESM(require("path"), 1);
 
 // ../myst-cli/dist/build/site/template.js
-var import_node_fs21 = __toESM(require("fs"), 1);
-var import_node_path27 = require("path");
+var import_node_fs20 = __toESM(require("fs"), 1);
+var import_node_path26 = require("path");
 
 // ../myst-templates/dist/template.js
-var import_node_fs19 = __toESM(require("fs"), 1);
-var import_node_path26 = require("path");
+var import_node_fs18 = __toESM(require("fs"), 1);
+var import_node_path25 = require("path");
 
 // ../myst-templates/dist/download.js
-var import_node_fs17 = __toESM(require("fs"), 1);
-var import_node_path24 = require("path");
+var import_node_fs16 = __toESM(require("fs"), 1);
+var import_node_path23 = require("path");
 var import_node_crypto3 = require("crypto");
 var import_adm_zip = __toESM(require_adm_zip(), 1);
 var TEMPLATE_YML = "template.yml";
@@ -291739,19 +291750,19 @@ function defaultPath(template, hash, opts) {
       subdirs.push(kind);
     subdirs.push((0, import_node_crypto3.createHash)("sha256").update(template).digest("hex"));
   } else {
-    subdirs.push((0, import_node_path24.join)(...template.split("/")));
+    subdirs.push((0, import_node_path23.join)(...template.split("/")));
   }
-  return (0, import_node_path24.join)(...subdirs);
+  return (0, import_node_path23.join)(...subdirs);
 }
 function resolveInputs(session, opts) {
   let templateUrl;
   let templatePath;
-  if (opts.template && import_node_fs17.default.existsSync(opts.template)) {
-    const { base: base5, dir } = (0, import_node_path24.parse)(opts.template);
-    if (base5 === TEMPLATE_YML || Object.values(KIND_TO_EXT).filter(Boolean).includes((0, import_node_path24.extname)(base5))) {
+  if (opts.template && import_node_fs16.default.existsSync(opts.template)) {
+    const { base: base5, dir } = (0, import_node_path23.parse)(opts.template);
+    if (base5 === TEMPLATE_YML || Object.values(KIND_TO_EXT).filter(Boolean).includes((0, import_node_path23.extname)(base5))) {
       templatePath = dir;
-    } else if (import_node_fs17.default.lstatSync(opts.template).isDirectory()) {
-      if (import_node_fs17.default.existsSync((0, import_node_path24.join)(opts.template, TEMPLATE_YML))) {
+    } else if (import_node_fs16.default.lstatSync(opts.template).isDirectory()) {
+      if (import_node_fs16.default.existsSync((0, import_node_path23.join)(opts.template, TEMPLATE_YML))) {
         templatePath = opts.template;
       }
     }
@@ -291774,26 +291785,26 @@ function resolveInputs(session, opts) {
 }
 async function unnestTemplate(session, path42) {
   var _a6;
-  const content3 = import_node_fs17.default.readdirSync(path42);
+  const content3 = import_node_fs16.default.readdirSync(path42);
   if (content3.includes(TEMPLATE_YML))
     return;
   let nestedPath;
   content3.forEach((dir) => {
-    const templateYmlFile2 = (0, import_node_path24.join)(path42, dir, TEMPLATE_YML);
-    if (!nestedPath && import_node_fs17.default.existsSync(templateYmlFile2)) {
-      nestedPath = (0, import_node_path24.join)(path42, dir);
+    const templateYmlFile2 = (0, import_node_path23.join)(path42, dir, TEMPLATE_YML);
+    if (!nestedPath && import_node_fs16.default.existsSync(templateYmlFile2)) {
+      nestedPath = (0, import_node_path23.join)(path42, dir);
     }
   });
   if (!nestedPath)
     return;
-  const templateYmlFile = (0, import_node_path24.join)(nestedPath, TEMPLATE_YML);
-  import_node_fs17.default.copyFileSync(templateYmlFile, (0, import_node_path24.join)(path42, TEMPLATE_YML));
-  const templateYml = js_yaml_default.load(import_node_fs17.default.readFileSync(templateYmlFile).toString());
+  const templateYmlFile = (0, import_node_path23.join)(nestedPath, TEMPLATE_YML);
+  import_node_fs16.default.copyFileSync(templateYmlFile, (0, import_node_path23.join)(path42, TEMPLATE_YML));
+  const templateYml = js_yaml_default.load(import_node_fs16.default.readFileSync(templateYmlFile).toString());
   if ((_a6 = templateYml.files) === null || _a6 === void 0 ? void 0 : _a6.length) {
     await Promise.all(templateYml.files.map(async (file) => {
-      const resolvedEntry = [...nestedPath.split(import_node_path24.sep), file].join("/");
+      const resolvedEntry = [...nestedPath.split(import_node_path23.sep), file].join("/");
       const matches4 = await glob(resolvedEntry);
-      matches4.map((match3) => match3.split("/").join(import_node_path24.sep)).filter((match3) => !isDirectory(match3)).forEach((match3) => {
+      matches4.map((match3) => match3.split("/").join(import_node_path23.sep)).filter((match3) => !isDirectory(match3)).forEach((match3) => {
         copyFileMaintainPath(session, match3, nestedPath, path42);
       });
     }));
@@ -291841,9 +291852,9 @@ async function downloadAndUnzipTemplate(session, downloadUrl, opts) {
     throw new Error(`Problem downloading template "${downloadUrl}": ${res.status} ${res.statusText}`);
   }
   const { templatePath } = opts;
-  const zipFile = (0, import_node_path24.join)(templatePath, "template.zip");
-  (0, import_node_fs17.mkdirSync)(templatePath, { recursive: true });
-  const fileStream = (0, import_node_fs17.createWriteStream)(zipFile);
+  const zipFile = (0, import_node_path23.join)(templatePath, "template.zip");
+  (0, import_node_fs16.mkdirSync)(templatePath, { recursive: true });
+  const fileStream = (0, import_node_fs16.createWriteStream)(zipFile);
   await new Promise((resolve7, reject) => {
     var _a6, _b;
     (_a6 = res.body) === null || _a6 === void 0 ? void 0 : _a6.pipe(fileStream);
@@ -291986,19 +291997,19 @@ function debugLogger(session) {
 }
 
 // ../myst-templates/dist/validators.js
-var import_node_fs18 = __toESM(require("fs"), 1);
-var import_node_path25 = __toESM(require("path"), 1);
+var import_node_fs17 = __toESM(require("fs"), 1);
+var import_node_path24 = __toESM(require("path"), 1);
 function validateFile(session, input3, opts) {
   const filename = validateString(input3, opts);
   if (!filename)
     return;
   let resolvedFile;
   if (opts.file) {
-    resolvedFile = import_node_path25.default.resolve(import_node_path25.default.dirname(opts.file), filename);
+    resolvedFile = import_node_path24.default.resolve(import_node_path24.default.dirname(opts.file), filename);
   } else {
-    resolvedFile = import_node_path25.default.resolve(filename);
+    resolvedFile = import_node_path24.default.resolve(filename);
   }
-  if (!import_node_fs18.default.existsSync(resolvedFile)) {
+  if (!import_node_fs17.default.existsSync(resolvedFile)) {
     return validationError(`unable to resolve file: ${filename}`, opts);
   }
   const { copyFolder, relativePathFrom } = opts;
@@ -292007,10 +292018,10 @@ function validateFile(session, input3, opts) {
     if (!hashedFile) {
       return validationError(`unable to copy file: ${resolvedFile} -> ${copyFolder}`, opts);
     }
-    resolvedFile = import_node_path25.default.join(copyFolder, hashedFile);
+    resolvedFile = import_node_path24.default.join(copyFolder, hashedFile);
   }
   if (relativePathFrom) {
-    return import_node_path25.default.relative(relativePathFrom, resolvedFile);
+    return import_node_path24.default.relative(relativePathFrom, resolvedFile);
   }
   return resolvedFile;
 }
@@ -292477,8 +292488,8 @@ function validateTemplateYml(session, input3, opts) {
       const fileOpts = incrementOptions(`files.${ind}`, opts);
       const file = validateString(val, fileOpts);
       if (file && opts.templateDir) {
-        const filePath = [...opts.templateDir.split(import_node_path25.default.sep), file].join("/");
-        const matches4 = globSync(filePath).map((match3) => match3.split("/").join(import_node_path25.default.sep));
+        const filePath = [...opts.templateDir.split(import_node_path24.default.sep), file].join("/");
+        const matches4 = globSync(filePath).map((match3) => match3.split("/").join(import_node_path24.default.sep));
         const files = matches4.filter((match3) => !isDirectory(match3));
         if (!matches4.length) {
           validationError(`file does not exist: ${filePath}`, fileOpts);
@@ -292492,12 +292503,12 @@ function validateTemplateYml(session, input3, opts) {
   if (defined(value.template)) {
     const templateOpts = incrementOptions("template", opts);
     const template = validateString(value.template, templateOpts);
-    if (template && output2.kind && import_node_path25.default.extname(template) !== KIND_TO_EXT[output2.kind]) {
-      validationError(`template extension "${import_node_path25.default.extname(template)}" must match kind "${KIND_TO_EXT[output2.kind]}"`, templateOpts);
+    if (template && output2.kind && import_node_path24.default.extname(template) !== KIND_TO_EXT[output2.kind]) {
+      validationError(`template extension "${import_node_path24.default.extname(template)}" must match kind "${KIND_TO_EXT[output2.kind]}"`, templateOpts);
     }
     if (template && opts.templateDir) {
-      const templatePath = [...opts.templateDir.split(import_node_path25.default.sep), template].join("/");
-      const matches4 = globSync(templatePath).map((match3) => match3.split("/").join(import_node_path25.default.sep));
+      const templatePath = [...opts.templateDir.split(import_node_path24.default.sep), template].join("/");
+      const matches4 = globSync(templatePath).map((match3) => match3.split("/").join(import_node_path24.default.sep));
       const files = matches4.filter((match3) => !isDirectory(match3));
       if (!matches4.length) {
         validationError(`template does not exist: ${templatePath}`, templateOpts);
@@ -292537,14 +292548,14 @@ var MystTemplate = class {
     this.kind = opts.kind;
   }
   getTemplateYmlPath() {
-    return (0, import_node_path26.join)(this.templatePath, TEMPLATE_YML);
+    return (0, import_node_path25.join)(this.templatePath, TEMPLATE_YML);
   }
   getTemplateYml() {
     const templateYmlPath = this.getTemplateYmlPath();
-    if (!import_node_fs19.default.existsSync(templateYmlPath)) {
+    if (!import_node_fs18.default.existsSync(templateYmlPath)) {
       throw new Error(`The template yml at "${templateYmlPath}" does not exist`);
     }
-    const content3 = import_node_fs19.default.readFileSync(templateYmlPath).toString();
+    const content3 = import_node_fs18.default.readFileSync(templateYmlPath).toString();
     return js_yaml_default.load(content3);
   }
   getValidatedTemplateYml() {
@@ -292625,7 +292636,7 @@ var MystTemplate = class {
     return validatedDoc;
   }
   async ensureTemplateExistsOnPath(force) {
-    if (!force && import_node_fs19.default.existsSync((0, import_node_path26.join)(this.templatePath, TEMPLATE_YML))) {
+    if (!force && import_node_fs18.default.existsSync((0, import_node_path25.join)(this.templatePath, TEMPLATE_YML))) {
       this.session.log.debug(`Template found: ${this.templatePath}`);
     } else if (!this.templateUrl) {
       throw new Error(`No template on path and no download URL to fetch from: ${this.templatePath}`);
@@ -292648,12 +292659,12 @@ To list valid templates, try the command "myst templates list"`);
     }
   }
   prepare(opts) {
-    if (!import_node_fs19.default.existsSync((0, import_node_path26.join)(this.templatePath, TEMPLATE_YML))) {
-      throw new Error(`The template at "${(0, import_node_path26.join)(this.templatePath, TEMPLATE_YML)}" does not exist`);
+    if (!import_node_fs18.default.existsSync((0, import_node_path25.join)(this.templatePath, TEMPLATE_YML))) {
+      throw new Error(`The template at "${(0, import_node_path25.join)(this.templatePath, TEMPLATE_YML)}" does not exist`);
     }
     const fileOpts = { copyFolder: opts.filesPath };
     if (opts.outputPath) {
-      fileOpts.relativePathFrom = (0, import_node_path26.dirname)(opts.outputPath);
+      fileOpts.relativePathFrom = (0, import_node_path25.dirname)(opts.outputPath);
     }
     const options = this.validateOptions(opts.options, opts.sourceFile, fileOpts);
     const parts = this.validateParts(opts.parts, options, opts.sourceFile);
@@ -292667,17 +292678,17 @@ To list valid templates, try the command "myst templates list"`);
     (_a6 = templateYml.files) === null || _a6 === void 0 ? void 0 : _a6.forEach((file) => {
       if (file === this.getTemplateFilename())
         return;
-      const source2 = (0, import_node_path26.join)(this.templatePath, ...file.split("/"));
-      const dest = (0, import_node_path26.join)(outputDir, ...file.split("/"));
-      if (import_node_fs19.default.existsSync(dest)) {
+      const source2 = (0, import_node_path25.join)(this.templatePath, ...file.split("/"));
+      const dest = (0, import_node_path25.join)(outputDir, ...file.split("/"));
+      if (import_node_fs18.default.existsSync(dest)) {
         if (!(opts === null || opts === void 0 ? void 0 : opts.force)) {
           this.session.log.debug(`Template files ${file} already exists, not copying.`);
           return;
         }
-        import_node_fs19.default.rmSync(dest);
+        import_node_fs18.default.rmSync(dest);
       }
-      import_node_fs19.default.mkdirSync((0, import_node_path26.dirname)(dest), { recursive: true });
-      import_node_fs19.default.copyFileSync(source2, dest);
+      import_node_fs18.default.mkdirSync((0, import_node_path25.dirname)(dest), { recursive: true });
+      import_node_fs18.default.copyFileSync(source2, dest);
     });
   }
 };
@@ -294001,7 +294012,7 @@ async function getMystTemplate(session, opts) {
 }
 async function installSiteTemplate(session, mystTemplate) {
   var _a6, _b;
-  if (import_node_fs21.default.existsSync((0, import_node_path27.join)(mystTemplate.templatePath, "node_modules")))
+  if (import_node_fs20.default.existsSync((0, import_node_path26.join)(mystTemplate.templatePath, "node_modules")))
     return;
   const toc = tic();
   session.log.info("\u2935\uFE0F  Installing web libraries (can take up to 60 s)");
@@ -294012,26 +294023,26 @@ async function installSiteTemplate(session, mystTemplate) {
 }
 
 // ../myst-cli/dist/build/utils/collectExportOptions.js
-var import_node_fs22 = __toESM(require("fs"), 1);
-var import_node_path29 = __toESM(require("path"), 1);
+var import_node_fs21 = __toESM(require("fs"), 1);
+var import_node_path28 = __toESM(require("path"), 1);
 
 // ../myst-cli/dist/build/utils/defaultNames.js
-var import_node_path28 = __toESM(require("path"), 1);
+var import_node_path27 = __toESM(require("path"), 1);
 function getDefaultExportFilename(session, file, projectPath) {
-  const { name: name3 } = import_node_path28.default.parse(file);
+  const { name: name3 } = import_node_path27.default.parse(file);
   const slugFromProject = projectPath ? selectPageSlug(session.store.getState(), projectPath, file) : void 0;
   const slug = slugFromProject || createSlug(name3);
   return slug;
 }
 function getDefaultExportFolder(session, file, format, projectPath) {
-  const subpaths = [projectPath || import_node_path28.default.parse(file).dir, "_build", "exports"];
+  const subpaths = [projectPath || import_node_path27.default.parse(file).dir, "_build", "exports"];
   if (format === ExportFormats.tex) {
     subpaths.push(`${getDefaultExportFilename(session, file, projectPath)}_tex`);
   }
   if (format === ExportFormats.typst) {
     subpaths.push(`${getDefaultExportFilename(session, file, projectPath)}_typst`);
   }
-  return import_node_path28.default.join(...subpaths);
+  return import_node_path27.default.join(...subpaths);
 }
 
 // ../myst-cli/dist/build/utils/collectExportOptions.js
@@ -294071,8 +294082,8 @@ function resolveTemplate(sourceFile, exp, disableTemplate) {
   if (disableTemplate)
     return null;
   if (exp.template) {
-    const resolvedTemplatePath = import_node_path29.default.resolve(import_node_path29.default.dirname(sourceFile), exp.template);
-    if (import_node_fs22.default.existsSync(resolvedTemplatePath)) {
+    const resolvedTemplatePath = import_node_path28.default.resolve(import_node_path28.default.dirname(sourceFile), exp.template);
+    if (import_node_fs21.default.existsSync(resolvedTemplatePath)) {
       return resolvedTemplatePath;
     }
   }
@@ -294086,7 +294097,7 @@ function resolveFormat(vfile2, exp) {
   let suggestedPdfFormat = ExportFormats.pdf;
   let suggestedOutputFormat;
   if (exp.output) {
-    const ext2 = import_node_path29.default.extname(exp.output);
+    const ext2 = import_node_path28.default.extname(exp.output);
     if (!ext2) {
       suggestedPdfFormat = ExportFormats.pdftex;
     } else {
@@ -294099,8 +294110,8 @@ function resolveFormat(vfile2, exp) {
     return ExportFormats.typst;
   if ((_c = exp.template) === null || _c === void 0 ? void 0 : _c.endsWith("-docx"))
     return ExportFormats.docx;
-  if (exp.template && import_node_fs22.default.existsSync(exp.template)) {
-    const templateFiles = import_node_fs22.default.readdirSync(exp.template);
+  if (exp.template && import_node_fs21.default.existsSync(exp.template)) {
+    const templateFiles = import_node_fs21.default.readdirSync(exp.template);
     const templateTexFiles = templateFiles.filter((file) => file.endsWith(".tex"));
     const templateTypFiles = templateFiles.filter((file) => file.endsWith(".typ"));
     if (templateTexFiles.length && !templateTypFiles.length)
@@ -294117,13 +294128,13 @@ function resolveArticles(session, sourceFile, vfile2, exp, projectPath) {
   const { articles, sub_articles } = exp;
   let resolved = { articles, sub_articles };
   if (exp.toc && !resolved.articles && !resolved.sub_articles) {
-    const resolvedToc = import_node_path29.default.resolve(import_node_path29.default.dirname(sourceFile), exp.toc);
+    const resolvedToc = import_node_path28.default.resolve(import_node_path28.default.dirname(sourceFile), exp.toc);
     if (validateTOC(session, resolvedToc)) {
       resolved = resolveArticlesFromTOC(session, exp, resolvedToc, vfile2);
     }
   }
-  if (!resolved.articles && SOURCE_EXTENSIONS.includes(import_node_path29.default.extname(sourceFile))) {
-    resolved.articles = [{ file: import_node_path29.default.resolve(sourceFile) }];
+  if (!resolved.articles && SOURCE_EXTENSIONS.includes(import_node_path28.default.extname(sourceFile))) {
+    resolved.articles = [{ file: import_node_path28.default.resolve(sourceFile) }];
   }
   if (((_a6 = resolved.articles) === null || _a6 === void 0 ? void 0 : _a6.length) === 1 && resolved.articles[0].level == null) {
     resolved.articles[0].level = 0;
@@ -294147,8 +294158,8 @@ function resolveArticles(session, sourceFile, vfile2, exp, projectPath) {
   resolved.articles = (_c = resolved.articles) === null || _c === void 0 ? void 0 : _c.map((article) => {
     if (!article.file)
       return article;
-    const resolvedFile = import_node_path29.default.resolve(import_node_path29.default.dirname(sourceFile), article.file);
-    if (!import_node_fs22.default.existsSync(resolvedFile)) {
+    const resolvedFile = import_node_path28.default.resolve(import_node_path28.default.dirname(sourceFile), article.file);
+    if (!import_node_fs21.default.existsSync(resolvedFile)) {
       fileError(vfile2, `Invalid export article - '${article.file}' does not exist`, {
         ruleId: RuleId.exportArticleExists
       });
@@ -294157,8 +294168,8 @@ function resolveArticles(session, sourceFile, vfile2, exp, projectPath) {
     return { ...article, file: resolvedFile };
   }).filter((article) => !!article);
   resolved.sub_articles = (_d2 = resolved.sub_articles) === null || _d2 === void 0 ? void 0 : _d2.map((file) => {
-    const resolvedFile = import_node_path29.default.resolve(import_node_path29.default.dirname(sourceFile), file);
-    if (!import_node_fs22.default.existsSync(resolvedFile)) {
+    const resolvedFile = import_node_path28.default.resolve(import_node_path28.default.dirname(sourceFile), file);
+    if (!import_node_fs21.default.existsSync(resolvedFile)) {
       fileError(vfile2, `Invalid export sub_article - '${file}' does not exist`, {
         ruleId: RuleId.exportArticleExists
       });
@@ -294183,7 +294194,7 @@ function resolveOutput(session, sourceFile, vfile2, exp, projectPath) {
   var _a6, _b, _c, _d2, _e;
   let output2;
   if (exp.output) {
-    output2 = import_node_path29.default.resolve(import_node_path29.default.dirname(sourceFile), exp.output);
+    output2 = import_node_path28.default.resolve(import_node_path28.default.dirname(sourceFile), exp.output);
   } else {
     output2 = getDefaultExportFolder(session, sourceFile, exp.format, projectPath);
   }
@@ -294194,16 +294205,16 @@ function resolveOutput(session, sourceFile, vfile2, exp, projectPath) {
     fileWarn(vfile2, `ignoring "zip: true" for export of format "${exp.format}"`);
     exp.zip = false;
   }
-  if (!import_node_path29.default.extname(output2)) {
+  if (!import_node_path28.default.extname(output2)) {
     const basename3 = getDefaultExportFilename(session, (_c = (_b = singleArticleWithFile(exp.articles)) === null || _b === void 0 ? void 0 : _b.file) !== null && _c !== void 0 ? _c : sourceFile, projectPath);
     const ext2 = exp.zip ? ".zip" : (_d2 = ALLOWED_EXTENSIONS[exp.format]) === null || _d2 === void 0 ? void 0 : _d2[0];
-    output2 = import_node_path29.default.join(output2, `${basename3}${ext2 !== null && ext2 !== void 0 ? ext2 : ""}`);
+    output2 = import_node_path28.default.join(output2, `${basename3}${ext2 !== null && ext2 !== void 0 ? ext2 : ""}`);
   }
-  if (!((_e = ALLOWED_EXTENSIONS[exp.format]) === null || _e === void 0 ? void 0 : _e.includes(import_node_path29.default.extname(output2)))) {
+  if (!((_e = ALLOWED_EXTENSIONS[exp.format]) === null || _e === void 0 ? void 0 : _e.includes(import_node_path28.default.extname(output2)))) {
     fileError(vfile2, `Output file "${output2}" has invalid extension for export format of "${exp.format}"`, { ruleId: RuleId.exportExtensionCorrect });
     return void 0;
   }
-  if (exp.zip && import_node_path29.default.extname(output2) !== ".zip") {
+  if (exp.zip && import_node_path28.default.extname(output2) !== ".zip") {
     fileWarn(vfile2, `Output file "${output2}" has non-zip extension but "zip: true" is specified; ignoring "zip: true"`, { ruleId: RuleId.exportExtensionCorrect });
   }
   return output2;
@@ -294252,10 +294263,10 @@ function filterAndMakeUnique(exports2) {
     const nMatch = (a2) => a2.filter((e2) => e2.output === exp.output).length;
     if (nMatch(arr) === 1)
       return { ...exp };
-    const { dir, name: name3, ext: ext2 } = import_node_path29.default.parse(exp.output);
+    const { dir, name: name3, ext: ext2 } = import_node_path28.default.parse(exp.output);
     return {
       ...exp,
-      output: import_node_path29.default.join(dir, `${name3}_${nMatch(arr.slice(0, ind))}${ext2}`)
+      output: import_node_path28.default.join(dir, `${name3}_${nMatch(arr.slice(0, ind))}${ext2}`)
     };
   });
 }
@@ -294272,7 +294283,7 @@ async function collectExportOptions(session, files, formats, opts) {
   await Promise.all(sourceFiles.map(async (file) => {
     let fileProjectPath;
     if (!projectPath) {
-      fileProjectPath = findCurrentProjectAndLoad(session, import_node_path29.default.dirname(file));
+      fileProjectPath = findCurrentProjectAndLoad(session, import_node_path28.default.dirname(file));
       if (fileProjectPath)
         await loadProjectFromDisk(session, fileProjectPath);
     } else {
@@ -294298,9 +294309,9 @@ async function resolvePageExports(session, file) {
     ExportFormats.xml,
     ExportFormats.meca
   ], {})).filter((exp) => {
-    return [".docx", ".pdf", ".zip", ".xml"].includes(import_node_path30.default.extname(exp.output));
+    return [".docx", ".pdf", ".zip", ".xml"].includes(import_node_path29.default.extname(exp.output));
   }).filter((exp) => {
-    return import_node_fs23.default.existsSync(exp.output);
+    return import_node_fs22.default.existsSync(exp.output);
   });
   const exportsAsDownloads = exports2.map((exp) => {
     const { format, output: output2 } = exp;
@@ -294309,7 +294320,7 @@ async function resolvePageExports(session, file) {
         ruleId: RuleId.exportFileCopied
       });
     });
-    return { format, filename: import_node_path30.default.basename(output2), url: `/${fileHash}` };
+    return { format, filename: import_node_path29.default.basename(output2), url: `/${fileHash}` };
   });
   return exportsAsDownloads;
 }
@@ -294333,7 +294344,7 @@ async function resolvePageDownloads(session, file, projectPath) {
   const resolvedDownloads = (_a6 = pageFrontmatter === null || pageFrontmatter === void 0 ? void 0 : pageFrontmatter.downloads) === null || _a6 === void 0 ? void 0 : _a6.map((download) => {
     var _a7;
     if (download.id && !expLookup[download.id]) {
-      addWarningForFile(session, file, `Locate download file by export id "${download.id}"`, "error", {
+      addWarningForFile(session, file, `Unable to locate download file by export id "${download.id}"`, "error", {
         ruleId: RuleId.exportFileCopied
       });
       return void 0;
@@ -294399,8 +294410,8 @@ async function localToManifestProject(session, projectPath, projectSlug) {
   const projConfigFile = selectors_exports.selectLocalConfigFile(state, projectPath);
   const exports2 = projConfigFile ? await resolvePageExports(session, projConfigFile) : [];
   const downloads = projConfigFile ? await resolvePageDownloads(session, projConfigFile, projectPath) : void 0;
-  const banner = await transformBanner(session, import_node_path30.default.join(projectPath, "myst.yml"), projFrontmatter, session.publicPath(), { altOutputFolder: "/" });
-  const thumbnail = await transformThumbnail(session, null, import_node_path30.default.join(projectPath, "myst.yml"), projFrontmatter, session.publicPath(), { altOutputFolder: "/" });
+  const banner = await transformBanner(session, import_node_path29.default.join(projectPath, "myst.yml"), projFrontmatter, session.publicPath(), { altOutputFolder: "/" });
+  const thumbnail = await transformThumbnail(session, null, import_node_path29.default.join(projectPath, "myst.yml"), projFrontmatter, session.publicPath(), { altOutputFolder: "/" });
   return {
     ...projFrontmatter,
     // TODO: a null in the project frontmatter should not fall back to index page
@@ -294464,8 +294475,8 @@ function resolveSiteAction(session, action, file, property) {
       static: false
     };
   }
-  const resolvedFile = import_node_path30.default.resolve(import_node_path30.default.dirname(file), action.url);
-  if (!import_node_fs23.default.existsSync(resolvedFile)) {
+  const resolvedFile = import_node_path29.default.resolve(import_node_path29.default.dirname(file), action.url);
+  if (!import_node_fs22.default.existsSync(resolvedFile)) {
     if (action.static) {
       addWarningForFile(session, file, `Could not find static resource at "${action.url}" in ${property}`, "error", { ruleId: RuleId.staticActionFileCopied });
       return void 0;
@@ -294498,12 +294509,12 @@ function resolveSiteAction(session, action, file, property) {
   if (!title) {
     addWarningForFile(session, file, `using filename for title of resource "${action.url}" in ${property}`);
   }
-  const filename = (_a6 = action.filename) !== null && _a6 !== void 0 ? _a6 : import_node_path30.default.basename(resolvedFile);
+  const filename = (_a6 = action.filename) !== null && _a6 !== void 0 ? _a6 : import_node_path29.default.basename(resolvedFile);
   return {
     title: (_b = action.title) !== null && _b !== void 0 ? _b : filename,
     url: `/${fileHash}`,
     filename,
-    format: (_c = action.format) !== null && _c !== void 0 ? _c : EXT_TO_FORMAT[import_node_path30.default.extname(resolvedFile)],
+    format: (_c = action.format) !== null && _c !== void 0 ? _c : EXT_TO_FORMAT[import_node_path29.default.extname(resolvedFile)],
     static: true
   };
 }
@@ -294907,15 +294918,15 @@ var Domains;
 })(Domains || (Domains = {}));
 
 // ../myst-cli/dist/process/loadIntersphinx.js
-var import_node_fs24 = __toESM(require("fs"), 1);
-var import_node_path31 = require("path");
+var import_node_fs23 = __toESM(require("fs"), 1);
+var import_node_path30 = require("path");
 function inventoryCacheFile(session, id, path42) {
   const hashcontent = `${id}${path42}`;
   const filename = `intersphinx-${computeHash(hashcontent)}.inv`;
-  const cacheFolder = (0, import_node_path31.join)(session.buildPath(), "cache");
-  if (!import_node_fs24.default.existsSync(cacheFolder))
-    import_node_fs24.default.mkdirSync(cacheFolder, { recursive: true });
-  return (0, import_node_path31.join)(cacheFolder, filename);
+  const cacheFolder = (0, import_node_path30.join)(session.buildPath(), "cache");
+  if (!import_node_fs23.default.existsSync(cacheFolder))
+    import_node_fs23.default.mkdirSync(cacheFolder, { recursive: true });
+  return (0, import_node_path30.join)(cacheFolder, filename);
 }
 async function loadIntersphinx(session, opts) {
   const state = session.store.getState();
@@ -294937,7 +294948,7 @@ async function loadIntersphinx(session, opts) {
     if (!cache.$externalReferences[key2] || opts.force) {
       const inventory = new Inventory({ id: key2, path: object.url });
       const cachePath = inventoryCacheFile(session, key2, inventory.path);
-      if (import_node_fs24.default.existsSync(cachePath) && !opts.force) {
+      if (import_node_fs23.default.existsSync(cachePath) && !opts.force) {
         const localInventory = new Inventory({ id: key2, path: cachePath });
         session.log.debug(`Loading cached inventory file for ${inventory.path}: ${cachePath}`);
         const toc = tic();
@@ -294971,7 +294982,7 @@ ${error === null || error === void 0 ? void 0 : error.stack}
       return null;
     }
     const cachePath = inventoryCacheFile(session, loader2.id, loader2.path);
-    if (!import_node_fs24.default.existsSync(cachePath) && isUrl(loader2.path)) {
+    if (!import_node_fs23.default.existsSync(cachePath) && isUrl(loader2.path)) {
       session.log.debug(`Saving remote inventory file to cache ${loader2.path}: ${cachePath}`);
       loader2.write(cachePath);
     }
@@ -295237,58 +295248,102 @@ function transformLiftCodeBlocksInJupytext(mdast2) {
 }
 
 // ../myst-cli/dist/transforms/dois.js
-var import_node_fs25 = __toESM(require("fs"), 1);
-var import_node_path32 = require("path");
-function doiBibtexCacheFile(session, normalizedDoi) {
-  const filename = `doi-${computeHash(normalizedDoi)}.bib`;
-  const cacheFolder = (0, import_node_path32.join)(session.buildPath(), "cache");
-  if (!import_node_fs25.default.existsSync(cacheFolder))
-    import_node_fs25.default.mkdirSync(cacheFolder, { recursive: true });
-  return (0, import_node_path32.join)(cacheFolder, filename);
+var import_node_fs24 = __toESM(require("fs"), 1);
+var import_node_path31 = require("path");
+var CSL_JSON_MIMETYPE = "application/vnd.citationstyles.csl+json";
+var BIBTEX_MIMETYPE = "application/x-bibtex";
+function doiCSLJSONCacheFile(session, normalizedDoi) {
+  const filename = `doi-${computeHash(normalizedDoi)}.csl.json`;
+  const cacheFolder = (0, import_node_path31.join)(session.buildPath(), "cache");
+  if (!import_node_fs24.default.existsSync(cacheFolder))
+    import_node_fs24.default.mkdirSync(cacheFolder, { recursive: true });
+  return (0, import_node_path31.join)(cacheFolder, filename);
 }
 function doiResolvesCacheFile(session, normalizedDoi) {
   const filename = `doi-${computeHash(normalizedDoi)}.txt`;
-  const cacheFolder = (0, import_node_path32.join)(session.buildPath(), "cache");
-  if (!import_node_fs25.default.existsSync(cacheFolder))
-    import_node_fs25.default.mkdirSync(cacheFolder, { recursive: true });
-  return (0, import_node_path32.join)(cacheFolder, filename);
+  const cacheFolder = (0, import_node_path31.join)(session.buildPath(), "cache");
+  if (!import_node_fs24.default.existsSync(cacheFolder))
+    import_node_fs24.default.mkdirSync(cacheFolder, { recursive: true });
+  return (0, import_node_path31.join)(cacheFolder, filename);
 }
-async function getDoiOrgBibtex(session, doiString) {
-  const normalizedDoi = doi.normalize(doiString);
-  const url = doi.buildUrl(normalizedDoi);
-  if (!doi.validate(doiString) || !normalizedDoi || !url)
-    return null;
-  const cachePath = doiBibtexCacheFile(session, normalizedDoi);
-  if (import_node_fs25.default.existsSync(cachePath)) {
-    const bibtex2 = import_node_fs25.default.readFileSync(cachePath).toString();
-    session.log.debug(`Loaded cached reference bibtex for doi:${normalizedDoi}`);
-    return bibtex2;
+async function resolveDOIAsBibTeX(session, url) {
+  session.log.debug("Fetching DOI BibTeX from doi.org");
+  const response = await session.fetch(url, {
+    headers: [["Accept", BIBTEX_MIMETYPE]]
+  }).catch(() => {
+    session.log.debug(`Request to ${url} failed.`);
+    return void 0;
+  });
+  if (!response || !response.ok) {
+    session.log.debug(`doi.org fetch failed for ${url}`);
+    return void 0;
   }
-  const toc = tic();
-  session.log.debug("Fetching DOI bibtex from doi.org");
+  const data = await response.text();
+  return parseBibTeX(data);
+}
+async function resolveDOIAsCSLJSON(session, url) {
+  session.log.debug("Fetching DOI CSL JSON from doi.org");
   const response = await session.fetch(url, {
-    headers: [["Accept", "application/x-bibtex"]]
+    headers: [["Accept", CSL_JSON_MIMETYPE]]
   }).catch(() => {
     session.log.debug(`Request to ${url} failed.`);
-    return null;
+    return void 0;
   });
   if (!response || !response.ok) {
-    session.log.debug(`doi.org fetch failed for ${doiString}`);
-    return null;
+    session.log.debug(`doi.org fetch failed for ${url}`);
+    return void 0;
   }
-  const bibtex = await response.text();
-  session.log.debug(toc(`Fetched reference bibtex for doi:${normalizedDoi} in %s`));
-  session.log.debug(`Saving doi bibtex to cache ${cachePath}`);
-  import_node_fs25.default.writeFileSync(cachePath, bibtex);
-  return bibtex;
+  const data = await response.json();
+  return parseCSLJSON([data]);
+}
+async function resolveDoiOrg(session, doiString) {
+  const normalizedDoi = doi.normalize(doiString);
+  const url = doi.buildUrl(doiString);
+  if (!doi.validate(doiString) || !normalizedDoi || !url)
+    return void 0;
+  const cachePath = doiCSLJSONCacheFile(session, normalizedDoi);
+  if (import_node_fs24.default.existsSync(cachePath)) {
+    const cached = import_node_fs24.default.readFileSync(cachePath).toString();
+    session.log.debug(`Loaded cached reference CSL-JSON for doi:${normalizedDoi}`);
+    return JSON.parse(cached);
+  }
+  const toc = tic();
+  let data;
+  try {
+    data = await resolveDOIAsBibTeX(session, url);
+    if (data) {
+      session.log.debug(toc(`Fetched reference BibTeX for doi:${normalizedDoi} in %s`));
+    } else {
+      session.log.debug(`BibTeX not available from doi.org for doi:${normalizedDoi}, trying CSL-JSON`);
+    }
+  } catch (error) {
+    session.log.debug(`BibTeX from doi.org was malformed for doi:${normalizedDoi}, trying CSL-JSON`);
+  }
+  if (!data) {
+    try {
+      data = await resolveDOIAsCSLJSON(session, url);
+      if (data) {
+        session.log.debug(toc(`Fetched reference CSL-JSON for doi:${normalizedDoi} in %s`));
+      } else {
+        session.log.debug(`CSL-JSON not available from doi.org for doi:${normalizedDoi}`);
+      }
+    } catch (error) {
+      session.log.debug(`CSL-JSON from doi.org was malformed for doi:${normalizedDoi}`);
+    }
+  }
+  if (!data)
+    return void 0;
+  session.log.debug(`Saving DOI CSL-JSON to cache ${cachePath}`);
+  import_node_fs24.default.writeFileSync(cachePath, JSON.stringify(data));
+  return data;
 }
 async function doiOrgResolves(session, doiString) {
   const normalizedDoi = doi.normalize(doiString);
-  const url = doi.buildUrl(normalizedDoi);
+  const url = doi.buildUrl(doiString);
   if (!doi.validate(doiString) || !normalizedDoi || !url)
     return false;
   const cachePath = doiResolvesCacheFile(session, normalizedDoi);
-  if (import_node_fs25.default.existsSync(cachePath)) {
+  if (import_node_fs24.default.existsSync(cachePath)) {
     session.log.debug(`Loaded cached resolution result for doi:${normalizedDoi}`);
     return true;
   }
@@ -295304,35 +295359,48 @@ async function doiOrgResolves(session, doiString) {
   }
   session.log.debug(toc(`Resolved doi existence for doi:${normalizedDoi} in %s`));
   session.log.debug(`Saving resolution result to cache ${cachePath}`);
-  import_node_fs25.default.writeFileSync(cachePath, "ok");
+  import_node_fs24.default.writeFileSync(cachePath, "ok");
   return true;
 }
 async function getCitation(session, vfile2, doiString, node3) {
   if (!doi.validate(doiString))
     return null;
-  const bibtex = await getDoiOrgBibtex(session, doiString);
-  if (!bibtex) {
+  const data = await resolveDoiOrg(session, doiString);
+  if (!data) {
     const resolves = await doiOrgResolves(session, doiString);
     const normalizedDoi = doi.normalize(doiString);
     let message;
     let note;
     if (resolves) {
-      message = `No bibtex available from doi.org for doi:${normalizedDoi}`;
-      note = `To resolve this error, visit ${doi.buildUrl(normalizedDoi)} and add citation info to .bib file`;
+      message = `Citation data from doi.org was not available or malformed for doi:${normalizedDoi}`;
+      note = `To resolve this error, visit ${doi.buildUrl(doiString)} and add citation info to local BibTeX file`;
     } else {
-      message = `Could not find DOI from link: ${doiString} as ${normalizedDoi}`;
+      message = `Could not find DOI "${doiString}" from doi.org as doi:${normalizedDoi}`;
+      note = "Please check the DOI and, if correct, add citation info to local BibTeX file";
     }
-    fileWarn(vfile2, message, {
+    fileError(vfile2, message, {
       node: node3,
       ruleId: RuleId.doiLinkValid,
       note
     });
     return null;
   }
-  const renderer = await getCitations(bibtex);
-  const id = Object.keys(renderer)[0];
-  const render3 = renderer[id];
-  return { id, render: render3 };
+  try {
+    const renderer = await getCitationRenderers(data);
+    const id = Object.keys(renderer)[0];
+    const render3 = renderer[id];
+    return { id, render: render3 };
+  } catch (error) {
+    fileError(vfile2, `Citation data from doi.org was malformed, please edit and add to your local references`, {
+      node: node3,
+      ruleId: RuleId.doiLinkValid,
+      note: `Citation data from ${doiString}:
+
+${JSON.stringify(data)}
+`
+    });
+    return null;
+  }
 }
 async function transformLinkedDOIs(session, vfile2, mdast2, doiRenderer, path42) {
   const toc = tic();
@@ -295366,11 +295434,12 @@ async function transformLinkedDOIs(session, vfile2, mdast2, doiRenderer, path42)
           return false;
       }
       doiRenderer[node3.url] = cite3;
-      renderer[cite3.id] = cite3.render;
+      const label = cite3.render.getLabel();
+      renderer[label] = cite3.render;
       const citeNode = node3;
       citeNode.type = "cite";
       citeNode.kind = "narrative";
-      citeNode.label = cite3.id;
+      citeNode.label = label;
       if (doi.validate(toText(citeNode.children))) {
         citeNode.children = [];
       }
@@ -295386,8 +295455,9 @@ async function transformLinkedDOIs(session, vfile2, mdast2, doiRenderer, path42)
           return false;
       }
       doiRenderer[node3.label] = cite3;
-      renderer[cite3.id] = cite3.render;
-      node3.label = cite3.id;
+      const label = cite3.render.getLabel();
+      renderer[label] = cite3.render;
+      node3.label = label;
       return true;
     })
   ]);
@@ -295537,6 +295607,54 @@ function embedTransform(session, mdast2, file, dependencies, state) {
   liftChildren(mdast2, "_lift");
 }
 
+// ../myst-cli/dist/transforms/include.js
+var import_node_path32 = __toESM(require("path"), 1);
+var import_node_fs25 = __toESM(require("fs"), 1);
+var makeFileResolver = (baseFile) => (relativeFile, sourceFile, vfile2) => {
+  const base5 = sourceFile.toLowerCase().endsWith(".tex") ? baseFile : sourceFile;
+  const fullFile = import_node_path32.default.resolve(import_node_path32.default.dirname(base5), relativeFile);
+  if (!import_node_fs25.default.existsSync(fullFile)) {
+    fileError(vfile2, `Include Directive: Could not find "${relativeFile}" relative to "${base5}"`, {
+      ruleId: RuleId.includeContentLoads
+    });
+    return;
+  }
+  return fullFile;
+};
+var makeFileLoader = (session, baseFile) => (fullFile) => {
+  session.store.dispatch(watch.actions.addLocalDependency({
+    path: baseFile,
+    dependency: fullFile
+  }));
+  return import_node_fs25.default.readFileSync(fullFile).toString();
+};
+var makeContentParser = (session) => async (filename, content3, vfile2) => {
+  var _a6;
+  if (filename.toLowerCase().endsWith(".html")) {
+    return [{ type: "html", value: content3 }];
+  }
+  if (filename.toLowerCase().endsWith(".tex")) {
+    const subTex = new TexParser(content3, vfile2);
+    return (_a6 = subTex.ast.children) !== null && _a6 !== void 0 ? _a6 : [];
+  }
+  if (filename.toLowerCase().endsWith(".ipynb")) {
+    const mdast2 = await processNotebook(session, filename, content3);
+    return mdast2.children;
+  }
+  return parseMyst(session, content3, filename).children;
+};
+async function includeFilesTransform(session, baseFile, tree, vfile2) {
+  const parseContent = makeContentParser(session);
+  const loadFile2 = makeFileLoader(session, baseFile);
+  const resolveFile = makeFileResolver(baseFile);
+  await includeDirectiveTransform(tree, vfile2, {
+    resolveFile,
+    loadFile: loadFile2,
+    parseContent,
+    sourceFile: baseFile
+  });
+}
+
 // ../myst-cli/dist/transforms/links.js
 var import_node_fs26 = __toESM(require("fs"), 1);
 var import_node_path33 = __toESM(require("path"), 1);
@@ -299279,24 +299397,6 @@ function cleanOutput(session, output2) {
 // ../myst-cli/dist/build/utils/bibtex.js
 var import_node_fs33 = __toESM(require("fs"), 1);
 var import_node_path47 = __toESM(require("path"), 1);
-function extractBibtex(key2, bibtex) {
-  const match3 = bibtex.match(new RegExp(`@[a-zA-Z]*{${key2}`, "g"));
-  if (!match3)
-    return;
-  const start = bibtex.indexOf(match3[0]);
-  let bracketCount = 0;
-  let ind = start + match3[0].length;
-  while (bibtex[ind] && (bibtex[ind] !== "}" || bracketCount !== 0)) {
-    if (bibtex[ind - 1] && bibtex[ind - 1] !== "\\") {
-      if (bibtex[ind] === "{")
-        bracketCount++;
-      if (bibtex[ind] === "}")
-        bracketCount--;
-    }
-    ind++;
-  }
-  return bibtex[ind] ? bibtex.substring(start, ind + 1) : void 0;
-}
 function writeBibtexFromCitationRenderers(session, output2, content3) {
   const order3 = content3.map(({ references }) => {
     var _a6, _b;
@@ -299308,13 +299408,7 @@ function writeBibtexFromCitationRenderers(session, output2, content3) {
   const citationLookup = {};
   Object.values(cache.$citationRenderers).forEach((renderers) => {
     Object.entries(renderers).forEach(([key2, renderer]) => {
-      var _a6;
-      const bibtexContent2 = renderer.cite._graph.find((item) => {
-        return item.type === "@biblatex/text";
-      });
-      if (bibtexContent2 === null || bibtexContent2 === void 0 ? void 0 : bibtexContent2.data) {
-        citationLookup[key2] = (_a6 = extractBibtex(key2, bibtexContent2.data)) !== null && _a6 !== void 0 ? _a6 : bibtexContent2.data;
-      }
+      citationLookup[key2] = renderer.exportBibTeX();
     });
   });
   const bibtexContent = [];
@@ -300642,10 +300736,10 @@ ${node3.value}
     state.write(`)`);
   },
   embed(node3, state) {
-    state.renderChildren(node3);
+    state.renderChildren(node3, 2);
   },
   include(node3, state) {
-    state.renderChildren(node3);
+    state.renderChildren(node3, 2);
   },
   footnoteReference(node3, state) {
     if (!node3.identifier)