chore(deps): update submissions

Dockerfile.dataset_submissions

@@ -1,4 +1,4 @@
-FROM public.ecr.aws/lambda/python:3.9
+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_failures

@@ -1,4 +1,4 @@
-FROM public.ecr.aws/lambda/python:3.8
+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:3.8
+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

@@ -1,24 +1,24 @@
-anndata==0.10.8
+anndata==0.11.1
 awscli
 boto3>=1.11.17
 botocore>=1.14.17
 cellxgene-schema
 dataclasses-json
-ddtrace==2.1.4
-numba==0.59.1
-numpy<2
+ddtrace==2.18.0
+numba==0.60.0
+numpy<3
 pandas>2,<3
 psutil>=5.9.0
 psycopg2-binary==2.*
 pyarrow>=1.0
 pydantic>=1.9.0
 python-json-logger
-pyvips==2.2.2
+pyvips==2.2.3
 requests>=2.22.0
-rpy2==3.5.16
+rpy2==3.5.17
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
-s3fs==0.4.2
-scanpy==1.9.8
+s3fs==2024.12.0
+scanpy==1.10.4
 SQLAlchemy==2.*
 tenacity
-tiledb==0.25.0  # Portal's tiledb version should always be the same or older than Explorer's
+tiledb==0.33.0  # Portal's tiledb version should always be the same or older than Explorer's

python_dependencies/upload_handler/requirements.txt

@@ -2,7 +2,7 @@ boto3
 dataclasses-json
 psycopg2-binary==2.*
 pyrsistent
-python-json-logger==2.0.7
+python-json-logger==3.2.1
 requests>=2.22.0
 rsa>=4.7 # not directly required, pinned by Snyk to avoid a vulnerability
 SQLAlchemy==2.*