MAINT: reorganise extension files

package.json

@@ -69,24 +69,24 @@
         "@myst-theme/frontmatter": "^0.5.21",
         "@myst-theme/providers": "^0.5.21",
         "katex": "^0.15.2",
-        "myst-common": "^1.1.21",
+        "myst-common": "^1.1.24",
         "myst-ext-card": "^1.0.5",
         "myst-ext-exercise": "^1.0.5",
         "myst-ext-grid": "^1.0.5",
-        "myst-ext-proof": "^1.0.7",
+        "myst-ext-proof": "^1.0.8",
         "myst-ext-tabs": "^1.0.5",
-        "myst-frontmatter": "^1.1.21",
-        "myst-parser": "^1.0.21",
-        "myst-to-html": "^1.0.21",
+        "myst-frontmatter": "^1.1.24",
+        "myst-parser": "^1.0.22",
+        "myst-to-html": "^1.0.22",
         "myst-to-react": "^0.5.21",
-        "myst-transforms": "^1.1.19"
+        "myst-transforms": "^1.2.1"
     },
     "devDependencies": {
         "@babel/core": "^7.0.0",
         "@babel/preset-env": "^7.0.0",
         "@jupyterlab/builder": "^4.0.0",
         "@jupyterlab/testutils": "^4.0.0",
-        "@myst-theme/styles": "^0.3.3",
+        "@myst-theme/styles": "^0.5.21",
         "@tailwindcss/typography": "^0.5.8",
         "@types/jest": "^29.2.0",
         "@types/json-schema": "^7.0.11",

src/MySTMarkdownCell.tsx

@@ -4,11 +4,11 @@ import { ActivityMonitor } from '@jupyterlab/coreutils';
 import { AttachmentsResolver } from '@jupyterlab/attachments';
 import { IMapChange } from '@jupyter/ydoc';
 import { IMySTMarkdownCell } from './types';
-import { getUserExpressions, metadataSection } from './metadata';
+import { getUserExpressions, metadataSection } from './userExpressions';
 import { IMySTModel, MySTModel, MySTWidget } from './widget';
 import { markdownParse, processCellMDAST, renderNotebook } from './myst';
 import { IRenderMime } from '@jupyterlab/rendermime-interfaces';
-import { ITaskItemChange } from './TaskItemControllerProvider';
+import { ITaskItemChange } from './providers';
 
 class IMySTWidget {}
 

src/actions.ts

@@ -8,7 +8,7 @@ import {
   getUserExpressions,
   setUserExpressions,
   deleteUserExpressions
-} from './metadata';
+} from './userExpressions';
 import {
   INotebookTracker,
   Notebook,

src/components/index.tsx

@@ -0,0 +1,2 @@
+export * from './inlineExpression';
+export * from './listItem';

src/inlineExpression.tsx → src/components/inlineExpression.tsx

@@ -1,14 +1,14 @@
 import React, { useEffect, useRef, useState } from 'react';
-import { useUserExpressions } from './UserExpressionsProvider';
+import { useUserExpressions } from '../providers';
 import { SingletonLayout, Widget } from '@lumino/widgets';
 import { IRenderMimeRegistry } from '@jupyterlab/rendermime';
 import {
+  IUserExpressionMetadata,
   IExpressionError,
   IExpressionResult,
   isError,
   isOutput
-} from './userExpressions';
-import { IUserExpressionMetadata } from './metadata';
+} from '../userExpressions';
 
 export interface IRenderedExpressionOptions {
   expression: string;
@@ -213,7 +213,7 @@ function MIMEBundleRenderer({
   return <div ref={ref} className="not-prose inline-block" />;
 }
 
-export function InlineRenderer({ value }: { value?: string }): JSX.Element {
+export function InlineExpression({ value }: { value?: string }): JSX.Element {
   const { expressions, rendermime, trusted } = useUserExpressions();
 
   if (!expressions || !rendermime) {

src/taskItem.tsx → src/components/listItem.tsx

@@ -1,7 +1,5 @@
 import React from 'react';
-import { NodeRenderer } from '@myst-theme/providers';
-import type { ListItem } from 'myst-spec-ext';
-import { useTaskItemController } from './TaskItemControllerProvider';
+import { useTaskItemController } from '../providers';
 import { MyST } from 'myst-to-react';
 
 function TaskItem({
@@ -10,7 +8,7 @@ function TaskItem({
   children
 }: {
   checked?: boolean;
-  children: React.ReactNode;
+  children?: React.ReactNode;
   line?: number;
 }) {
   // The rendering waiting on promises from Jupyter is slow
@@ -38,23 +36,29 @@ function TaskItem({
   );
 }
 
-export const listItem: NodeRenderer<ListItem & { checked?: boolean }> = ({
-  node
-}) => {
-  if (node.checked === null) {
+export function ListItem({
+  checked,
+  line,
+  children
+}: {
+     checked?: boolean,
+     line?: number,
+     children?: any[]
+
+   }): JSX.Element {
+  if (checked === null) {
     return (
-      <li key={node.key}>
-        <MyST ast={node.children} />
+      <li>
+        <MyST ast={children} />
       </li>
     );
   }
   return (
     <TaskItem
-      key={node.key}
-      checked={node.checked}
-      line={node.position?.start.line}
+      checked={checked}
+      line={line}
     >
-      <MyST ast={node.children} />
+      <MyST ast={children} />
     </TaskItem>
   );
 };

src/mime.tsx

@@ -11,8 +11,8 @@ export class RenderedMySTMarkdown
   extends MySTWidget
   implements IRenderMime.IRenderer
 {
-  readonly resolver: IRenderMime.IResolver | undefined;
-  readonly linkHandler: IRenderMime.ILinkHandler | undefined;
+  readonly resolver?: IRenderMime.IResolver;
+  readonly linkHandler?: IRenderMime.ILinkHandler;
 
   constructor(options: IRenderMime.IRendererOptions) {
     super({

src/myst.ts

@@ -30,11 +30,8 @@ import { exerciseDirectives } from 'myst-ext-exercise';
 import { StaticNotebook } from '@jupyterlab/notebook';
 import { IRenderMimeRegistry } from '@jupyterlab/rendermime';
 import { IRenderMime } from '@jupyterlab/rendermime-interfaces';
-import { imageUrlSourceTransform } from './images';
-import { internalLinksTransform } from './links';
-import { addCiteChildrenPlugin } from './citations';
-import { evalRole } from './roles';
-import { IUserExpressionMetadata } from './metadata';
+import { imageUrlSourceTransform, internalLinksTransform, addCiteChildrenPlugin } from './transforms';
+import { IUserExpressionMetadata } from './userExpressions';
 import { IMySTMarkdownCell } from './types';
 import { Cell, ICellModel } from '@jupyterlab/cells';
 import { MySTModel } from './widget';
@@ -60,7 +57,7 @@ export function markdownParse(text: string): Root {
         ...tabDirectives,
         ...exerciseDirectives
       ],
-      roles: [evalRole]
+      roles: []
     });
   };
 
@@ -96,21 +93,21 @@ export async function processArticleMDAST(
   };
 
   const { frontmatter: frontmatterRaw } = getFrontmatter(file, mdast, {
-    removeYaml: true,
-    removeHeading: true
   });
   const frontmatter = validatePageFrontmatter(frontmatterRaw, {
     property: 'frontmatter',
     messages: {}
   });
 
-  const state = new ReferenceState({
+  const state = new ReferenceState(
+	  "<PATH>",
+  {
     numbering: frontmatter.numbering,
-    file
+    vfile: file
   });
   unified()
     .use(mathPlugin, { macros: frontmatter?.math ?? {} }) // This must happen before enumeration, as it can add labels
-    .use(glossaryPlugin, { state }) // This should be before the enumerate plugins
+    .use(glossaryPlugin) // This should be before the enumerate plugins
     .use(abbreviationPlugin, { abbreviations: frontmatter.abbreviations })
     .use(enumerateTargetsPlugin, { state })
     .use(linksPlugin, { transformers: linkTransforms })
@@ -163,8 +160,6 @@ export async function processNotebookMDAST(
     // This is the first cell, which might have a YAML block or header.
     mdast.children[0] as any,
     {
-      removeYaml: true,
-      removeHeading: true
     }
   );
 
@@ -173,14 +168,14 @@ export async function processNotebookMDAST(
     messages: {}
   });
 
-  const state = new ReferenceState({
+  const state = new ReferenceState("<PATH>",{
     numbering: frontmatter.numbering,
-    file
+    vfile: file
   });
 
   unified()
     .use(mathPlugin, { macros: frontmatter?.math ?? {} }) // This must happen before enumeration, as it can add labels
-    .use(glossaryPlugin, { state }) // This should be before the enumerate plugins
+    .use(glossaryPlugin) // This should be before the enumerate plugins
     .use(abbreviationPlugin, { abbreviations: frontmatter.abbreviations })
     .use(enumerateTargetsPlugin, { state })
     .use(linksPlugin, { transformers: linkTransforms })
@@ -231,6 +226,7 @@ export async function renderNotebook(notebook: StaticNotebook) {
     frontmatter,
     mdast: processedMDAST
   } = await processNotebookMDAST(
+
     mdast,
     notebook.rendermime.resolver ?? undefined
   );

src/providers/index.tsx

@@ -0,0 +1,3 @@
+export * from './sanitizer';
+export * from './taskItem';
+export * from './userExpressions';

src/UserExpressionsProvider.tsx → src/providers/userExpressions.tsx

@@ -1,5 +1,5 @@
 import React, { createContext, useContext } from 'react';
-import { IUserExpressionMetadata } from './metadata';
+import { IUserExpressionMetadata } from '../userExpressions';
 import { IRenderMimeRegistry } from '@jupyterlab/rendermime';
 
 type UserExpressionsState = {

src/renderers.tsx

@@ -2,17 +2,18 @@ import React from 'react';
 import { DEFAULT_RENDERERS } from 'myst-to-react';
 import { MermaidNodeRenderer } from '@myst-theme/diagrams';
 import { NodeRenderer } from '@myst-theme/providers';
-import { InlineRenderer } from './inlineExpression';
-import { listItem } from './taskItem';
-import { useSanitizer } from './SanitizerProvider';
+import { InlineExpression,  ListItem } from './components';
+import { useSanitizer } from './providers';
 
 export const renderers: Record<string, NodeRenderer> = {
   ...DEFAULT_RENDERERS,
   mermaid: MermaidNodeRenderer,
   inlineExpression: ({ node }) => {
-    return <InlineRenderer value={node.value} />;
+    return <InlineExpression value={node.value} />;
+  },
+  listItem: ({ node }) => {
+    return <ListItem checked={node.checked} line={node.position?.start.line} children={node.children}/>;
   },
-  listItem,
   html: ({ node }, children) => {
     const { sanitizer } = useSanitizer();
     if (sanitizer !== undefined) {

src/transforms/index.ts

@@ -0,0 +1,3 @@
+export * from './citations';
+export * from './images';
+export * from './links';

src/types.ts

@@ -2,6 +2,7 @@ import { MarkdownCell } from '@jupyterlab/cells';
 import { IMySTModel } from './widget';
 import { IRenderMime } from '@jupyterlab/rendermime-interfaces';
 
+
 export type IMySTMarkdownCell = MarkdownCell & {
   readonly fragmentMDAST: any | undefined;
   readonly attachmentsResolver: IRenderMime.IResolver;