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 06:48:12 +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
15 changed files with 59 additions and 245 deletions
@@ -12,7 +12,7 @@ jobs:
  main:
    runs-on: ubuntu-latest
    steps:
-      - uses: amannn/action-semantic-pull-request@40166f00814508ec3201fc8595b393d451c8cd80@v3.4.1
+      - uses: amannn/action-semantic-pull-request@v3.4.1
        with:
          validateSingleCommit: true
        env:
@@ -69,10 +69,21 @@ jobs:
      - name: Install dependencies
        run: make pydist install-dist dev-env-server
      - name: Unit tests
-        run: |
-          make unit-test-server unit-test-client
-          bash <(curl -s https://codecov.io/bash) -y .codecov.yml -k server -cF server,python,unitTest
-          cd client && ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,unitTest
+        run: make unit-test-server unit-test-client
+      - name: Generate server coverage XML
+        run: coverage xml -o server/coverage.xml
+      - 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
@@ -102,9 +113,7 @@ jobs:
          pip install setuptools
          make pydist install-dist
      - name: Smoke tests (without annotations feature)
-        run: |
-          cd client && make smoke-test
-          ./node_modules/codecov/bin/codecov --yml=../.codecov.yml --root=../ --gcov-root=../ -C -F frontend,javascript,smokeTest
+        run: cd client && make smoke-test

  # TODO: reinstate: https://github.com/chanzuckerberg/cellxgene/issues/2544
  # smoke-tests-annotations:
@@ -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
@@ -82,6 +82,13 @@ extension could be directly contributed, which would make it available for a wid

 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.

+### 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.
+
+
 ### Security

 If you believe you have found a security issue, we would appreciate notification. Please send email to <security@chanzuckerberg.com>.
@@ -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).
@@ -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",
@@ -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 @@
        "node": ">= 0.8"
      }
    },
-    "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 @@
        "node": ">= 6"
      }
    },
-    "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 @@
        "node": ">= 0.4.0"
      }
    },
-    "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 @@
      "integrity": "sha512-RpAVKQA5T63xEj6/giIbUEtZwJ4UFIc3ZtvEkiaUERylqe8xb5IvqcgOurZLahv93CLKfxcw5YI+DZcUBRyLXA==",
      "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 @@
      "resolved": "https://registry.npmjs.org/fast-levenshtein/-/fast-levenshtein-2.0.6.tgz",
      "integrity": "sha512-DCXu6Ifhqcks7TZKY3Hxp3y6qphY5SJZmrWMDrKcERSOXWQdMhU9Ig/PYrzyw/ul9jOIyh0N4M0tbC5hodg8dw=="
    },
-    "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,
-      "requires": {
-        "punycode": "^1.3.2"
-      },
-      "dependencies": {
-        "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
-        }
-      }
-    },
    "fastest-levenshtein": {
      "version": "1.0.12",
      "resolved": "https://registry.npmjs.org/fastest-levenshtein/-/fastest-levenshtein-1.0.12.tgz",
@@ -26382,15 +26242,6 @@
      "resolved": "https://registry.npmjs.org/ignore/-/ignore-4.0.6.tgz",
      "integrity": "sha512-cyFDKrqc/YdcWFniJhzI42+AzS+gNwmUzOSFcRCQYwySuBBBy/KjuxWLZ/FHEH6Moq1NizMOBWyTcv8O4OZIMg=="
    },
-    "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 @@
      "integrity": "sha512-RwNA9Z/7PrK06rYLIzFMlaF+l73iwpzsqRIFgbMLbTcLD6cOao82TaWefPXQvB2fOC4AjuYSEndS7N/mTCbkdQ==",
      "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 @@
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      "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",
@@ -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",
@@ -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)}
@@ -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():
-                raise click.UsageError(f"obs {set_obs_names} not found, options are: {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: {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():
-                raise click.UsageError(f"var {set_var_names} not found, options are: {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: {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)
@@ -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
@@ -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:
@@ -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:
@@ -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
@@ -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):
@@ -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),
-            )
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