chore(deps): update wmg and cellguide pipeline

Author: renovate[bot]

Dockerfile.cellguide_pipeline

@@ -1,6 +1,6 @@
 ARG BASE_TAG=branch-main
 
-FROM python:3.10
+FROM python:3.14
 
 # Update AWS root Certificates
 ADD https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem /etc/ssl/certs/rds-global-bundle.pem

Dockerfile.wmg_pipeline

@@ -1,6 +1,6 @@
 ARG BASE_TAG=branch-main
 
-FROM python:3.10
+FROM python:3.14
 
 # Update AWS root Certificates
 ADD https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem /etc/ssl/certs/rds-global-bundle.pem

python_dependencies/cellguide_pipeline/requirements.txt

@@ -1,19 +1,19 @@
 anndata>=0.10.1
-awscli==1.29.34
-boto3==1.28.7
+awscli==1.43.3
+boto3==1.41.3
 cellxgene-census>=1.16.2
-cellxgene-ontology-guide~=1.4.2
-ddtrace==2.1.4
+cellxgene-ontology-guide~=1.9.0
+ddtrace==4.0.0
 numba>=0.58.0
-numpy>=1.24.0,<2.1.0
-openai==0.27.7
-pandas==2.2.1
-psutil==5.9.5
-pydantic==2.6.4
+numpy>=2.3.5,<3.0.0
+openai==2.8.1
+pandas==2.3.3
+psutil==7.1.3
+pydantic==2.12.4
 requests==2.31.0
-scipy==1.11.1
+scipy==1.16.3
 tiledb
 tiledbsoma>=1.15.3
 urllib3==1.26.16
-pyarrow==12.0.0
-dask==2023.8.1
+pyarrow==22.0.0
+dask==2025.11.0

python_dependencies/wmg_processing/requirements.txt

@@ -1,27 +1,27 @@
-alembic==1.11.1
+alembic==1.17.2
 anndata>=0.10.1
-boto3==1.28.7
-botocore>=1.31.7, <1.32.0
+boto3==1.41.3
+botocore>=1.41.3, <1.42.0
 cellxgene-census>=1.16.2 # WMG pipeline always reads the latest version of Census so we need to use the latest package version
-cellxgene-ontology-guide~=1.0.0
-dataclasses-json==0.5.7
-ddtrace==2.1.4
+cellxgene-ontology-guide~=1.9.0
+dataclasses-json==0.6.7
+ddtrace==4.0.0
 numba>=0.58.0
-numpy>=1.24.0,<2.1.0
-openai==0.27.7
-pandas==2.2.1
-psutil==5.9.5
-pyarrow==12.0.0
+numpy>=2.3.5,<3.0.0
+openai==2.8.1
+pandas==2.3.3
+psutil==7.1.3
+pyarrow==22.0.0
 pydantic<3
-pygraphviz==1.11
-python-json-logger==2.0.7
+pygraphviz==1.14
+python-json-logger==4.0.0
 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==1.11.5
+scipy==1.16.3
+SQLAlchemy==2.0.44
+SQLAlchemy-Utils==0.42.0
+tenacity==9.1.2
 tiledb
 tiledbsoma>=1.15.3 # WMG pipeline always reads the latest version of Census so we need to use the latest package version
-dask==2023.8.1
+dask==2025.11.0