CLI commands fail when a flow consists of several python modules

[vladfeigin]

My flow consists several Python modules:
E.g. those are folders in my app:
my-app (root)
flow/flow.flex.yaml
rag/rag.py
search/search.py
...

The flow entry class uses code from other modules, e.g. from rag module.
When I run one of CLI commands like
pf flow build --source ./flow --output ./deployment --format docker
I get the error:
["Failed to load python module from file '../../flow/flow.py': (ModuleNotFoundError) No module named 'rag.rag'; 'rag' is not a package"]

I set PYTHONPATH env variable but still the problem persists.

System Info:
{
"promptflow": "1.16.1",
"promptflow-azure": "1.16.1",
"promptflow-core": "1.16.1",
"promptflow-devkit": "1.16.1",
"promptflow-tracing": "1.16.1"
}

Python (Darwin) 3.11.10 (main, Sep 7 2024, 01:03:31) [Clang 15.0.0 (clang-1500.3.9.4)]
OS Version: Darwin Kernel Version 24.0.0: Tue Sep 24 23:39:07 PDT 2024; root:xnu-11215.1.12~1/RELEASE_ARM64_T6000
Python Version: 3.11.10 (main, Sep 7 2024, 01:03:31) [Clang 15.0.0 (clang-1500.3.9.4)]