chore(deps): update wmg and cellguide pipeline

Dockerfile.cellguide_pipeline

@@ -1,6 +1,6 @@
 ARG BASE_TAG=branch-main
 
-FROM python:3.10
+FROM python:3.12
 RUN /usr/local/bin/python -m pip install --upgrade pip && \
     apt update && apt -y install graphviz graphviz-dev && \
     rm -rf /var/lib/apt/lists/*

Dockerfile.wmg_pipeline

@@ -1,6 +1,6 @@
 ARG BASE_TAG=branch-main
 
-FROM python:3.10
+FROM python:3.12
 RUN /usr/local/bin/python -m pip install --upgrade pip && \
     apt update && apt -y install graphviz graphviz-dev && \
     rm -rf /var/lib/apt/lists/* && \

python_dependencies/cellguide_pipeline/requirements.txt

@@ -1,37 +1,37 @@
-anndata==0.9.2
-annotated-types==0.5.0
-awscli==1.29.34
-boto3==1.28.25
-botocore==1.31.34
-cellxgene-ontology-guide==0.8.0
-certifi==2023.7.22
+anndata==0.10.7
+annotated-types==0.7.0
+awscli==1.32.116
+boto3==1.34.116
+botocore==1.34.116
+cellxgene-ontology-guide==1.0.0
+certifi==2024.2.2
 chardet==5.2.0
-charset-normalizer==3.2.0
-ddtrace==2.1.4
-fastobo==0.12.2
-h5py==3.9.0
+charset-normalizer==3.3.2
+ddtrace==2.8.5
+fastobo==0.12.3
+h5py==3.11.0
 idna==3.7
 jmespath==1.0.1
 llvmlite==0.42.0
 natsort==8.4.0
-networkx==3.1
+networkx==3.3
 numba==0.59.1
-numpy==1.24.4
-openai==0.27.7
-packaging==23.1
-pandas==2.0.3
-psutil==5.9.5
-pydantic==2.6.4
-pydantic_core==2.16.3
-python-dateutil==2.8.2
-pytz==2023.3
+numpy==1.26.4
+openai==1.30.5
+packaging==24.0
+pandas==2.2.2
+psutil==5.9.8
+pydantic==2.7.2
+pydantic_core==2.18.3
+python-dateutil==2.9.0.post0
+pytz==2024.1
 requests==2.31.0
-s3transfer==0.6.1
-scipy==1.11.1
+s3transfer==0.10.1
+scipy==1.13.1
 six==1.16.0
 tiledb
-typing_extensions==4.11.0
-tzdata==2023.3
+typing_extensions==4.12.0
+tzdata==2024.1
 urllib3==1.26.16
-pyarrow==12.0.0
-dask==2023.8.1
+pyarrow==16.1.0
+dask==2024.5.1

python_dependencies/wmg_processing/requirements.txt

@@ -1,29 +1,29 @@
-alembic==1.11.1
-anndata==0.8.0
-boto3==1.28.7
-botocore>=1.31.7, <1.32.0
+alembic==1.13.1
+anndata==0.10.7
+boto3==1.34.116
+botocore>=1.34.116, <1.35.0
 cellxgene-census>=1.10.0 # WMG pipeline always reads the latest version of Census so we need to use the latest package version
-cellxgene-ontology-guide==0.8.0
-dataclasses-json==0.5.7
-ddtrace==2.1.4
+cellxgene-ontology-guide==1.0.0
+dataclasses-json==0.6.6
+ddtrace==2.8.5
 furl==2.1.3
-jsonschema==4.18.4
+jsonschema==4.22.0
 moto>=5.0.0
 numba>=0.58.0
-numpy==1.23.5
-openai==0.27.7
-pandas==2.2.1
-psutil==5.9.5
+numpy==1.26.4
+openai==1.30.5
+pandas==2.2.2
+psutil==5.9.8
 pyarrow==12.0.0
 pydantic==1.10.7
-pygraphviz==1.11
+pygraphviz==1.13
 python-json-logger==2.0.7
 requests>=2.22.0
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
-scanpy==1.9.3
-scipy==1.10.1
-SQLAlchemy==1.4.49
-SQLAlchemy-Utils==0.41.1
-tenacity==8.2.2
+scanpy==1.10.1
+scipy==1.13.1
+SQLAlchemy==2.0.30
+SQLAlchemy-Utils==0.41.2
+tenacity==8.3.0
 tiledbsoma>=1.7.0 # WMG pipeline always reads the latest version of Census so we need to use the latest package version
-dask==2023.8.1
+dask==2024.5.1