chore(deps): update submissions

Author: renovate[bot]

Dockerfile.processing

@@ -1,4 +1,4 @@
-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.upload_failures

@@ -1,4 +1,4 @@
-FROM public.ecr.aws/lambda/python:3.10
+FROM public.ecr.aws/lambda/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

Dockerfile.upload_success

@@ -1,4 +1,4 @@
-FROM public.ecr.aws/lambda/python:3.10
+FROM public.ecr.aws/lambda/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

python_dependencies/processing/requirements.txt

@@ -2,22 +2,22 @@ anndata # uses the version supplied by cellxgene-schema
 awscli
 boto3>=1.11.17
 cellxgene-schema==7.0.1
-dask==2024.12.0
+dask==2025.10.0
 dataclasses-json
-ddtrace==2.1.4
-numba==0.59.1
-numpy<2
+ddtrace==3.17.2
+numba==0.62.1
+numpy<3
 pandas>2,<3
 psutil>=5.9.0
 psycopg2-binary==2.*
 pyarrow>=1.0
 pydantic<3
 python-json-logger
-pyvips==2.2.2
+pyvips==3.0.0
 requests>=2.22.0
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
-s3fs==0.4.2
-scanpy==1.9.8
+s3fs==2025.9.0
+scanpy==1.11.5
 SQLAlchemy==2.*
 tenacity
-tiledb==0.25.0  # Portal's tiledb version should always be the same or older than Explorer's
+tiledb==0.35.1  # Portal's tiledb version should always be the same or older than Explorer's

python_dependencies/upload_handler/requirements.txt

@@ -3,7 +3,7 @@ dataclasses-json
 pydantic<3
 psycopg2-binary==2.*
 pyrsistent
-python-json-logger==2.0.7
+python-json-logger==4.0.0
 requests>=2.22.0
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
 SQLAlchemy==2.*