Update dependencies for template cuda flavor #1220
Description
Background
Currently, it's not possible to install the pytorch 2.7.1 for Cuda 12.9 in the template cuda flavor,, as this pytorch version depends on a newer version of protobuf.
Acceptance Criteria
Update protobuf and optionally other packages in the template cuda flavor, such that pytorch version 2.7.1=cuda129_generic_py310_h919abc8_203 can be installed in it.