Thanks for the PR! I rebased it and changed the following things in the Makefile: 

1. Moved the virtual env directory to a hidden directory.
2. Instead of making targets depend on setup, I made them depend on .venv/bin/activate, so that the virtual env creation and pip install code only runs if the virtual env is missing.
3. Made nuitka use an icon in the project repository instead of a system-dependent path.
4. Removed the deactivate logic in targets: there’s no need to cleanup after activating the virtual env since each shell command of the Makefile get executed in a different subprocess anyway.

Hope that is ok. If so, I think this can be merged!

Looks good to me! I"ll merge it!