About a year ago, I moved all my projects to the pattern that Pyramid uses itself...
* /src/PROJECT
* /tests
* /MANIFEST.in
* /pyproject.toml
* /setup.cfg
* /setup.py
* /tox.ini
That has eliminated 99% of the packaging issues I've encountered in the past.
IIRC, that became the standardized repo design for Python projects a few years ago, due to constant issues in package/file discovery.