chore: update BE dependencies (#571)

chore: update BE dependencies

.github/workflows/push_tests.yml

@@ -19,10 +19,10 @@ jobs:
       - uses: actions/checkout@v2
       - run: |
           git fetch --depth=1 origin +${{github.base_ref}}
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.8
       - name: Node cache
         uses: actions/cache@v1
         with:
@@ -48,10 +48,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.8
       - name: Python cache
         uses: actions/cache@v1
         with:
@@ -79,10 +79,10 @@ jobs:
     timeout-minutes: 20
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.8
       - name: Python cache
         uses: actions/cache@v1
         with:

.github/workflows/scale-test.yml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v1
         with:
-          python-version: 3.7
+          python-version: 3.8
       - name: Install dependencies
         run: |
           pip install -r server/tests/locust/requirements-locust.txt

hosted/Dockerfile

@@ -17,7 +17,7 @@ RUN apt-get update && \
 
 COPY hosted/nginx.conf /etc/nginx/nginx.conf
 
-ADD hosted/requirements.txt .
+ADD server/requirements.txt .
 RUN python3 -m pip install -r requirements.txt
 
 ADD Makefile Makefile

server/dataset/cxg_dataset.py

@@ -94,7 +94,7 @@ def get_name(self):
         return "cellxgene cxg adaptor version"
 
     def get_library_versions(self):
-        return dict(tiledb=tiledb.__version__)
+        return dict(tiledb=tiledb.version.version)
 
     def get_path(self, *urls):
         return path_join(self.url, *urls)

server/requirements.txt

@@ -1,24 +1,23 @@
-anndata>=0.7.6 # we need to_memory(), added in 0.7.6
-bitarray>=2.3.6
-boto3>=1.12.18
-envyaml>=1.9
-Flask~=2.2
-Flask-Compress>=1.4.0
-Flask-Cors>=3.0.9  # CVE-2020-25032
-Flask-RESTful>=0.3.9
-flask-server-timing>=0.1.2
-flask-talisman>=0.7.0
+anndata==0.8.0
+bitarray==2.7.3
+boto3==1.26.94
+click==8.1.3
+envyaml==1.10.211231
+flask==2.2.3
+flask-compress==1.13
+flask-cors==3.0.10
+flask-restful==0.3.9
+flask-talisman==1.0.0
 flatbuffers>=1.11.0,<2.0.0 # cellxgene is not compatible with 2.0.0. Requires migration
-flatten-dict>=0.2.0
+flatten_dict==0.4.2
 fsspec>=0.4.4,<0.8.0
-gunicorn>=20.0.4
-numba>=0.51.2
-numpy>=1.17
-pydantic<2
-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
-tiledb==0.16.5  # Explorer's major/minor tiledb version should always be the >= Portal's tiledb major/minor version (for read/write compatibility)
+gunicorn[gevent]==20.0.4
+numba==0.56.4
+numpy==1.23.5
+pandas==1.5.3
+pydantic==1.10.6
+requests==2.28.2
+scipy==1.10.1
+flask-server-timing==0.1.2
 s3fs==0.4.2
+tiledb==0.21.1 # Explorer's major/minor tiledb version should always be the >= Portal's tiledb major/minor version (for read/write compatibility)