Merge branch 'main' into 375-query-by-set

.gitignore

@@ -15,7 +15,6 @@ logs
 npm-debug.log*
 yarn-debug.log*
 yarn-error.log*
-lerna-debug.log*
 .pnpm-debug.log*
 
 # Diagnostic reports (https://nodejs.org/api/report.html)
@@ -163,3 +162,4 @@ sketch
 
 # End of https://www.toptal.com/developers/gitignore/api/react,node,joed
 .turbo/cookies/0.cookie
+.turbo/

e2e-tests/common.ts

@@ -1,7 +1,7 @@
 import { Page } from '@playwright/test';
-import mockData from '../playwright/mock-data/simpsons/simpsons_data.json';
-import mockAnnotations from '../playwright/mock-data/simpsons/simpsons_annotations.json';
-import mockAltText from '../playwright/mock-data/simpsons/simpsons_alttxt.json';
+import mockData from '../playwright/mock-data/simpsons/simpsons_data.json' assert { type: 'json' };
+import mockAnnotations from '../playwright/mock-data/simpsons/simpsons_annotations.json' assert { type: 'json' };
+import mockAltText from '../playwright/mock-data/simpsons/simpsons_alttxt.json' assert { type: 'json' };
 
 export const alttxt = {
   upsetIntroduction: 'This is an UpSet plot that visualizes set intersection. To learn about UpSet plots, visit https://upset.app.',

e2e-tests/elementView.spec.ts

@@ -217,7 +217,7 @@ async function setQuery(page: Page, att: string, type: string, query: string): P
 test('Query Selection', async ({ page }) => {
   await page.goto('http://localhost:3000/?workspace=Upset+Examples&table=simpsons&sessionId=193');
   await page.getByLabel('Element View Sidebar Toggle').click();
-  await page.locator('[id="Subset_School\\~\\&\\~Male"] g').filter({ hasText: /^Blue Hair$/ }).locator('circle').click();
+  await page.locator('[id="Subset_School\\~\\&\\~Male"]').getByLabel('Blue Hair').locator('circle').click();
 
   // Selected elements for testing
   const ralphCell = page.getByRole('cell', { name: 'Ralph' });

package.json

@@ -1,6 +1,7 @@
 {
   "name": "upset-monorepo",
   "private": true,
+  "type": "module",
   "workspaces": [
     "packages/*"
   ],
@@ -10,9 +11,6 @@
     "storybook": "turbo run storybook",
     "test": "playwright test",
     "build": "turbo run build --force",
-    "prepublish": "lerna run prepublish",
-    "publish-canary": "echo 'Do something'",
-    "publish-stable": "echo 'Do something'",
     "lint": "turbo run lint --parallel --no-cache",
     "doc": "typedoc --options typedoc.json"
   },
@@ -27,27 +25,19 @@
     "eslint-plugin-jsx-a11y": "^6.5.1",
     "eslint-plugin-react": "^7.28.0",
     "eslint-plugin-react-hooks": "^4.3.0",
-    "lerna": "^4.0.0",
     "rollup-plugin-postcss": "^4.0.2",
-    "turbo": "^1.0.24",
+    "turbo": "^2.4.1",
     "typedoc": "^0.25.12",
     "typedoc-plugin-missing-exports": "^2.2.0",
     "typescript": "^4.5.5"
   },
-  "prettier": {
-    "printWidth": 80,
-    "semi": true,
-    "singleQuote": true,
-    "trailingComma": "all"
-  },
   "packageManager": "yarn@1.22.19",
   "dependencies": {
     "@playwright/test": "^1.49.1",
-    "@vitejs/plugin-react": "^4.0.4",
+    "@vitejs/plugin-react": "^4.3.4",
     "eslint-config-react-app": "^7.0.1",
-    "react": "^18.0.2",
-    "vite": "^4.4.9",
-    "vite-plugin-dts": "^3.5.1",
-    "vite-tsconfig-paths": "^4.2.0"
+    "react": "^18.3.1",
+    "vite": "^6.1.0",
+    "vite-plugin-dts": "^3.5.1"
   }
 }

packages/app/package.json

@@ -2,6 +2,7 @@
   "name": "@visdesignlab/app",
   "version": "0.1.0",
   "private": true,
+  "type": "module",
   "dependencies": {
     "@emotion/css": "^11.10.5",
     "@emotion/react": "^11.10.5",
@@ -18,23 +19,21 @@
     "@types/jest": "^27.4.0",
     "@types/node": "^16.11.22",
     "@types/react": "^17.0.39",
-    "@types/react-dom": "^17.0.11",
-    "@visdesignlab/upset2-core": "^0.1.0",
-    "@visdesignlab/upset2-react": "^0.1.0",
+    "@types/react-dom": "^18.3.1",
+    "@visdesignlab/upset2-core": "*",
+    "@visdesignlab/upset2-react": "*",
     "localforage": "^1.10.0",
     "multinet": "0.23.3",
-    "react": "^18.0.2",
+    "react": "^18.3.1",
     "react-dom": "^18.0.2",
     "react-router-dom": "^6.14.1",
     "recoil": "^0.6.1",
     "typescript": "^4.5.5",
     "web-vitals": "^2.1.4"
   },
   "scripts": {
-    "start": "vite --port 3000",
-    "dev": "yarn start",
-    "build": "vite build",
-    "serve": "vite preview"
+    "dev": "vite dev --port 3000",
+    "build": "vite build"
   },
   "eslintConfig": {
     "extends": [
@@ -55,7 +54,7 @@
     ]
   },
   "devDependencies": {
-    "@vitejs/plugin-react": "^4.0.4",
-    "vite": "^4.4.9"
+    "@vitejs/plugin-react": "^4.3.4",
+    "vite": "^6.1.0"
   }
 }

packages/app/src/App.tsx

@@ -7,7 +7,7 @@ import {
 } from '@visdesignlab/upset2-react';
 import { useRecoilValue, useSetRecoilState } from 'recoil';
 import { BrowserRouter, Route, Routes } from 'react-router-dom';
-import { convertConfig, DefaultConfig, UpsetConfig } from '@visdesignlab/upset2-core';
+import { convertConfig, deepCopy, DefaultConfig, UpsetConfig } from '@visdesignlab/upset2-core';
 import { CircularProgress } from '@mui/material';
 import { ProvenanceGraph } from '@trrack/core/graph/graph-slice';
 import { dataSelector, encodedDataAtom } from './atoms/dataAtom';
@@ -18,6 +18,7 @@ import { queryParamAtom } from './atoms/queryParamAtom';
 import { getMultinetSession } from './api/session';
 
 /** @jsxImportSource @emotion/react */
+// eslint-disable-next-line @typescript-eslint/no-unused-vars
 
 const defaultVisibleSets = 6;
 
@@ -79,7 +80,7 @@ function App() {
       );
 
       if (sessionState && sessionState !== 'not found') {
-        prov.importObject(structuredClone(sessionState));
+        prov.importObject(deepCopy(sessionState));
       }
 
       // Make sure the config atom stays up-to-date with the provenance

packages/app/src/components/Body.tsx

@@ -1,5 +1,5 @@
 import { AltText, Upset, getAltTextConfig } from '@visdesignlab/upset2-react';
-import { CoreUpsetData, UpsetConfig } from '@visdesignlab/upset2-core';
+import { CoreUpsetData, deepCopy, UpsetConfig } from '@visdesignlab/upset2-core';
 import { useRecoilValue, useRecoilState } from 'recoil';
 import {
   useCallback, useContext, useEffect, useState,
@@ -83,7 +83,7 @@ export const Body = ({ data, config }: Props) => {
   const getAltText: () => Promise<AltText> = useCallback(async () => {
     const state = provObject.provenance.getState();
     // Rows must be cloned to avoid a recoil error triggered far down in this call chain when a function writes rows
-    const ATConfig = getAltTextConfig(state, data, structuredClone(rows));
+    const ATConfig = getAltTextConfig(state, data, deepCopy(rows));
 
     if (ATConfig.firstAggregateBy !== 'None') {
       throw new Error("Alt text generation is not yet supported for aggregated plots. To generate an alt text, set aggregation to 'None' in the left sidebar.");

packages/app/src/index.tsx

@@ -6,8 +6,8 @@ import '@fontsource/roboto/700.css';
 
 import { Box, CircularProgress, ThemeProvider } from '@mui/material';
 import React, { Suspense } from 'react';
-import ReactDOM from 'react-dom';
 import { RecoilRoot } from 'recoil';
+import { createRoot } from 'react-dom/client';
 
 import App from './App';
 import DefaultTheme from './components/theme';
@@ -61,7 +61,9 @@ oAuth.maybeRestoreLogin().then(() => {
     invalidateSharedLoginCookie();
   }
 
-  ReactDOM.render(
+  const container = document.getElementById('root') as HTMLElement
+  const root = createRoot(container);
+  root.render(
     <React.StrictMode>
       <ThemeProvider theme={DefaultTheme}>
         <RecoilRoot>
@@ -86,12 +88,6 @@ oAuth.maybeRestoreLogin().then(() => {
           </Suspense>
         </RecoilRoot>
       </ThemeProvider>
-    </React.StrictMode>,
-    document.getElementById('root'),
+    </React.StrictMode>
   );
 });
-
-// If you want to start measuring performance in your app, pass a function
-// to log results (for example: reportWebVitals(console.log))
-// or send to an analytics endpoint. Learn more: https://bit.ly/CRA-vitals
-// reportWebVitals(console.log);

packages/app/src/utils/oneHotEncoding.ts

@@ -1,8 +1,8 @@
-import { CoreUpsetData, process } from "@visdesignlab/upset2-core";
+import { CoreUpsetData, deepCopy, process } from "@visdesignlab/upset2-core";
 
 export const oneHotEncode = (encodeList: string[], data: CoreUpsetData, empty?: boolean) => {
     const newColNames: string[] = []
-    const encodedData: CoreUpsetData = structuredClone(data);
+    const encodedData: CoreUpsetData = deepCopy(data);
 
     // close the error window
     if (empty) {

packages/core/package.json

@@ -1,20 +1,26 @@
 {
   "name": "@visdesignlab/upset2-core",
-  "version": "0.1.0",
+  "version": "1.0.0",
   "license": "MIT",
-  "main": "dist/index.js",
+  "type": "module",
+  "main": "dist/index.cjs",
   "typings": "dist/index.d.ts",
-  "module": "dist/index.mjs",
+  "module": "dist/index.js",
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "require": "./dist/index.cjs"
+    }
+  },
   "files": [
     "dist",
     "src"
   ],
   "engines": {
-    "node": ">=10"
+    "node": ">=18"
   },
   "scripts": {
-    "start": "vite build --watch",
-    "dev": "yarn run start",
+    "dev": "vite build --watch",
     "build": "vite build",
     "lint": "eslint src --fix"
   },
@@ -24,23 +30,10 @@
       "pre-commit": "eslint src"
     }
   },
-  "author": "Kiran Gadhave (kirangadhave2@gmail.com), Jake Wagoner",
-  "size-limit": [
-    {
-      "path": "dist/packagescore.cjs.production.min.js",
-      "limit": "10 KB"
-    },
-    {
-      "path": "dist/packagescore.esm.js",
-      "limit": "10 KB"
-    }
-  ],
+  "author": "Kiran Gadhave (kirangadhave2@gmail.com), Jake Wagoner, Nate Lanza",
   "devDependencies": {
-    "@size-limit/preset-small-lib": "^7.0.5",
     "@types/d3": "^7.1.0",
     "husky": "^7.0.4",
-    "size-limit": "^7.0.5",
-    "tsdx": "^0.14.1",
     "tslib": "^2.3.1",
     "typescript": "^4.5.4"
   },

packages/core/src/convertConfig.ts

@@ -241,8 +241,6 @@ export function convertConfig(config: unknown): UpsetConfig {
     default:
       void 0;
   }
-  /* eslint-enable no-fallthrough */
-  /* eslint-enable no-void */
 
   if (!isUpsetConfig(config)) {
     // eslint-disable-next-line no-console

packages/core/src/process.ts

@@ -1,11 +1,12 @@
 import { DSVRowArray } from 'd3-dsv';
 
 import {
- max, mean, median, min, quantile,
+  max, mean, median, min, quantile,
 } from 'd3-array';
 
 import {
   AttributeList,
+  BaseIntersection,
   ColumnDefs,
   ColumnName,
   CoreUpsetData,
@@ -223,11 +224,14 @@ function getSets(
       type: 'Set',
       size: setMembership[col].length,
       setMembership: { ...setMembershipStatus, [col]: 'Yes' },
-      attributes: getSixNumberSummary(
-        items,
-        setMembership[col],
-        attributeColumns,
-      ),
+      attributes: {
+        ...getSixNumberSummary(
+          items,
+          setMembership[col],
+          attributeColumns,
+        ),
+        deviation: 0,
+      },
     };
 
     sets[set.id] = set;

packages/core/src/utils.ts

@@ -4,7 +4,7 @@ import {
 } from './types';
 
 /**
- * DEPRECATED: Currently serves only as an alias for structuredClone; use that instead.
+ * Version safe deep copy using structured cloning.
  * Create a deep copy (with all fields recursively copied) of an object using structured cloning;
  * if structured cloning fails, falls back to JSON serialization.
  * @param obj the object to copy

packages/core/vite.config.js

@@ -1,9 +1,7 @@
-/// <reference types="vitest" />
 import { defineConfig } from 'vite';
 
 import { join } from 'path';
 import dts from 'vite-plugin-dts';
-import viteTsConfigPaths from 'vite-tsconfig-paths';
 
 export default defineConfig({
   cacheDir: '../../node_modules/.vite/core',
@@ -13,10 +11,6 @@ export default defineConfig({
       // Faster builds by skipping tests. Set this to false to enable type checking.
       skipDiagnostics: true,
     }),
-
-    viteTsConfigPaths({
-      root: '../../',
-    }),
   ],
   server: { hmr: process.env.NODE_TESTING !== 'true' },
 
@@ -29,7 +23,7 @@ export default defineConfig({
       // Could also be a dictionary or array of multiple entry points.
       entry: 'src/index.ts',
       fileName: 'index',
-      formats: ['es'],
+      formats: ['es', 'cjs'],
     },
     rollupOptions: {
       // External packages that should not be bundled into your library.