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 06:58:11 +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
14 changed files with 52 additions and 267 deletions
@@ -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
@@ -17,4 +17,4 @@ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -1,20 +0,0 @@
-The MIT License (MIT)
-
-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
-the Software without restriction, including without limitation the rights to
-use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
-the Software, and to permit persons to whom the Software is furnished to do so,
-subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
-FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
-COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
-IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -1,2 +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).
+# 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 @@
      "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",
@@ -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