flakey test

* Bump version: 1.2.0 → 1.3.0-rc.0

* Bump version: 1.3.0-rc.0 → 1.3.0

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 1.3.0
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 

.github/workflows/compatibility_tests.yml

@@ -7,6 +7,10 @@ on:
     branches:
       - main
 
+  # For debug - uncomment below to run on all PRs
+  pull_request:
+    branches: "*"
+
 env:
   JEST_ENV: prod
 
@@ -14,9 +18,9 @@ jobs:
   docker-build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Build docker image
@@ -29,23 +33,23 @@ jobs:
       fail-fast: false
       matrix:
         # note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
-        os: [ubuntu-latest, macos-latest, macos-11]
+        os: [ubuntu-latest, macos-latest, macos-13]
-        python-version: [3.8, 3.9, 3.10, 3.11]
+        python-version: ["3.10", "3.11"]
         cellxgene_build: [main, latest]
         # add anndata pinned version test for subset of matrix configurations,
         # in order to reduce matrix cross-product explosion
         include:
-          - python-version: 3.9
+          - python-version: 3.11
             cellxgene_build: latest
             # TODO: dynamically use the literal version in requirements.txt,
             # to avoid having to update this in manually in the future
             # TODO: Do not bother running this if anndata latest version
             # matches this pinned version, to avoid a redundant test
-            anndata_version: "==0.10.3"
+            anndata_version: "==0.10.9"
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache env vars
@@ -55,14 +59,14 @@ jobs:
         run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
       # FIXME: Only working for Linux
       - name: Python cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.PIP_CACHE }}
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -70,7 +74,7 @@ jobs:
             ${{ runner.os }}-node-
       - name: Brew cache (MacOS)
         if: startsWith(matrix.os, 'macos')
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ${{ env.BREW_CACHE }}
           key: ${{ runner.os }}-brew-
@@ -96,6 +100,7 @@ jobs:
           # keep same pip pkg versions as in the cxg release
           sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
           pip install -r server/requirements-dev.txt
+          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas
       - name: Install anndata version per matrix variable
         run: pip install anndata${{ matrix.anndata_version }}
       - name: Install node

.github/workflows/push_tests.yml

@@ -14,15 +14,15 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - run: |
           git fetch --depth=1 origin +${{github.base_ref}}
-      - name: Set up Python 3.9
+      - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -45,22 +45,22 @@ jobs:
   unit-test:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
-      - name: Set up Python 3.9 (pyenv) # pyenv needed for mlflow in cli annotate tests
+      - name: Set up Python 3.12 (pyenv) # pyenv needed for mlflow in cli annotate tests
         uses: gabrielfalcao/pyenv-action@v9
         with:
-          default: 3.9
+          default: 3.12
           command: pip install -U pip # upgrade pip after installing python
       - run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
       - name: Python cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -78,27 +78,29 @@ jobs:
     runs-on: macos-latest
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
-      - name: Set up Python 3.9
+      - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.12
       - name: Python cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
           restore-keys: |
             ${{ runner.os }}-node-
       - name: Install dependencies
-        run: make pydist install-dist
+        run: |
+          pip install setuptools
+          make pydist install-dist
       - name: Smoke tests (without annotations feature)
         run: |
           cd client && make smoke-test

README.md

@@ -1,4 +1,4 @@
-<img src="./docs/cellxgene-logo.png" width="300">
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/cellxgene-logo.png)
 
 _an interactive explorer for single-cell transcriptomics data_
 
@@ -11,7 +11,8 @@ CZ CELLxGENE Annotate (pronounced "cell-by-gene") is an interactive data explore
 
 Whether you need to visualize one thousand cells or one million, CELLxGENE Annotate helps you gain insight into your single-cell data.
 
-<img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/crossfilter.gif" width="350" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/category-breakdown.gif" width="350" height="200" hspace="30">
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/crossfilter.gif)
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/category-breakdown.gif)
 
 # Getting started
 
@@ -27,7 +28,7 @@ Whether you need to visualize one thousand cells or one million, CELLxGENE Annot
 
 ### Quick start
 
-To install CELLxGENE Annotate you need Python 3.6+. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
+To install CELLxGENE Annotate you need Python 3.10+. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
 
 Install the package.
 
@@ -58,7 +59,7 @@ Please [file an issue](https://github.com/chanzuckerberg/cellxgene/issues/new/ch
 ### Finding help
 
 We'd love to hear from you!
-For questions, suggestions, or accolades, [join the `#cellxgene-users` channel on the CZI Science Slack](https://join-cellxgene-users.herokuapp.com/) and say "hi!".
+For questions, suggestions, or accolades, join the `#cellxgene-users` channel on the [CZI Science Community Slack](https://czi.co/science-slack) and say "hi!".
 
 For any errors, [report bugs on Github](https://github.com/chanzuckerberg/cellxgene/issues).
 
@@ -66,22 +67,21 @@ For any errors, [report bugs on Github](https://github.com/chanzuckerberg/cellxg
 
 ### Contributing
 
-We warmly welcome contributions from the community! Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CELLxGENE Annotate. Please see the [dev_docs](https://github.com/chanzuckerberg/cellxgene/tree/main/dev_docs) for pull request suggestions, unit test details, local documentation preview, and other development specifics. 
+We warmly welcome contributions from the community! Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CELLxGENE Annotate. Please see the [dev_docs](https://github.com/chanzuckerberg/cellxgene/tree/main/dev_docs) for pull request suggestions, unit test details, local documentation preview, and other development specifics.
 
 This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/master/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.
 
 ### Reuse
 
-This project was started with the sole goal of empowering the scientific community to explore and understand their data. 
+This project was started with the sole goal of empowering the scientific community to explore and understand their data.
-As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from 
+As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
 this project. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT).
 
+Before extending CELLxGENE Annotate, we encourage you to reach out to us with ideas or questions. It might be possible that an
+extension could be directly contributed, which would make it available for a wider audience, or that it's on our
+[roadmap](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/roadmap.md) and under active development.
 
-Before extending CELLxGENE Annotate, we encourage you to reach out to us with ideas or questions. It might be possible that an 
+See the [CELLxGENE extensions](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/community-extensions.md) section of our documentation for examples of community use and CELLxGENE extensions.
-extension could be directly contributed, which would make it available for a wider audience, or that it's on our 
-[roadmap](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/roadmap.md) and under active development. 
-
-See the [CELLxGENE extensions](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/community-extensions.md) section of our documentation for examples of community use and CELLxGENE extensions. 
 
 ### Security
 

client/.nvmrc

@@ -0,0 +1 @@
+18.17.0

client/__tests__/e2e/config.js

@@ -1,4 +1,4 @@
-import * as ENV_DEFAULT from "../../../environment.default.json";
+import * as ENV_DEFAULT from "Code/cellxgene/environment.default.json";
 
 export const jestEnv = process.env.JEST_ENV || ENV_DEFAULT.JEST_ENV;
 export const appUrlBase =

client/__tests__/e2e/puppeteer.setup.js

@@ -5,15 +5,15 @@
  */
 
 import { setDefaultOptions } from "expect-puppeteer";
+import * as ENV_DEFAULT from "Code/cellxgene/environment.default.json";
 import { isDebug, isDev } from "./config";
-import * as ENV_DEFAULT from "../../../environment.default.json";
 
 // (thuang): This is the max time a test can take to run.
 // Since when debugging, we run slowMo and !headless, this means
 // a test can take more time to finish, so we don't want
 // jest to shut off the test too soon
 jest.setTimeout(2 * 60 * 1000);
-setDefaultOptions({ timeout: 20 * 1000 });
+setDefaultOptions({ timeout: 60 * 1000 });
 
 jest.retryTimes(ENV_DEFAULT.RETRY_ATTEMPTS);
 

client/__tests__/util/promiseLimit.test.js

@@ -76,7 +76,7 @@ describe("PromiseLimit", () => {
     const plimit = new PromiseLimit(1);
 
     let finishOrder = 0;
-    const callback = () => async () => {
+    const callback = async () => {
       await delay(100);
       const result = finishOrder;
       finishOrder += 1;
@@ -84,11 +84,11 @@ describe("PromiseLimit", () => {
     };
 
     const result = await Promise.all([
-      plimit.add(callback()),
+      plimit.add(callback),
-      plimit.priorityAdd(4, callback()),
+      plimit.priorityAdd(4, callback),
-      plimit.priorityAdd(0, callback()),
+      plimit.priorityAdd(0, callback),
-      plimit.priorityAdd(1, callback()),
+      plimit.priorityAdd(1, callback),
-      plimit.priorityAdd(-1, callback()),
+      plimit.priorityAdd(-1, callback),
     ]);
 
     expect(result).toEqual([0, 4, 2, 3, 1]);

client/configuration/eslint/eslint.js

@@ -82,13 +82,14 @@ module.exports = {
       },
       // Can't extend in overrides: https://github.com/eslint/eslint/issues/8813
       // "extends": ["plugin:jest/recommended"]
-      plugins: ["jest"],
+      plugins: ["jest", "no-floating-promise"],
       rules: {
         "jest/no-disabled-tests": "warn",
         "jest/no-focused-tests": "error",
         "jest/no-identical-title": "error",
         "jest/prefer-to-have-length": "warn",
         "jest/valid-expect": "error",
+        "no-floating-promise/no-floating-promise": 2,
       },
     },
   ],

client/jest-puppeteer.config.js

@@ -14,6 +14,7 @@ const DEFAULT_LAUNCH_CONFIG = {
   headless: !isHeadful,
   args: ["--ignore-certificate-errors", "--ignore-ssl-errors"],
   ignoreHTTPSErrors: true,
+  timeout: 90000,
   defaultViewport: {
     width: 1280,
     height: 960,

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "1.2.0",
+  "version": "1.3.0",
   "license": "MIT",
   "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
   "repository": "https://github.com/chanzuckerberg/cellxgene",
@@ -10,15 +10,16 @@
     "dev": "npm run build -- configuration/webpack/webpack.config.dev.js",
     "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js",
     "e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.js",
-    "fmt": "eslint --fix src __tests__",
+    "fmt": "eslint --fix __tests__",
-    "lint": "eslint --fix src __tests__",
+    "lint": "eslint --fix __tests__",
     "prod": "npm run build -- configuration/webpack/webpack.config.prod.js",
     "test": "jest --testPathIgnorePatterns e2e",
     "prepare": "cd .. && husky install client/.husky"
   },
   "engineStrict": true,
   "engines": {
-    "npm": ">=3.0.0"
+    "npm": ">=9.6.7",
+    "node": "^18.17.0"
   },
   "eslintConfig": {
     "extends": "./configuration/eslint/eslint.js"
@@ -77,7 +78,7 @@
     "whatwg-fetch": "^3.2.0"
   },
   "devDependencies": {
-    "@babel/core": "^7.13.16",
+    "@babel/core": "^7.25.2",
     "@babel/plugin-proposal-class-properties": "^7.10.4",
     "@babel/plugin-proposal-decorators": "^7.13.15",
     "@babel/plugin-proposal-export-namespace-from": "^7.10.4",
@@ -91,7 +92,7 @@
     "@babel/preset-react": "^7.13.13",
     "@babel/register": "^7.13.16",
     "@babel/runtime": "^7.13.16",
-    "@blueprintjs/eslint-plugin": "^0.3.0",
+    "@blueprintjs/eslint-plugin": "^6.1.4",
     "@sentry/webpack-plugin": "^1.15.0",
     "babel-jest": "^26.1.0",
     "babel-loader": "^8.1.0",
@@ -103,15 +104,16 @@
     "codecov": "^3.7.1",
     "css-loader": "^5.2.4",
     "css-minimizer-webpack-plugin": "^4.0.0",
-    "eslint": "^7.24.0",
+    "eslint": "^8.56.0",
-    "eslint-config-airbnb": "^18.2.0",
+    "eslint-config-airbnb": "^19.0.4",
     "eslint-config-prettier": "^8.2.0",
     "eslint-plugin-compat": "^4.2.0",
     "eslint-plugin-eslint-comments": "^3.2.0",
     "eslint-plugin-filenames": "^1.3.2",
     "eslint-plugin-import": "^2.24.2",
-    "eslint-plugin-jest": "^24.3.5",
+    "eslint-plugin-jest": "^28.8.3",
     "eslint-plugin-jsx-a11y": "^6.3.1",
+    "eslint-plugin-no-floating-promise": "^2.0.0",
     "eslint-plugin-react": "^7.23.2",
     "eslint-plugin-react-hooks": "^4.0.8",
     "expect-puppeteer": "^5.0.0",
@@ -123,7 +125,7 @@
     "jest-circus": "^27.0.6",
     "jest-environment-puppeteer": "^5.0.1",
     "jest-fetch-mock": "^3.0.3",
-    "jest-puppeteer": "^5.0.1",
+    "jest-puppeteer": "^6.2.0",
     "json-loader": "^0.5.7",
     "lint-staged": "^10.2.11",
     "lodash": "^4.17.21",
@@ -134,11 +136,11 @@
     "lodash.zip": "^4.2.0",
     "mini-css-extract-plugin": "^1.5.0",
     "prettier": "^2.0.5",
-    "puppeteer": "^8.0.0",
+    "puppeteer": "^10.4.0",
     "rimraf": "^3.0.2",
     "serve-favicon": "^2.5.0",
     "terser-webpack-plugin": "^5.1.1",
-    "webpack": "^5.88.2",
+    "webpack": "^5.94.0",
     "webpack-cli": "^4.6.0",
     "webpack-dev-middleware": "^4.1.0",
     "webpack-merge": "^5.0.9",

client/src/components/brushableHistogram/error.js

@@ -1,8 +1,8 @@
 import React from "react";
 import * as globals from "../../globals";
 
-const ErrorLoading = ({ displayName, zebra }) => (
+function ErrorLoading({ displayName, zebra }) {
-    <div
+  return <div
       style={{
         backgroundColor: zebra ? globals.lightestGrey : "white",
         fontStyle: "italic",
@@ -10,6 +10,6 @@ const ErrorLoading = ({ displayName, zebra }) => (
     >
       <span>{`Failure loading ${displayName}`}</span>
     </div>
-  );
+}
 
 export default ErrorLoading;

client/src/components/brushableHistogram/histogram.js

@@ -5,7 +5,7 @@ import * as d3 from "d3";
 import maybeScientific from "../../util/maybeScientific";
 import clamp from "../../util/clamp";
 
-const Histogram = ({
+function Histogram({
   field,
   fieldForId,
   display,
@@ -18,7 +18,7 @@ const Histogram = ({
   isColorBy,
   selectionRange,
   mini,
-}) => {
+}) {
   const svgRef = useRef(null);
   const [brush, setBrush] = useState(null);
 
@@ -186,6 +186,6 @@ const Histogram = ({
       ref={svgRef}
     />
   );
-};
+}
 
 export default Histogram;

client/src/components/brushableHistogram/loading.js

@@ -3,12 +3,8 @@ import { Button } from "@blueprintjs/core";
 
 import * as globals from "../../globals";
 
-const StillLoading = ({ zebra, displayName }) => 
+function StillLoading({ zebra, displayName }) {
-  /*
+  return <div
-    Render a loading indicator for the field.
-    */
-   (
-    <div
       data-testclass="gene-loading-spinner"
       style={{
         padding: globals.leftSidebarSectionPadding,
@@ -37,7 +33,6 @@ const StillLoading = ({ zebra, displayName }) =>
         </div>
       </div>
     </div>
-  )
+}
-;
 
 export default StillLoading;

client/src/components/categorical/category/annoDialogAddLabel.js

@@ -71,8 +71,7 @@ class Category extends React.PureComponent {
     const { metadataField, annotations, obsCrossfilter } = this.props;
 
     return (
-      <>
+      <AnnoDialog
-        <AnnoDialog
           isActive={
             annotations.isAddingNewLabel &&
             annotations.categoryAddingNewLabel === metadataField
@@ -105,7 +104,6 @@ class Category extends React.PureComponent {
             />
           }
         />
-      </>
     );
   }
 }

client/src/components/categorical/category/annoDialogEditCategoryName.js

@@ -105,8 +105,7 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
     const { metadataField, annotations } = this.props;
 
     return (
-      <>
+      <AnnoDialog
-        <AnnoDialog
           isActive={
             annotations.isEditingCategoryName &&
             annotations.categoryBeingEdited === metadataField
@@ -141,7 +140,6 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
             />
           }
         />
-      </>
     );
   }
 }

client/src/components/categorical/category/index.js

@@ -288,11 +288,8 @@ class Category extends React.PureComponent {
 
 export default Category;
 
-const StillLoading = ({ metadataField, checkboxID }) => (
+function StillLoading({ metadataField, checkboxID }) {
-  /*
+  return <div
-  We are still loading this category, so render a "busy" signal.
-  */
-  <div
     style={{
       maxWidth: globals.maxControlsWidth,
     }}
@@ -335,8 +332,8 @@ const StillLoading = ({ metadataField, checkboxID }) => (
       </div>
     </div>
   </div>
-);
+}
-const ErrorLoading = ({ metadataField, error }) => {
+function ErrorLoading({ metadataField, error }) {
   console.error(error); // log error to console as it is unexpected.
   return (
     <div style={{ marginBottom: 10, marginTop: 4 }}>
@@ -352,7 +349,7 @@ const ErrorLoading = ({ metadataField, error }) => {
       </span>
     </div>
   );
-};
+}
 
 const CategoryHeader = React.memo(
   ({

client/src/components/categorical/value/index.js

@@ -162,7 +162,7 @@ class CategoryValue extends React.Component {
     );
   };
 
-  shouldComponentUpdate = (nextProps, nextState) => {
+  shouldComponentUpdate(nextProps, nextState) {
     /*
     Checks to see if at least one of the following changed:
     * world state

client/src/components/embedding/index.js

@@ -109,7 +109,7 @@ const loadAllEmbeddingCounts = async ({ annoMatrix, available }) => {
   }));
 };
 
-const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }) => {
+function EmbeddingChoices({ onChange, annoMatrix, layoutChoice }) {
   const { available } = layoutChoice;
   const { data, error, isPending } = useAsync({
     promiseFn: loadAllEmbeddingCounts,
@@ -149,4 +149,4 @@ const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }) => {
     );
   }
   return null;
-};
+}

client/src/components/framework/logo.js

@@ -1,7 +1,7 @@
 import React from "react";
 import icon from "../../images/icon.png";
 
-const Logo = (props) => {
+function Logo(props) {
   const { size } = props;
   return (
     <img
@@ -11,6 +11,6 @@ const Logo = (props) => {
       alt="CELLxGENE Annotate Logo"
      />
   );
-};
+}
 
 export default Logo;

client/src/components/geneExpression/menus/addGeneToGenesetDialogue.js

@@ -53,8 +53,7 @@ class AddGeneToGenesetDialogue extends React.PureComponent {
     const { genesToAdd } = this.state;
 
     return (
-      <>
+      <AnnoDialog
-        <AnnoDialog
           isActive={genesetsUI.isAddingGenesToGeneset === geneset}
           inputProps={{ "data-testid": `${geneset}:create-label-dialog` }}
           primaryButtonProps={{
@@ -81,7 +80,6 @@ class AddGeneToGenesetDialogue extends React.PureComponent {
           handleSubmit={this.handleAddGeneToGeneSet}
           handleCancel={this.disableAddGeneMode}
         />
-      </>
     );
   }
 }

client/src/components/geneExpression/menus/createGenesetDialogue.js

@@ -125,8 +125,7 @@ class CreateGenesetDialogue extends React.PureComponent {
     const { genesetsUI, genesets } = this.props;
 
     return (
-      <>
+      <Dialog
-        <Dialog
           icon="tag"
           title="Create gene set"
           isOpen={genesetsUI.createGenesetModeActive}
@@ -210,7 +209,6 @@ class CreateGenesetDialogue extends React.PureComponent {
             </div>
           </form>
         </Dialog>
-      </>
     );
   }
 }

client/src/components/geneExpression/menus/editGenesetNameDialogue.js

@@ -109,8 +109,7 @@ class RenameGeneset extends React.PureComponent {
     } = this.props;
 
     return (
-      <>
+      <AnnoDialog
-        <AnnoDialog
           isActive={genesetsUI.isEditingGenesetName === originalGenesetName}
           inputProps={{
             "data-testid": `${genesetsUI.isEditingGenesetName}:rename-geneset-dialog`,
@@ -161,7 +160,6 @@ class RenameGeneset extends React.PureComponent {
           handleSubmit={this.renameGeneset}
           handleCancel={this.disableEditGenesetNameMode}
         />
-      </>
     );
   }
 }

client/src/components/graph/graph.js

@@ -935,7 +935,7 @@ class Graph extends React.Component {
   }
 }
 
-const ErrorLoading = ({ displayName, error, width, height }) => {
+function ErrorLoading({ displayName, error, width, height }) {
   console.log(error); // log to console as this is an unepected error
   return (
     <div
@@ -949,14 +949,10 @@ const ErrorLoading = ({ displayName, error, width, height }) => {
       <span>{`Failure loading ${displayName}`}</span>
     </div>
   );
-};
+}
 
-const StillLoading = ({ displayName, width, height }) => 
+function StillLoading({ displayName, width, height }) {
-  /*
+  return <div
-  Render a busy/loading indicator
-  */
-   (
-    <div
       style={{
         position: "fixed",
         fontWeight: 500,
@@ -976,7 +972,6 @@ const StillLoading = ({ displayName, width, height }) =>
         <span style={{ fontStyle: "italic" }}>Loading {displayName}</span>
       </div>
     </div>
-  )
+}
-;
 
 export default Graph;

client/src/components/graph/overlays/centroidLabels.js

@@ -167,7 +167,7 @@ class CentroidLabels extends PureComponent {
   }
 }
 
-const Label = ({
+function Label({
   label,
   dilatedValue,
   coords,
@@ -177,7 +177,7 @@ const Label = ({
   displayLabel,
   onMouseEnter,
   onMouseOut,
-}) => {
+}) {
   /*
   Render a label at a given coordinate.
   */
@@ -215,4 +215,4 @@ const Label = ({
       </text>
     </g>
   );
-};
+}

client/src/components/labelInput.js

@@ -159,8 +159,7 @@ export default class LabelInput extends React.PureComponent {
     };
     const { queryResults } = this.state;
     return (
-      <>
+      <Suggest
-        <Suggest
           fill
           inputValueRenderer={(i) => i.target}
           items={queryResults}
@@ -172,7 +171,6 @@ export default class LabelInput extends React.PureComponent {
           inputProps={inputProps}
           onKeyDown={this.handleKeyDown}
         />
-      </>
     );
   }
 }

client/src/components/leftSidebar/infoMenu.js

@@ -16,7 +16,7 @@ const InformationMenu = React.memo((props) => {
             rel="noopener"
           />
           <MenuItem
-            href="https://join-cellxgene-users.herokuapp.com/"
+            href="https://czi.co/science-slack"
             target="_blank"
             icon="chat"
             text="Chat"

client/src/components/miniHistogram/index.js

@@ -35,11 +35,11 @@ export default class MiniHistogram extends React.PureComponent {
     }
   };
 
-  componentDidMount = () => {
+  componentDidMount() {
     this.drawHistogram();
   };
 
-  componentDidUpdate = (prevProps) => {
+  componentDidUpdate(prevProps) {
     const { obsOrVarContinuousFieldDisplayName, bins } = this.props;
     if (
       prevProps.obsOrVarContinuousFieldDisplayName !==

client/src/components/miniStackedBar/index.js

@@ -42,12 +42,12 @@ export default class MiniStackedBar extends React.PureComponent {
     }
   };
 
-  componentDidUpdate = (prevProps) => {
+  componentDidUpdate(prevProps) {
     const { occupancy } = this.props;
     if (occupancy !== prevProps.occupancy) this.drawStacks();
   };
 
-  componentDidMount = () => {
+  componentDidMount() {
     this.drawStacks();
   };
 

client/src/components/util/truncate.js

@@ -32,7 +32,7 @@ const SECOND_HALF_INNER_STYLE = {
   right: 0,
 };
 
-export default (props) => {
+export default function(props) {
   const { children, isGenesetDescription, tooltipAddendum = "" } = props;
   // Truncate only support a single child with a text child
 

client/src/globals.js

@@ -1,6 +1,6 @@
 import { Colors } from "@blueprintjs/core";
+import ENV_DEFAULT from "Code/cellxgene/environment.default.json";
 import { dispatchNetworkErrorMessageToUser } from "./util/actionHelpers";
-import ENV_DEFAULT from "../../environment.default.json";
 
 /* overflow category values are created  using this string */
 export const overflowCategoryLabel = ": all other labels";

dev_docs/developer_guidelines.md

@@ -3,7 +3,7 @@
 ## Requirements
 
 - npm
-- Python 3.6+
+- Python 3.10+
 - Chrome
 
 [See dev section of README](../README.md)
@@ -148,6 +148,6 @@ If you would like to run the smoke tests against a hot-reloaded version of the c
 
 ### Tips
 
-- You can also install/launch the server side code from npm scrips (requires python3.6 with virtualenv) with the `scripts/backend_dev` script.
+- You can also install/launch the server side code from npm scrips (requires python3.10 with virtualenv) with the `scripts/backend_dev` script.
 
-- Check out [e2e Tests](e2e_tests.md) for more details
+- Check out [e2e Tests](e2e_tests.md) for more details

dev_docs/developer_scripts.md

@@ -11,9 +11,10 @@ $PROJECT_ROOT`.
 ### Build
 
 **Usage:** from the `$PROJECT_ROOT` directory run:
-* `make build` builds whole app client and server
+
-* `make build-client` runs webpack build
+- `make build` builds whole app client and server
-* `make build-for-server-dev` builds client and copies output directly into
+- `make build-client` runs webpack build
+- `make build-for-server-dev` builds client and copies output directly into
   source tree (only for server devlopment)
 
 ### Clean
@@ -21,17 +22,19 @@ $PROJECT_ROOT`.
 Deletes generated files.
 
 **Usage:** from the `$PROJECT_ROOT` directory run:
-* `make clean` cleans everything including node modules (means build with take
+
+- `make clean` cleans everything including node modules (means build with take
   a while
-* `make clean-lite` cleans built directories
+- `make clean-lite` cleans built directories
-* `make clean-server` cleans source tree
+- `make clean-server` cleans source tree
 
 ### Distribution
 
 Creates distribution for python module to upload to pypi.
 
 **Usage:** from the `$PROJECT_ROOT` directory run:
-* `make pydist` builds code and then builds sdist
+
+- `make pydist` builds code and then builds sdist
 
 ### Release
 
@@ -42,16 +45,18 @@ See `release_process.md`.
 Installs requirements files.
 
 **Usage:** from the `$PROJECT_ROOT` directory run:
-* `make dev-env` installs requirements and requirments-dev (for building code)
+
+- `make dev-env` installs requirements and requirments-dev (for building code)
 
 ### Installing cellxgene packages
 
 **Usage:** from the `$PROJECT_ROOT` directory:
-* `install-dev` - installs from local source tree
+
-* `install-release-test` - installs from test pypi
+- `install-dev` - installs from local source tree
-* `install-release` - installs from pypi
+- `install-release-test` - installs from test pypi
-* `install-dist` - installs from local dist folder
+- `install-release` - installs from pypi
-* `uninstall` - uninstalls cellxgene
+- `install-dist` - installs from local dist folder
+- `uninstall` - uninstalls cellxgene
 
 ## Client-level scripts
 
@@ -62,8 +67,9 @@ Installs requirements files.
 **About** Serve the current client javascript independently from the `server` code.
 
 **Requires**
-* The server to be running. Best way to do this is with [backend_dev](#backend_dev).
+
-* `make ci` to install the necessary node modules
+- The server to be running. Best way to do this is with [backend_dev](#backend_dev).
+- `make ci` to install the necessary node modules
 
 **Usage:** from the `$PROJECT_ROOT/client` directory run `make start-frontend`
 
@@ -75,23 +81,24 @@ the FE developer gets the current version of the backend with a single command
 and no knowledge of python necessary. It creates and activates a virtual
 environment and installs cellxgene from the current branch.
 
-**Requires** `Python3.6+`, `virtual-env`, `pip`
+**Requires** `Python3.10+`, `virtual-env`, `pip`
 
 **Usage:** from the `$PROJECT_ROOT` directory run `./scripts/backend_dev`
 
 **Options:**
-* In parallel, you can then launch the node development server to serve the
+
+- In parallel, you can then launch the node development server to serve the
   current state of the FE with [`start-frontend`](#start-frontend), usually in
   a different terminal tab.
-* You can also select a specific dataset using `DATASET=<dataset path> ./scripts/backend_dev`.
+- You can also select a specific dataset using `DATASET=<dataset path> ./scripts/backend_dev`.
-* You can also use `CXG_OPTIONS` to pass options to the `cellxgene launch`
+- You can also use `CXG_OPTIONS` to pass options to the `cellxgene launch`
   command, as in `CXG_OPTIONS='--disable-annotations' ./scripts/backend_dev`.
 
 **Breakdown**
 
 | command                                  | purpose                                                    |
 | ---------------------------------------- | ---------------------------------------------------------- |
-| python3.6 -m venv cellxgene              | creates cellxgene virtual environment                      |
+| python3.12 -m venv cellxgene             | creates cellxgene virtual environment                      |
 | source cellxgene/bin/activate            | activates virtual environment                              |
 | yes \| pip uninstall cellxgene \|\| true | uninstalls cellxgene (if installed)                        |
 | pip install -e .                         | installs current local version of cellxgene                |
@@ -102,14 +109,15 @@ environment and installs cellxgene from the current branch.
 Methods used to test the client javascript code
 
 **Usage:** from the `$PROJECT_ROOT/client` directory run:
-* `make unit-test` Runs all unit tests. It excludes any tests in the e2e
+
+- `make unit-test` Runs all unit tests. It excludes any tests in the e2e
   folder. This is used by travis to run unit tests.
-* `make smoke-test` Starts backend development server and runs end to end
+- `make smoke-test` Starts backend development server and runs end to end
   tests. This is what travis runs. It depends on the `e2e` and the
   `backend-dev` targets. One starts the server, the other runs the tests. If
   developing a front-end feature and just checking if tests pass, this is
   probabaly the one you want to run.
-* `npm run e2e` Runs backend tests without starting the server. You will need to
+- `npm run e2e` Runs backend tests without starting the server. You will need to
   start the rest api separately with the pbmc3k.h5ad file. Note you can use
   the `JEST_ENV` environment variable to change how JEST runs in the browser.
   The test runs against `localhost:3000` by default. You can use the

server/__init__.py

@@ -2,7 +2,7 @@ import logging
 import sys
 from server.common.utils.utils import import_plugins
 
-__version__ = "1.2.0"
+__version__ = "1.3.0"
 display_version = "cellxgene v" + __version__
 
 try:

server/common/config/dataset_config.py

@@ -176,7 +176,7 @@ class DatasetConfig(BaseConfig):
         self.validate_correct_type_of_configuration_attribute("diffexp__top_n", int)
 
         data_adaptor = self.get_data_adaptor()
-        if self.diffexp__enable and data_adaptor.parameters.get("diffexp_may_be_slow", False):
+        if self.diffexp__enable and data_adaptor.parameters.get("diffexp-may-be-slow", False):
             context["messagefn"](
                 "CAUTION: due to the size of your dataset, " "running differential expression may take longer or fail."
             )

server/common/utils/type_conversion_utils.py

@@ -116,7 +116,7 @@ def _get_type_info(array: Union[np.ndarray, pd.Series, pd.Index]) -> Tuple[np.dt
         raise TypeError("Unsupported data type.")
 
     dtype = array.dtype
-
+    
     res = _get_type_info_from_dtype(dtype)
     if res is not None:
         return res
@@ -140,7 +140,6 @@ def _get_type_info(array: Union[np.ndarray, pd.Series, pd.Index]) -> Tuple[np.dt
 
     if dtype.kind in ["i", "u"] and _can_cast_array_values_to_int32(array):
         return (np.int32, {"type": "int32"})
-
     if dtype.kind == "f":
         _float64_warning(array.dtype)
         return (np.float32, {"type": "float32"})

server/data_anndata/anndata_adaptor.py

@@ -211,7 +211,7 @@ class AnndataAdaptor(DataAdaptor):
         # heuristic
         n_values = self.data.shape[0] * self.data.shape[1]
         if (n_values > 1e8 and self.server_config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
-            self.parameters.update({"diffexp_may_be_slow": True})
+            self.parameters.update({"diffexp-may-be-slow": True})
 
     def _is_valid_layout(self, arr):
         """return True if this layout data is a valid array for front-end presentation:

server/requirements-annotate.txt

@@ -1,2 +1,2 @@
-mlflow==1.27.0
+mlflow==2.16.0
 scanpy

server/requirements.txt

@@ -7,16 +7,17 @@ Flask-Cors>=3.0.9
 Flask-RESTful>=0.3.6
 flask-server-timing>=0.1.2
 flask-talisman>=0.7.0
-flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
+flatbuffers==2.0.7
 flatten-dict>=0.2.0
 fsspec>0.8.0
 gunicorn>=20.0.4
 h5py>=3.0.0
-numba>=0.51.2
+numba>=0.60.0
-numpy>1.22
+numpy==2.0.1
 packaging>=20.0
-pandas<2.0.0
+pandas>=2.2.2
 PyYAML>=5.4  # CVE-2020-14343
 requests>=2.22.0
 s3fs==0.4.2
-scipy>=1.4
+scipy>=1.4
+setuptools

setup.py

@@ -14,7 +14,7 @@ with open("server/requirements-annotate.txt") as fh:
 
 setup(
     name="cellxgene",
-    version="1.2.0",
+    version="1.3.0",
     packages=find_packages(),
     url="https://github.com/chanzuckerberg/cellxgene",
     license="MIT",
@@ -24,7 +24,7 @@ setup(
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=requirements,
-    python_requires=">=3.6",
+    python_requires=">=3.10",
     include_package_data=True,
     zip_safe=False,
     classifiers=[
@@ -37,8 +37,9 @@ setup(
         "Operating System :: MacOS :: MacOS X",
         "Programming Language :: JavaScript",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.6",
+        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
         "Programming Language :: Python :: 3 :: Only",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],

test/unit/compute/test_est_dist.py

@@ -65,13 +65,13 @@ class EstDistTest(unittest.TestCase):
 
         # non-finites
         self.assertEqual(estimate_approximate_distribution(np.array([np.nan])), XApproximateDistribution.NORMAL)
-        self.assertEqual(estimate_approximate_distribution(np.array([np.PINF])), XApproximateDistribution.NORMAL)
+        self.assertEqual(estimate_approximate_distribution(np.array([np.inf])), XApproximateDistribution.NORMAL)
-        self.assertEqual(estimate_approximate_distribution(np.array([np.NINF])), XApproximateDistribution.NORMAL)
+        self.assertEqual(estimate_approximate_distribution(np.array([np.inf])), XApproximateDistribution.NORMAL)
         self.assertEqual(
-            estimate_approximate_distribution(np.array([np.PINF, np.NINF, 0])), XApproximateDistribution.NORMAL
+            estimate_approximate_distribution(np.array([np.inf, np.inf, 0])), XApproximateDistribution.NORMAL
         )
         self.assertEqual(
-            estimate_approximate_distribution(np.array([np.nan, np.PINF, np.NINF])), XApproximateDistribution.NORMAL
+            estimate_approximate_distribution(np.array([np.nan, np.inf, np.inf])), XApproximateDistribution.NORMAL
         )
 
         raw = np.random.exponential(scale=1000, size=(50, 3))
@@ -82,15 +82,15 @@ class EstDistTest(unittest.TestCase):
             XApproximateDistribution.COUNT,
         )
         self.assertEqual(
-            estimate_approximate_distribution(put(raw, [1], [np.PINF])),
+            estimate_approximate_distribution(put(raw, [1], [np.inf])),
             XApproximateDistribution.COUNT,
         )
         self.assertEqual(
-            estimate_approximate_distribution(put(raw, [1], [np.NINF])),
+            estimate_approximate_distribution(put(raw, [1], [np.inf])),
             XApproximateDistribution.COUNT,
         )
         self.assertEqual(
-            estimate_approximate_distribution(put(raw, [1, 3, 88], [np.nan, np.PINF, np.NINF])),
+            estimate_approximate_distribution(put(raw, [1, 3, 88], [np.nan, np.inf, np.inf])),
             XApproximateDistribution.COUNT,
         )
         self.assertEqual(
@@ -103,15 +103,15 @@ class EstDistTest(unittest.TestCase):
             XApproximateDistribution.NORMAL,
         )
         self.assertEqual(
-            estimate_approximate_distribution(put(logged, [1], [np.PINF])),
+            estimate_approximate_distribution(put(logged, [1], [np.inf])),
             XApproximateDistribution.NORMAL,
         )
         self.assertEqual(
-            estimate_approximate_distribution(put(logged, [1], [np.NINF])),
+            estimate_approximate_distribution(put(logged, [1], [np.inf])),
             XApproximateDistribution.NORMAL,
         )
         self.assertEqual(
-            estimate_approximate_distribution(put(logged, [1, 3, 88], [np.nan, np.PINF, np.NINF])),
+            estimate_approximate_distribution(put(logged, [1, 3, 88], [np.nan, np.inf, np.inf])),
             XApproximateDistribution.NORMAL,
         )
         self.assertEqual(

test/unit/utils/test_jsonify_strict.py

@@ -16,10 +16,10 @@ class TestJsonifyStrict(unittest.TestCase):
             jsonify_strict({"nan": [np.nan]})
 
         with self.assertRaises(ValueError):
-            jsonify_strict({"pinf": [np.PINF]})
+            jsonify_strict({"pinf": [np.inf]})
 
         with self.assertRaises(ValueError):
-            jsonify_strict({"ninf": [np.NINF]})
+            jsonify_strict({"ninf": [np.inf]})
 
     def test_jsonify_numpy_ndarray(self):
         values = {

test/unit/utils/test_type_conversion_utils.py

@@ -42,7 +42,7 @@ class TestTypeConversionUtils(unittest.TestCase):
             with self.assertRaises(TypeError):
                 get_schema_type_hint_from_dtype(np.dtype(dtype))
 
-        for dtype in [np.float16, np.float32, np.float64]:
+        for dtype in [np.float32, np.float64]:
             self.assertEqual(get_schema_type_hint_from_dtype(np.dtype(dtype)), {"type": "float32"})
 
         for dtype in [np.dtype(object), np.dtype(str)]:
@@ -123,17 +123,18 @@ int_OK_cases = [
 
 float_OK_cases = [
     {
+        "test_case": "float_OK_cases",
         "data": data,
         "expected_encoding_dtype": np.float32,
         "expected_schema_hint": {"type": "float32"},
-        "logs": None if data.dtype != np.float64 else {"level": logging.WARNING, "output": "may lose precision"},
+        "logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
     }
-    for dtype in [np.float16, np.float32, np.float64]
+    for dtype in [np.float32, np.float64]
     for data in [
         np.arange(-128, 1000, dtype=dtype),
         pd.Series(np.arange(-128, 1000, dtype=dtype)),
         pd.Index(np.arange(-129, 1000, dtype=dtype)),
-        np.array([-np.nan, np.NINF, -1, np.NZERO, 0, np.PZERO, 1, np.PINF, np.nan], dtype=dtype),
+        np.array([-np.nan, -np.inf, -1, -0.0, 0, 0.0, 1, np.inf, np.nan], dtype=dtype),
         np.array([np.finfo(dtype).min, 0, np.finfo(dtype).max], dtype=dtype),
         sparse.csr_matrix((10, 100), dtype=dtype),
     ]
@@ -198,12 +199,13 @@ category_numeric_OK_cases = [
     # numeric, no NA/NaN, float
     *[
         {
+            "test_case": "numeric, no NA/NaN, float",
             "data": data,
             "expected_encoding_dtype": np.float32,
             "expected_schema_hint": {"type": "categorical"},
-            "logs": {"level": logging.WARNING, "output": "may lose precision"},
+            "logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
         }
-        for dtype in [np.float16, np.float32, np.float64]
+        for dtype in [np.float32, np.float64]
         for data in [
             pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category"),
             pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category").cat.remove_categories([1]),
@@ -213,10 +215,11 @@ category_numeric_OK_cases = [
     # numeric, has NA-induced cast to float32
     *[
         {
+            "test_case": "numeric, has NA-induced cast to float32",
             "data": data,
             "expected_encoding_dtype": np.float32,
             "expected_schema_hint": {"type": "categorical"},
-            "logs": {"level": logging.WARNING, "output": "may lose precision"},
+            "logs": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
         }
         for dtype in [
             np.int8,
@@ -227,7 +230,6 @@ category_numeric_OK_cases = [
             np.uint32,
             np.int64,
             np.uint64,
-            np.float16,
             np.float32,
             np.float64,
         ]
@@ -312,7 +314,6 @@ class TestTypeInference(unittest.TestCase, AssertNoLog):
                     self.assertEqual(encoding_dtype, self.expected_encoding_dtype)
                     self.assertEqual(schema_hint, self.expected_schema_hint)
                     self.assertIn(logs["output"], logger.output[0])
-
             else:
                 with self.assertNoLogs(logging.getLogger(), logging.WARNING):
                     encoding_dtype, schema_hint = get_dtype_and_schema_of_array(self.data)