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

Yeah that makes sense! Mergingg

.bumpversion.cfg

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

.github/workflows/compatibility_tests.yml

@@ -7,10 +7,6 @@ on:
     branches:
       - main
 
-  # For debug - uncomment below to run on all PRs
-  # pull_request:
-  #   branches: "*"
-
 env:
   JEST_ENV: prod
 
@@ -32,14 +28,13 @@ 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]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         cellxgene_build: [main, latest]
         # add anndata pinned version test for subset of matrix configurations,
         # in order to reduce matrix cross-product explosion
         include:
-          - python-version: 3.11
+          - 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
@@ -100,7 +95,7 @@ jobs:
           # keep same pip pkg versions as in the cxg release
           sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
           pip install -r server/requirements-dev.txt
-          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas
+          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

@@ -17,10 +17,10 @@ jobs:
       - uses: actions/checkout@v4
       - run: |
           git fetch --depth=1 origin +${{github.base_ref}}
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: Node cache
         uses: actions/cache@v4
         with:
@@ -46,10 +46,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python 3.11 (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: 3.11
+          default: 3.12
           command: pip install -U pip # upgrade pip after installing python
       - run: pip install virtualenv # virtualenv needed for mlflow in cli annotate tests
       - name: Python cache
@@ -69,20 +69,31 @@ 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@v4
-      - name: Set up Python 3.11
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.12
       - name: Python cache
         uses: actions/cache@v4
         with:
@@ -98,11 +109,11 @@ jobs:
           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:

LICENSE

@@ -1,6 +1,6 @@
-The MIT License (MIT)
+# The MIT License (MIT)
 
-Copyright (c) 2017-2023 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

README.md

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

SECURITY.md

@@ -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).

client/.nvmrc

@@ -1 +1 @@
-16.20.0
+18.17.0

client/jest-puppeteer.config.js

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

client/package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "cellxgene",
-  "version": "1.2.0",
+  "version": "1.3.0",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "cellxgene",
-      "version": "1.2.0",
+      "version": "1.3.0",
       "license": "MIT",
       "dependencies": {
         "@babel/eslint-parser": "^7.15.0",
@@ -71,7 +71,6 @@
         "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",
@@ -116,8 +115,8 @@
         "webpack-obsolete-plugin": "^1.0.5"
       },
       "engines": {
-        "node": "^16.0.0",
+        "node": "^18.17.0",
-        "npm": ">=3.0.0"
+        "npm": ">=9.6.7"
       }
     },
     "node_modules/@ampproject/remapping": {
@@ -5371,16 +5370,6 @@
         "sprintf-js": "~1.0.2"
       }
     },
-    "node_modules/argv": {
-      "version": "0.0.2",
-      "resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
-      "integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
-      "deprecated": "Package no longer supported. Contact Support at https://www.npmjs.com/support for more info.",
-      "dev": true,
-      "engines": {
-        "node": ">=0.6.10"
-      }
-    },
     "node_modules/aria-query": {
       "version": "4.2.2",
       "resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
@@ -6448,26 +6437,6 @@
         "node": ">=0.10.0"
       }
     },
-    "node_modules/codecov": {
-      "version": "3.8.3",
-      "resolved": "https://registry.npmjs.org/codecov/-/codecov-3.8.3.tgz",
-      "integrity": "sha512-Y8Hw+V3HgR7V71xWH2vQ9lyS358CbGCldWlJFR0JirqoGtOoas3R3/OclRTvgUYFK29mmJICDPauVKmpqbwhOA==",
-      "deprecated": "https://about.codecov.io/blog/codecov-uploader-deprecation-plan/",
-      "dev": true,
-      "dependencies": {
-        "argv": "0.0.2",
-        "ignore-walk": "3.0.4",
-        "js-yaml": "3.14.1",
-        "teeny-request": "7.1.1",
-        "urlgrey": "1.0.0"
-      },
-      "bin": {
-        "codecov": "bin/codecov"
-      },
-      "engines": {
-        "node": ">=4.0"
-      }
-    },
     "node_modules/collect-v8-coverage": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
@@ -9173,21 +9142,6 @@
       "resolved": "https://registry.npmjs.org/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz",
       "integrity": "sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw=="
     },
-    "node_modules/fast-url-parser": {
-      "version": "1.1.3",
-      "resolved": "https://registry.npmjs.org/fast-url-parser/-/fast-url-parser-1.1.3.tgz",
-      "integrity": "sha512-5jOCVXADYNuRkKFzNJ0dCCewsZiYo0dz8QNYljkOpFC6r2U4OBmKtvm/Tsuh4w1YYdDqDb31a8TVhBJ2OJKdqQ==",
-      "dev": true,
-      "dependencies": {
-        "punycode": "^1.3.2"
-      }
-    },
-    "node_modules/fast-url-parser/node_modules/punycode": {
-      "version": "1.4.1",
-      "resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
-      "integrity": "sha512-jmYNElW7yvO7TV33CjSmvSiE2yco3bV2czu/OzDKdMNVZQWfxCblURLhf+47syQRBntjfLdd/H0egrzIG+oaFQ==",
-      "dev": true
-    },
     "node_modules/fastest-levenshtein": {
       "version": "1.0.12",
       "resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
@@ -10251,15 +10205,6 @@
         "node": ">= 4"
       }
     },
-    "node_modules/ignore-walk": {
-      "version": "3.0.4",
-      "resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.4.tgz",
-      "integrity": "sha512-PY6Ii8o1jMRA1z4F2hRkH/xN59ox43DavKvD3oDpfurRlOJyAHpifIwpbdv1n4jt4ov0jSpw3kQ4GhJnpBL6WQ==",
-      "dev": true,
-      "dependencies": {
-        "minimatch": "^3.0.4"
-      }
-    },
     "node_modules/import-fresh": {
       "version": "3.3.0",
       "resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz",
@@ -16921,15 +16866,6 @@
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       }
     },
-    "node_modules/stream-events": {
-      "version": "1.0.5",
-      "resolved": "https://registry.npmjs.org/stream-events/-/stream-events-1.0.5.tgz",
-      "integrity": "sha512-E1GUzBSgvct8Jsb3v2X15pjzN1tYebtbLaMg+eBOUOAxgbLoSbT2NS91ckc5lJD1KfLjId+jXJRgo0qnV5Nerg==",
-      "dev": true,
-      "dependencies": {
-        "stubs": "^3.0.0"
-      }
-    },
     "node_modules/string_decoder": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz",
@@ -17089,12 +17025,6 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
-    "node_modules/stubs": {
-      "version": "3.0.0",
-      "resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
-      "integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
-      "dev": true
-    },
     "node_modules/stylehacks": {
       "version": "5.1.0",
       "resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
@@ -17353,22 +17283,6 @@
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       }
     },
-    "node_modules/teeny-request": {
-      "version": "7.1.1",
-      "resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
-      "integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
-      "dev": true,
-      "dependencies": {
-        "http-proxy-agent": "^4.0.0",
-        "https-proxy-agent": "^5.0.0",
-        "node-fetch": "^2.6.1",
-        "stream-events": "^1.0.5",
-        "uuid": "^8.0.0"
-      },
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/terminal-link": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
@@ -17957,15 +17871,6 @@
         "requires-port": "^1.0.0"
       }
     },
-    "node_modules/urlgrey": {
-      "version": "1.0.0",
-      "resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-1.0.0.tgz",
-      "integrity": "sha512-hJfIzMPJmI9IlLkby8QrsCykQ+SXDeO2W5Q9QTW3QpqZVTx4a/K7p8/5q+/isD8vsbVaFgql/gvAoQCRQ2Cb5w==",
-      "dev": true,
-      "dependencies": {
-        "fast-url-parser": "^1.1.3"
-      }
-    },
     "node_modules/use": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
@@ -17996,15 +17901,6 @@
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       }
     },
-    "node_modules/uuid": {
-      "version": "8.3.2",
-      "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
-      "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
-      "dev": true,
-      "bin": {
-        "uuid": "dist/bin/uuid"
-      }
-    },
     "node_modules/v8-compile-cache": {
       "version": "2.3.0",
       "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",
@@ -22694,12 +22590,6 @@
         "sprintf-js": "~1.0.2"
       }
     },
-    "argv": {
-      "version": "0.0.2",
-      "resolved": "https://registry.npmjs.org/argv/-/argv-0.0.2.tgz",
-      "integrity": "sha512-dEamhpPEwRUBpLNHeuCm/v+g0anFByHahxodVO/BbAarHVBBg2MccCwf9K+o1Pof+2btdnkJelYVUWjW/VrATw==",
-      "dev": true
-    },
     "aria-query": {
       "version": "4.2.2",
       "resolved": "https://registry.npmjs.org/aria-query/-/aria-query-4.2.2.tgz",
@@ -23489,19 +23379,6 @@
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       "dev": true
     },
-    "codecov": {
-      "version": "3.8.3",
-      "resolved": "https://registry.npmjs.org/codecov/-/codecov-3.8.3.tgz",
-      "integrity": "sha512-Y8Hw+V3HgR7V71xWH2vQ9lyS358CbGCldWlJFR0JirqoGtOoas3R3/OclRTvgUYFK29mmJICDPauVKmpqbwhOA==",
-      "dev": true,
-      "requires": {
-        "argv": "0.0.2",
-        "ignore-walk": "3.0.4",
-        "js-yaml": "3.14.1",
-        "teeny-request": "7.1.1",
-        "urlgrey": "1.0.0"
-      }
-    },
     "collect-v8-coverage": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/collect-v8-coverage/-/collect-v8-coverage-1.0.1.tgz",
@@ -25575,23 +25452,6 @@
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-    "fast-url-parser": {
-      "version": "1.1.3",
-      "resolved": "https://registry.npmjs.org/fast-url-parser/-/fast-url-parser-1.1.3.tgz",
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-      "dev": true,
-      "requires": {
-        "punycode": "^1.3.2"
-      },
-      "dependencies": {
-        "punycode": {
-          "version": "1.4.1",
-          "resolved": "https://registry.npmjs.org/punycode/-/punycode-1.4.1.tgz",
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-          "dev": true
-        }
-      }
-    },
     "fastest-levenshtein": {
       "version": "1.0.12",
       "resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
@@ -26382,15 +26242,6 @@
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-    "ignore-walk": {
-      "version": "3.0.4",
-      "resolved": "https://registry.npmjs.org/ignore-walk/-/ignore-walk-3.0.4.tgz",
-      "integrity": "sha512-PY6Ii8o1jMRA1z4F2hRkH/xN59ox43DavKvD3oDpfurRlOJyAHpifIwpbdv1n4jt4ov0jSpw3kQ4GhJnpBL6WQ==",
-      "dev": true,
-      "requires": {
-        "minimatch": "^3.0.4"
-      }
-    },
     "import-fresh": {
       "version": "3.3.0",
       "resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.3.0.tgz",
@@ -31562,15 +31413,6 @@
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       "dev": true
     },
-    "stream-events": {
-      "version": "1.0.5",
-      "resolved": "https://registry.npmjs.org/stream-events/-/stream-events-1.0.5.tgz",
-      "integrity": "sha512-E1GUzBSgvct8Jsb3v2X15pjzN1tYebtbLaMg+eBOUOAxgbLoSbT2NS91ckc5lJD1KfLjId+jXJRgo0qnV5Nerg==",
-      "dev": true,
-      "requires": {
-        "stubs": "^3.0.0"
-      }
-    },
     "string_decoder": {
       "version": "1.1.1",
       "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-1.1.1.tgz",
@@ -31693,12 +31535,6 @@
       "resolved": "https://registry.npmjs.org/strip-json-comments/-/strip-json-comments-3.1.1.tgz",
       "integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig=="
     },
-    "stubs": {
-      "version": "3.0.0",
-      "resolved": "https://registry.npmjs.org/stubs/-/stubs-3.0.0.tgz",
-      "integrity": "sha512-PdHt7hHUJKxvTCgbKX9C1V/ftOcjJQgz8BZwNfV5c4B6dcGqlpelTbJ999jBGZ2jYiPAwcX5dP6oBwVlBlUbxw==",
-      "dev": true
-    },
     "stylehacks": {
       "version": "5.1.0",
       "resolved": "https://registry.npmjs.org/stylehacks/-/stylehacks-5.1.0.tgz",
@@ -31896,19 +31732,6 @@
         }
       }
     },
-    "teeny-request": {
-      "version": "7.1.1",
-      "resolved": "https://registry.npmjs.org/teeny-request/-/teeny-request-7.1.1.tgz",
-      "integrity": "sha512-iwY6rkW5DDGq8hE2YgNQlKbptYpY5Nn2xecjQiNjOXWbKzPGUfmeUBCSQbbr306d7Z7U2N0TPl+/SwYRfua1Dg==",
-      "dev": true,
-      "requires": {
-        "http-proxy-agent": "^4.0.0",
-        "https-proxy-agent": "^5.0.0",
-        "node-fetch": "^2.6.1",
-        "stream-events": "^1.0.5",
-        "uuid": "^8.0.0"
-      }
-    },
     "terminal-link": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/terminal-link/-/terminal-link-2.1.1.tgz",
@@ -32347,15 +32170,6 @@
         "requires-port": "^1.0.0"
       }
     },
-    "urlgrey": {
-      "version": "1.0.0",
-      "resolved": "https://registry.npmjs.org/urlgrey/-/urlgrey-1.0.0.tgz",
-      "integrity": "sha512-hJfIzMPJmI9IlLkby8QrsCykQ+SXDeO2W5Q9QTW3QpqZVTx4a/K7p8/5q+/isD8vsbVaFgql/gvAoQCRQ2Cb5w==",
-      "dev": true,
-      "requires": {
-        "fast-url-parser": "^1.1.3"
-      }
-    },
     "use": {
       "version": "3.1.1",
       "resolved": "https://registry.npmjs.org/use/-/use-3.1.1.tgz",
@@ -32380,12 +32194,6 @@
       "integrity": "sha512-pMZTvIkT1d+TFGvDOqodOclx0QWkkgi6Tdoa8gC8ffGAAqz9pzPTZWAybbsHHoED/ztMtkv/VoYTYyShUn81hA==",
       "dev": true
     },
-    "uuid": {
-      "version": "8.3.2",
-      "resolved": "https://registry.npmjs.org/uuid/-/uuid-8.3.2.tgz",
-      "integrity": "sha512-+NYs2QeMWy+GWFOEm9xnn6HCDp0l7QBD7ml8zLUmJ+93Q5NF0NocErnwkTkXVFNiX3/fpC6afS8Dhb/gz7R7eg==",
-      "dev": true
-    },
     "v8-compile-cache": {
       "version": "2.3.0",
       "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "1.2.0",
+  "version": "1.3.0",
   "license": "MIT",
   "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
   "repository": "https://github.com/chanzuckerberg/cellxgene",
@@ -18,8 +18,8 @@
   },
   "engineStrict": true,
   "engines": {
-    "npm": ">=3.0.0",
+    "npm": ">=9.6.7",
-    "node": "^16.0.0"
+    "node": "^18.17.0"
   },
   "eslintConfig": {
     "extends": "./configuration/eslint/eslint.js"
@@ -101,7 +101,6 @@
     "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",

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

@@ -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)}

dev_docs/developer_guidelines.md

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

dev_docs/developer_scripts.md

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

server/__init__.py

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

server/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 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)

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].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

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 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:

server/data_anndata/anndata_adaptor.py

@@ -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):
@@ -173,13 +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
+            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)
@@ -302,11 +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) is 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:

server/requirements-dev.txt

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

server/requirements.txt

@@ -7,7 +7,7 @@ Flask-Cors>=3.0.9
 Flask-RESTful>=0.3.6
 flask-server-timing>=0.1.2
 flask-talisman>=0.7.0
-flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
+flatbuffers==2.0.7
 flatten-dict>=0.2.0
 fsspec>0.8.0
 gunicorn>=20.0.4
@@ -19,4 +19,5 @@ pandas>=2.2.2
 PyYAML>=5.4  # CVE-2020-14343
 requests>=2.22.0
 s3fs==0.4.2
-scipy>=1.4
+scipy>=1.4
+setuptools

setup.py

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

test/unit/data_anndata/test_anndata_adaptor.py

@@ -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):

test/unit/data_anndata/test_anndata_adaptor_errors.py

@@ -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),
-            )

test/unit/utils/test_type_conversion_utils.py

@@ -134,7 +134,7 @@ float_OK_cases = [
         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.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),
     ]