update requirements.txt

server/requirements.txt

@@ -1,25 +1,171 @@
-# NOTE: If you update 'anndata' min version, also update the 'anndata_version'
-# matrix value in .github/workflows/compatibility_tests.yml
-anndata>=0.7.6 # we need to_memory(), added in 0.7.6
-boto3>=1.12.18
-click>=7.1.2
-Flask>=1.0.2
-Flask-Compress>=1.4.0
-Flask-Cors>=3.0.9  # CVE-2020-25032
-Flask-RESTful>=0.3.6
-flask-server-timing>=0.1.2
-flask-talisman>=0.7.0
-flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
-flatten-dict>=0.2.0
-fsspec>=0.4.4,<0.8.0
-gunicorn>=20.0.4
-h5py>=3.0.0
-matplotlib>=3.5.0
-numba>=0.51.2
-numpy>=1.17.5
-packaging>=20.0
-pandas>=1.0,!=1.1  # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446
-PyYAML>=5.4  # CVE-2020-14343
-scipy>=1.4
-requests>=2.22.0
+alembic==1.4.2
+aniso8601==8.0.0
+anndata==0.8.0
+appdirs==1.4.4
+astroid==2.4.2
+attrs==19.3.0
+Authlib==0.14.3
+autopep8==1.5.4
+aws-sam-translator==1.25.0
+aws-xray-sdk==2.6.0
+bitarray==2.7.3
+black==23.12.1
+bleach==3.1.5
+boto==2.49.0
+boto3==1.26.94
+botocore==1.29.165
+Brotli==1.0.7
+bump2version==1.0.0
+bumpversion==0.6.0
+-e git+git@github.com:chanzuckerberg/cellxgene.git@7d61f47a31a661f49cef6c7d2356228d0aeb044c#egg=cellxgene
+certifi==2020.4.5.1
+cffi==1.14.0
+cfn-lint==0.34.0
+chalice==1.12.0
+chardet==3.0.4
+charset-normalizer==3.3.2
+click==8.1.3
+clickclick==1.2.2
+codecov==2.1.3
+connexion==2.7.0
+contourpy==1.1.1
+coverage==7.4.0
+cryptography==2.9.2
+cycler==0.10.0
+decorator==4.4.2
+docker==4.2.2
+docutils==0.15.2
+ecdsa==0.18.0
+enum-compat==0.0.3
+envyaml==1.10.211231
+fastobo==0.7.2
+flake8==7.0.0
+flake8-black==0.2.0
+Flask==2.2.3
+Flask-Caching==1.8.0
+Flask-Compress==1.13
+Flask-Cors==3.0.10
+Flask-RESTful==0.3.9
+flask-server-timing==0.1.2
+flask-talisman==1.0.0
+flatbuffers==1.12
+flatten-dict==0.4.2
+fonttools==4.47.2
+fsspec==0.7.4
+furl==2.1.0
+future==0.18.2
+get-version==2.1
+gevent==23.9.1
+greenlet==3.0.3
+gunicorn==20.0.4
+h5py==3.10.0
+idna==2.8
+importlib-metadata==7.0.1
+importlib-resources==6.1.1
+inflection==0.5.0
+isort==4.3.21
+itsdangerous==2.1.2
+Jinja2==3.1.3
+jmespath==0.10.0
+joblib==0.16.0
+jsondiff==1.1.2
+jsonpatch==1.26
+jsonpickle==1.4.1
+jsonpointer==2.0
+jsonschema==3.2.0
+junit-xml==1.9
+keyring==21.2.1
+kiwisolver==1.2.0
+lazy-object-proxy==1.4.3
+legacy-api-wrap==1.2
+llvmlite==0.39.1
+Mako==1.1.3
+MarkupSafe==2.1.4
+matplotlib==3.7.4
+mccabe==0.7.0
+mock==4.0.2
+more-itertools==8.3.0
+moto==1.3.14
+mypy==1.8.0
+mypy-extensions==0.4.3
+natsort==7.0.1
+networkx==2.4
+numba==0.56.4
+numexpr==2.7.1
+numpy==1.23.5
+openapi-spec-validator==0.2.8
+orderedmultidict==1.0.1
+Owlready2==0.24
+packaging==20.4
+pandas==1.5.3
+parameterized==0.7.4
+pathlib2==2.3.5
+pathspec==0.12.1
+patsy==0.5.1
+Pillow==7.2.0
+pkginfo==1.5.0.1
+platformdirs==4.1.0
+pluggy==0.13.1
+psycopg2-binary==2.8.5
+py==1.8.1
+pyasn1==0.4.8
+pycodestyle==2.11.1
+pycparser==2.20
+pydantic==1.10.6
+pyflakes==3.2.0
+Pygments==2.6.1
+pylint==2.5.3
+PyMySQL==0.9.3
+pyparsing==2.4.7
+pyrsistent==0.16.0
+pytest==5.4.2
+pytest-subtests==0.11.0
+python-dateutil==2.8.1
+python-editor==1.0.4
+python-jose==3.3.0
+python-json-logger==2.0.7
+pytz==2020.1
+PyYAML==6.0.1
+readme-renderer==26.0
+regex==2020.5.14
+requests==2.28.2
+requests-toolbelt==0.9.1
+responses==0.10.15
+rsa==4.9
 s3fs==0.4.2
+s3transfer==0.6.2
+scanpy==1.4.6
+scikit-learn==0.23.2
+scipy==1.10.1
+seaborn==0.10.1
+setuptools-scm==4.1.2
+sinfo==0.3.1
+six==1.15.0
+SQLAlchemy==1.3.19
+sshpubkeys==3.1.0
+statsmodels==0.12.0rc0
+stdlib-list==0.7.0
+swagger-ui-bundle==0.0.6
+tables==3.6.1
+threadpoolctl==2.1.0
+tiledb==0.21.4
+toml==0.10.1
+tomli==2.0.1
+tqdm==4.46.0
+twine==3.1.1
+typed-ast==1.4.1
+types-PyYAML==6.0.12.12
+types-requests==2.31.0.20240106
+types-setuptools==69.0.0.20240115
+typing-extensions==3.7.4.3
+umap-learn==0.4.6
+urllib3==1.25.9
+wcwidth==0.2.2
+webencodings==0.5.1
+websocket-client==0.57.0
+Werkzeug==2.2.3
+wrapt==1.12.1
+xmltodict==0.12.0
+zipp==3.1.0
+zope.event==5.0
+zope.interface==6.1