chore: upgrade dependencies

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.3.0
+current_version = 1.1.2
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 

.github/workflows/compatibility_tests.yml

@@ -14,9 +14,9 @@ jobs:
   docker-build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Build docker image
@@ -28,23 +28,35 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, macos-13]
+        # note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
-        python-version: ["3.10", "3.11", "3.12"]
+        os: [ubuntu-latest, macos-latest, macos-11]
+        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: 3.12
+          - python-version: 3.9
             cellxgene_build: latest
             # TODO: dynamically use the literal version in requirements.txt,
             # to avoid having to update this in manually in the future
             # TODO: Do not bother running this if anndata latest version
             # matches this pinned version, to avoid a redundant test
-            anndata_version: "==0.10.9"
+            anndata_version: "==0.10.3"
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Cache env vars
@@ -54,14 +66,14 @@ jobs:
         run: echo "BREW_CACHE=`brew --cache`" >> $GITHUB_ENV
       # FIXME: Only working for Linux
       - name: Python cache
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         with:
           path: ${{ env.PIP_CACHE }}
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -69,7 +81,7 @@ jobs:
             ${{ runner.os }}-node-
       - name: Brew cache (MacOS)
         if: startsWith(matrix.os, 'macos')
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         with:
           path: ${{ env.BREW_CACHE }}
           key: ${{ runner.os }}-brew-
@@ -95,7 +107,6 @@ jobs:
           # keep same pip pkg versions as in the cxg release
           sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
           pip install -r server/requirements-dev.txt
-          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas flatbuffers==2.0.7
       - name: Install anndata version per matrix variable
         run: pip install anndata${{ matrix.anndata_version }}
       - name: Install node

.github/workflows/push_tests.yml

@@ -14,15 +14,15 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v2
       - run: |
           git fetch --depth=1 origin +${{github.base_ref}}
-      - name: Set up Python 3.12
+      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.12
+          python-version: 3.9
       - name: Node cache
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         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@v4
+      - uses: actions/checkout@v2
-      - name: Set up Python 3.12 (pyenv) # pyenv needed for mlflow in cli annotate tests
+      - name: Set up Python 3.9 (pyenv) # pyenv needed for mlflow in cli annotate tests
         uses: gabrielfalcao/pyenv-action@v9
         with:
-          default: 3.12
+          default: 3.9
           command: pip install -U pip # upgrade pip after installing python
       - run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
       - name: Python cache
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
@@ -69,51 +69,40 @@ jobs:
       - name: Install dependencies
         run: make pydist install-dist dev-env-server
       - name: Unit tests
-        run: make unit-test-server unit-test-client
+        run: |
-      - name: Generate server coverage XML
+          make unit-test-server unit-test-client
-        run: coverage xml -o server/coverage.xml
+          bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
-      - name: Upload server coverage
+          cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
-        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@v4
+      - uses: actions/checkout@v2
-      - name: Set up Python 3.12
+      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.12
+          python-version: 3.9
       - name: Python cache
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements*.txt') }}
           restore-keys: |
             ${{ runner.os }}-pip-
       - name: Node cache
-        uses: actions/cache@v4
+        uses: actions/cache@v1
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
           restore-keys: |
             ${{ runner.os }}-node-
       - name: Install dependencies
-        run: |
+        run: make pydist install-dist
-          pip install setuptools
-          make pydist install-dist
       - name: Smoke tests (without annotations feature)
-        run: cd client && make smoke-test
+        run: |
+          cd client && make smoke-test
+          ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
 
   # TODO: reinstate: https://github.com/chanzuckerberg/cellxgene/issues/2544
   # smoke-tests-annotations:

LICENSE.txt

@@ -1,6 +1,6 @@
-# The MIT License (MIT)
+The MIT License (MIT)
 
-Copyright (c) 2017-2026 Chan Zuckerberg Initiative
+Copyright (c) 2017-2023 Chan Zuckerberg Initiative
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in

README.md

@@ -27,7 +27,7 @@ Whether you need to visualize one thousand cells or one million, CELLxGENE Annot
 
 ### Quick start
 
-To install CELLxGENE Annotate you need Python 3.10+. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
+To install CELLxGENE Annotate you need Python 3.6+. We recommend [installing Annotate into a conda or virtual environment.](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/desktop/install.md)
 
 Install the package.
 
@@ -58,7 +58,7 @@ Please [file an issue](https://github.com/chanzuckerberg/cellxgene/issues/new/ch
 ### Finding help
 
 We'd love to hear from you!
-For questions, suggestions, or accolades, join the `#cellxgene-users` channel on the [CZI Science Community Slack](https://czi.co/science-slack) and say "hi!".
+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 any errors, [report bugs on Github](https://github.com/chanzuckerberg/cellxgene/issues).
 
@@ -66,28 +66,22 @@ For any errors, [report bugs on Github](https://github.com/chanzuckerberg/cellxg
 
 ### Contributing
 
-We warmly welcome contributions from the community! Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CELLxGENE Annotate. Please see the [dev_docs](https://github.com/chanzuckerberg/cellxgene/tree/main/dev_docs) for pull request suggestions, unit test details, local documentation preview, and other development specifics.
+We warmly welcome contributions from the community! Please see our [contributing guide](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/contribute.md) and don't hesitate to open an issue or send a pull request to improve CELLxGENE Annotate. Please see the [dev_docs](https://github.com/chanzuckerberg/cellxgene/tree/main/dev_docs) for pull request suggestions, unit test details, local documentation preview, and other development specifics. 
 
 This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/master/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to opensource@chanzuckerberg.com.
 
 ### Reuse
 
-This project was started with the sole goal of empowering the scientific community to explore and understand their data.
+This project was started with the sole goal of empowering the scientific community to explore and understand their data. 
-As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from
+As such, we encourage other scientific tool builders in academia or industry to adopt the patterns, tools, and code from 
 this project. All code is freely available for reuse under the [MIT license](https://opensource.org/licenses/MIT).
 
-Before extending CELLxGENE Annotate, we encourage you to reach out to us with ideas or questions. It might be possible that an
-extension could be directly contributed, which would make it available for a wider audience, or that it's on our
-[roadmap](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/roadmap.md) and under active development.
 
-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.
+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 
-### Trademarks
+[roadmap](https://github.com/chanzuckerberg/cellxgene-documentation/blob/main/roadmap.md) and under active development. 
-
-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
 

SECURITY.md

@@ -1,3 +0,0 @@
-# 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).

client/.nvmrc

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

client/__tests__/e2e/puppeteer.setup.js

@@ -13,7 +13,7 @@ import * as ENV_DEFAULT from "../../../environment.default.json";
 // a test can take more time to finish, so we don't want
 // jest to shut off the test too soon
 jest.setTimeout(2 * 60 * 1000);
-setDefaultOptions({ timeout: 60 * 1000 });
+setDefaultOptions({ timeout: 20 * 1000 });
 
 jest.retryTimes(ENV_DEFAULT.RETRY_ATTEMPTS);
 

client/jest-puppeteer.config.js

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

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "1.3.0",
+  "version": "1.1.2",
   "license": "MIT",
   "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
   "repository": "https://github.com/chanzuckerberg/cellxgene",
@@ -18,8 +18,7 @@
   },
   "engineStrict": true,
   "engines": {
-    "npm": ">=9.6.7",
+    "npm": ">=3.0.0"
-    "node": "^18.17.0"
   },
   "eslintConfig": {
     "extends": "./configuration/eslint/eslint.js"
@@ -78,7 +77,7 @@
     "whatwg-fetch": "^3.2.0"
   },
   "devDependencies": {
-    "@babel/core": "^7.25.2",
+    "@babel/core": "^7.13.16",
     "@babel/plugin-proposal-class-properties": "^7.10.4",
     "@babel/plugin-proposal-decorators": "^7.13.15",
     "@babel/plugin-proposal-export-namespace-from": "^7.10.4",
@@ -101,6 +100,7 @@
     "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",
@@ -123,7 +123,7 @@
     "jest-circus": "^27.0.6",
     "jest-environment-puppeteer": "^5.0.1",
     "jest-fetch-mock": "^3.0.3",
-    "jest-puppeteer": "^6.2.0",
+    "jest-puppeteer": "^5.0.1",
     "json-loader": "^0.5.7",
     "lint-staged": "^10.2.11",
     "lodash": "^4.17.21",
@@ -134,11 +134,11 @@
     "lodash.zip": "^4.2.0",
     "mini-css-extract-plugin": "^1.5.0",
     "prettier": "^2.0.5",
-    "puppeteer": "^10.4.0",
+    "puppeteer": "^8.0.0",
     "rimraf": "^3.0.2",
     "serve-favicon": "^2.5.0",
     "terser-webpack-plugin": "^5.1.1",
-    "webpack": "^5.94.0",
+    "webpack": "^5.88.2",
     "webpack-cli": "^4.6.0",
     "webpack-dev-middleware": "^4.1.0",
     "webpack-merge": "^5.0.9",

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

@@ -150,7 +150,7 @@ class CentroidLabels extends PureComponent {
                   dilatedValue={dilatedValue}
                   coords={coords}
                   inverseTransform={inverseTransform}
-                  opacity={selected ? 1 : deselectOpacity}
+                  opactity={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)}

client/src/components/leftSidebar/infoMenu.js

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

dev_docs/developer_guidelines.md

@@ -3,7 +3,7 @@
 ## Requirements
 
 - npm
-- Python 3.10+
+- Python 3.6+
 - 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 python3.10 with virtualenv) with the `scripts/backend_dev` script.
+- You can also install/launch the server side code from npm scrips (requires python3.6 with virtualenv) with the `scripts/backend_dev` script.
 
-- Check out [e2e Tests](e2e_tests.md) for more details
+- Check out [e2e Tests](e2e_tests.md) for more details

dev_docs/developer_scripts.md

@@ -11,10 +11,9 @@ $PROJECT_ROOT`.
 ### Build
 
 **Usage:** from the `$PROJECT_ROOT` directory run:
-
+* `make build` builds whole app client and server
-- `make build` builds whole app client and server
+* `make build-client` runs webpack build
-- `make build-client` runs webpack build
+* `make build-for-server-dev` builds client and copies output directly into
-- `make build-for-server-dev` builds client and copies output directly into
   source tree (only for server devlopment)
 
 ### Clean
@@ -22,19 +21,17 @@ $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
 
@@ -45,18 +42,16 @@ 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-dev` - installs from local source tree
+* `install-release-test` - installs from test pypi
-- `install-release-test` - installs from test pypi
+* `install-release` - installs from pypi
-- `install-release` - installs from pypi
+* `install-dist` - installs from local dist folder
-- `install-dist` - installs from local dist folder
+* `uninstall` - uninstalls cellxgene
-- `uninstall` - uninstalls cellxgene
 
 ## Client-level scripts
 
@@ -67,9 +62,8 @@ 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).
-- The server to be running. Best way to do this is with [backend_dev](#backend_dev).
+* `make ci` to install the necessary node modules
-- `make ci` to install the necessary node modules
 
 **Usage:** from the `$PROJECT_ROOT/client` directory run `make start-frontend`
 
@@ -81,24 +75,23 @@ 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** `Python3.10+`, `virtual-env`, `pip`
+**Requires** `Python3.6+`, `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                                                    |
 | ---------------------------------------- | ---------------------------------------------------------- |
-| python3.12 -m venv cellxgene             | creates cellxgene virtual environment                      |
+| python3.6 -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                |
@@ -109,15 +102,14 @@ environment and installs cellxgene from the current branch.
 Methods used to test the client javascript code
 
 **Usage:** from the `$PROJECT_ROOT/client` directory run:
-
+* `make unit-test` Runs all unit tests. It excludes any tests in the e2e
-- `make unit-test` Runs all unit tests. It excludes any tests in the e2e
   folder. This is used by travis to run unit tests.
-- `make smoke-test` Starts backend development server and runs end to end
+* `make smoke-test` Starts backend development server and runs end to end
   tests. This is what travis runs. It depends on the `e2e` and the
   `backend-dev` targets. One starts the server, the other runs the tests. If
   developing a front-end feature and just checking if tests pass, this is
   probabaly the one you want to run.
-- `npm run e2e` Runs backend tests without starting the server. You will need to
+* `npm run e2e` Runs backend tests without starting the server. You will need to
   start the rest api separately with the pbmc3k.h5ad file. Note you can use
   the `JEST_ENV` environment variable to change how JEST runs in the browser.
   The test runs against `localhost:3000` by default. You can use the

server/__init__.py

@@ -2,7 +2,7 @@ import logging
 import sys
 from server.common.utils.utils import import_plugins
 
-__version__ = "1.3.0"
+__version__ = "1.1.2"
 display_version = "cellxgene v" + __version__
 
 try:

server/cli/prepare.py

@@ -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 list(adata.obs.keys()):
+            if set_obs_names not in adata.obs_keys():
-                raise click.UsageError(f"obs {set_obs_names} not found, options are: {list(adata.obs.keys())}")
+                raise click.UsageError(f"obs {set_obs_names} not found, options are: {adata.obs_keys()}")
             adata.obs_names = adata.obs[set_obs_names]
         if not set_var_names == "":
-            if set_var_names not in list(adata.var.keys()):
+            if set_var_names not in adata.var_keys():
-                raise click.UsageError(f"var {set_var_names} not found, options are: {list(adata.var.keys())}")
+                raise click.UsageError(f"var {set_var_names} not found, options are: {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)

server/common/colors.py

@@ -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].astype('category').cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
+            zip(data.obs[category_name].cat.categories, [convert_color_to_hex_format(c) for c in data.uns[uns_key]])
         )
     return cxg_colors

server/common/config/dataset_config.py

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

server/common/corpora.py

@@ -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 list(adata.uns.keys()):
+    if "version" not in adata.uns_keys():
         return None
     version = adata.uns["version"]
     if not isinstance(version, collections.abc.Mapping) or "corpora_schema_version" not in version:

server/common/utils/type_conversion_utils.py

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

server/data_anndata/anndata_adaptor.py

@@ -1,5 +1,4 @@
 import warnings
-import importlib.metadata
 
 import anndata
 import numpy as np
@@ -17,7 +16,7 @@ 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(importlib.metadata.version('anndata'))).release
+anndata_version = version.parse(str(anndata.__version__)).release
 
 
 def anndata_version_is_pre_070():
@@ -64,7 +63,7 @@ class AnndataAdaptor(DataAdaptor):
         return "cellxgene anndata adaptor version"
 
     def get_library_versions(self):
-        return dict(anndata=str(importlib.metadata.version('anndata')))
+        return dict(anndata=str(anndata.__version__))
 
     @staticmethod
     def _create_unique_column_name(df, col_name_prefix):
@@ -174,24 +173,13 @@ class AnndataAdaptor(DataAdaptor):
             )
         except MemoryError:
             raise DatasetAccessError("Out of memory - file is too large for available memory.")
-        except Exception as e:
+        except Exception:
             import traceback
-            error_msg = str(e)
-
-            # 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."
-                )
 
+            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)
@@ -223,7 +211,7 @@ class AnndataAdaptor(DataAdaptor):
         # heuristic
         n_values = self.data.shape[0] * self.data.shape[1]
         if (n_values > 1e8 and self.server_config.adaptor__anndata_adaptor__backed is True) or (n_values > 5e8):
-            self.parameters.update({"diffexp-may-be-slow": True})
+            self.parameters.update({"diffexp_may_be_slow": True})
 
     def _is_valid_layout(self, arr):
         """return True if this layout data is a valid array for front-end presentation:
@@ -314,11 +302,11 @@ class AnndataAdaptor(DataAdaptor):
         layouts = self.dataset_config.embeddings__names
 
         if layouts is None or len(layouts) == 0:
-            layouts = [key[2:] for key in list(self.data.obsm.keys()) if type(key) is str and key.startswith("X_")]
+            layouts = [key[2:] for key in self.data.obsm_keys() if type(key) is str and key.startswith("X_")]
 
         # remove invalid layouts
         valid_layouts = []
-        obsm_keys = list(self.data.obsm.keys())
+        obsm_keys = self.data.obsm_keys()
         for layout in layouts:
             layout_name = f"X_{layout}"
             if layout_name not in obsm_keys:

server/requirements-annotate.txt

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

server/requirements-dev.txt

@@ -1,6 +1,6 @@
 black
 bumpversion>=0.5
-coverage>=5.0
+codecov>=2.0.15
 parameterized>=0.7.0
 pytest>=3.6.3
 python-jose>=3.2.0

server/requirements.txt

@@ -1,23 +1,22 @@
-anndata>=0.8.0
+anndata==0.10.3
-boto3>=1.12.18
+boto3==1.29.5
-click>=7.1.2
+click==8.1.7
-Flask>=3.0.0
+Flask==3.0.0
-Flask-Compress>=1.4.0
+Flask-Compress==1.14
-Flask-Cors>=3.0.9
+Flask-Cors==4.0.0
-Flask-RESTful>=0.3.6
+Flask-RESTful==0.3.10
-flask-server-timing>=0.1.2
+flask-server-timing==0.1.2
-flask-talisman>=0.7.0
+flask-talisman==1.1.0
-flatbuffers==2.0.7
+flatbuffers==1.12
-flatten-dict>=0.2.0
+flatten-dict==0.4.2
-fsspec>0.8.0
+fsspec==2023.10.0
-gunicorn>=20.0.4
+gunicorn==21.2.0
-h5py>=3.0.0
+h5py==3.10.0
-numba>=0.60.0
+numba==0.58.1
-numpy==2.0.1
+numpy==1.26.2
-packaging>=20.0
+packaging==23.2
-pandas>=2.2.2
+pandas<2.0.0
-PyYAML>=5.4  # CVE-2020-14343
+PyYAML==6.0.1
-requests>=2.22.0
+requests==2.31.0
 s3fs==0.4.2
-scipy>=1.4
+scipy==1.11.4
-setuptools

setup.py

@@ -14,7 +14,7 @@ with open("server/requirements-annotate.txt") as fh:
 
 setup(
     name="cellxgene",
-    version="1.3.0",
+    version="1.1.2",
     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=">=3.10",
+    python_requires=">=3.6",
     include_package_data=True,
     zip_safe=False,
     classifiers=[
@@ -37,9 +37,8 @@ setup(
         "Operating System :: MacOS :: MacOS X",
         "Programming Language :: JavaScript",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.7",
-        "Programming Language :: Python :: 3.12",
         "Programming Language :: Python :: 3 :: Only",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],

test/unit/cli/fixtures/__init__.py

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

test/unit/compute/test_est_dist.py

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

test/unit/data_anndata/test_anndata_adaptor.py

@@ -36,6 +36,7 @@ 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):

test/unit/data_anndata/test_anndata_adaptor_errors.py

@@ -0,0 +1,23 @@
+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),
+            )

test/unit/utils/test_jsonify_strict.py

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

test/unit/utils/test_type_conversion_utils.py

@@ -42,7 +42,7 @@ class TestTypeConversionUtils(unittest.TestCase):
             with self.assertRaises(TypeError):
                 get_schema_type_hint_from_dtype(np.dtype(dtype))
 
-        for dtype in [np.float32, np.float64]:
+        for dtype in [np.float16, 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)]:
@@ -123,18 +123,17 @@ 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 dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
+        "logs": None if data.dtype != np.float64 else {"level": logging.WARNING, "output": "may lose precision"},
     }
-    for dtype in [np.float32, np.float64]
+    for dtype in [np.float16, 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.inf, -1, -0.0, 0, 0.0, 1, np.inf, np.nan], dtype=dtype),
+        np.array([-np.nan, np.NINF, -1, np.NZERO, 0, np.PZERO, 1, np.PINF, np.nan], dtype=dtype),
         np.array([np.finfo(dtype).min, 0, np.finfo(dtype).max], dtype=dtype),
         sparse.csr_matrix((10, 100), dtype=dtype),
     ]
@@ -199,13 +198,12 @@ 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": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
+            "logs": {"level": logging.WARNING, "output": "may lose precision"},
         }
-        for dtype in [np.float32, np.float64]
+        for dtype in [np.float16, 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]),
@@ -215,11 +213,10 @@ 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": None if dtype == np.float32 else {"level": logging.WARNING, "output": "may lose precision"},
+            "logs": {"level": logging.WARNING, "output": "may lose precision"},
         }
         for dtype in [
             np.int8,
@@ -230,6 +227,7 @@ category_numeric_OK_cases = [
             np.uint32,
             np.int64,
             np.uint64,
+            np.float16,
             np.float32,
             np.float64,
         ]
@@ -314,6 +312,7 @@ 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)