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

.bumpversion.cfg

@@ -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 = 

LICENSE.txt

@@ -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

client/package-lock.json

@@ -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",
+      "version": "0.21.4",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.4.tgz",
-      "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==",
+      "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",
+      "version": "1.14.8",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.2.tgz",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.8.tgz",
-      "integrity": "sha512-yLR6WaE2lbF0x4K2qE2p9PEXKLDjUjnR/xmjS3wHAYxtlsI9MLLBJUZirAHKzUZDGLxje7w/cXR49WOUo4rbsA==",
+      "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",
+      "version": "3.3.1",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.1.25.tgz",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.1.tgz",
-      "integrity": "sha512-rdwtIXaXCLFAQbnfqDRnI6jaRHp9fTcYBjtFKE8eezcZ7LuLjhUaQGNeMXf1HmRoCH32CLz6XwX0TtxEOS/A3Q==",
+      "integrity": "sha512-n6Vs/3KGyxPQd6uO0eH4Bv0ojGSUvuLlIHtC3Y0kEO23YRge8H9x1GCzLn28YX0H66pMkxuaeESFq4tKISKwdw==",
       "dev": true,
       "bin": {
         "nanoid": "bin/nanoid.cjs"
@@ -21005,9 +21005,9 @@
       ]
     },
     "node_modules/simple-get": {
-      "version": "3.1.0",
+      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.1.tgz",
-      "integrity": "sha512-bCR6cP+aTdScaQCnQKbPKtJOKDp/hj9EDLJo3Nw4y1QksqaovlW/bnptB6/c1e+qmNIDHRK+oXFDdEqBT8WzUA==",
+      "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",
+      "version": "1.0.5",
-      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.4.tgz",
+      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.5.tgz",
-      "integrity": "sha1-I2QN17QtAEM5ERQIIOXPRA5SHdE=",
+      "integrity": "sha512-3f0uOEAQwIqGuWW2MVzYg8fV/QNnc/IpuJNG837rLuczAaLVHslWHZQj4IGiEl5Hs3kkbhwL9Ab7Hrsmuj+Smw==",
       "dev": true
     },
     "node_modules/to-fast-properties": {
@@ -27379,12 +27379,12 @@
       "dev": true
     },
     "axios": {
-      "version": "0.21.1",
+      "version": "0.21.4",
-      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.1.tgz",
+      "resolved": "https://registry.npmjs.org/axios/-/axios-0.21.4.tgz",
-      "integrity": "sha512-dKQiRHxGD9PPRIUNIWvZhPTPpl1rf/OxTYKsqKUDjBwYylTvV7SjSHJb9ratfyzM6wCdLCOYLzs73qpg5c4iGA==",
+      "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",
+      "version": "1.14.8",
-      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.2.tgz",
+      "resolved": "https://registry.npmjs.org/follow-redirects/-/follow-redirects-1.14.8.tgz",
-      "integrity": "sha512-yLR6WaE2lbF0x4K2qE2p9PEXKLDjUjnR/xmjS3wHAYxtlsI9MLLBJUZirAHKzUZDGLxje7w/cXR49WOUo4rbsA==",
+      "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",
+      "version": "3.3.1",
-      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.1.25.tgz",
+      "resolved": "https://registry.npmjs.org/nanoid/-/nanoid-3.3.1.tgz",
-      "integrity": "sha512-rdwtIXaXCLFAQbnfqDRnI6jaRHp9fTcYBjtFKE8eezcZ7LuLjhUaQGNeMXf1HmRoCH32CLz6XwX0TtxEOS/A3Q==",
+      "integrity": "sha512-n6Vs/3KGyxPQd6uO0eH4Bv0ojGSUvuLlIHtC3Y0kEO23YRge8H9x1GCzLn28YX0H66pMkxuaeESFq4tKISKwdw==",
       "dev": true
     },
     "nanomatch": {
@@ -40147,9 +40147,9 @@
       "dev": true
     },
     "simple-get": {
-      "version": "3.1.0",
+      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.0.tgz",
+      "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.1.tgz",
-      "integrity": "sha512-bCR6cP+aTdScaQCnQKbPKtJOKDp/hj9EDLJo3Nw4y1QksqaovlW/bnptB6/c1e+qmNIDHRK+oXFDdEqBT8WzUA==",
+      "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",
+      "version": "1.0.5",
-      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.4.tgz",
+      "resolved": "https://registry.npmjs.org/tmpl/-/tmpl-1.0.5.tgz",
-      "integrity": "sha1-I2QN17QtAEM5ERQIIOXPRA5SHdE=",
+      "integrity": "sha512-3f0uOEAQwIqGuWW2MVzYg8fV/QNnc/IpuJNG837rLuczAaLVHslWHZQj4IGiEl5Hs3kkbhwL9Ab7Hrsmuj+Smw==",
       "dev": true
     },
     "to-fast-properties": {

client/package.json

@@ -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",

server/__init__.py

@@ -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:

server/data_anndata/anndata_adaptor.py

@@ -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:

setup.py

@@ -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",

test/unit/data_anndata/test_anndata_adaptor.py

@@ -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):

test/unit/data_anndata/test_anndata_adaptor_errors.py

@@ -0,0 +1,23 @@
+import unittest
+
+from parameterized import parameterized_class
+
+from server.common.errors import DatasetAccessError
+from test import FIXTURES_ROOT
+from test.unit import app_config
+
+
+@parameterized_class(
+    ("data_locator", "backed", "X_approximate_distribution"),
+    [
+        (f"{FIXTURES_ROOT}/pbmc3k_16.h5ad", True, "auto"),  # 16 bit conversion tests
+    ],
+)
+class AdaptorLoadErrorTest(unittest.TestCase):
+    def test_float16_backed_raises_err(self):
+        with self.assertRaises(DatasetAccessError):
+            config = app_config(
+                self.data_locator,
+                backed=self.backed,
+                extra_dataset_config=dict(X_approximate_distribution=self.X_approximate_distribution),
+            )