From 044a4fccfe80690d02c78ec62360dfa1d8173387 Mon Sep 17 00:00:00 2001
From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com>
Date: Mon, 23 Dec 2024 20:55:48 +0000
Subject: [PATCH] chore(deps): update wmg and cellguide pipeline

---
 Dockerfile.cellguide_pipeline                 |  2 +-
 Dockerfile.wmg_pipeline                       |  2 +-
 .../cellguide_pipeline/requirements.txt       | 26 ++++++------
 .../wmg_processing/requirements.txt           | 40 +++++++++----------
 4 files changed, 35 insertions(+), 35 deletions(-)

diff --git a/Dockerfile.cellguide_pipeline b/Dockerfile.cellguide_pipeline
index 365327ec354e8..f40a909f6ed31 100644
--- a/Dockerfile.cellguide_pipeline
+++ b/Dockerfile.cellguide_pipeline
@@ -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
diff --git a/Dockerfile.wmg_pipeline b/Dockerfile.wmg_pipeline
index 592a04baffeb8..8e92cf4370da6 100644
--- a/Dockerfile.wmg_pipeline
+++ b/Dockerfile.wmg_pipeline
@@ -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
diff --git a/python_dependencies/cellguide_pipeline/requirements.txt b/python_dependencies/cellguide_pipeline/requirements.txt
index fb1e903dfcaf0..c6bb7af852d0b 100644
--- a/python_dependencies/cellguide_pipeline/requirements.txt
+++ b/python_dependencies/cellguide_pipeline/requirements.txt
@@ -1,19 +1,19 @@
-anndata==0.8.0
-awscli==1.29.34
-boto3==1.28.7
+anndata==0.11.1
+awscli==1.36.28
+boto3==1.35.87
 cellxgene-census>=1.10.0
-cellxgene-ontology-guide~=1.0.0
-ddtrace==2.1.4
+cellxgene-ontology-guide~=1.3.1
+ddtrace==2.18.1
 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>=2.2.1,<3.0.0
+openai==1.58.1
+pandas==2.2.3
+psutil==6.1.1
+pydantic==2.10.4
 requests==2.31.0
-scipy==1.11.1
+scipy==1.14.1
 tiledb
 tiledbsoma>=1.7.0
 urllib3==1.26.16
-pyarrow==12.0.0
-dask==2023.8.1
+pyarrow==18.1.0
+dask==2024.12.1
diff --git a/python_dependencies/wmg_processing/requirements.txt b/python_dependencies/wmg_processing/requirements.txt
index 90f8a1de08f2b..22b386a23e20b 100644
--- a/python_dependencies/wmg_processing/requirements.txt
+++ b/python_dependencies/wmg_processing/requirements.txt
@@ -1,26 +1,26 @@
-alembic==1.11.1
-anndata==0.8.0
-boto3==1.28.7
-botocore>=1.31.7, <1.32.0
+alembic==1.14.0
+anndata==0.11.1
+boto3==1.35.87
+botocore>=1.35.87, <1.36.0
 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~=1.0.0
-dataclasses-json==0.5.7
-ddtrace==2.1.4
+cellxgene-ontology-guide~=1.3.1
+dataclasses-json==0.6.7
+ddtrace==2.18.1
 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>=2.2.1,<3.0.0
+openai==1.58.1
+pandas==2.2.3
+psutil==6.1.1
+pyarrow==18.1.0
 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==1.14.1
+SQLAlchemy==2.0.36
+SQLAlchemy-Utils==0.41.2
+tenacity==9.0.0
 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==2024.12.1