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chore(deps): update wmg and cellguide pipeline #7101

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chore(deps): update wmg and cellguide pipeline #7101

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2 changes: 1 addition & 1 deletion Dockerfile.cellguide_pipeline
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
ARG BASE_TAG=branch-main

FROM python:3.10
FROM python:3.13

# Update AWS root Certificates
ADD https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem /etc/ssl/certs/rds-global-bundle.pem
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2 changes: 1 addition & 1 deletion Dockerfile.wmg_pipeline
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
ARG BASE_TAG=branch-main

FROM python:3.10
FROM python:3.13

# Update AWS root Certificates
ADD https://truststore.pki.rds.amazonaws.com/global/global-bundle.pem /etc/ssl/certs/rds-global-bundle.pem
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24 changes: 12 additions & 12 deletions python_dependencies/cellguide_pipeline/requirements.txt
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@@ -1,19 +1,19 @@
anndata>=0.10.1
awscli==1.29.34
boto3==1.28.7
awscli==1.37.15
boto3==1.36.15
cellxgene-census>=1.16.2
cellxgene-ontology-guide~=1.0.0
ddtrace==2.1.4
cellxgene-ontology-guide~=1.4.2
ddtrace==2.20.0
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>=2.2.2,<3.0.0
openai==1.61.1
pandas==2.2.3
psutil==6.1.1
pydantic==2.10.6
requests==2.31.0
scipy==1.11.1
scipy==1.15.1
tiledb
tiledbsoma>=1.15.3
urllib3==1.26.16
pyarrow==12.0.0
dask==2023.8.1
pyarrow==19.0.0
dask==2025.1.0
38 changes: 19 additions & 19 deletions python_dependencies/wmg_processing/requirements.txt
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@@ -1,27 +1,27 @@
alembic==1.11.1
alembic==1.14.1
anndata>=0.10.1
boto3==1.28.7
botocore>=1.31.7, <1.32.0
boto3==1.36.15
botocore>=1.36.15, <1.37.0
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~=1.4.2
dataclasses-json==0.6.7
ddtrace==2.20.0
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>=2.2.2,<3.0.0
openai==1.61.1
pandas==2.2.3
psutil==6.1.1
pyarrow==19.0.0
pydantic==1.10.7
pygraphviz==1.11
python-json-logger==2.0.7
pygraphviz==1.14
python-json-logger==3.2.1
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==1.10.4
scipy==1.15.1
SQLAlchemy==2.0.38
SQLAlchemy-Utils==0.41.2
tenacity==9.0.0
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==2025.1.0