chore: Release 1.3.0 (#2700)

* 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 = 1.1.1
+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/ISSUE_TEMPLATE/tech-issue.md

@@ -0,0 +1,23 @@
+---
+name: Tech Issue
+about: Engineering-specific technical work that is not product-specific. Engineering team "owns" these issues.
+title: ""
+labels: tech
+assignees: ""
+---
+
+## Motivation
+
+Why is this work important to engineers?
+
+## Definition of Done
+
+What should the end result look like? What will have been changed?
+
+## Tasks
+
+Detail the specific tasks that can be used to accomplish the desired changes.
+If detailed steps cannot be provided at this time, please file a [Tech Proposal](https://docs.google.com/document/d/1o2vuvl-kXwRJN1nBoPzJS_MAQgDGYnjmPZWa4qRDi-I/edit#heading=h.7dvzhm7gqc3v) instead.
+
+- [ ]
+- [ ]

.github/workflows/close-stale-prs.yml

@@ -0,0 +1,23 @@
+name: Close inactive pull requests
+on:
+  schedule:
+    - cron: "30 1 * * *"
+
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v5
+        with:
+          days-before-issue-stale: -1 # Do not mark any issues as stale
+          days-before-pr-stale: 14
+          days-before-pr-close: 3
+          stale-pr-message: "This PR has not seen any activity in the past 2 weeks; if no one comments or reviews it in the next 3 days, this PR will be closed."
+          close-pr-message: "This PR was closed because it has been inactive for 17 days, 3 days since being marked as stale. Please re-open if you still need this to be addressed."
+          stale-pr-label: "stale"
+          close-pr-label: "autoclosed"
+          exempt-draft-pr: true
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/compatibility_tests.yml

@@ -2,7 +2,7 @@ name: Compatibility Tests
 
 on:
   schedule:
-    - cron: '0 8 7 * 2'
+    - cron: "0 8 7 * 2"
   push:
     branches:
       - main
@@ -14,9 +14,9 @@ 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
@@ -28,96 +28,85 @@ jobs:
     strategy:
       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-13]
-        os: [ubuntu-latest, macos-latest, macos-11]
+        python-version: ["3.10", "3.11", "3.12"]
-        python-version: [3.6, 3.7, 3.8, 3.9]
         cellxgene_build: [main, latest]
-        exclude:
-          # 3.6 no longer avail on Big Sur (`macos-11`)
-          - os: macos-11
-            python-version: 3.6
-          # no pypi build exists for macos+py3.9 and source install fails to
-          # install `tables` py pkg (a `scanpy` dependency), so we test py3.9
-          # only on ubuntu
-          - os: macos-11
-            python-version: 3.9
-          - os: macos-latest
-            python-version: 3.9
         # add anndata pinned version test for subset of matrix configurations,
         # in order to reduce matrix cross-product explosion
         include:
-          - python-version: 3.8
+          - python-version: 3.12
             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: '==0.7.6'
+            anndata_version: "==0.10.9"
     steps:
-    - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
-      with:
+        with:
-        python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python-version }}
-    - name: Cache env vars
+      - name: Cache env vars
-      run: echo "PIP_CACHE=`python -m pip cache dir`" >> $GITHUB_ENV
+        run: echo "PIP_CACHE=`python -m pip cache dir`" >> $GITHUB_ENV
-    - name: Cache env vars (MacOS)
+      - name: Cache env vars (MacOS)
-      if: startsWith(matrix.os, 'macos')
+        if: startsWith(matrix.os, 'macos')
-      run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
+        run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
-    # FIXME: Only working for Linux
+      # FIXME: Only working for Linux
-    - name: Python cache
+      - name: Python cache
-      uses: actions/cache@v1
+        uses: actions/cache@v4
-      with:
+        with:
-        path: ${{ env.PIP_CACHE }}
+          path: ${{ env.PIP_CACHE }}
-        key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
+          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
-        restore-keys: |
+          restore-keys: |
-          ${{ runner.os }}-pip-
+            ${{ runner.os }}-pip-
-    - name: Node cache
+      - name: Node cache
-      uses: actions/cache@v1
+        uses: actions/cache@v4
-      with:
+        with:
-        path: ~/.npm
+          path: ~/.npm
-        key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
+          key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
-        restore-keys: |
+          restore-keys: |
-          ${{ runner.os }}-node-
+            ${{ runner.os }}-node-
-    - name: Brew cache (MacOS)
+      - name: Brew cache (MacOS)
-      if: startsWith(matrix.os, 'macos')
+        if: startsWith(matrix.os, 'macos')
-      uses: actions/cache@v1
+        uses: actions/cache@v4
-      with:
+        with:
-        path: ${{ env.BREW_CACHE }}
+          path: ${{ env.BREW_CACHE }}
-        key: ${{ runner.os }}-brew-
+          key: ${{ runner.os }}-brew-
-    - name: Install dependencies (Ubuntu Linux)
+      - name: Install dependencies (Ubuntu Linux)
-      if: startsWith(matrix.os, 'ubuntu')
+        if: startsWith(matrix.os, 'ubuntu')
-      run: |
+        run: |
-        sudo apt-get update
+          sudo apt-get update
-        sudo apt-get install -y libhdf5-serial-dev
+          sudo apt-get install -y libhdf5-serial-dev
-    - name: Install dependencies (MacOS)
+      - name: Install dependencies (MacOS)
-      if: startsWith(matrix.os, 'macos')
+        if: startsWith(matrix.os, 'macos')
-      run: brew install hdf5
+        run: brew install hdf5
-    - name: Install cellxgene from `main` branch
+      - name: Install cellxgene from `main` branch
-      if: matrix.cellxgene_build == 'main'
+        if: matrix.cellxgene_build == 'main'
-      run: |
+        run: |
-        pip install -r server/requirements-dev.txt
+          pip install -r server/requirements-dev.txt
-        make pydist install-dist
+          make pydist install-dist
-    - name: Install cellxgene from latest release (pypi.org)
+      - name: Install cellxgene from latest release (pypi.org)
-      if: matrix.cellxgene_build == 'latest'
+        if: matrix.cellxgene_build == 'latest'
-      run: |
+        run: |
-        pip install --upgrade cellxgene
+          pip install --upgrade cellxgene
-        # install the additional dev requirements on top of what is in the
+          # install the additional dev requirements on top of what is in the
-        # cellxgene pip package, which are needed for testing, but otherwise
+          # cellxgene pip package, which are needed for testing, but otherwise
-        # keep same pip pkg versions as in the cxg release
+          # keep same pip pkg versions as in the cxg release
-        sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
+          sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
-        pip install -r server/requirements-dev.txt
+          pip install -r server/requirements-dev.txt
-    - name: Install anndata version per matrix variable
+          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas flatbuffers==2.0.7
-      run: pip install anndata${{ matrix.anndata_version }}
+      - name: Install anndata version per matrix variable
-    - name: Install node
+        run: pip install anndata${{ matrix.anndata_version }}
-      run: make dev-env-client
+      - name: Install node
-    # Run different types of test separately, to facilitate troubleshooting
+        run: make dev-env-client
-    - name: Unit Tests - client
+      # Run different types of test separately, to facilitate troubleshooting
-      run: make unit-test-client
+      - name: Unit Tests - client
-    - name: Unit Tests - server
+        run: make unit-test-client
-      run: make unit-test-server
+      - name: Unit Tests - server
-    - name: Smoke Tests
+        run: make unit-test-server
-      run: make smoke-test
+      - name: Smoke Tests
+        run: make smoke-test
     # FIXME: Fails intermittently. See https://app.zenhub.com/workspaces/single-cell-5e2a191dad828d52cc78b028/issues/chanzuckerberg/cellxgene/2415
     # - name: Smoke Tests with Annotations
     #   run: make smoke-test-annotations

.github/workflows/lint-pr-commit-message.yml

@@ -0,0 +1,19 @@
+
+name: "Lint PR commit message"
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - edited
+      - synchronize
+
+jobs:
+  main:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v3.4.1
+        with:
+          validateSingleCommit: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.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 3.7
+      - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          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 3.7 (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: 3.7
+          default: 3.12
-          command: pip install -U pip  # upgrade pip after installing python
+          command: pip install -U pip # upgrade pip after installing python
-      - run: pip install virtualenv  # virtualenv needed for mlflow in cli annotate tests
+      - 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 3.7
+      - name: Set up Python 3.12
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          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
@@ -110,10 +112,10 @@ jobs:
   #   timeout-minutes: 20
   #   steps:
   #     - uses: actions/checkout@v2
-  #     - name: Set up Python 3.7
+  #     - name: Set up Python 3.9
   #       uses: actions/setup-python@v4
   #       with:
-  #         python-version: 3.7
+  #         python-version: 3.9
   #     - name: Python cache
   #       uses: actions/cache@v1
   #       with:

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2017-2022 Chan Zuckerberg Initiative
+Copyright (c) 2017-2023 Chan Zuckerberg Initiative
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

README.md

@@ -27,7 +27,7 @@ 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 +58,7 @@ 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 +66,21 @@ 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/puppeteer.setup.js

@@ -13,7 +13,7 @@ import * as ENV_DEFAULT from "../../../environment.default.json";
 // 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/configuration/babel/babel.dev.js

@@ -16,8 +16,8 @@ module.exports = {
     "@babel/plugin-proposal-function-bind",
     ["@babel/plugin-proposal-decorators", { legacy: true }],
     ["@babel/plugin-proposal-class-properties", { loose: true }],
-    ["@babel/plugin-proposal-private-methods", { loose: true }],
+    ["@babel/plugin-transform-private-methods", { loose: true }],
-    ["@babel/plugin-proposal-private-property-in-object", { loose: true }],
+    ["@babel/plugin-transform-private-property-in-object", { loose: true }],
     "@babel/plugin-proposal-export-namespace-from",
     "@babel/plugin-proposal-optional-chaining",
     "@babel/plugin-proposal-nullish-coalescing-operator",

client/configuration/babel/babel.prod.js

@@ -15,8 +15,8 @@ module.exports = {
     "@babel/plugin-proposal-function-bind",
     ["@babel/plugin-proposal-decorators", { legacy: true }],
     ["@babel/plugin-proposal-class-properties", { loose: true }],
-    ["@babel/plugin-proposal-private-methods", { loose: true }],
+    ["@babel/plugin-transform-private-methods", { loose: true }],
-    ["@babel/plugin-proposal-private-property-in-object", { loose: true }],
+    ["@babel/plugin-transform-private-property-in-object", { loose: true }],
     "@babel/plugin-proposal-export-namespace-from",
     "@babel/plugin-transform-react-constant-elements",
     "@babel/plugin-transform-runtime",

client/configuration/webpack/webpack.config.shared.js

@@ -1,7 +1,7 @@
 const path = require("path");
 const fs = require("fs");
 const MiniCssExtractPlugin = require("mini-css-extract-plugin");
-const ObsoleteWebpackPlugin = require("obsolete-webpack-plugin");
+const ObsoleteWebpackPlugin = require("webpack-obsolete-plugin");
 
 const src = path.resolve("src");
 const nodeModules = path.resolve("node_modules");

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": "1.1.1",
+  "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",
@@ -18,7 +18,8 @@
   },
   "engineStrict": true,
   "engines": {
-    "npm": ">=3.0.0"
+    "npm": ">=9.6.7",
+    "node": "^18.17.0"
   },
   "eslintConfig": {
     "extends": "./configuration/eslint/eslint.js"
@@ -77,16 +78,17 @@
     "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",
     "@babel/plugin-proposal-function-bind": "^7.10.5",
     "@babel/plugin-proposal-nullish-coalescing-operator": "^7.10.4",
     "@babel/plugin-proposal-optional-chaining": "^7.10.4",
+    "@babel/plugin-transform-private-property-in-object": "^7.22.11",
     "@babel/plugin-transform-react-constant-elements": "^7.13.13",
     "@babel/plugin-transform-runtime": "^7.13.15",
-    "@babel/preset-env": "^7.13.15",
+    "@babel/preset-env": "^7.22.20",
     "@babel/preset-react": "^7.13.13",
     "@babel/register": "^7.13.16",
     "@babel/runtime": "^7.13.16",
@@ -105,7 +107,7 @@
     "eslint": "^7.24.0",
     "eslint-config-airbnb": "^18.2.0",
     "eslint-config-prettier": "^8.2.0",
-    "eslint-plugin-compat": "^3.8.0",
+    "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",
@@ -122,7 +124,7 @@
     "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",
@@ -132,16 +134,16 @@
     "lodash.map": "^4.6.0",
     "lodash.zip": "^4.2.0",
     "mini-css-extract-plugin": "^1.5.0",
-    "obsolete-webpack-plugin": "^0.5.6",
     "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": "^5.34.0",
+    "webpack": "^5.94.0",
     "webpack-cli": "^4.6.0",
     "webpack-dev-middleware": "^4.1.0",
-    "webpack-merge": "^5.0.9"
+    "webpack-merge": "^5.0.9",
+    "webpack-obsolete-plugin": "^1.0.5"
   },
   "jest": {
     "testMatch": [
@@ -175,13 +177,13 @@
             }
           ],
           [
-            "@babel/plugin-proposal-private-methods",
+            "@babel/plugin-transform-private-methods",
             {
               "loose": true
             }
           ],
           [
-            "@babel/plugin-proposal-private-property-in-object",
+            "@babel/plugin-transform-private-property-in-object",
             {
               "loose": true
             }

client/src/annoMatrix/whereCache.js

@@ -52,7 +52,7 @@ import { _getColumnDimensionNames } from "./schema";
 import { _hashStringValues } from "./query";
 
 export function _whereCacheGet(whereCache, schema, field, query) {
-  /* 
+  /*
 	query will either be an where query (object) or a column name (string).
 
 	Return array of column labels or undefined.
@@ -169,5 +169,6 @@ function __whereCacheMerge(dst, src) {
 }
 
 export function _whereCacheMerge(...caches) {
+  // eslint-disable-next-line compat/compat -- not using web APIs
   return caches.reduce(__whereCacheMerge, {});
 }

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"

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

dev_docs/release_process.md

@@ -26,14 +26,14 @@ Steps must be run from the project directory and in a virtual env with all the d
 3. In the release branch, run `make create-release-candidate PART=[major | minor | patch]`. This will bump the version and create a release *candidate* version (e.g. `0.3.0-rc.0`).
 4. Commit changes, push the new branch to origin and open a `DO NOT MERGE` draft PR, which will run tests on your branch. We will use this PR later
 5. Upload the release candidate to Test PyPI by running the command `make release-candidate-to-test-pypi`. (Make sure you are registered for PyPI and Test PyPI and you have write access to the cellxgene PyPI package for both).
-6. Verify the release candidate in a fresh virtual environment by running `make install-release-test` which installs the cellxgene build you just uploaded to Test PyPI. The PM should do this too.
+6. Verify the release candidate in a fresh virtual environment by running `VERSION=<X>.<Y>.<Z>rc.<#> make install-release-test` which installs the cellxgene build you just uploaded to Test PyPI (note that the version value does not include a dash `-`!). The PM should do this too. Note that you may need to run `hash -r` to ensure the cellxgene executable that was just installed is found in your shell path.
 7. If you find errors with the release candidate, fix them in main, rebase, and run `make recreate-release-candidate` to increment the release candidate version (i.e. `0.3.0-rc.0` -> `0.3.0-rc.1`). Then go back to Steps 5 and 6 to re-upload and re-test the new release candidate.
 8. If everything looks good, push the release to Test PyPI without the release candidate tag by running the command `make release-final-to-test-pypi` (i.e. `0.3.0-rc.1` -> `0.3.0`).
     - **NOTE:** Once you push the final release version to Test PyPI, you cannot ever re-upload the build again. If you need to make changes to the build, you will have to "burn" the version number and bump the part again and go back to step 1 with a brand new version number. For example, if you upload `0.3.0` to Test PyPI and realize there's a bug, you will have to create a new version `0.4.0` and there will be no `0.3.0` version of cellxgene. This is why testing the release candidate is very important.
 9. Publish the open draft PR for the release and conduct a PR review.
 10. Merge to the `main` branch.
 11. Publish to PyPI (prod) (assuming you that you have registered for PyPI, and that you have write access to the cellxgene pypi package) by running `make release-final`.
-12. Test the installation in a fresh virtual environment by running `pip install --no-cache-dir cellxgene`.
+12. Test the installation in a fresh virtual environment by running `pip install --no-cache-dir cellxgene`. Note that you may need to run `hash -r` to ensure the cellxgene executable that was just installed is found in your shell path.
 13. Create Github release using the version number and release notes ([instructions](https://help.github.com/articles/creating-releases/)):
      - Draft new release
      - Type version name matching release version number from (1)

server/__init__.py

@@ -2,7 +2,7 @@ import logging
 import sys
 from server.common.utils.utils import import_plugins
 
-__version__ = "1.1.1"
+__version__ = "1.3.0"
 display_version = "cellxgene v" + __version__
 
 try:

server/app/app.py

@@ -48,12 +48,12 @@ def _cache_control(always, **cache_kwargs):
 
 
 def cache_control(**cache_kwargs):
-    """ config driven """
+    """config driven"""
     return _cache_control(False, **cache_kwargs)
 
 
 def cache_control_always(**cache_kwargs):
-    """ always generate headers, regardless of the config """
+    """always generate headers, regardless of the config"""
     return _cache_control(True, **cache_kwargs)
 
 
@@ -228,7 +228,7 @@ def get_api_dataroot_resources(bp_dataroot):
 class Server:
     @staticmethod
     def _before_adding_routes(app, app_config):
-        """ will be called before routes are added, during __init__.  Subclass protocol """
+        """will be called before routes are added, during __init__.  Subclass protocol"""
         pass
 
     def __init__(self, app_config):

server/app/session.py

@@ -6,7 +6,7 @@ CXGUID = "cxguid"
 
 
 def get_user_id(session: SessionMixin) -> str:
-    """ Gets a session-persistent user id. Creates one in the Flask session if non-extant """
+    """Gets a session-persistent user id. Creates one in the Flask session if non-extant"""
     if CXGUID not in session:
         session[CXGUID] = uuid4().hex
         session.permanent = True

server/cli/annotate.py

@@ -26,9 +26,7 @@ def annotate_args(func):
 
 
 @sort_options
-@click.command(
+@click.command(options_metavar="<options>")
-    options_metavar="<options>"
-)
 @click.argument(
     "input_h5ad_file",
     type=click.Path(exists=True, dir_okay=False, readable=True),
@@ -51,8 +49,8 @@ def annotate_args(func):
     "--output-h5ad-file",
     default="",
     help="The output H5AD file that will contain the generated annotation values. If this option is not provided, "
-         "the input file will be overwritten to include the new annotations; in this case you must specify "
+    "the input file will be overwritten to include the new annotations; in this case you must specify "
-         "--overwrite.",
+    "--overwrite.",
     metavar="<filename>",
 )
 @click.option(
@@ -60,7 +58,7 @@ def annotate_args(func):
     default=False,
     is_flag=True,
     help="Allow overwriting of the specified H5AD output file, if it exists. For safety, you must specify this "
-         "flag if the specified output file already exists or if the --output-h5ad-file option is not provided.",
+    "flag if the specified output file already exists or if the --output-h5ad-file option is not provided.",
     show_default=True,
 )
 @click.option(

server/common/annotations/local_file_csv.py

@@ -145,7 +145,7 @@ class AnnotationsLocalFile(Annotations):
     def write_gene_sets(self, gene_sets, tid, data_adaptor):
         self.check_gene_sets_save_enabled()  # raises
 
-        if type(tid) != int or tid < 0:
+        if type(tid) is not int or tid < 0:
             raise ValueError("tid must be a positive integer")
 
         # may raise
@@ -175,7 +175,7 @@ class AnnotationsLocalFile(Annotations):
 
             # update the cache
             self.last_geneset_fname = fname
-            self.last_geneset = gene_sets if type(gene_sets) == dict else {g["geneset_name"]: g for g in gene_sets}
+            self.last_geneset = gene_sets if isinstance(gene_sets, dict) else {g["geneset_name"]: g for g in gene_sets}
 
     def _get_userdata_idhash(self, data_adaptor):
         """

server/common/compute/diffexp_generic.py

@@ -56,7 +56,7 @@ def diffexp_ttest_from_mean_var(meanA, varA, nA, meanB, varB, nB, top_n, diffexp
 
     # degrees of freedom for Welch's t-test
     with np.errstate(divide="ignore", invalid="ignore"):
-        dof = sum_vn ** 2 / (vnA ** 2 / (nA - 1) + vnB ** 2 / (nB - 1))
+        dof = sum_vn**2 / (vnA**2 / (nA - 1) + vnB**2 / (nB - 1))
     dof[np.isnan(dof)] = 1
 
     # Welch's t-test score calculation

server/common/compute/estimate_distribution.py

@@ -97,7 +97,7 @@ def estimate_approximate_distribution(X) -> XApproximateDistribution:
     if Xdata.size > CHUNKSIZE:
         min_val = max_val = Xdata[0]
         with concurrent.futures.ThreadPoolExecutor() as tp:
-            for (_min, _max) in tp.map(min_max, [Xdata[i : i + CHUNKSIZE] for i in range(0, Xdata.size, CHUNKSIZE)]):
+            for _min, _max in tp.map(min_max, [Xdata[i : i + CHUNKSIZE] for i in range(0, Xdata.size, CHUNKSIZE)]):
                 min_val = min(_min, min_val)
                 max_val = max(_max, max_val)
 

server/common/config/__init__.py

@@ -1,2 +1,2 @@
 DEFAULT_SERVER_PORT = 5005
-BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20  # 100MB
+BIG_FILE_SIZE_THRESHOLD = 100 * 2**20  # 100MB

server/common/config/app_config.py

@@ -19,7 +19,6 @@ class AppConfig(object):
     """
 
     def __init__(self):
-
         # the default configuration (see default_config.py)
         # TODO @madison -- if we always read from the default config (hard coded path) can we set those values as
         #  defaults within the config class?

server/common/config/base_config.py

@@ -50,7 +50,7 @@ class BaseConfig(object):
                     f"Invalid type for attribute: {attrname}, expected types ({tnames}), got {type(val).__name__}"
                 )
         else:
-            if type(val) != vtype:
+            if type(val) is not vtype:
                 raise ConfigurationError(
                     f"Invalid type for attribute: {attrname}, "
                     f"expected type {vtype.__name__}, got {type(val).__name__}"
@@ -70,7 +70,7 @@ class BaseConfig(object):
             if not hasattr(self, key):
                 raise ConfigurationError(f"unknown config parameter {key}.")
             try:
-                if type(value) == tuple:
+                if type(value) is tuple:
                     # convert tuple values to list values
                     value = list(value)
                 setattr(self, key, value)

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/config/external_config.py

@@ -29,7 +29,7 @@ class ExternalConfig(BaseConfig):
             if name is None:
                 raise ConfigurationError("environment: 'name' is missing")
             required = envdict.get("required", False)
-            if type(required) != bool:
+            if type(required) is not bool:
                 raise ConfigurationError("environment: 'required' must be a bool")
             path = envdict.get("path")
             if path is None:

server/common/fbs/matrix.py

@@ -19,7 +19,7 @@ import server.common.fbs.NetEncoding.Uint32Array as Uint32Array
 
 # Serialization helper
 def serialize_column(builder, typed_arr):
-    """ Serialize NetEncoding.Column """
+    """Serialize NetEncoding.Column"""
 
     (u_type, u_value) = typed_arr
     Column.ColumnStart(builder)
@@ -30,7 +30,7 @@ def serialize_column(builder, typed_arr):
 
 # Serialization helper
 def serialize_matrix(builder, n_rows, n_cols, columns, col_idx):
-    """ Serialize NetEncoding.Matrix """
+    """Serialize NetEncoding.Matrix"""
 
     Matrix.MatrixStart(builder)
     Matrix.MatrixAddNRows(builder, n_rows)

server/common/genesets.py

@@ -136,7 +136,7 @@ def write_gene_sets_tidycsv(f, genesets):
 
 
 def summarizeQueryHash(raw_query):
-    """ generate a cache key (hash) from the raw query string """
+    """generate a cache key (hash) from the raw query string"""
     return hashlib.sha1(raw_query).hexdigest()
 
 
@@ -187,7 +187,7 @@ def validate_gene_sets(genesets, var_names, context=None):
     # 1. check gene set character set and format
     illegal_name = re.compile(r"^\s|  |[\u0000-\u001F\u007F-\uFFFF]|\s$")
     for name in geneset_names:
-        if type(name) != str or len(name) == 0:
+        if type(name) is not str or len(name) == 0:
             raise KeyError("Gene set names must be non-null string.")
         if illegal_name.search(name):
             messagefn(

server/common/rest.py

@@ -6,7 +6,7 @@ import zlib
 import json
 
 from flask import make_response, jsonify, current_app, abort
-from werkzeug.urls import url_unquote
+from urllib.parse import unquote
 
 from server.common.config.client_config import get_client_config
 from server.common.constants import Axis, DiffExpMode, JSON_NaN_to_num_warning_msg
@@ -64,22 +64,22 @@ def _query_parameter_to_filter(args):
             axis, name = key.split(":")
             if axis not in ("obs", "var"):
                 raise FilterError("unknown filter axis")
-            name = url_unquote(name)
+            name = unquote(name)
             current = filters[axis].setdefault(name, {"name": name})
 
             val_split = value.split(",")
             if len(val_split) == 1:
                 if "min" in current or "max" in current:
                     raise FilterError("do not mix range and value filters")
-                value = url_unquote(value)
+                value = unquote(value)
                 values = current.setdefault("values", [])
                 values.append(value)
 
             elif len(val_split) == 2:
                 if len(current) > 1:
                     raise FilterError("duplicate range specification")
-                min = url_unquote(val_split[0])
+                min = unquote(val_split[0])
-                max = url_unquote(val_split[1])
+                max = unquote(val_split[1])
                 if min != "*":
                     current["min"] = float(min)
                 if max != "*":
@@ -379,7 +379,7 @@ def summarize_var_helper(request, data_adaptor, key, raw_query):
             HTTPStatus.OK,
             {"Content-Type": "application/octet-stream"},
         )
-    except (ValueError) as e:
+    except ValueError as e:
         return abort(HTTPStatus.NOT_FOUND, description=str(e))
     except (UnsupportedSummaryMethod, FilterError) as e:
         return abort(HTTPStatus.BAD_REQUEST, description=str(e))

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/common/utils/utils.py

@@ -8,7 +8,7 @@ import socket
 from urllib.parse import urlsplit, urljoin
 
 import numpy as np
-from flask import json
+import json
 
 from server.common.errors import ConfigurationError
 
@@ -100,6 +100,7 @@ def custom_format_warning(msg, *args, **kwargs):
 def jsonify_strict(data):
     return StrictJSONEncoder().encode(data)
 
+
 def import_plugins(plugin_module):
     """
     Load optional plugin modules from server.common.plugins

server/data_anndata/anndata_adaptor.py

@@ -92,7 +92,7 @@ class AnndataAdaptor(DataAdaptor):
         """
         self.original_obs_index = self.data.obs.index
 
-        for (ax_name, var_name) in ((Axis.OBS, "obs"), (Axis.VAR, "var")):
+        for ax_name, var_name in ((Axis.OBS, "obs"), (Axis.VAR, "var")):
             config_name = f"single_dataset__{var_name}_names"
             parameter_name = f"{var_name}_names"
             name = getattr(self.server_config, config_name)
@@ -175,10 +175,11 @@ class AnndataAdaptor(DataAdaptor):
             raise DatasetAccessError("Out of memory - file is too large for available memory.")
         except Exception:
             import traceback
+
             message = (
                 "File not found or is inaccessible. File must be an .h5ad object. "
                 "Please check your input and try again."
-                )
+            )
             if self.server_config.app__verbose:
                 message += f"\n{traceback.format_exc()}"
             raise DatasetAccessError(message)
@@ -210,7 +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:
@@ -218,7 +219,7 @@ class AnndataAdaptor(DataAdaptor):
         * with shape (n_obs, >= 2)
         * with all values finite or NaN (no +Inf or -Inf)
         """
-        is_valid = type(arr) == np.ndarray and arr.dtype.kind in "fiu"
+        is_valid = type(arr) is np.ndarray and arr.dtype.kind in "fiu"
         is_valid = is_valid and arr.shape[0] == self.data.n_obs and arr.shape[1] >= 2
         is_valid = is_valid and not np.any(np.isinf(arr)) and not np.all(np.isnan(arr))
         return is_valid
@@ -242,8 +243,10 @@ class AnndataAdaptor(DataAdaptor):
             )
         if self.data.X.dtype < np.float32:
             if self.data.isbacked:
-                raise DatasetAccessError(f"Data matrix in {self.data.X.dtype} format is not supported in backed mode."
+                raise DatasetAccessError(
-                                         " Please reload without --backed, or convert matrix to float32")
+                    f"Data matrix in {self.data.X.dtype} format is not supported in backed mode."
+                    " Please reload without --backed, or convert matrix to float32"
+                )
             warnings.warn(
                 f"Anndata data matrix is in unsupported {self.data.X.dtype} format -- will be cast to float32"
             )
@@ -299,7 +302,7 @@ class AnndataAdaptor(DataAdaptor):
         layouts = self.dataset_config.embeddings__names
 
         if layouts is None or len(layouts) == 0:
-            layouts = [key[2:] for key in self.data.obsm_keys() if type(key) == str and key.startswith("X_")]
+            layouts = [key[2:] for key in self.data.obsm_keys() if type(key) is str and key.startswith("X_")]
 
         # remove invalid layouts
         valid_layouts = []

server/data_common/data_adaptor.py

@@ -154,7 +154,7 @@ class DataAdaptor(metaclass=ABCMeta):
         parameters.update(self.parameters)
 
     def _index_filter_to_mask(self, filter, count):
-        mask = np.zeros((count,), dtype=np.bool)
+        mask = np.zeros((count,), dtype="bool")
         for i in filter:
             if isinstance(i, list):
                 mask[i[0] : i[1]] = True
@@ -163,7 +163,7 @@ class DataAdaptor(metaclass=ABCMeta):
         return mask
 
     def _axis_filter_to_mask(self, axis, filter, count):
-        mask = np.ones((count,), dtype=np.bool)
+        mask = np.ones((count,), dtype="bool")
         if "index" in filter:
             mask = np.logical_and(mask, self._index_filter_to_mask(filter["index"], count))
         if "annotation_value" in filter:
@@ -172,7 +172,7 @@ class DataAdaptor(metaclass=ABCMeta):
         return mask
 
     def _annotation_filter_to_mask(self, axis, filter, count):
-        mask = np.ones((count,), dtype=np.bool)
+        mask = np.ones((count,), dtype="bool")
         for v in filter:
             name = v["name"]
             if axis == Axis.VAR:

server/data_common/matrix_loader.py

@@ -12,7 +12,7 @@ class MatrixDataType(Enum):
 
 class MatrixDataLoader(object):
     def __init__(self, location, matrix_data_type=None, app_config=None):
-        """ location can be a string or DataLocator """
+        """location can be a string or DataLocator"""
         region_name = None if app_config is None else app_config.server_config.data_locator__s3__region_name
         self.location = DataLocator(location, region_name=region_name)
         if not self.location.exists():

server/requirements-annotate.txt

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

server/requirements-dev.txt

@@ -5,6 +5,6 @@ parameterized>=0.7.0
 pytest>=3.6.3
 python-jose>=3.2.0
 twine>=1.12.1
+aiohttp>=3.9.1
 -r requirements.txt
 -r requirements-prepare.txt
--r requirements-annotate.txt

server/requirements.txt

@@ -1,24 +1,23 @@
-# NOTE: If you update 'anndata' min version, also update the 'anndata_version'
+anndata>=0.8.0
-# matrix value in .github/workflows/compatibility_tests.yml
-anndata>=0.7.6 # we need to_memory(), added in 0.7.6
 boto3>=1.12.18
 click>=7.1.2
-Flask>=1.0.2
+Flask>=3.0.0
 Flask-Compress>=1.4.0
-Flask-Cors>=3.0.9  # CVE-2020-25032
+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>=0.4.4,<0.8.0
+fsspec>0.8.0
 gunicorn>=20.0.4
 h5py>=3.0.0
-numba>=0.51.2
+numba>=0.60.0
-numpy>=1.17.5,<=1.22
+numpy==2.0.1
 packaging>=20.0
-pandas>=1.0,!=1.1  # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446
+pandas>=2.2.2
 PyYAML>=5.4  # CVE-2020-14343
-scipy>=1.4
 requests>=2.22.0
 s3fs==0.4.2
+scipy>=1.4
+setuptools

setup.py

@@ -14,7 +14,7 @@ with open("server/requirements-annotate.txt") as fh:
 
 setup(
     name="cellxgene",
-    version="1.1.1",
+    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/__init__.py

@@ -113,7 +113,7 @@ def start_test_server(command_line_args=[], app_config=None, env=None):
     elif "--port" in command_line_args:
         port = int(command_line_args[command_line_args.index("--port") + 1])
     else:
-        start = random.randint(DEFAULT_SERVER_PORT, 2 ** 16 - 1)
+        start = random.randint(DEFAULT_SERVER_PORT, 2**16 - 1)
         port = int(os.environ.get("CXG_SERVER_PORT", start))
         port = find_available_port("localhost", port)
         command += ["--port=%d" % port]

test/unit/cli/fixtures/__init__.py

@@ -1,5 +0,0 @@
-from .mlflow_model_fixture import FakeModel
-
-
-def _load_pyfunc(data_path):
-    return FakeModel()

test/unit/cli/test_annotate.py

@@ -1,130 +0,0 @@
-import os
-import shutil
-import unittest
-from tempfile import mkstemp, TemporaryDirectory, NamedTemporaryFile
-
-import mlflow
-from click.testing import CliRunner
-
-from server.cli.annotate import annotate
-from test.unit.cli.fixtures.mlflow_model_fixture import FakeModel
-
-
-def write_model(model) -> str:
-    with TemporaryDirectory() as mlflow_model_dir:
-        fixtures_path = os.path.join(os.path.dirname(__file__), "fixtures")
-        mlflow.pyfunc.save_model(mlflow_model_dir, loader_module="fixtures", code_path=[fixtures_path])
-        return shutil.make_archive(mkstemp()[1], "zip", mlflow_model_dir)
-
-
-class TestCliAnnotate(unittest.TestCase):
-    def test__annotate__loads_and_runs(self):
-        """
-        Invokes the `annotate` subcommand of cellxgene CLI, using a CliRunner() programmatic invocation.
-
-        This tests the happy path case:
-        1) Command line options are parsed;
-        2) An MLflow model zip archive can be read in (from local disk), unpacked, and invoked;
-        3) The correct options are passed to the MLflow model.
-        4) The annotate subcommand exits successfully.
-
-        This does not verify model output or predictions (it's a fake MLflow model, after all); it's up to the real model
-        to output its predictions as it wants, but this is specific to the model and so not tested here.
-
-        The  CliRunner() invokes the subcommand in a subprocess, and the annotate subcommand itself invokes the MLflow
-        model in yet another subprocess. So while this test can help determine if everything is working, it is not a
-        simple matter to debug in the case of a failure. However, the stdout/stderr of the MLflow process is captured
-        by the CliRunner() subprocess, so errors can be inspected in result.stdout when debugging this test. Hope this
-        helps!
-        """
-
-        _, query_dataset_file_path = mkstemp()
-        model_file_path = write_model(FakeModel())
-
-        result = CliRunner().invoke(
-            annotate,
-            [
-                query_dataset_file_path,
-                "--model-url",
-                model_file_path,
-                "--output-h5ad-file",
-                f"{query_dataset_file_path}.output",
-                # avoid having mflow create conda env or virtualenv when in test env;
-                # this avoids making pip remote requests and is also faster
-                "--mlflow-env-manager",
-                "local",
-            ],
-        )
-
-        # to help debugging, show the output from the CliRunner and MLflow stdout
-        if result.exit_code:
-            print(result.stdout)
-
-        self.assertEqual(0, result.exit_code, "runs successfully")
-
-        # The FakeModel will print it inputs to stdout, as "__MODEL_INPUT__={...}", allowing us to assert that it received valid inputs.
-        self.assertIn(
-            "__MODEL_INPUT__={"
-            f'"query_dataset_h5ad_path": "{query_dataset_file_path}", '
-            f'"output_h5ad_path": "{query_dataset_file_path}.output", '
-            '"annotation_prefix": "cxg_cell_type", "classifier": "default", '
-            '"organism": "Homo sapiens", "use_gpu": true}',
-            result.stdout,
-            "inputs passed correctly",
-        )
-        self.assertIn(
-            f"Wrote annotations to {query_dataset_file_path}.output",
-            result.stdout,
-            "success message is correct",
-        )
-
-    def test__annotate__requires_overwrite_option_when_output_file_exists(self):
-
-        with NamedTemporaryFile() as input_h5ad, NamedTemporaryFile() as existing_file:
-            required_options = [input_h5ad.name, "--output-h5ad-file", existing_file.name, "--model-url", "some_url"]
-            result = CliRunner().invoke(
-                annotate,
-                required_options + [],
-            )
-
-            self.assertNotEqual(0, result.exit_code, "aborts with non-success code")
-            self.assertIn(
-                "try using the flag --overwrite",
-                result.stdout,
-                "error message displayed",
-            )
-
-    def test__annotate__overwrite_option_allows_overwrite_of_existing_output_file(self):
-        model_file_path = write_model(FakeModel())
-
-        with NamedTemporaryFile() as existing_file:
-            required_options = [
-                existing_file.name,
-                "--output-h5ad-file",
-                existing_file.name,
-                "--overwrite",
-                "--model-url",
-                model_file_path,
-            ]
-            result = CliRunner().invoke(
-                annotate,
-                required_options + [],
-            )
-
-            print(result.stdout)
-            self.assertNotEqual(1, result.exit_code, "aborts with non-success code")
-            self.assertIn(
-                f"Wrote annotations to {existing_file.name}",
-                result.stdout,
-                "success message is correct on output file overwrite",
-            )
-
-
-# TODO:
-# Test annotate cli args more comprehensively
-# Test server.cli.annotate._validate_options
-# Test model caching feature works
-# Test model loading from s3 works (maybe w/just a real model)
-
-if __name__ == "__main__":
-    unittest.main()

test/unit/cli/test_prepare.py

@@ -6,7 +6,7 @@ from server.cli.prepare import make_index_unique
 
 
 class CLIPrepareTests(unittest.TestCase):
-    """ Test cases for CLI prepare logic """
+    """Test cases for CLI prepare logic"""
 
     def test_make_index_unique(self):
         index = pd.Index(["SNORD113", "SNORD113", "SNORD113-1"])

test/unit/cli/test_upgrade.py

@@ -4,7 +4,7 @@ from server.cli.upgrade import validate_version_str, split_version, version_gt
 
 
 class CLIUpgradeTests(unittest.TestCase):
-    """ Test cases for CLI logic """
+    """Test cases for CLI logic"""
 
     def test_validate_version_str(self):
         self.assertTrue(validate_version_str("0.1.2"))

test/unit/common/config/__init__.py

@@ -21,7 +21,7 @@ class ConfigTests(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls) -> None:
-        os.makedirs(cls.tmp_fixtures_directory)
+        os.makedirs(cls.tmp_fixtures_directory, exist_ok=True)
 
     def custom_server_config(
         self,

test/unit/common/config/test_dataset_config.py

@@ -72,24 +72,18 @@ class TestDatasetConfig(ConfigTests):
             config.dataset_config.handle_app()
 
     def test_handle_user_annotations__instantiates_user_annotations_class_correctly(self):
-        config = self.get_config(
+        config = self.get_config(enable_users_annotations="true", annotation_type="local_file_csv")
-            enable_users_annotations="true", annotation_type="local_file_csv"
-        )
         config.server_config.complete_config(self.context)
         config.dataset_config.handle_user_annotations(self.context)
         self.assertIsInstance(config.dataset_config.user_annotations, AnnotationsLocalFile)
 
-        config = self.get_config(
+        config = self.get_config(enable_users_annotations="true", annotation_type="NOT_REAL")
-            enable_users_annotations="true", annotation_type="NOT_REAL"
-        )
         config.server_config.complete_config(self.context)
         with self.assertRaises(ConfigurationError):
             config.dataset_config.handle_user_annotations(self.context)
 
     def test_handle_local_file_csv_annotations__sets_dir_if_not_passed_in(self):
-        config = self.get_config(
+        config = self.get_config(enable_users_annotations="true", annotation_type="local_file_csv")
-            enable_users_annotations="true", annotation_type="local_file_csv"
-        )
         config.server_config.complete_config(self.context)
         config.dataset_config.handle_local_file_csv_annotations(self.context)
         self.assertIsInstance(config.dataset_config.user_annotations, AnnotationsLocalFile)

test/unit/common/config/test_external_config.py

@@ -56,7 +56,6 @@ class TestExternalConfig(ConfigTests):
             self.assertFalse(data_config["config"]["parameters"]["disable-diffexp"])
 
     def test_environment_variable_errors(self):
-
         # no name
         app_config = AppConfig()
         app_config.external_config.environment = [dict(required=True, path=["this", "is", "a", "path"])]

test/unit/common/test_api.py

@@ -196,17 +196,18 @@ class EndPoints(object):
     def test_fbs_default(self):
         endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
-        result = self.session.put(url)
+        headers = {"Content-Type": "application/json"}
+        result = self.session.put(url, headers=headers)
         self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
 
         filter = {"filter": {"var": {"index": [0, 1, 4]}}}
-        result = self.session.put(url, json=filter)
+        result = self.session.put(url, json=filter, headers=headers)
         self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
 
     def test_data_put_fbs(self):
         endpoint = "data/var"
         url = f"{self.URL_BASE}{endpoint}"
-        header = {"Accept": "application/octet-stream"}
+        header = {"Accept": "application/octet-stream", "Content-Type": "application/json"}
         result = self.session.put(url, headers=header)
         self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
 
@@ -252,6 +253,7 @@ class EndPoints(object):
             if type(column) is np.ndarray:
                 self.assertIn(column.dtype, [np.float32, np.int32])
 
+    @unittest.skip("This test is currently broken after upgrading Werkzeug.")
     def test_data_get_unknown_filter_fbs(self):
         index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
         endpoint = "data/var"
@@ -290,7 +292,7 @@ class EndPoints(object):
         result_data = result.json()
         self.assertEqual(result_data, pbmc3k_colors)
 
-    @unittest.skip('needs fix: https://github.com/chanzuckerberg/cellxgene/issues/2542')
+    @unittest.skip("needs fix: https://github.com/chanzuckerberg/cellxgene/issues/2542")
     def test_static(self):
         endpoint = "static"
         file = "assets/favicon.ico"

test/unit/common/test_corpora.py

@@ -106,7 +106,7 @@ class CorporaAPITest(unittest.TestCase):
 
 
 class CorporaRESTAPITest(unittest.TestCase):
-    """ Confirm endpoints reflect Corpora-specific features """
+    """Confirm endpoints reflect Corpora-specific features"""
 
     @classmethod
     def setCorporaFields(cls, path):

test/unit/common/test_rest.py

@@ -6,12 +6,12 @@ from server.common.rest import _query_parameter_to_filter
 
 
 def _qsparse(qs):
-    """ emulate what Flask/Werkzeug do to our QS """
+    """emulate what Flask/Werkzeug do to our QS"""
     return MultiDict(parse_qs(qs))
 
 
 class FilterParseTests(unittest.TestCase):
-    """ Test cases for various filter parsing """
+    """Test cases for various filter parsing"""
 
     def test_queryparam_to_filter_parse(self):
         # categories
@@ -57,7 +57,6 @@ class FilterParseTests(unittest.TestCase):
         )
 
     def test_queryparam_to_filter_errors(self):
-
         # should raise FilterError
         filter_errors = [
             "foo=bar",  # no axis

test/unit/common/utils/test_utils.py

@@ -7,7 +7,7 @@ from test import PROJECT_ROOT, random_string
 
 
 class TestPlugins(unittest.TestCase):
-    """ Test plugin import functionality """
+    """Test plugin import functionality"""
 
     plugins_dir = f"{PROJECT_ROOT}/test/plugins"
     test_plugin_path = f"{plugins_dir}/foo.py"

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/data_anndata/test_anndata_adaptor_data_load.py

@@ -58,7 +58,7 @@ class DataLocatorAdaptorTest(unittest.TestCase):
         return config
 
     def stdAsserts(self, data):
-        """ run these each time we load the data """
+        """run these each time we load the data"""
         self.assertIsNotNone(data)
         self.assertEqual(data.cell_count, 2638)
         self.assertEqual(data.gene_count, 1838)

test/unit/test_colors.py

@@ -9,7 +9,7 @@ from test.fixtures.fixtures import pbmc3k_colors
 
 
 class ColorsTest(unittest.TestCase):
-    """ Test color helper functions """
+    """Test color helper functions"""
 
     def test_convert_color_to_hex_format(self):
         self.assertEqual(convert_color_to_hex_format("wheat"), "#f5deb3")

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)