Chore: update dependencies

requirements/base-pypi.txt

-boto3>=1.26,<1.29
-boto3-stubs[s3]>=1.26,<1.29
-psycopg>=3,<3.2
-shapely>=2.0.1,<3
+boto3>=1.28,<1.34
+boto3-stubs[s3]>=1.28,<1.34
+psycopg>=3.1,<3.2
+shapely>=2.0.2,<2.1
 typing-extensions>=4,<5 ; python_version < '3.11'