📦 Update for footnotes and JATS

.changeset/rude-bikes-run.md

@@ -0,0 +1,9 @@
+---
+'myst-to-react': patch
+'myst-demo': patch
+'@myst-theme/providers': patch
+'@myst-theme/jupyter': patch
+'@myst-theme/site': patch
+---
+
+Update packages to latest versions. Add JATS support.

.changeset/tame-mugs-work.md

@@ -0,0 +1,5 @@
+---
+'@myst-theme/jupyter': patch
+---
+
+Remove console.log

docs/package.json

@@ -25,7 +25,7 @@
   },
   "dependencies": {
     "@myst-theme/frontmatter": "*",
-    "myst-frontmatter": "^0.0.9",
+    "myst-frontmatter": "*",
     "myst-to-react": "*"
   }
 }

packages/jupyter/package.json

@@ -27,8 +27,8 @@
     "ansi-to-react": "^6.1.6",
     "buffer": "^6.0.3",
     "classnames": "^2.3.2",
-    "myst-common": "^0.0.14",
-    "myst-config": "^0.0.10",
+    "myst-common": "^0.0.15",
+    "myst-config": "^0.0.11",
     "myst-spec": "^0.0.4",
     "nanoid": "^4.0.0",
     "nbtx": "^0.2.3",

packages/jupyter/src/output.tsx

@@ -52,8 +52,6 @@ export function Output(node: GenericNode) {
     );
   }
 
-  console.log('Output', allSafe, outputs);
-
   return (
     <figure
       key={node.key}

packages/myst-demo/package.json

@@ -22,20 +22,21 @@
     "@heroicons/react": "^2.0.13",
     "classnames": "^2.3.2",
     "js-yaml": "^4.1.0",
-    "myst-common": "^0.0.14",
-    "myst-config": "^0.0.10",
-    "myst-ext-card": "^0.0.4",
-    "myst-ext-grid": "^0.0.4",
-    "myst-ext-tabs": "^0.0.4",
-    "myst-frontmatter": "^0.0.9",
-    "myst-parser": "^0.0.23",
+    "myst-common": "^0.0.15",
+    "myst-config": "^0.0.11",
+    "myst-directives": "^0.0.24",
+    "myst-ext-card": "^0.0.5",
+    "myst-ext-grid": "^0.0.5",
+    "myst-ext-tabs": "^0.0.5",
+    "myst-frontmatter": "^0.0.10",
+    "myst-parser": "^0.0.24",
     "myst-spec": "^0.0.4",
-    "myst-to-docx": "^0.0.18",
-    "myst-to-html": "^0.0.23",
-    "myst-to-jats": "^0.0.20",
+    "myst-to-docx": "^0.0.19",
+    "myst-to-html": "^0.0.24",
+    "myst-to-jats": "^0.0.21",
     "myst-to-react": "^0.1.33",
-    "myst-to-tex": "^0.0.21",
-    "myst-transforms": "^0.0.23",
+    "myst-to-tex": "^0.0.22",
+    "myst-transforms": "^0.0.24",
     "unified": "^10.1.2",
     "unist-util-visit": "^4.1.1",
     "vfile": "^5.3.6",

packages/myst-demo/src/index.tsx

@@ -27,13 +27,11 @@ function downloadBlob(filename: string, blob: Blob) {
   a.click();
 }
 
-async function saveDocxFile(filename: string, mdast: any, footnotes?: any) {
+async function saveDocxFile(filename: string, mdast: any) {
   const { unified } = await import('unified');
   const { mystToDocx, fetchImagesAsBuffers } = await import('myst-to-docx');
   // Clone the tree
   const tree = JSON.parse(JSON.stringify(mdast));
-  // Put the footnotes back in
-  if (footnotes) tree.children.push(...Object.values(footnotes));
   const opts = await fetchImagesAsBuffers(tree);
   const docxBlob = await (unified()
     .use(mystToDocx, opts)
@@ -44,7 +42,11 @@ async function saveDocxFile(filename: string, mdast: any, footnotes?: any) {
 async function parse(
   text: string,
   defaultFrontmatter?: PageFrontmatter,
-  options?: { renderers?: Record<string, NodeRenderer>; removeHeading?: boolean },
+  options?: {
+    renderers?: Record<string, NodeRenderer>;
+    removeHeading?: boolean;
+    jats?: { fullArticle?: boolean };
+  },
 ) {
   // Ensure that any imports from myst are async and scoped to this function
   const { visit } = await import('unist-util-visit');
@@ -112,7 +114,7 @@ async function parse(
     .use(mathPlugin, { macros: frontmatter?.math ?? {} }) // This must happen before enumeration, as it can add labels
     .use(enumerateTargetsPlugin, { state })
     .use(linksPlugin, { transformers: linkTransforms })
-    .use(footnotesPlugin, { references })
+    .use(footnotesPlugin)
     .use(resolveReferencesPlugin, { state })
     .use(keysPlugin)
     .runSync(mdast as any, file);
@@ -122,7 +124,7 @@ async function parse(
     .stringify(mdast as any, texFile).result as LatexResult;
   const jatsFile = new VFile();
   const jats = unified()
-    .use(mystToJats, { spaces: 2 })
+    .use(mystToJats, { spaces: 2, fullArticle: options?.jats?.fullArticle, frontmatter })
     .stringify(mdast as any, jatsFile).result as JatsResult;
   const content = useParse(mdast as any, options?.renderers);
   return {
@@ -173,7 +175,11 @@ export function MySTRenderer({
 
   useEffect(() => {
     const ref = { current: true };
-    parse(text, { numbering }, { renderers, removeHeading: !!TitleBlock }).then((result) => {
+    parse(
+      text,
+      { numbering },
+      { renderers, removeHeading: !!TitleBlock, jats: { fullArticle: true } },
+    ).then((result) => {
       if (!ref.current) return;
       setFrontmatter(result.frontmatter);
       setYaml(result.yaml);
@@ -305,7 +311,7 @@ export function MySTRenderer({
             <div>
               <button
                 className="rounded border p-3"
-                onClick={() => saveDocxFile('demo.docx', references.article, references.footnotes)}
+                onClick={() => saveDocxFile('demo.docx', references.article)}
                 title={`Download Micorsoft Word`}
                 aria-label={`Download Micorsoft Word`}
               >

packages/myst-to-react/package.json

@@ -23,14 +23,14 @@
     "@popperjs/core": "^2.11.6",
     "buffer": "^6.0.3",
     "classnames": "^2.3.2",
-    "myst-common": "^0.0.14",
-    "myst-config": "^0.0.10",
+    "myst-common": "^0.0.15",
+    "myst-config": "^0.0.11",
     "myst-spec": "^0.0.4",
     "nanoid": "^4.0.0",
     "react-popper": "^2.3.0",
     "react-syntax-highlighter": "^15.5.0",
     "swr": "^1.3.0",
-    "unist-util-select": "^4.0.1"
+    "unist-util-select": "^4.0.3"
   },
   "peerDependencies": {
     "@types/react": "^16.8 || ^17.0 || ^18.0",

packages/myst-to-react/src/footnotes.tsx

@@ -3,10 +3,13 @@ import type { NodeRenderer } from '@myst-theme/providers';
 import { useReferences } from '@myst-theme/providers';
 import { useParse } from '.';
 import { ClickPopover } from './components/ClickPopover';
+import { select } from 'unist-util-select';
 
 export function FootnoteDefinition({ identifier }: { identifier: string }) {
   const references = useReferences();
-  const node = references?.footnotes?.[identifier];
+  const node =
+    (references as any)?.footnotes?.[identifier] ??
+    select(`footnoteDefinition[identifier=${identifier}]`, references?.article);
   const children = useParse(node as GenericParent);
   return <>{children}</>;
 }
@@ -25,6 +28,8 @@ export const FootnoteReference: NodeRenderer = (node) => {
 
 const FOOTNOTE_RENDERERS = {
   footnoteReference: FootnoteReference,
+  // Do not render the definitions, they get pulled in by a handler
+  footnoteDefinition: () => null,
 };
 
 export default FOOTNOTE_RENDERERS;

packages/providers/package.json

@@ -17,9 +17,9 @@
     "build": "npm-run-all -l clean -p build:cjs build:types"
   },
   "dependencies": {
-    "myst-common": "^0.0.14",
-    "myst-config": "^0.0.10",
-    "myst-frontmatter": "^0.0.9"
+    "myst-common": "^0.0.15",
+    "myst-config": "^0.0.11",
+    "myst-frontmatter": "^0.0.10"
   },
   "peerDependencies": {
     "@types/react": "^16.8 || ^17.0 || ^18.0",

packages/site/package.json

@@ -22,8 +22,8 @@
     "@myst-theme/providers": "^0.1.33",
     "classnames": "^2.3.2",
     "lodash.throttle": "^4.1.1",
-    "myst-common": "^0.0.14",
-    "myst-config": "^0.0.10",
+    "myst-common": "^0.0.15",
+    "myst-config": "^0.0.11",
     "myst-demo": "^0.1.33",
     "myst-to-react": "^0.1.33",
     "nbtx": "^0.2.3",