fix ci

Author: rowanc1

docs/diagrams.md

@@ -37,3 +37,19 @@ npm install -g @mermaid-js/mermaid-cli
 ```
 
 :::
+
+:::{note .dropdown} For CI Environments
+
+The Mermaid CLI uses Puppeteer which may require special configuration in CI environments. MyST automatically handles this by detecting the `CI` environment variable or you can manually control it:
+
+```bash
+# Automatic detection (recommended for CI)
+CI=true npm run build
+
+# Manual control
+MERMAID_NO_SANDBOX=true npm run build
+```
+
+This automatically creates a Puppeteer configuration file with `--no-sandbox` flag to resolve sandbox issues in Linux CI environments.
+
+:::

packages/jtex/tests/download.spec.ts

@@ -4,57 +4,53 @@ import { TemplateKind } from 'myst-common';
 import MystTemplate, { downloadTemplate, resolveInputs, Session } from 'myst-templates';
 import { renderTemplate } from '../src';
 
-describe(
-  'Download Template',
-  () => {
-    it('Download default template', async () => {
-      const session = new Session();
-      const inputs = resolveInputs(session, { buildDir: '_build', kind: TemplateKind.tex });
-      await downloadTemplate(session, {
-        templatePath: inputs.templatePath,
-        templateUrl: inputs.templateUrl as string,
-      });
-      expect(fs.existsSync('_build/templates/tex/myst/plain_latex/template.zip')).toBe(true);
-      expect(fs.existsSync('_build/templates/tex/myst/plain_latex/template.yml')).toBe(true);
-      expect(fs.existsSync('_build/templates/tex/myst/plain_latex/template.tex')).toBe(true);
+describe('Download Template', { timeout: 15000 }, () => {
+  it('Download default template', async () => {
+    const session = new Session();
+    const inputs = resolveInputs(session, { buildDir: '_build', kind: TemplateKind.tex });
+    await downloadTemplate(session, {
+      templatePath: inputs.templatePath,
+      templateUrl: inputs.templateUrl as string,
     });
-    it('Bad template paths to throw', async () => {
-      const jtex = new MystTemplate(new Session(), {
-        template: 'not-there',
-        kind: TemplateKind.tex,
-      });
-      expect(() => jtex.prepare({} as any)).toThrow(/does not exist/);
+    expect(fs.existsSync('_build/templates/tex/myst/plain_latex/template.zip')).toBe(true);
+    expect(fs.existsSync('_build/templates/tex/myst/plain_latex/template.yml')).toBe(true);
+    expect(fs.existsSync('_build/templates/tex/myst/plain_latex/template.tex')).toBe(true);
+  });
+  it('Bad template paths to throw', async () => {
+    const jtex = new MystTemplate(new Session(), {
+      template: 'not-there',
+      kind: TemplateKind.tex,
     });
-    it('Render out the template', async () => {
-      const jtex = new MystTemplate(new Session(), {
-        kind: TemplateKind.tex,
-        template: `${__dirname}/example`,
-      });
-      renderTemplate(jtex, {
-        contentOrPath: `${__dirname}/test.tex`,
-        outputPath: '_build/out/article.tex',
-        frontmatter: {
-          title: 'test',
-          description: 'test',
-          date: new Date(2022, 6, 22).toISOString(),
-          authors: [
-            { name: 'Rowan Cockett', affiliations: ['Curvenote'] },
-            { name: 'Steve Purves', affiliations: ['Curvenote'], orcid: '0000' },
-          ],
-        },
-        options: {
-          keywords: '',
-        },
-        parts: {
-          abstract: 'My abstract!',
-        },
-      });
-      expect(fs.existsSync('_build/out/article.tex')).toBe(true);
-      const content = fs.readFileSync('_build/out/article.tex').toString();
-      expect(content.includes('Volcanic Archipelago')).toBe(true);
-      expect(content.includes('Rowan Cockett')).toBe(true);
-      expect(content.includes('My abstract!')).toBe(true);
+    expect(() => jtex.prepare({} as any)).toThrow(/does not exist/);
+  });
+  it('Render out the template', async () => {
+    const jtex = new MystTemplate(new Session(), {
+      kind: TemplateKind.tex,
+      template: `${__dirname}/example`,
     });
-  },
-  { timeout: 15000 },
-);
+    renderTemplate(jtex, {
+      contentOrPath: `${__dirname}/test.tex`,
+      outputPath: '_build/out/article.tex',
+      frontmatter: {
+        title: 'test',
+        description: 'test',
+        date: new Date(2022, 6, 22).toISOString(),
+        authors: [
+          { name: 'Rowan Cockett', affiliations: ['Curvenote'] },
+          { name: 'Steve Purves', affiliations: ['Curvenote'], orcid: '0000' },
+        ],
+      },
+      options: {
+        keywords: '',
+      },
+      parts: {
+        abstract: 'My abstract!',
+      },
+    });
+    expect(fs.existsSync('_build/out/article.tex')).toBe(true);
+    const content = fs.readFileSync('_build/out/article.tex').toString();
+    expect(content.includes('Volcanic Archipelago')).toBe(true);
+    expect(content.includes('Rowan Cockett')).toBe(true);
+    expect(content.includes('My abstract!')).toBe(true);
+  });
+});

packages/myst-cli/src/build/jats/single.ts

@@ -14,6 +14,17 @@ import { resolveFrontmatterParts } from '../../utils/resolveFrontmatterParts.js'
 import type { ExportWithOutput, ExportFnOptions } from '../types.js';
 import { cleanOutput } from '../utils/cleanOutput.js';
 import { getFileContent } from '../utils/getFileContent.js';
+import { mermaidPlugin } from '../../transforms/mermaid.js';
+import type { TransformSpec } from 'myst-common';
+
+const mermaidTransform: TransformSpec = {
+  name: 'mermaid',
+  stage: 'document',
+  plugin: mermaidPlugin,
+  options: {
+    format: 'png',
+  },
+};
 
 /**
  * Build a MyST project as JATS XML
@@ -39,6 +50,7 @@ export async function runJatsExport(
       projectPath,
       imageExtensions: KNOWN_IMAGE_EXTENSIONS,
       extraLinkTransformers,
+      transforms: [mermaidTransform],
       preFrontmatters: [
         filterKeys(article, [...PAGE_FRONTMATTER_KEYS, ...Object.keys(FRONTMATTER_ALIASES)]),
       ], // only apply to article, not sub_articles