🔧 Fix single file export references by building project files

.changeset/cyan-moles-leave.md

@@ -0,0 +1,5 @@
+---
+'myst-cli': patch
+---
+
+Fix crosslinked content for single file exports

.changeset/lucky-moles-mix.md

@@ -0,0 +1,6 @@
+---
+'myst-directives': patch
+'myst-parser': patch
+---
+
+Remove identifier from embed node

.changeset/poor-toes-work.md

@@ -0,0 +1,5 @@
+---
+'myst-to-tex': patch
+---
+
+Remove {name} template from getting printed into single article exports

.github/workflows/ci.yml

@@ -33,6 +33,7 @@ jobs:
         with:
           fetch-depth: 2
           submodules: recursive
+      - run: sudo apt-get update
       - run: sudo apt-get install -y libxml2-utils
       - name: Setup Node.js environment
         uses: actions/setup-node@v2

packages/myst-cli/src/build/utils/collectExportOptions.ts

@@ -39,7 +39,7 @@ async function prepareExportOptions(
   exportOptions.forEach((exp) => {
     // If no files are specified, use the sourceFile for article
     if (!exp.article && SOURCE_EXTENSIONS.includes(path.extname(sourceFile))) {
-      exp.article = sourceFile;
+      exp.article = path.resolve(sourceFile);
     }
     // Also validate that sub_articles exist
     if (exp.sub_articles) {

packages/myst-cli/src/build/utils/getFileContent.ts

@@ -35,12 +35,14 @@ export async function getFileContent(
   const toc = tic();
   files = files.map((file) => resolve(file));
   projectPath = projectPath ?? resolve('.');
-  const { project } = await loadProject(session, projectPath);
+  const { project, pages } = await loadProject(session, projectPath);
+  const projectFiles = pages.map((page) => page.file);
+  const allFiles = [...new Set([...files, ...projectFiles])];
   await Promise.all([
     // Load all citations (.bib)
     ...project.bibliography.map((path) => loadFile(session, path, '.bib')),
     // Load all content (.md and .ipynb)
-    ...files.map((file) => loadFile(session, file, undefined, { minifyMaxCharacters: 0 })),
+    ...allFiles.map((file) => loadFile(session, file, undefined, { minifyMaxCharacters: 0 })),
     // Load up all the intersphinx references
     loadIntersphinx(session, { projectPath }) as Promise<any>,
   ]);
@@ -55,7 +57,7 @@ export async function getFileContent(
   //   extraTransforms.push(...opts.extraTransforms);
   // }
   await Promise.all(
-    files.map(async (file) => {
+    allFiles.map(async (file) => {
       await transformMdast(session, {
         file,
         imageWriteFolder,
@@ -68,7 +70,7 @@ export async function getFileContent(
   );
   const pageReferenceStates = selectPageReferenceStates(
     session,
-    files.map((file) => {
+    allFiles.map((file) => {
       return { file };
     }),
   );
@@ -82,6 +84,12 @@ export async function getFileContent(
       return selectedFile;
     }),
   );
-  session.log.info(toc(`📚 Built ${files.length} pages for export from ${projectPath} in %s.`));
+  session.log.info(
+    toc(
+      `📚 Built ${allFiles.length} pages for export (including ${
+        allFiles.length - files.length
+      } dependencies) from ${projectPath} in %s.`,
+    ),
+  );
   return selectedFiles;
 }

packages/myst-directives/src/embed.ts

@@ -16,12 +16,11 @@ export const embedDirective: DirectiveSpec = {
     },
   },
   run(data: DirectiveData): GenericNode[] {
-    const { label, identifier } = normalizeLabel(data.options?.label as string) || {};
+    const { label } = normalizeLabel(data.options?.label as string) || {};
     return [
       {
         type: 'embed',
         label,
-        identifier,
         'remove-input': data.options?.['remove-input'],
         'remove-output': data.options?.['remove-output'],
       },

packages/myst-parser/tests/directives/embed.yml

@@ -17,5 +17,4 @@ cases:
           children:
             - type: embed
               label: hi
-              identifier: hi
               remove-output: true

packages/myst-to-jats/jest.config.cjs

@@ -17,7 +17,7 @@ module.exports = {
   verbose: true,
   testEnvironment: 'node',
   transformIgnorePatterns: [
-    '<rootDir>/node_modules/(?!(vfile|formdata-polyfill|chalk|fetch-blob|vfile-message|unified|bail|trough|zwitch|unist-|hast-|html-|rehype-|mdast-|micromark-|trim-|web-namespaces|property-information|space-separated-tokens|comma-separated-tokens|get-port|stringify-entities|character-entities-html4|ccount))',
+    '<rootDir>/node_modules/(?!(vfile|formdata-polyfill|chalk|fetch-blob|vfile-message|unified|bail|trough|zwitch|unist-|hast-|html-|rehype-|mdast-|micromark-|trim-|web-namespaces|property-information|space-separated-tokens|comma-separated-tokens|get-port|stringify-entities|character-entities-html4|ccount|is-plain-obj|nanoid))',
   ],
   testPathIgnorePatterns: ['/node_modules/', '/.yalc/', '/dist/'],
 };

packages/myst-to-jats/package.json

@@ -50,13 +50,18 @@
     "myst-frontmatter": "^0.0.12",
     "myst-spec": "^0.0.4",
     "myst-spec-ext": "^0.0.10",
+    "unified": "^10.1.2",
     "unist-util-select": "^4.0.3",
     "vfile-reporter": "^7.0.4",
     "xml-js": "^1.6.11"
   },
   "devDependencies": {
     "@types/jest": "^28.1.6",
+    "@types/js-yaml": "^4.0.5",
+    "@types/mdast": "^3.0.11",
     "jest": "^28.1.3",
+    "js-yaml": "^4.1.0",
+    "myst-cli-utils": "^0.0.11",
     "npm-run-all": "^4.1.5",
     "prettier": "^2.6.1",
     "rimraf": "^3.0.2",

packages/myst-to-jats/tests/basic.spec.ts

@@ -7,6 +7,8 @@ import yaml from 'js-yaml';
 import { VFile } from 'vfile';
 import mystToJats, { writeJats } from '../src';
 
+const TEST_DTD = false;
+
 type TestFile = {
   cases: TestCase[];
 };
@@ -39,6 +41,19 @@ const testLogger = new Session({
   },
 });
 
+function addHeader(data: string) {
+  return `<?xml version="1.0" encoding="UTF-8"?>
+    <!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD with MathML3 v1.3 20210610//EN" "http://jats.nlm.nih.gov/publishing/1.3/JATS-archivearticle1-3-mathml3.dtd">
+    <article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" dtd-version="1.3" xml:lang="en">
+      <front>
+        <article-meta/>
+      </front>
+      <body>
+        ${data}
+      </body>
+    </article>`;
+}
+
 async function writeValidateDelete(data: string) {
   const testXml = path.join(__dirname, 'test.xml');
   fs.writeFileSync(testXml, data);
@@ -49,11 +64,12 @@ async function writeValidateDelete(data: string) {
 
 describe('Basic JATS body', () => {
   const cases = loadCases('basic.yml');
-  test.each(cases.map((c): [string, TestCase] => [c.title, c]))('%s', (_, { tree, jats }) => {
+  test.each(cases.map((c): [string, TestCase] => [c.title, c]))('%s', async (_, { tree, jats }) => {
     const pipe = unified().use(mystToJats);
     pipe.runSync(tree as any);
     const vfile = pipe.stringify(tree as any);
     expect(vfile.result).toEqual(jats);
+    if (TEST_DTD) expect(await writeValidateDelete(addHeader(vfile.result as string))).toBeTruthy();
   });
 });
 
@@ -69,7 +85,7 @@ describe('JATS full article', () => {
       pipe.runSync(tree as any);
       const vfile = pipe.stringify(tree as any);
       expect(vfile.result).toEqual(jats);
-      expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
+      if (TEST_DTD) expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
     },
   );
 });
@@ -86,7 +102,7 @@ describe('JATS full article with bibliography', () => {
       pipe.runSync(tree as any);
       const vfile = pipe.stringify(tree as any);
       expect(vfile.result).toEqual(jats);
-      expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
+      if (TEST_DTD) expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
     },
   );
 });
@@ -106,7 +122,7 @@ describe('JATS multi-article', () => {
         },
       );
       expect(vfile.result).toEqual(jats);
-      expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
+      if (TEST_DTD) expect(await writeValidateDelete(vfile.result as string)).toBeTruthy();
     },
   );
 });
@@ -115,7 +131,7 @@ describe('JATS SI units', () => {
   const cases = loadCases('siunit.yml');
   test.each(cases.map((c): [string, TestCase] => [c.title, c]))(
     '%s',
-    (_, { tree, jats, frontmatter, citations }) => {
+    async (_, { tree, jats, frontmatter, citations }) => {
       const vfile = writeJats(
         new VFile(),
         { mdast: tree as any, frontmatter, citations },
@@ -124,6 +140,9 @@ describe('JATS SI units', () => {
         },
       );
       expect(vfile.result).toEqual(jats);
+      if (TEST_DTD) {
+        expect(await writeValidateDelete(addHeader(vfile.result as string))).toBeTruthy();
+      }
     },
   );
 });

packages/myst-to-tex/src/index.ts

@@ -220,7 +220,8 @@ const handlers: Record<string, Handler> = {
   captionNumber: () => undefined,
   crossReference(node, state) {
     // Look up reference and add the text
-    const text = (node.template ?? toText(node))?.replace(/\s/g, '~') || '%s';
+    const usedTemplate = node.template?.includes('%s') ? node.template : undefined;
+    const text = (usedTemplate ?? toText(node))?.replace(/\s/g, '~') || '%s';
     const id = node.label;
     state.write(text.replace(/%s/g, `\\ref{${id}}`));
   },