release version 1.0.1 (#2497 )

* Bump version: 1.0.0 → 1.0.1-rc.0 * Bump version: 1.0.1-rc.0 → 1.0.1
chore(deps): bump nanoid from 3.1.25 to 3.3.1 in /client (#2488 )
2026-09-26 07:18:11 +08:00 · 2022-02-28 15:18:21 -08:00 · 2022-02-25 09:57:22 -08:00 · 2022-02-24 14:20:17 -08:00 · 2022-02-24 14:05:26 -08:00 · 2022-02-24 13:46:07 -08:00
10 changed files with 71 additions and 40 deletions
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.0
+current_version = 1.0.1
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 
@@ -1,6 +1,6 @@
 The MIT License (MIT)

-Copyright (c) 2017-2021 Chan Zuckerberg Initiative
+Copyright (c) 2017-2022 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
@@ -1,12 +1,12 @@
 {
  "name": "cellxgene",
-  "version": "1.0.0",
+  "version": "1.0.1",
  "lockfileVersion": 2,
  "requires": true,
  "packages": {
    "": {
      "name": "cellxgene",
-      "version": "1.0.0",
+      "version": "1.0.1",
      "license": "MIT",
      "dependencies": {
        "@babel/eslint-parser": "^7.15.0",
@@ -4807,12 +4807,12 @@
      }
    },
    "node_modules/axios": {
-      "version": "0.21.1",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz",
-      "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==",
+      "version": "0.21.4",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.4.tgz",
+      "integrity": "sha512-ut5vewkiu8jjGBdqpM44XxjuCjq9LAKeHVmoVfHVzy8eHgxxq8SbAVQNovDA8mVi05kP0Ea/n/UzcSHcTJQfNg==",
      "dev": true,
      "dependencies": {
-        "follow-redirects": "^1.10.0"
+        "follow-redirects": "^1.14.0"
      }
    },
    "node_modules/axobject-query": {
@@ -9642,9 +9642,9 @@
      }
    },
    "node_modules/follow-redirects": {
-      "version": "1.14.2",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.2.tgz",
-      "integrity": "sha512-yLR6WaE2lbF0x4K2qE2p9PEXKLDjUjnR/xmjS3wHAYxtlsI9MLLBJUZirAHKzUZDGLxje7w/cXR49WOUo4rbsA==",
+      "version": "1.14.8",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.8.tgz",
+      "integrity": "sha512-1x0S9UVJHsQprFcEC/qnNzBLcIxsjAV905f/UkQxbclCsoTWlacCNOpQa/anodLl2uaEKFhfWOvM2Qg77+15zA==",
      "dev": true,
      "funding": [
        {
@@ -14492,9 +14492,9 @@
      "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w=="
    },
    "node_modules/nanoid": {
-      "version": "3.1.25",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.1.25.tgz",
-      "integrity": "sha512-rdwtIXaXCLFAQbnfqDRnI6jaRHp9fTcYBjtFKE8eezcZ7LuLjhUaQGNeMXf1HmRoCH32CLz6XwX0TtxEOS/A3Q==",
+      "version": "3.3.1",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.1.tgz",
+      "integrity": "sha512-n6Vs/3KGyxPQd6uO0eH4Bv0ojGSUvuLlIHtC3Y0kEO23YRge8H9x1GCzLn28YX0H66pMkxuaeESFq4tKISKwdw==",
      "dev": true,
      "bin": {
        "nanoid": "bin/nanoid.cjs"
@@ -21005,9 +21005,9 @@
      ]
    },
    "node_modules/simple-get": {
-      "version": "3.1.0",
-      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.0.tgz",
-      "integrity": "sha512-bCR6cP+aTdScaQCnQKbPKtJOKDp/hj9EDLJo3Nw4y1QksqaovlW/bnptB6/c1e+qmNIDHRK+oXFDdEqBT8WzUA==",
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.1.tgz",
+      "integrity": "sha512-CQ5LTKGfCpvE1K0n2us+kuMPbk/q0EKl82s4aheV9oXjFEz6W/Y7oQFVJuU6QG77hRT4Ghb5RURteF5vnWjupA==",
      "dev": true,
      "dependencies": {
        "decompress-response": "^4.2.0",
@@ -22398,9 +22398,9 @@
      "integrity": "sha512-ppJZNDuKGgxzkHihX8v9v9G5f+18gzaTfrukGrq6ueg0lmH4nqVnA2IPG0AEH3jKEk2GRJCUhDoqpoiw3PHLBA=="
    },
    "node_modules/tmpl": {
-      "version": "1.0.4",
-      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.4.tgz",
-      "integrity": "sha1-I2QN17QtAEM5ERQIIOXPRA5SHdE=",
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.5.tgz",
+      "integrity": "sha512-3f0uOEAQwIqGuWW2MVzYg8fV/QNnc/IpuJNG837rLuczAaLVHslWHZQj4IGiEl5Hs3kkbhwL9Ab7Hrsmuj+Smw==",
      "dev": true
    },
    "node_modules/to-fast-properties": {
@@ -27379,12 +27379,12 @@
      "dev": true
    },
    "axios": {
-      "version": "0.21.1",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz",
-      "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==",
+      "version": "0.21.4",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.4.tgz",
+      "integrity": "sha512-ut5vewkiu8jjGBdqpM44XxjuCjq9LAKeHVmoVfHVzy8eHgxxq8SbAVQNovDA8mVi05kP0Ea/n/UzcSHcTJQfNg==",
      "dev": true,
      "requires": {
-        "follow-redirects": "^1.10.0"
+        "follow-redirects": "^1.14.0"
      }
    },
    "axobject-query": {
@@ -31199,9 +31199,9 @@
      }
    },
    "follow-redirects": {
-      "version": "1.14.2",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.2.tgz",
-      "integrity": "sha512-yLR6WaE2lbF0x4K2qE2p9PEXKLDjUjnR/xmjS3wHAYxtlsI9MLLBJUZirAHKzUZDGLxje7w/cXR49WOUo4rbsA==",
+      "version": "1.14.8",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.8.tgz",
+      "integrity": "sha512-1x0S9UVJHsQprFcEC/qnNzBLcIxsjAV905f/UkQxbclCsoTWlacCNOpQa/anodLl2uaEKFhfWOvM2Qg77+15zA==",
      "dev": true
    },
    "for-in": {
@@ -35041,9 +35041,9 @@
      "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w=="
    },
    "nanoid": {
-      "version": "3.1.25",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.1.25.tgz",
-      "integrity": "sha512-rdwtIXaXCLFAQbnfqDRnI6jaRHp9fTcYBjtFKE8eezcZ7LuLjhUaQGNeMXf1HmRoCH32CLz6XwX0TtxEOS/A3Q==",
+      "version": "3.3.1",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.1.tgz",
+      "integrity": "sha512-n6Vs/3KGyxPQd6uO0eH4Bv0ojGSUvuLlIHtC3Y0kEO23YRge8H9x1GCzLn28YX0H66pMkxuaeESFq4tKISKwdw==",
      "dev": true
    },
    "nanomatch": {
@@ -40147,9 +40147,9 @@
      "dev": true
    },
    "simple-get": {
-      "version": "3.1.0",
-      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.0.tgz",
-      "integrity": "sha512-bCR6cP+aTdScaQCnQKbPKtJOKDp/hj9EDLJo3Nw4y1QksqaovlW/bnptB6/c1e+qmNIDHRK+oXFDdEqBT8WzUA==",
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.1.tgz",
+      "integrity": "sha512-CQ5LTKGfCpvE1K0n2us+kuMPbk/q0EKl82s4aheV9oXjFEz6W/Y7oQFVJuU6QG77hRT4Ghb5RURteF5vnWjupA==",
      "dev": true,
      "requires": {
        "decompress-response": "^4.2.0",
@@ -41281,9 +41281,9 @@
      "integrity": "sha512-ppJZNDuKGgxzkHihX8v9v9G5f+18gzaTfrukGrq6ueg0lmH4nqVnA2IPG0AEH3jKEk2GRJCUhDoqpoiw3PHLBA=="
    },
    "tmpl": {
-      "version": "1.0.4",
-      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.4.tgz",
-      "integrity": "sha1-I2QN17QtAEM5ERQIIOXPRA5SHdE=",
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.5.tgz",
+      "integrity": "sha512-3f0uOEAQwIqGuWW2MVzYg8fV/QNnc/IpuJNG837rLuczAaLVHslWHZQj4IGiEl5Hs3kkbhwL9Ab7Hrsmuj+Smw==",
      "dev": true
    },
    "to-fast-properties": {
@@ -1,6 +1,6 @@
 {
  "name": "cellxgene",
-  "version": "1.0.0",
+  "version": "1.0.1",
  "license": "MIT",
  "description": "cellxgene is a web application for the interactive exploration of single cell sequence data.",
  "repository": "https://github.com/chanzuckerberg/cellxgene",
@@ -2,7 +2,7 @@ import logging
 import sys
 from server.common.utils.utils import import_plugins

-__version__ = "1.0.0"
+__version__ = "1.0.1"
 display_version = "cellxgene v" + __version__

 try:
@@ -236,6 +236,14 @@ class AnndataAdaptor(DataAdaptor):
            warnings.warn(
                f"Anndata data matrix is in {self.data.X.dtype} format not float32. " f"Precision may be truncated."
            )
+        if self.data.X.dtype < np.float32:
+            if self.data.isbacked:
+                raise DatasetAccessError(f"Data matrix in {self.data.X.dtype} format is not supported in backed mode."
+                                         " Please reload without --backed, or convert matrix to float32")
+            warnings.warn(
+                f"Anndata data matrix is in unsupported {self.data.X.dtype} format -- will be cast to float32"
+            )
+            self.data.X = self.data.X.astype(np.float32)
        for ax in Axis:
            curr_axis = getattr(self.data, str(ax))
            for ann in curr_axis:
@@ -11,7 +11,7 @@ with open("server/requirements-prepare.txt") as fh:

 setup(
    name="cellxgene",
-    version="1.0.0",
+    version="1.0.1",
    packages=find_packages(),
    url="https://github.com/chanzuckerberg/cellxgene",
    license="MIT",
@@ -1,5 +1,4 @@
 import json
-import sys
 import time
 import unittest

@@ -37,6 +36,7 @@ Test the anndata adaptor using the pbmc3k data set.
        (f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", True, "normal"),
        (f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", True, "normal"),
        (f"{FIXTURES_ROOT}/pbmc3k_64.h5ad", False, "auto"),  # 64 bit conversion tests
+        (f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", False, "auto"),  # 16 bit conversion tests
    ],
 )
 class AdaptorTest(unittest.TestCase):
@@ -0,0 +1,23 @@
+import unittest
+
+from parameterized import parameterized_class
+
+from server.common.errors import DatasetAccessError
+from test import FIXTURES_ROOT
+from test.unit import app_config
+
+
+@parameterized_class(
+    ("data_locator", "backed", "X_approximate_distribution"),
+    [
+        (f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", True, "auto"),  # 16 bit conversion tests
+    ],
+)
+class AdaptorLoadErrorTest(unittest.TestCase):
+    def test_float16_backed_raises_err(self):
+        with self.assertRaises(DatasetAccessError):
+            config = app_config(
+                self.data_locator,
+                backed=self.backed,
+                extra_dataset_config=dict(X_approximate_distribution=self.X_approximate_distribution),
+            )
Author	SHA1	Message	Date
Severiano Badajoz	002c9a5c7f	release version 1.0.1 (#2497 ) * Bump version: 1.0.0 → 1.0.1-rc.0 * Bump version: 1.0.1-rc.0 → 1.0.1	2022-02-28 15:18:21 -08:00
dependabot[bot]	e6a0351079	chore(deps): bump nanoid from 3.1.25 to 3.3.1 in /client (#2488 ) Bumps [nanoid](https://github.com/ai/nanoid) from 3.1.25 to 3.3.1. - [Release notes](https://github.com/ai/nanoid/releases) - [Changelog](https://github.com/ai/nanoid/blob/main/CHANGELOG.md) - [Commits](https://github.com/ai/nanoid/compare/3.1.25...3.3.1) --- updated-dependencies: - dependency-name: nanoid dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2022-02-25 09:57:22 -08:00
dependabot[bot]	38fdc649f5	chore(deps): bump axios from 0.21.1 to 0.21.4 in /client (#2491 ) Bumps [axios](https://github.com/axios/axios) from 0.21.1 to 0.21.4. - [Release notes](https://github.com/axios/axios/releases) - [Changelog](https://github.com/axios/axios/blob/master/CHANGELOG.md) - [Commits](https://github.com/axios/axios/compare/v0.21.1...v0.21.4) --- updated-dependencies: - dependency-name: axios dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2022-02-24 14:20:17 -08:00
dependabot[bot]	69a5d5e837	chore(deps): bump tmpl from 1.0.4 to 1.0.5 in /client (#2490 ) Bumps [tmpl](https://github.com/daaku/nodejs-tmpl) from 1.0.4 to 1.0.5. - [Release notes](https://github.com/daaku/nodejs-tmpl/releases) - [Commits](https://github.com/daaku/nodejs-tmpl/commits/v1.0.5) --- updated-dependencies: - dependency-name: tmpl dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2022-02-24 14:05:26 -08:00
dependabot[bot]	b854c58eea	chore(deps): bump simple-get from 3.1.0 to 3.1.1 in /client (#2489 ) Bumps [simple-get](https://github.com/feross/simple-get) from 3.1.0 to 3.1.1. - [Release notes](https://github.com/feross/simple-get/releases) - [Commits](https://github.com/feross/simple-get/compare/v3.1.0...v3.1.1) --- updated-dependencies: - dependency-name: simple-get dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2022-02-24 13:46:07 -08:00
dependabot[bot]	2d650ba50d	chore(deps): bump follow-redirects from 1.14.2 to 1.14.8 in /client (#2484 ) Bumps [follow-redirects](https://github.com/follow-redirects/follow-redirects) from 1.14.2 to 1.14.8. - [Release notes](https://github.com/follow-redirects/follow-redirects/releases) - [Commits](https://github.com/follow-redirects/follow-redirects/compare/v1.14.2...v1.14.8) --- updated-dependencies: - dependency-name: follow-redirects dependency-type: indirect ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>	2022-02-24 11:57:08 -08:00
Ben MR	8bac98f25c	Fix float16 support [#2379 ] (#2483 ) * Fix float16 support [#2379] Convert to float32 on startup unless backed, in which case error. scipy does not support complex slicing from float16 data so this is the easiest fix for now. * minor msg change	2022-02-10 15:20:47 -08:00
maniarathi	ceb0cc6f27	Update license to 2022. (#2478 )	2022-01-14 14:07:35 -05:00