fix: correct opacity prop typo and style object in centroid labels (#2767 )

fix: Handle non-categorical columns with colors + update deprecated AnnData API (#2758 )
Yeah that makes sense! Mergingg
2026-09-26 18:58:12 +08:00 · 2026-03-09 13:39:56 -07:00 · 2026-02-24 13:37:57 -08:00 · 2026-01-16 09:28:12 -08:00 · 2026-01-15 15:18:45 -08:00 · 2026-01-14 09:22:22 -08:00
76 changed files with 5909 additions and 3699 deletions
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.1
+current_version = 1.3.0
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 
@@ -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.
 - [ ]
 - [ ]
@@ -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 }}
@@ -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
@@ -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: ${{ secrets.GITHUB_TOKEN }}
@@ -14,15 +14,15 @@ jobs:
  lint:
    runs-on: ubuntu-latest
    steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
      - run: |
          git fetch --depth=1 origin +${{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') }}
@@ -69,40 +69,51 @@ jobs:
      - name: Install dependencies
        run: make pydist install-dist dev-env-server
      - name: Unit tests
-        run: |
+        run: make unit-test-server unit-test-client
-          make unit-test-server unit-test-client
+      - name: Generate server coverage XML
-          bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
+        run: coverage xml -o server/coverage.xml
-          cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
+      - name: Upload server coverage
        uses: codecov/codecov-action@v5
        with:
          flags: server,python,unitTest
          files: ./server/coverage.xml
          fail_ci_if_error: false
      - name: Upload client coverage
        uses: codecov/codecov-action@v5
        with:
          flags: frontend,javascript,unitTest
          files: ./client/coverage/lcov.info
          fail_ci_if_error: false
  smoke-tests:
    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
      - name: Smoke tests (without annotations feature)
        run: |
-          cd client && make smoke-test
+          pip install setuptools
-          ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
+          make pydist install-dist
      - name: Smoke tests (without annotations feature)
        run: cd client && make smoke-test
  # TODO: reinstate: https://github.com/chanzuckerberg/cellxgene/issues/2544
  # smoke-tests-annotations:
@@ -110,10 +121,10 @@ 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:
@@ -1,6 +1,6 @@
-The MIT License (MIT)
+# The MIT License (MIT)
-Copyright (c) 2017-2022 Chan Zuckerberg Initiative
+Copyright (c) 2017-2026 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
@@ -7,27 +7,27 @@ _an interactive explorer for single-cell transcriptomics data_
 [![Compatibility Tests](https://github.com/chanzuckerberg/cellxgene/workflows/Compatibility%20Tests/badge.svg)](https://github.com/chanzuckerberg/cellxgene/actions?query=workflow%3A%22Compatibility+Tests%22)
 ![Code Coverage](https://codecov.io/gh/chanzuckerberg/cellxgene/branch/main/graph/badge.svg)
-cellxgene Desktop (pronounced "cell-by-gene") is an interactive data explorer for single-cell datasets, such as those coming from the [Human Cell Atlas](https://humancellatlas.org). Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.
+CZ CELLxGENE Annotate (pronounced "cell-by-gene") is an interactive data explorer for single-cell datasets, such as those coming from the [Human Cell Atlas](https://humancellatlas.org). Leveraging modern web development techniques to enable fast visualizations of at least 1 million cells, we hope to enable biologists and computational researchers to explore their data.
-Whether you need to visualize one thousand cells or one million, cellxgene Desktop helps you gain insight into your single-cell data.
+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">
 # Getting started
-### The comprehensive guide to cellxgene Desktop
+### The comprehensive guide to CZ CELLxGENE Annotate
-[The cellxgene documentation is your one-stop-shop for information about cellxgene Desktop](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/README.md)! You may be particularly interested in:
+[The CZ CELLxGENE Annotate documentation is your one-stop-shop for information about CELLxGENE Annotate](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/README.md)! You may be particularly interested in:
- Seeing [what cellxgene Desktop can do](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/explore-data/explorer-tutorials.md)
+- Seeing [what Annotate can do](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/explore-data/explorer-tutorials.md)
- Learning more about cellxgene [installation](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md) and [usage](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/quick-start.md#quick-start-1)
+- Learning more about Annotate [installation](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md) and [usage](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/quick-start.md#quick-start-1)
- [Preparing your own data](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/data-reqs.md) for use in cellxgene Desktop
+- [Preparing your own data](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/data-reqs.md) for use in Annotate
 - Checking out [our roadmap](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/roadmap.md) for future development
- [Contributing](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) to cellxgene Desktop
+- [Contributing](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) to Annotate
 ### Quick start
-To install cellxgene Desktop you need Python 3.6+. We recommend [installing cellxgene Desktop 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.
@@ -35,19 +35,19 @@ Install the package.
 pip install cellxgene
 ```
-Launch cellxgene Desktop with an example [anndata](https://anndata.readthedocs.io/en/latest/) file
+Launch Annotate with an example [anndata](https://anndata.readthedocs.io/en/latest/) file
 ```bash
 cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad
 ```
-To explore more datasets already formatted for cellxgene Desktop, check out the [Demo data](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/quick-start.md#example-datasets) or
+To explore more datasets already formatted for Annotate, check out the [Demo data](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/quick-start.md#example-datasets) or
 see [Preparing your data](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/data-reqs.md) to learn more about formatting your own
-data for cellxgene Desktop.
+data for CELLxGENE Annotate.
 ### Supported browsers
-cellxgene Desktop currently supports the following browsers:
+CELLxGENE Annotate currently supports the following browsers:
 - Google Chrome 61+
 - Edge 15+
@@ -58,30 +58,36 @@ 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).
-# Developing with cellxgene Desktop
+# Developing with CZ CELLxGENE Annotate
 ### 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 Desktop. 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, 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. 
+### Trademarks
 CZ CELLXGENE, CZ CELLXGENE DISCOVER, and CZ CELLXGENE ANNOTATE are trademarks of the Chan Zuckerberg Initiative. All rights reserved.
 Use, reuse, modification, and re-distribution of the source code in this repository is subject to the terms of the applicable open source [license](LICENSE.txt). However, that license does not grant permission to use the trademarks without separate, express permission from the Chan Zuckerberg Initiative.
 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
@@ -0,0 +1,3 @@
 # Reporting Security Issues
 If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).
@@ -0,0 +1 @@
 18.17.0
@@ -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);
@@ -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",
@@ -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",
@@ -9,6 +9,7 @@ const sharedConfig = require("./webpack.config.shared");
 const babelOptions = require("../babel/babel.dev");
 const fonts = path.resolve("src/fonts");
 const images = path.resolve("src/images");
 const nodeModules = path.resolve("node_modules");
 const devConfig = {
@@ -28,11 +29,11 @@ const devConfig = {
      {
        test: /\.(jpg|png|gif|eot|svg|ttf|woff|woff2|otf)$/i,
        loader: "file-loader",
-        include: [nodeModules, fonts],
+        include: [nodeModules, fonts, images],
        options: {
          name: "static/assets/[name].[ext]",
          // (thuang): This is needed to make sure @font url path is '/static/assets/'
-          publicPath: "/",
+          publicPath: "..",
        },
      },
    ],
@@ -14,6 +14,7 @@ const CspHashPlugin = require("./cspHashPlugin");
 const sharedConfig = require("./webpack.config.shared");
 const fonts = path.resolve("src/fonts");
 const images = path.resolve("src/images");
 const nodeModules = path.resolve("node_modules");
 const prodConfig = {
@@ -43,11 +44,11 @@ const prodConfig = {
      {
        test: /\.(jpg|png|gif|eot|svg|ttf|woff|woff2|otf)$/i,
        loader: "file-loader",
-        include: [nodeModules, fonts],
+        include: [nodeModules, fonts, images],
        options: {
          name: "static/assets/[name]-[contenthash].[ext]",
          // (thuang): This is needed to make sure @font url path is '../static/assets/'
-          publicPath: "static/",
+          publicPath: "..",
        },
      },
    ],
@@ -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");
@@ -3,7 +3,7 @@
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <title>cell&times;gene</title>
+    <title>CELL&times;GENE | Annotate</title>
    <style>
      html,
      body,
@@ -3,7 +3,7 @@
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <title>cell&times;gene</title>
+    <title>CELL&times;GENE | Annotate</title>
    <style>
      html,
      body,
@@ -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,
@@ -1,6 +1,6 @@
 {
  "name": "cellxgene",
-  "version": "1.0.1",
+  "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",
@@ -99,13 +101,12 @@
    "cheerio": "^1.0.0-rc.6",
    "clean-css": "^5.1.2",
    "clean-webpack-plugin": "^4.0.0-alpha.0",
    "codecov": "^3.7.1",
    "css-loader": "^5.2.4",
    "css-minimizer-webpack-plugin": "^4.0.0",
    "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 +123,7 @@
    "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 +133,16 @@
    "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 +176,13 @@
            }
          ],
          [
-            "@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
            }
@@ -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, {});
 }
@@ -41,7 +41,7 @@ class App extends React.Component {
    const { loading, error, graphRenderCounter } = this.props;
    return (
      <Container>
-        <Helmet title="cellxgene" />
+        <Helmet title="CELL&times;GENE | Annotate" />
        {loading ? (
          <div
            style={{
@@ -1,17 +1,15 @@
 import React from "react";
-import * as globals from "../../globals";
+import icon from "../../images/icon.png";
 const Logo = (props) => {
  const { size } = props;
  return (
-    <svg width={size} height={size} viewBox="0 0 48 48" fill="none">
+    <img
-      <rect width="48" height="48" fill="white" />
+      src={icon}
-      <rect width="48" height="48" fill={globals.logoColor} />
+      height={size}
-      <rect x="19" y="19" width="22" height="22" fill="white" />
+      width={size}
-      <rect x="24" y="24" width="12" height="12" fill={globals.logoColor} />
+      alt="CELLxGENE Annotate Logo"
-      <rect x="7" y="19" width="7" height="22" fill="white" />
+     />
      <rect x="19" y="7" width="22" height="7" fill="white" />
    </svg>
  );
 };
@@ -150,7 +150,7 @@ class CentroidLabels extends PureComponent {
                  dilatedValue={dilatedValue}
                  coords={coords}
                  inverseTransform={inverseTransform}
-                  opactity={selected ? 1 : deselectOpacity}
+                  opacity={selected ? 1 : deselectOpacity}
                  colorAccessor={colorAccessor}
                  displayLabel={displayLabel}
                  onMouseEnter={this.handleMouseEnter}
@@ -205,7 +205,7 @@ const Label = ({
          fontWeight,
          fill: "black",
          userSelect: "none",
-          opacity: { opacity },
+          opacity,
        }}
        onMouseEnter={(e) => onMouseEnter(e, colorAccessor, label)}
        onMouseOut={(e) => onMouseOut(e, colorAccessor, label)}
@@ -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"
@@ -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
@@ -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
@@ -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)
@@ -2,7 +2,7 @@ import logging
 import sys
 from server.common.utils.utils import import_plugins
-__version__ = "1.0.1"
+__version__ = "1.3.0"
 display_version = "cellxgene v" + __version__
 try:
@@ -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):
@@ -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
@@ -4,7 +4,7 @@ import os.path
 import shlex
 import shutil
 import subprocess
-import sys
+from os.path import isfile
 from subprocess import STDOUT, PIPE
 from tempfile import NamedTemporaryFile
@@ -26,24 +26,41 @@ def annotate_args(func):
@sort_options
-@click.command(
+@click.command(options_metavar="<options>")
-    short_help="Annotate H5AD file columns. Run `cellxgene annotation --help` for more information.",
+@click.argument(
-    options_metavar="<options>",
+    "input_h5ad_file",
-)
+    type=click.Path(exists=True, dir_okay=False, readable=True),
-@click.option(
+    nargs=1,
-    "-i",
+    metavar="<path to H5AD input file>",
    "--input-h5ad-file",
    required=True,
    type=str,
    help="The input H5AD file containing the missing annotations.",
 )
@click.option(
    "-m",
    "--model-url",
    # Making this a required "option", rather than an "argument", since we support automatic model selection in the
    # future, in which case the user would not need to specify this option at all and we can make it optional at
    # that time.
    required=True,
    help="The URL of the model used to prediction annotated labels. May be a local filesystem directory "
    "or S3 path (s3://)",
 )
@click.option(
    "-o",
    "--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 "
    "--overwrite.",
    metavar="<filename>",
 )
@click.option(
    "--overwrite",
    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.",
    show_default=True,
 )
@click.option(
    "-l",
    "--counts-layer",
@@ -53,8 +70,8 @@ def annotate_args(func):
@click.option(
    "-g",
    "--gene-column-name",
-    help="The name of the `var` column that contains gene identifiers. The values in this column will be used to match "
+    help="The name of the `var` column that contains gene names. The values in this column will be used to match "
-    "genes between the query and reference datasets. If not specified, the gene identifiers are expected to exist "
+    "genes between the query and reference datasets. If not specified, the gene names are expected to exist "
    "in `var.index`.",
 )
 # TODO: Useful if we want to support discoverability of models
@@ -91,19 +108,6 @@ def annotate_args(func):
    "will store the predicted annotation values and confidence scores. This can be used to allow multiple "
    "annotation predictions to be run on a single AnnData object.",
 )
@click.option(
    "-u",
    "--update-h5ad-file",
    is_flag=True,
    help="Flag indicating whether to update the input h5ad file with annotation values.  This option is mutually "
    "exclusive with --output-h5ad-file.",
 )
@click.option(
    "-o",
    "--output-h5ad-file",
    help="The output H5AD file that will contain the generated annotation values. This option is mutually "
    "exclusive with --update-h5ad-file.",
 )
@click.option("--use-model-cache/--no-use-model-cache", default=True)
@click.option(
    "--use-gpu/--no-use-gpu",
@@ -141,6 +145,9 @@ def annotate_args(func):
 )
@click.help_option("--help", "-h", help="Show this message and exit.")
 def annotate(**cli_args):
    """
    Add predicted annotations to an H5AD file. Run `cellxgene annotate --help` for more information.
    """
    _validate_options(cli_args)
    print(f"Reading query dataset {cli_args['input_h5ad_file']}...")
@@ -149,7 +156,11 @@ def annotate(**cli_args):
        filter(None, [cli_args.get("annotation_prefix"), cli_args.get("annotation_type"), cli_args.get("run_name")])
    )
-    output_h5ad_file = cli_args["input_h5ad_file"] if cli_args["update_h5ad_file"] else cli_args["output_h5ad_file"]
+    output_h5ad_file = (
        cli_args["input_h5ad_file"]
        if cli_args["overwrite"] and not cli_args["output_h5ad_file"]
        else cli_args["output_h5ad_file"]
    )
    model_url = cli_args.get("model_url")
    local_model_path = _retrieve_model(cli_args.get("model_cache_dir"), model_url, cli_args.get("use_model_cache"))
@@ -196,7 +207,7 @@ def annotate(**cli_args):
            p.wait()
            if p.returncode == 0:
-                print(f"Wrote annotations to {cli_args.get('output_h5ad_file')}")
+                print(f"Wrote annotations to {output_h5ad_file}")
            else:
                print("Annotation failed!")
    else:
@@ -218,13 +229,11 @@ def _retrieve_model(model_cache_dir, model_url, use_cache=True):
 def _validate_options(cli_args):
-    # TODO(atolopko): Use cloup library for this logic
+    output = cli_args["output_h5ad_file"]
-    if cli_args["update_h5ad_file"] and cli_args["output_h5ad_file"]:
+    overwrite = cli_args["overwrite"]
-        click.echo("--update_h5ad_file and --output_h5ad_file are mutually exclusive")
+
-        sys.exit(1)
+    if isfile(output) and not overwrite:
-    if not (cli_args["update_h5ad_file"] or cli_args["output_h5ad_file"]):
+        raise click.UsageError(f"Cannot overwrite existing file {output}, try using the flag --overwrite")
        click.echo("--update_h5ad_file or --output_h5ad_file must be specified")
        sys.exit(1)
 if __name__ == "__main__":
@@ -128,12 +128,12 @@ def prepare(
            raise click.FileError(data, hint="not a valid file or path")
        if not set_obs_names == "":
-            if set_obs_names not in adata.obs_keys():
+            if set_obs_names not in list(adata.obs.keys()):
-                raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
+                raise click.UsageError(f"obs {set_obs_names} not found, options are: {list(adata.obs.keys())}")
            adata.obs_names = adata.obs[set_obs_names]
        if not set_var_names == "":
-            if set_var_names not in adata.var_keys():
+            if set_var_names not in list(adata.var.keys()):
-                raise click.UsageError(f"var {set_var_names} not found, options are: {adata.var_keys()}")
+                raise click.UsageError(f"var {set_var_names} not found, options are: {list(adata.var.keys())}")
            adata.var_names = adata.var[set_var_names]
        if make_obs_names_unique:
            adata.obs.index = make_index_unique(adata.obs.index)
@@ -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):
        """
@@ -228,6 +228,6 @@ def convert_anndata_category_colors_to_cxg_category_colors(data):
        # create the cellxgene color entry for this category
        cxg_colors[category_name] = dict(
-            zip(data.obs[category_name].cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
+            zip(data.obs[category_name].astype('category').cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
        )
    return cxg_colors
@@ -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
@@ -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)
@@ -1,2 +1,2 @@
 DEFAULT_SERVER_PORT = 5005
-BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20  # 100MB
+BIG_FILE_SIZE_THRESHOLD = 100 * 2**20  # 100MB
@@ -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?
@@ -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)
@@ -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."
            )
@@ -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:
@@ -22,7 +22,7 @@ def corpora_get_versions_from_anndata(adata):
    """
    # per Corpora AnnData spec, this is a corpora file if the following is true
-    if "version" not in adata.uns_keys():
+    if "version" not in list(adata.uns.keys()):
        return None
    version = adata.uns["version"]
    if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:
@@ -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)
@@ -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(
@@ -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))
@@ -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"})
@@ -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
@@ -98,7 +98,7 @@ def custom_format_warning(msg, *args, **kwargs):
 def jsonify_strict(data):
-    return json.dumps(data, cls=StrictJSONEncoder, allow_nan=False)
+    return StrictJSONEncoder().encode(data)
 def import_plugins(plugin_module):
@@ -1,4 +1,5 @@
 import warnings
 import importlib.metadata
 import anndata
 import numpy as np
@@ -16,7 +17,7 @@ from server.common.utils.type_conversion_utils import get_schema_type_hint_of_ar
 from server.data_common.data_adaptor import DataAdaptor
 from server.common.fbs.matrix import encode_matrix_fbs
-anndata_version = version.parse(str(anndata.__version__)).release
+anndata_version = version.parse(str(importlib.metadata.version('anndata'))).release
 def anndata_version_is_pre_070():
@@ -63,7 +64,7 @@ class AnndataAdaptor(DataAdaptor):
        return "cellxgene anndata adaptor version"
    def get_library_versions(self):
-        return dict(anndata=str(anndata.__version__))
+        return dict(anndata=str(importlib.metadata.version('anndata')))
    @staticmethod
    def _create_unique_column_name(df, col_name_prefix):
@@ -92,7 +93,7 @@ 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)
@@ -173,12 +174,24 @@ class AnndataAdaptor(DataAdaptor):
            )
        except MemoryError:
            raise DatasetAccessError("Out of memory - file is too large for available memory.")
-        except Exception:
+        except Exception as e:
            import traceback
-            message = (
+            error_msg = str(e)
-                "File not found or is inaccessible. File must be an .h5ad object. "
+
-                "Please check your input and try again."
+            # IMPROVEMENT: Broadly catch ANY version incompatibility
            if "No read method registered" in error_msg and "IOSpec" in error_msg:
                message = (
                    "Error loading file: This H5AD file uses a newer internal format that "
                    "your version of 'anndata' cannot read.\n"
                    f"The specific error was: {error_msg}\n"
                    "Please upgrade anndata in your environment (pip install --upgrade anndata)."
                )
            else:
                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 +223,7 @@ 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 +231,7 @@ 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 +255,10 @@ 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"
            )
@@ -299,11 +314,11 @@ 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 list(self.data.obsm.keys()) if type(key) is str and key.startswith("X_")]
        # remove invalid layouts
        valid_layouts = []
-        obsm_keys = self.data.obsm_keys()
+        obsm_keys = list(self.data.obsm.keys())
        for layout in layouts:
            layout_name = f"X_{layout}"
            if layout_name not in obsm_keys:
@@ -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:
@@ -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():
@@ -1,2 +1,2 @@
-mlflow
+mlflow==2.16.0
 scanpy
@@ -1,10 +1,10 @@
 black
 bumpversion>=0.5
-codecov>=2.0.15
+coverage>=5.0
 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
@@ -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
@@ -14,7 +14,7 @@ with open("server/requirements-annotate.txt") as fh:
 setup(
    name="cellxgene",
-    version="1.0.1",
+    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",
    ],
@@ -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]
@@ -1,5 +0,0 @@
 from .mlflow_model_fixture import FakeModel
 def _load_pyfunc(data_path):
    return FakeModel()
@@ -1,111 +0,0 @@
 import os
 import shutil
 import unittest
 from tempfile import mkstemp, TemporaryDirectory
 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,
            [
                "--input-h5ad-file",
                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",
        )
    def test__annotate__verifies_mutually_exclusive_options(self):
        required_options = ["--input-h5ad-file", "some.h5ad", "--model-url", "some_url"]
        result = CliRunner().invoke(
            annotate,
            required_options + [],
        )
        self.assertNotEqual(0, result.exit_code, "aborts with non-success code")
        self.assertIn(
            "--update_h5ad_file or --output_h5ad_file must be specified",
            result.stdout,
            "error message displayed",
        )
        result = CliRunner().invoke(
            annotate, required_options + ["--output-h5ad-file", "some_arg", "--update-h5ad-file"]
        )
        self.assertNotEqual(0, result.exit_code, "aborts with non-success code")
        self.assertIn(
            "--update_h5ad_file and --output_h5ad_file are mutually exclusive",
            result.stdout,
            "error message displayed",
        )
 # 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()
@@ -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"])
@@ -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"))
@@ -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,
@@ -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)
@@ -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"])]
@@ -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"
@@ -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):
@@ -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
@@ -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"
@@ -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(
@@ -36,7 +36,6 @@ Test the anndata adaptor using the pbmc3k data set.
        (f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", True, "normal"),
        (f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", True, "normal"),
        (f"{FIXTURES_ROOT}/pbmc3k_64.h5ad", False, "auto"),  # 64 bit conversion tests
        (f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", False, "auto"),  # 16 bit conversion tests
    ],
 )
 class AdaptorTest(unittest.TestCase):
@@ -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)
@@ -1,23 +0,0 @@
 import unittest
 from parameterized import parameterized_class
 from server.common.errors import DatasetAccessError
 from test import FIXTURES_ROOT
 from test.unit import app_config
@parameterized_class(
    ("data_locator", "backed", "X_approximate_distribution"),
    [
        (f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", True, "auto"),  # 16 bit conversion tests
    ],
 )
 class AdaptorLoadErrorTest(unittest.TestCase):
    def test_float16_backed_raises_err(self):
        with self.assertRaises(DatasetAccessError):
            config = app_config(
                self.data_locator,
                backed=self.backed,
                extra_dataset_config=dict(X_approximate_distribution=self.X_approximate_distribution),
            )
@@ -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")
@@ -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 = {
@@ -54,5 +54,5 @@ class TestJsonifyStrict(unittest.TestCase):
        # the actual test!
        self.assertEqual(
            jsonify_strict(values),
-            '{"floating": [100.0, 101.0, 102.0], "integer": [0, 1, 2, 3, 4, 5, 6, 7]}',
+            '{"integer": [0, 1, 2, 3, 4, 5, 6, 7], "floating": [100.0, 101.0, 102.0]}',
        )
@@ -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)
Author	SHA1	Message	Date
LiudengZhang	76a39fcf92	fix: correct opacity prop typo and style object in centroid labels (#2767 )	2026-03-09 13:39:56 -07:00
rwbaber	5eb3021752	fix: Handle non-categorical columns with colors + update deprecated AnnData API (#2758 ) Yeah that makes sense! Mergingg	2026-02-24 13:37:57 -08:00
Timmy HuangandClaude Opus 4.5	7c7203bdfe	chore: replace deprecated codecov with GitHub Action (#2747 ) Migrate from the deprecated codecov npm package and bash uploader to the official codecov/codecov-action@v5. This fixes gcov errors on macOS runners and provides better reliability for coverage uploads. Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>	2026-01-16 09:28:12 -08:00
rwbaber	5ac256fc8b	fix: remove incompatible float16 fixture from general adaptor tests (#2746 ) * test: remove incompatible float16 fixture from generic adaptor tests * test: remove obsolete error test file for float16	2026-01-15 15:18:45 -08:00
rwbaber Copilot Timmy Huang	2b86f8e600	fix: improve anndata error msg (#2743 ) * feat: improve error message for anndata version mismatches * fix: Remove mentioning of python update and only mention upgrading anndata * Update server/data_anndata/anndata_adaptor.py Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> --------- Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>	2026-01-14 09:22:22 -08:00
Timmy Huang	0fddcd042a	docs: Add open source required docs (#2745 )	2026-01-14 09:13:54 -08:00
Justin Kiggins	eb1dc8944f	Update README.md (#2725 ) CodeQL Scan / Analyze (javascript) (push) Has been cancelled CodeQL Scan / Analyze (python) (push) Has been cancelled Compatibility Tests / docker-build (push) Has been cancelled Compatibility Tests / cxg:latest os: py:3.12 anndata:==0.10.9 (push) Has been cancelled Compatibility Tests / cxg:latest os:macos-13 py:3.10 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:macos-13 py:3.11 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:macos-13 py:3.12 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:macos-latest py:3.10 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:macos-latest py:3.11 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:macos-latest py:3.12 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:ubuntu-latest py:3.10 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:ubuntu-latest py:3.11 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:latest os:ubuntu-latest py:3.12 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:macos-13 py:3.10 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:macos-13 py:3.11 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:macos-13 py:3.12 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:macos-latest py:3.10 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:macos-latest py:3.11 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:macos-latest py:3.12 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:ubuntu-latest py:3.10 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:ubuntu-latest py:3.11 anndata:latest (push) Has been cancelled Compatibility Tests / cxg:main os:ubuntu-latest py:3.12 anndata:latest (push) Has been cancelled Close inactive pull requests / close-issues (push) Has been cancelled Trademark	2025-05-14 12:03:19 -07:00
Ronen	fd8b47b78e	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	2024-09-12 16:05:14 -04:00
Ronen	487bd13ff8	chore: add support for python 3.12 (#2694 )	2024-09-12 14:16:46 -04:00
Ronen	eb743efd9a	fix: webpack upgrade (#2691 )	2024-09-09 13:34:44 -04:00
Ronen	67d152e108	fix: mlflow critical upgrade (#2690 )	2024-09-09 12:29:09 -04:00
Timmy Huang	c425d2e0b0	fix: underscore snakecase notation to hyphenated snakecase for diffexp-may-be-slow (#2687 )	2024-09-05 10:09:13 -07:00
Timmy Huangandkaloster	7bf5add6ef	chore: Fix compatibility tests (#2685 ) * chore: Fix compatibility tests * DEBUGGGG * fix: update deps, fix unit tests * fix: FE deps * chore: update compatibility matrix --------- Co-authored-by: kaloster <rkalo@contractor.chanzuckerberg.com>	2024-09-05 09:26:40 -07:00
dependabot[bot]andTimmy Huang	4281a8f816	chore(deps-dev): bump follow-redirects from 1.15.1 to 1.15.6 in /client (#2661 ) Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.15.1 to 1.15.6. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.15.1...v1.15.6) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Timmy Huang <tihuan@users.noreply.github.com>	2024-04-18 14:54:49 +00:00
Emanuele Bezzi	53e9edfec1	docs: change link to the CZI science community Slack (#2662 )	2024-03-19 10:19:28 -07:00
atarashansky	74fbec35fe	chore: Release version 1.2.0 (#2652 ) * Bump version: 1.1.2 → 1.2.0-rc.0 * Bump version: 1.2.0-rc.0 → 1.2.0	2023-12-19 14:13:08 -08:00
atarashansky	5d4c782f3a	chore: lower pinned requirements for backend server (#2651 ) * chore: lower pinned requirements for backend server * update one requirement	2023-12-19 13:39:47 -08:00
atarashansky	6505f6cbf5	chore: upgrade backend dependencies (#2641 ) chore: upgrade backend dependencies (#2641)	2023-11-29 14:16:39 -08:00
Severiano BadajozandSeve Badajoz	4bb9a2b834	chore: update dependencies (#2636 ) * chore: update dependencies * fix babel plugins and lint errors * switch out obselete browser plugin * add babel config for jest * revert some babel/jest package bumps * npm install * tmp remove werkzeug pin --------- Co-authored-by: Seve Badajoz <severiano.badajoz@chanzuckerberg.com>	2023-10-20 21:08:09 -04:00
maniarathi	2d7aab3a9a	fix: override default so that issues are not marked as stale (#2627 )	2023-08-23 21:22:17 -04:00
maniarathi	f749733d54	feat: Add a Github Action that automatically closes stale PRs. (#2626 )	2023-08-22 22:08:22 -04:00
atarashanskyandatarashansky	ffcf6eb5d8	chore: Release version 1.1.2 (#2611 ) * Bump version: 1.1.1 → 1.1.2-rc.0 * fix: release candidate 1.1.2 * Bump version: 1.1.2-rc.0 → 1.1.2 * promote --------- Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net>	2023-04-26 15:01:57 -04:00
atarashanskyandatarashansky	c209a9bca7	fix: pin flask requirement to be less than 2.3 (#2609 ) Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.hsd1.ma.comcast.net>	2023-04-26 13:58:40 -04:00
Kuni Katsuya	85319d45a4	chore: tech issue template	2023-02-06 15:46:54 -08:00
Andrew Tolopko	514f1627ea	Update license copyright year (#2600 )	2023-02-03 16:01:53 -05:00
Severiano Badajoz	127de34a20	feat: Add PR Linting (#2560 )	2022-10-24 18:08:25 +00:00
Andrew Tolopko	54ab9d79b6	docs: fix test pypi install command (#2515 ) fix test pypi install command in release_process.md	2022-09-29 19:30:11 +00:00
Andrew Tolopko	f48d06fb90	Bump version: 1.1.0 → 1.1.1 (#2572 )	2022-09-21 15:33:28 -04:00
Severiano BadajozandSeve Badajoz	84563291a0	fix: fix static file serving in webpack (#2574 ) Co-authored-by: Seve Badajoz <severiano.badajoz@chanzuckerberg.com>	2022-09-21 18:03:03 +00:00
Andrew Tolopko	ddb601c103	feat: annotate command improvements (#2568 ) * Replace --input-h5ad-file with a positional argument, for consistency with other CLI commands * Replace --update-h5ad-file with --overwrite, for consistency with `prepare` command. * Fix/clarify various help descriptions * Fix final output message when input file is overwritten * Fix annotate top-level help description	2022-09-15 11:55:58 -04:00
ashin-czi	450261f109	chore: updating Annotate favicon and logo icon (#2556 ) * chore: replacing html icon with png icon and updating favicon	2022-08-25 16:01:03 +00:00
ashin-czi	c0f4ad6dfa	docs: updating readme and display version for rebranding (#2550 ) * docs: updating readme and display version for rebranding - CELLxGENE -> CELLxGENE Annotate - reverting __init__.py display_version back to "cellxgene" - changing page titles to "CELLxGENE \| Annotate"	2022-08-25 15:41:26 +00:00
atarashanskyandatarashansky	ff5da77372	fix unit tests (#2562 ) Co-authored-by: atarashansky <atarashansky@CZIMACOS3990.local>	2022-08-25 08:02:58 -07:00
Andrew Tolopko Seve Badajoz Severiano Badajoz	a9044b01df	release version 1.1.0 (#2548 ) * Bump version: 1.0.1 → 1.1.0-rc.0 * bump version to v1.1.0 * Bump version: 1.1.0-rc.0 → 1.1.0-rc.1 * bump version to v1.1.0 rc1 rc0 was previously used by an aborted release attempt * Bump version: 1.1.0-rc.1 → 1.1.0 Co-authored-by: Seve Badajoz <severiano.badajoz@chanzuckerberg.com> Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com>	2022-08-23 10:02:23 -07:00
ashin-czi	11b948369f	fix: reverting back to old icon	2022-08-18 14:49:59 -04:00
ashin-czi	a2dc0c25b1	chore: updating Annotate favicon	2022-08-11 13:30:19 -04:00
		`@@ -0,0 +1,3 @@`
							`# Reporting Security Issues`

							`If you believe you have found a security issue, please responsibly disclose by contacting us at [security@chanzuckerberg.com](mailto:security@chanzuckerberg.com).`
`@@ -1,2 +1,2 @@`
	`DEFAULT_SERVER_PORT = 5005`	`DEFAULT_SERVER_PORT = 5005`
	`BIG_FILE_SIZE_THRESHOLD = 100 * 2 ** 20 # 100MB`	`BIG_FILE_SIZE_THRESHOLD = 100 * 2**20 # 100MB`