Say you want want to create a programming project that mixes C++ and Python. The Foo C++ project structure uses CMake, a
If the C++ application has no use outside the Python package that will contain it:
You can pretty safely place the C++ code within the python package that owns it. Have the "foo" directory within the "bar" directory within your example. This will make packaging the final Python module a bit easier.
If the C++ application is reusable:
I would definitely try to think of things in terms of "packages", where independent parts are self-contained. All independent parts live on the same level. If one part depends on another, you import from its corresponding "package" from the same level. This is how dependencies typically work.
I would NOT include one within the other, because one does not strictly belong to the other. What if you started a third project that needed "foo", but did not need "bar"?
I would place both "foo" and "bar" packages into the same "project" directory (and I would probably give each package it's own code repository so each package can be easily maintained and installed).