chore: upgrade dependencies

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 1.1.2
 commit = True
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<prerel>rc)\.(?P<prerelversion>\d+))?
 serialize = 

.github/workflows/compatibility_tests.yml

@@ -30,8 +30,19 @@ jobs:
       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-11]
-        python-version: [3.8, 3.9, 3.10, 3.11]
+        python-version: [3.6, 3.7, 3.8, 3.9]
         cellxgene_build: [main, latest]
+        exclude:
+          # 3.6 no longer avail on Big Sur (`macos-11`)
+          - os: macos-11
+            python-version: 3.6
+          # no pypi build exists for macos+py3.9 and source install fails to
+          # install `tables` py pkg (a `scanpy` dependency), so we test py3.9
+          # only on ubuntu
+          - os: macos-11
+            python-version: 3.9
+          - os: macos-latest
+            python-version: 3.9
         # add anndata pinned version test for subset of matrix configurations,
         # in order to reduce matrix cross-product explosion
         include:

client/package.json

@@ -1,6 +1,6 @@
 {
   "name": "cellxgene",
-  "version": "1.2.0",
+  "version": "1.1.2",
   "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__ = "1.2.0"
+__version__ = "1.1.2"
 display_version = "cellxgene v" + __version__
 
 try:

server/requirements.txt

@@ -1,22 +1,22 @@
-anndata>=0.8.0
+anndata==0.10.3
-boto3>=1.12.18
+boto3==1.29.5
-click>=7.1.2
+click==8.1.7
-Flask>=3.0.0
+Flask==3.0.0
-Flask-Compress>=1.4.0
+Flask-Compress==1.14
-Flask-Cors>=3.0.9
+Flask-Cors==4.0.0
-Flask-RESTful>=0.3.6
+Flask-RESTful==0.3.10
-flask-server-timing>=0.1.2
+flask-server-timing==0.1.2
-flask-talisman>=0.7.0
+flask-talisman==1.1.0
-flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
+flatbuffers==1.12
-flatten-dict>=0.2.0
+flatten-dict==0.4.2
-fsspec>0.8.0
+fsspec==2023.10.0
-gunicorn>=20.0.4
+gunicorn==21.2.0
-h5py>=3.0.0
+h5py==3.10.0
-numba>=0.51.2
+numba==0.58.1
-numpy>1.22
+numpy==1.26.2
-packaging>=20.0
+packaging==23.2
 pandas<2.0.0
-PyYAML>=5.4  # CVE-2020-14343
+PyYAML==6.0.1
-requests>=2.22.0
+requests==2.31.0
 s3fs==0.4.2
-scipy>=1.4
+scipy==1.11.4

setup.py

@@ -14,7 +14,7 @@ with open("server/requirements-annotate.txt") as fh:
 
 setup(
     name="cellxgene",
-    version="1.2.0",
+    version="1.1.2",
     packages=find_packages(),
     url="https://github.com/chanzuckerberg/cellxgene",
     license="MIT",

test/unit/cli/fixtures/__init__.py

@@ -0,0 +1,5 @@
+from .mlflow_model_fixture import FakeModel
+
+
+def _load_pyfunc(data_path):
+    return FakeModel()