@myst-theme/site 0.1.35 → 0.1.37

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@myst-theme/site",
-  "version": "0.1.35",
+  "version": "0.1.37",
   "main": "./src/index.ts",
   "types": "./src/index.ts",
   "files": [
@@ -16,20 +16,21 @@
   "dependencies": {
     "@headlessui/react": "^1.7.13",
     "@heroicons/react": "^2.0.14",
-    "@myst-theme/diagrams": "^0.1.35",
-    "@myst-theme/frontmatter": "^0.1.35",
-    "@myst-theme/jupyter": "^0.1.35",
-    "@myst-theme/providers": "^0.1.35",
+    "@myst-theme/diagrams": "^0.1.37",
+    "@myst-theme/frontmatter": "^0.1.37",
+    "@myst-theme/jupyter": "^0.1.37",
+    "@myst-theme/providers": "^0.1.37",
     "classnames": "^2.3.2",
     "lodash.throttle": "^4.1.1",
     "myst-common": "^0.0.16",
-    "myst-config": "^0.0.12",
-    "myst-demo": "^0.1.35",
-    "myst-to-react": "^0.1.35",
+    "myst-config": "^0.0.14",
+    "myst-demo": "^0.1.37",
+    "myst-to-react": "^0.1.37",
     "nbtx": "^0.2.3",
     "node-cache": "^5.1.2",
     "node-fetch": "^2.6.7",
-    "unist-util-select": "^4.0.1"
+    "unist-util-select": "^4.0.1",
+    "thebe-react": "^0.0.7"
   },
   "peerDependencies": {
     "@remix-run/node": "^1.12.0",

package/src/components/ComputeControls.tsx

@@ -0,0 +1,124 @@
+import { Spinner } from './Spinner';
+import PlayCircleIcon from '@heroicons/react/24/outline/PlayCircleIcon';
+import ArrowPathIcon from '@heroicons/react/24/outline/ArrowPathIcon';
+import MinusCircleIcon from '@heroicons/react/24/outline/MinusCircleIcon';
+import ArrowTopRightOnSquareIcon from '@heroicons/react/24/outline/ArrowTopRightOnSquareIcon';
+import classNames from 'classnames';
+import type { NotebookExecuteOptions } from 'thebe-react';
+import { useThebeServer } from 'thebe-react';
+import type { IThebeCellExecuteReturn } from 'thebe-core';
+import { useMDASTNotebook, useNotebookCellExecution } from '@myst-theme/jupyter';
+
+export function Run({
+  ready,
+  executing,
+  disabled,
+  execute,
+}: {
+  ready: boolean;
+  executing: boolean;
+  disabled?: boolean;
+  execute: (
+    options?: NotebookExecuteOptions | undefined,
+  ) => Promise<(IThebeCellExecuteReturn | null)[]>;
+}) {
+  return (
+    <div className="flex relative text-sm">
+      <button
+        className={classNames(
+          'cursor-pointer text-gray-700 active:text-green-700 hover:opacity-100',
+          {
+            'opacity-10 hover:opacity-10': executing,
+            'opacity-60': !executing,
+          },
+        )}
+        disabled={disabled || !ready || executing}
+        onClick={() => execute()}
+      >
+        <PlayCircleIcon className="h-6 w-6 inline-block align-top" title="run all cells" />
+      </button>
+      {executing && (
+        <span className="absolute top-0 left-0 z-10 w-[22px] h-[22px] opacity-100">
+          <Spinner size={24} />
+        </span>
+      )}
+    </div>
+  );
+}
+
+export function Clear({
+  ready,
+  executing,
+  disabled,
+  clear,
+}: {
+  ready: boolean;
+  executing: boolean;
+  disabled?: boolean;
+  clear: () => void;
+}) {
+  return (
+    <button
+      className="flex cursor-pointer text-gray-700 active:text-green-700 opacity-60 hover:opacity-100"
+      disabled={disabled || !ready || executing}
+      onClick={() => clear()}
+    >
+      <MinusCircleIcon className="h-6 w-6 inline-block align-top" title="clear all outputs" />
+    </button>
+  );
+}
+
+export function RunCell({ id }: { id: string }) {
+  const exec = useNotebookCellExecution(id);
+  if (!exec?.ready) return null;
+  const { ready, executing, notebookIsExecuting, execute } = exec;
+  return (
+    <Run ready={ready} executing={executing} disabled={notebookIsExecuting} execute={execute} />
+  );
+}
+
+export function ClearCell({ id }: { id: string }) {
+  const exec = useNotebookCellExecution(id);
+  if (!exec?.ready) return null;
+  const { ready, executing, notebookIsExecuting, clear } = exec;
+  return <Clear ready={ready} executing={executing} disabled={notebookIsExecuting} clear={clear} />;
+}
+
+export function NotebookRunAll() {
+  const { ready: serverReady, server } = useThebeServer();
+  const exec = useMDASTNotebook();
+
+  if (!exec?.ready) return null;
+  const { ready, executing, executeAll, restart, clear } = exec;
+
+  const clickLaunchInJupyter = () => {
+    if (!serverReady || !server?.settings) return;
+    window.open(server.settings.baseUrl, '_blank');
+  };
+
+  return (
+    <div className="flex">
+      <div className="group flex relative space-x-1">
+        <Run ready={ready} executing={executing} execute={executeAll} />
+        <button
+          className="flex items-center cursor-pointer text-gray-700 active:text-green-700 opacity-60 hover:opacity-100"
+          disabled={!ready || executing}
+          onClick={() => restart()}
+        >
+          <ArrowPathIcon className="h-6 w-6" title="restart kernel" />
+        </button>
+        <Clear ready={ready} executing={executing} clear={clear} />
+        <button
+          className="flex items-center cursor-pointer text-gray-700 active:text-green-700 opacity-60 hover:opacity-100"
+          disabled={!ready}
+          onClick={clickLaunchInJupyter}
+        >
+          <ArrowTopRightOnSquareIcon
+            className="h-6 w-6 inline-block align-top"
+            title="launch in juptyer"
+          />
+        </button>
+      </div>
+    </div>
+  );
+}

package/src/components/ContentBlocks.tsx

@@ -1,9 +1,28 @@
 import { useParse, DEFAULT_RENDERERS } from 'myst-to-react';
-import type { Parent } from 'myst-spec';
+import type { GenericParent, SourceFileKind } from 'myst-common';
 import { useNodeRenderers } from '@myst-theme/providers';
 import classNames from 'classnames';
+import { ClearCell, RunCell } from './ComputeControls';
 
-function Block({ id, node, className }: { id: string; node: Parent; className?: string }) {
+function isACodeCell(node: GenericParent) {
+  return (
+    node.type === 'block' &&
+    node.children.length === 2 &&
+    node.children[0].type === 'code' &&
+    node.children[1].type === 'output'
+  );
+}
+
+function Block({
+  id,
+  node,
+  className,
+}: {
+  id: string;
+  pageKind: SourceFileKind;
+  node: GenericParent;
+  className?: string;
+}) {
   const renderers = useNodeRenderers() ?? DEFAULT_RENDERERS;
   const children = useParse(node, renderers);
   const subGrid = 'article-grid article-subgrid-gap col-screen';
@@ -13,23 +32,40 @@ function Block({ id, node, className }: { id: string; node: Parent; className?:
     (dataClassName && dataClassName.includes('col-')) || (className && className.includes('col-'));
   return (
     <div
+      key={id}
       id={id}
-      className={classNames(className, dataClassName, {
+      className={classNames('relative group/block', className, dataClassName, {
         [subGrid]: !noSubGrid,
       })}
     >
       {children}
+      {isACodeCell(node) && (
+        <div className="hidden group-hover/block:flex md:flex-col absolute -top-[28px] md:top-0 right-0 md:-right-[28px] mt-8">
+          <RunCell id={id} />
+          <ClearCell id={id} />
+        </div>
+      )}
     </div>
   );
 }
 
-export function ContentBlocks({ mdast, className }: { mdast: Parent; className?: string }) {
-  const blocks = mdast.children as Parent[];
+export function ContentBlocks({
+  name,
+  pageKind,
+  mdast,
+  className,
+}: {
+  name: string;
+  pageKind: SourceFileKind;
+  mdast: GenericParent;
+  className?: string;
+}) {
+  const blocks = mdast.children as GenericParent[];
   return (
     <>
-      {blocks.map((node, index) => {
-        return <Block key={(node as any).key} id={`${index}`} node={node} className={className} />;
-      })}
+      {blocks.map((node) => (
+        <Block key={node.key} id={node.key} pageKind={pageKind} node={node} className={className} />
+      ))}
     </>
   );
 }

package/src/components/DocumentOutline.tsx

@@ -1,3 +1,4 @@
+import { useNavigation } from '@remix-run/react';
 import classNames from 'classnames';
 import throttle from 'lodash.throttle';
 import { useCallback, useEffect, useRef, useState } from 'react';
@@ -155,32 +156,51 @@ const useIntersectionObserver = (highlight: () => void, onScreen: Set<HTMLHeadin
 const DOC_OUTLINE_CLASS =
   'fixed z-10 bottom-0 right-[max(0px,calc(50%-45rem))] w-[14rem] lg:w-[18rem] py-10 px-4 lg:px-8 overflow-y-auto hidden lg:block';
 
+export function useOutlineHeight<T extends HTMLElement = HTMLElement>() {
+  const container = useRef<T>(null);
+  const outline = useRef<T>(null);
+  const transitionState = useNavigation().state;
+  const setHeight = () => {
+    if (!container.current || !outline.current) return;
+    const height = container.current.offsetHeight - window.scrollY;
+    outline.current.style.display = height < 50 ? 'none' : '';
+    outline.current.style.height = height > window.innerHeight ? '' : `${height}px`;
+    outline.current.style.opacity = height && height > 300 ? '' : '0';
+    outline.current.style.pointerEvents = height && height > 300 ? '' : 'none';
+  };
+  useEffect(() => {
+    setHeight();
+    setTimeout(setHeight, 100); // Some lag sometimes
+    const handleScroll = () => setHeight();
+    window.addEventListener('scroll', handleScroll);
+    return () => {
+      window.removeEventListener('scroll', handleScroll);
+    };
+  }, [container, outline, transitionState]);
+  return { container, outline };
+}
+
 export const DocumentOutline = ({
+  outlineRef,
   top,
-  height,
   className = DOC_OUTLINE_CLASS,
 }: {
+  outlineRef?: React.RefObject<HTMLElement>;
   top?: number;
   height?: number;
   className?: string;
 }) => {
   const { activeId, headings, highlight } = useHeaders();
-  if (height && height < 50) return null;
   if (headings.length <= 1) return <nav suppressHydrationWarning />;
   return (
     <nav
+      ref={outlineRef}
       aria-label="Document Outline"
       suppressHydrationWarning
       className={classNames('not-prose transition-opacity overflow-y-auto', className)}
       style={{
         top: top ?? 0,
-        height:
-          typeof document === 'undefined' || (height && height > window.innerHeight)
-            ? undefined
-            : height,
         maxHeight: `calc(100vh - ${(top ?? 0) + 20}px)`,
-        opacity: height && height > 300 ? undefined : 0,
-        pointerEvents: height && height > 300 ? undefined : 'none',
       }}
     >
       <div className="text-slate-900 mb-4 text-sm leading-6 dark:text-slate-100 uppercase">

package/src/components/EnableCompute.tsx

@@ -0,0 +1,64 @@
+import { useThebeCore, useThebeServer, useThebeSession } from 'thebe-react';
+import PowerIcon from '@heroicons/react/24/outline/PowerIcon';
+import { useHasNotebookProvider } from '@myst-theme/jupyter';
+import { useNavigation } from '@remix-run/react';
+import { useEffect, useState } from 'react';
+
+export function EnableCompute({
+  canCompute,
+  children,
+}: React.PropsWithChildren<{ canCompute: boolean }>) {
+  const { load, loading, core } = useThebeCore();
+  const { connect, connecting, ready: serverReady, error: serverError } = useThebeServer();
+  const {
+    start,
+    starting,
+    shutdown,
+    session,
+    ready: sessionReady,
+    error: sessionError,
+  } = useThebeSession();
+  const hasNotebookProvider = useHasNotebookProvider();
+  const navigation = useNavigation();
+  const [enabling, setEnabling] = useState(false);
+  const [enabled, setEnabled] = useState(false);
+  const busy = enabling || loading || connecting || starting;
+
+  useEffect(() => {
+    if (!enabling) return;
+    if (!core) return load();
+    if (!serverReady) return connect();
+    if (!sessionReady) start();
+    if (sessionReady) {
+      setEnabled(true);
+      setEnabling(false);
+    }
+  }, [enabling, core, serverReady, sessionReady]);
+
+  if (!canCompute || !hasNotebookProvider) return null;
+  let classes = 'flex text-center mr-1 cursor-pointer rounded-full';
+  const idleClasses = 'text-blue-700 hover:opacity-100 opacity-60';
+  const busyClasses = 'bg-yellow-700 text-yellow-700 opacity-100 font-semibold';
+  const readyClasses = 'bg-green-700 text-green-700 opacity-100 font-semibold';
+  const errorClasses = 'bg-red-700 text-red-700 opacity-100';
+
+  if (busy) classes += busyClasses;
+  else if (serverReady && sessionReady) classes += readyClasses;
+  else if (serverError || sessionError) classes += errorClasses;
+  else classes += idleClasses;
+
+  useEffect(() => {
+    if (navigation.state === 'loading') {
+      shutdown();
+    }
+  }, [shutdown, navigation]);
+
+  return (
+    <div className="flex mx-1 items-center">
+      <button className={classes} onClick={() => setEnabling(true)} disabled={enabling || enabled}>
+        <PowerIcon className="h-6 w-6 mx-1 inline-block align-top" title="enable compute" />
+      </button>
+      {enabled && <>{children}</>}
+    </div>
+  );
+}

package/src/components/FooterLinksBlock.tsx

@@ -1,8 +1,10 @@
 import classNames from 'classnames';
 import { Link } from '@remix-run/react';
-import { ArrowLeftIcon, ArrowRightIcon } from '@heroicons/react/24/outline';
+import ArrowLeftIcon from '@heroicons/react/24/outline/ArrowLeftIcon';
+import ArrowRightIcon from '@heroicons/react/24/outline/ArrowRightIcon';
 import type { FooterLinks, NavigationLink } from '../types';
 import { useUrlbase, withUrlbase } from '@myst-theme/providers';
+import { useEffect, useState } from 'react';
 
 const FooterLink = ({ title, url, group, right }: NavigationLink & { right?: boolean }) => {
   const urlbase = useUrlbase();

package/src/components/Navigation/Navigation.tsx

@@ -5,14 +5,14 @@ export function Navigation({
   children,
   projectSlug,
   top,
-  height,
+  tocRef,
   hide_toc,
   footer,
 }: {
   children?: React.ReactNode;
   projectSlug?: string;
   top?: number;
-  height?: number;
+  tocRef?: React.RefObject<HTMLDivElement>;
   hide_toc?: boolean;
   footer?: React.ReactNode;
 }) {
@@ -23,11 +23,12 @@ export function Navigation({
       {open && (
         <div
           className="fixed inset-0 bg-black opacity-50 z-30"
+          style={{ marginTop: top }}
           onClick={() => setOpen(false)}
         ></div>
       )}
       {children}
-      <TableOfContents projectSlug={projectSlug} top={top} height={height} footer={footer} />
+      <TableOfContents tocRef={tocRef} projectSlug={projectSlug} top={top} footer={footer} />
     </>
   );
 }

package/src/components/Navigation/TableOfContents.tsx

@@ -1,6 +1,6 @@
-import React from 'react';
+import React, { useEffect, useRef } from 'react';
 import classNames from 'classnames';
-import { NavLink, useParams, useLocation } from '@remix-run/react';
+import { NavLink, useParams, useLocation, useNavigation } from '@remix-run/react';
 import type { SiteManifest } from 'myst-config';
 import { useNavOpen, useSiteManifest, useUrlbase, withUrlbase } from '@myst-theme/providers';
 import { getProjectHeadings } from '../../loaders';
@@ -102,14 +102,39 @@ const Headings = ({ folder, headings, sections }: Props) => {
   );
 };
 
+export function useTocHeight<T extends HTMLElement = HTMLElement>(top?: number) {
+  const container = useRef<T>(null);
+  const toc = useRef<HTMLDivElement>(null);
+  const transitionState = useNavigation().state;
+  const setHeight = () => {
+    if (!container.current || !toc.current) return;
+    const height = container.current.offsetHeight - window.scrollY;
+    const div = toc.current.firstChild as HTMLDivElement;
+    const MAGIC_PADDING = 16; // I dunno, just go with it ...
+    if (div) div.style.height = `min(calc(100vh - ${top ?? 0}px), ${height + MAGIC_PADDING}px)`;
+    const nav = toc.current.querySelector('nav');
+    if (nav) nav.style.opacity = height > 150 ? '1' : '0';
+  };
+  useEffect(() => {
+    setHeight();
+    setTimeout(setHeight, 100); // Some lag sometimes
+    const handleScroll = () => setHeight();
+    window.addEventListener('scroll', handleScroll);
+    return () => {
+      window.removeEventListener('scroll', handleScroll);
+    };
+  }, [container, toc, transitionState]);
+  return { container, toc };
+}
+
 export const TableOfContents = ({
   projectSlug,
   top,
-  height,
+  tocRef,
   footer,
 }: {
   top?: number;
-  height?: number;
+  tocRef?: React.RefObject<HTMLDivElement>;
   projectSlug?: string;
   footer?: React.ReactNode;
 }) => {
@@ -124,13 +149,13 @@ export const TableOfContents = ({
   if (!headings) return null;
   return (
     <div
+      ref={tocRef}
       className={classNames(
         'fixed xl:article-grid article-grid-gap xl:w-screen z-30 xl:pointer-events-none overflow-auto max-xl:min-w-[300px]',
         { hidden: !open },
       )}
       style={{
         top: top ?? 0,
-        height: `min(calc(100vh - ${top ?? 0}px), ${height}px)`,
       }}
     >
       <div
@@ -149,7 +174,6 @@ export const TableOfContents = ({
         <nav
           aria-label="Table of Contents"
           className="flex-grow overflow-y-auto transition-opacity mt-6 pb-3 ml-3 xl:ml-0 mr-3"
-          style={{ opacity: height && height > 150 ? undefined : 0 }}
         >
           <Headings folder={resolvedProjectSlug} headings={headings} sections={config?.projects} />
         </nav>

package/src/components/Navigation/ThemeButton.tsx

@@ -1,6 +1,6 @@
 import { useTheme } from '@myst-theme/providers';
-import { MoonIcon } from '@heroicons/react/24/solid';
-import { SunIcon } from '@heroicons/react/24/outline';
+import MoonIcon from '@heroicons/react/24/solid/MoonIcon';
+import SunIcon from '@heroicons/react/24/outline/SunIcon';
 import classNames from 'classnames';
 
 export function ThemeButton({ className = 'mx-3 h-8 w-8' }: { className?: string }) {
@@ -8,7 +8,7 @@ export function ThemeButton({ className = 'mx-3 h-8 w-8' }: { className?: string
   return (
     <button
       className={classNames(
-        'theme rounded-full border border-white border-solid overflow-hidden text-white hover:text-stone-500 hover:bg-white',
+        'theme rounded-full border border-stone-700 dark:border-white hover:bg-neutral-100 border-solid overflow-hidden text-stone-700 dark:text-white hover:text-stone-500 dark:hover:text-neutral-800',
         className,
       )}
       title={`Change theme to ${isDark ? 'light' : 'dark'} mode.`}

package/src/components/Navigation/TopNav.tsx

@@ -2,11 +2,9 @@ import { Link, NavLink } from '@remix-run/react';
 import { Fragment } from 'react';
 import classNames from 'classnames';
 import { Menu, Transition } from '@headlessui/react';
-import {
-  EllipsisVerticalIcon,
-  Bars3Icon as MenuIcon,
-  ChevronDownIcon,
-} from '@heroicons/react/24/solid';
+import EllipsisVerticalIcon from '@heroicons/react/24/solid/EllipsisVerticalIcon';
+import MenuIcon from '@heroicons/react/24/solid/Bars3Icon';
+import ChevronDownIcon from '@heroicons/react/24/solid/ChevronDownIcon';
 import type { SiteManifest, SiteNavItem } from 'myst-config';
 import { ThemeButton } from './ThemeButton';
 import { useNavOpen, useSiteManifest } from '@myst-theme/providers';
@@ -58,7 +56,7 @@ function NavItem({ item }: { item: SiteNavItem }) {
           to={item.url ?? ''}
           className={({ isActive }) =>
             classNames(
-              'inline-flex items-center justify-center w-full mx-2 py-1 text-md font-medium text-white focus:outline-none focus-visible:ring-2 focus-visible:ring-white focus-visible:ring-opacity-75',
+              'inline-flex items-center justify-center w-full mx-2 py-1 text-md font-medium dark:text-white focus:outline-none focus-visible:ring-2 focus-visible:ring-white focus-visible:ring-opacity-75',
               {
                 'border-b border-stone-200': isActive,
               },
@@ -73,12 +71,9 @@ function NavItem({ item }: { item: SiteNavItem }) {
   return (
     <Menu as="div" className="relative grow-0 inline-block mx-2">
       <div className="inline-block">
-        <Menu.Button className="inline-flex items-center justify-center w-full mx-2 py-1 text-md font-medium text-white rounded-md focus:outline-none focus-visible:ring-2 focus-visible:ring-white focus-visible:ring-opacity-75">
+        <Menu.Button className="inline-flex items-center justify-center w-full mx-2 py-1 text-md font-medium text-stone-900 dark:text-white rounded-md focus:outline-none focus-visible:ring-2 focus-visible:ring-white focus-visible:ring-opacity-75">
           <span>{item.title}</span>
-          <ChevronDownIcon
-            className="w-5 h-5 ml-2 -mr-1 text-violet-200 hover:text-violet-100"
-            aria-hidden="true"
-          />
+          <ChevronDownIcon className="w-5 h-5 ml-2 -mr-1 text-violet-200 hover:text-violet-100" />
         </Menu.Button>
       </div>
       <Transition
@@ -184,11 +179,15 @@ function HomeLink({ logo, logoText, name }: { logo?: string; logoText?: string;
   const nothingSet = !logo && !logoText;
   return (
     <Link
-      className="flex items-center text-white w-fit ml-3 md:ml-5 xl:ml-7"
+      className="flex items-center dark:text-white w-fit ml-3 md:ml-5 xl:ml-7"
       to="/"
       prefetch="intent"
     >
-      {logo && <img src={logo} className="h-9 mr-3" alt={logoText || name} height="2.25rem"></img>}
+      {logo && (
+        <div className="dark:bg-white dark:rounded p-1 mr-3">
+          <img src={logo} className="h-9" alt={logoText || name} height="2.25rem"></img>
+        </div>
+      )}
       <span
         className={classNames('text-md sm:text-xl tracking-tight sm:mr-5', {
           'sr-only': !(logoText || nothingSet),
@@ -205,18 +204,18 @@ export function TopNav() {
   const config = useSiteManifest();
   const { logo, logo_text, logoText, actions, title, nav } = config ?? ({} as SiteManifest);
   return (
-    <div className="bg-stone-700 p-3 md:px-8 fixed w-screen top-0 z-30 h-[60px]">
+    <div className="bg-white/80 backdrop-blur dark:bg-stone-900/80 shadow dark:shadow-stone-700 p-3 md:px-8 fixed w-screen top-0 z-30 h-[60px]">
       <nav className="flex items-center justify-between flex-wrap max-w-[1440px] mx-auto">
         <div className="flex flex-row xl:min-w-[19.5rem] mr-2 sm:mr-7 justify-start items-center">
           <div className="block xl:hidden">
             <button
-              className="flex items-center text-stone-200 border-stone-400 hover:text-white"
+              className="flex items-center border-stone-400 text-stone-800 hover:text-stone-900 dark:text-stone-200 hover:dark:text-stone-100"
               onClick={() => {
                 setOpen(!open);
               }}
             >
+              <MenuIcon className="h-8 w-8 p-1" />
               <span className="sr-only">Open Menu</span>
-              <MenuIcon className="fill-current h-8 w-8 p-1" />
             </button>
           </div>
           <HomeLink name={title} logo={logo} logoText={logo_text || logoText} />
@@ -232,7 +231,7 @@ export function TopNav() {
             {actions?.map((action, index) => (
               <ExternalOrInternalLink
                 key={action.url || index}
-                className="inline-block text-md px-4 py-2 mx-1 leading-none border rounded text-white border-white hover:border-transparent hover:text-stone-500 hover:bg-white mt-0"
+                className="inline-block text-md px-4 py-2 mx-1 leading-none border rounded border-stone-700 dark:border-white text-stone-700 dark:text-white hover:text-stone-500 dark:hover:text-neutral-800 hover:bg-neutral-100 mt-0"
                 to={action.url}
               >
                 {action.title}

package/src/components/Navigation/index.tsx

@@ -1,5 +1,5 @@
 export { ThemeButton } from './ThemeButton';
 export { TopNav, DEFAULT_NAV_HEIGHT } from './TopNav';
 export { Navigation } from './Navigation';
-export { TableOfContents } from './TableOfContents';
+export { TableOfContents, useTocHeight } from './TableOfContents';
 export { LoadingBar } from './Loading';

package/src/components/Spinner.tsx

@@ -0,0 +1,23 @@
+export function Spinner({ size }: { size: number }) {
+  return (
+    <div role="status">
+      <svg
+        aria-hidden="true"
+        className={`w-[${size}px] h-[${size}px] mr-2 text-gray-200 animate-spin dark:text-gray-600 fill-green-600`}
+        viewBox="0 0 100 101"
+        fill="none"
+        xmlns="http://www.w3.org/2000/svg"
+      >
+        <path
+          d="M100 50.5908C100 78.2051 77.6142 100.591 50 100.591C22.3858 100.591 0 78.2051 0 50.5908C0 22.9766 22.3858 0.59082 50 0.59082C77.6142 0.59082 100 22.9766 100 50.5908ZM9.08144 50.5908C9.08144 73.1895 27.4013 91.5094 50 91.5094C72.5987 91.5094 90.9186 73.1895 90.9186 50.5908C90.9186 27.9921 72.5987 9.67226 50 9.67226C27.4013 9.67226 9.08144 27.9921 9.08144 50.5908Z"
+          fill="currentColor"
+        />
+        <path
+          d="M93.9676 39.0409C96.393 38.4038 97.8624 35.9116 97.0079 33.5539C95.2932 28.8227 92.871 24.3692 89.8167 20.348C85.8452 15.1192 80.8826 10.7238 75.2124 7.41289C69.5422 4.10194 63.2754 1.94025 56.7698 1.05124C51.7666 0.367541 46.6976 0.446843 41.7345 1.27873C39.2613 1.69328 37.813 4.19778 38.4501 6.62326C39.0873 9.04874 41.5694 10.4717 44.0505 10.1071C47.8511 9.54855 51.7191 9.52689 55.5402 10.0491C60.8642 10.7766 65.9928 12.5457 70.6331 15.2552C75.2735 17.9648 79.3347 21.5619 82.5849 25.841C84.9175 28.9121 86.7997 32.2913 88.1811 35.8758C89.083 38.2158 91.5421 39.6781 93.9676 39.0409Z"
+          fill="currentFill"
+        />
+      </svg>
+      <span className="sr-only">Loading...</span>
+    </div>
+  );
+}

package/src/components/index.ts

@@ -1,5 +1,5 @@
 export { ContentBlocks } from './ContentBlocks';
-export { DocumentOutline } from './DocumentOutline';
+export { DocumentOutline, useOutlineHeight } from './DocumentOutline';
 export { FooterLinksBlock } from './FooterLinksBlock';
 export { ContentReload } from './ContentReload';
 export { Bibliography } from './Bibliography';

package/src/index.ts

@@ -4,4 +4,3 @@ export * from './loaders';
 export * from './components';
 export * from './pages';
 export * from './seo';
-export * from './hooks';

package/src/pages/Article.tsx

@@ -1,26 +1,54 @@
-import { ReferencesProvider } from '@myst-theme/providers';
+import React from 'react';
+import { ReferencesProvider, useComputeOptions } from '@myst-theme/providers';
 import { FrontmatterBlock } from '@myst-theme/frontmatter';
 import { Bibliography, ContentBlocks, FooterLinksBlock } from '../components';
 import { ErrorDocumentNotFound } from './ErrorDocumentNotFound';
 import { ErrorProjectNotFound } from './ErrorProjectNotFound';
 import type { PageLoader } from '../types';
+import { ThebeSessionProvider } from 'thebe-react';
+import type { GenericParent } from 'myst-common';
+import { SourceFileKind } from 'myst-common';
+import { EnableCompute } from '../components/EnableCompute';
+import { NotebookRunAll } from '../components/ComputeControls';
+import { NotebookProvider, BinderBadge } from '@myst-theme/jupyter';
 
-export function ArticlePage({ article }: { article: PageLoader }) {
-  const { hide_title_block, hide_footer_links } = (article.frontmatter as any)?.design ?? {};
+export const ArticlePage = React.memo(function ({ article }: { article: PageLoader }) {
+  const computeOptions = useComputeOptions();
+  const canCompute = computeOptions.canCompute && (article.frontmatter as any)?.thebe !== false;
+  const { hide_title_block, hide_footer_links, binder } =
+    (article.frontmatter as any)?.design ?? {};
+  const isJupyter = article?.kind && article.kind === SourceFileKind.Notebook;
   return (
     <ReferencesProvider
       references={{ ...article.references, article: article.mdast }}
       frontmatter={article.frontmatter}
     >
-      {!hide_title_block && (
-        <FrontmatterBlock kind={article.kind} frontmatter={article.frontmatter} />
-      )}
-      <ContentBlocks mdast={article.mdast} />
-      <Bibliography />
-      {!hide_footer_links && <FooterLinksBlock links={article.footer} />}
+      <ThebeSessionProvider start={false} name={article.slug}>
+        {!hide_title_block && (
+          <FrontmatterBlock kind={article.kind} frontmatter={article.frontmatter} />
+        )}
+        <NotebookProvider siteConfig={false} page={article}>
+          <div className="flex items-center">
+            <div className="flex-grow"></div>
+            {binder && <BinderBadge binder={binder} />}
+            {canCompute && isJupyter && (
+              <EnableCompute canCompute={true} key={article.slug}>
+                <NotebookRunAll />
+              </EnableCompute>
+            )}
+          </div>
+          <ContentBlocks
+            name={article.slug}
+            pageKind={article.kind}
+            mdast={article.mdast as GenericParent}
+          />
+          <Bibliography />
+          {!hide_footer_links && <FooterLinksBlock links={article.footer} />}
+        </NotebookProvider>
+      </ThebeSessionProvider>
     </ReferencesProvider>
   );
-}
+});
 
 export function ProjectPageCatchBoundary() {
   return <ErrorProjectNotFound />;

package/src/pages/Root.tsx

@@ -16,6 +16,8 @@ import { ContentReload, renderers } from '../components';
 import { Analytics } from '../seo';
 import { ErrorSiteNotFound } from './ErrorSiteNotFound';
 import classNames from 'classnames';
+import { ThebeCoreProvider } from 'thebe-react';
+import { ConfiguredThebeServerProvider } from '@myst-theme/jupyter';
 
 export function Document({
   children,
@@ -47,7 +49,11 @@ export function Document({
       </head>
       <body className="m-0 transition-colors duration-500 bg-white dark:bg-stone-900">
         <ThemeProvider theme={theme} renderers={renderers} Link={RemixLink as any}>
-          <SiteProvider config={config}>{children}</SiteProvider>
+          <ThebeCoreProvider>
+            <SiteProvider config={config}>
+              <ConfiguredThebeServerProvider>{children}</ConfiguredThebeServerProvider>
+            </SiteProvider>
+          </ThebeCoreProvider>
         </ThemeProvider>
         <ScrollRestoration />
         <Scripts />

package/src/hooks/index.ts

@@ -1,23 +0,0 @@
-import { useTransition } from '@remix-run/react';
-import { useEffect, useRef, useState } from 'react';
-
-export function useNavigationHeight<T extends HTMLElement = HTMLElement>() {
-  const ref = useRef<T>(null);
-  const [height, setHeightState] = useState(1000);
-  const transitionState = useTransition().state;
-  const setHeight = () => {
-    if (ref.current) {
-      setHeightState(ref.current.offsetHeight - window.scrollY);
-    }
-  };
-  useEffect(() => {
-    setHeight();
-    setTimeout(setHeight, 100); // Some lag sometimes
-    const handleScroll = () => setHeight();
-    window.addEventListener('scroll', handleScroll);
-    return () => {
-      window.removeEventListener('scroll', handleScroll);
-    };
-  }, [ref, transitionState]);
-  return { ref, height };
-}