currently, zipapp’s notion of __main__.py is very different from the usual. the root directory of a zipapp is not a module, therefore __init__.py isn’t used and relative imports from __main__.py don’t work. i propose that the zipapp functionality is amended/changed to 1. allow more than one target directory (bundle multiple modules) 2. allow creation of a __main__.py that contains a runpy-powered module runner so maybe we could specify the module itself as entry point to get this behavior zipapp -m my_module dependency.py my_module should create my_module.pyz ├ __main__.py → ...runpy.run_module('my_module') ├ dependency.py └ my_module ├ __init__.py └ __main__.py → from . import ... or there would be another option to specify it.