Right now, py_binary has an implicit output ({name}.zip}) and output group (python_zip_file) that builds a zip file of the py_binary. This zip file is a "zipapp", basically a zip file with a top-level __main__.py file. See https://peps.python.org/pep-0441/ and https://docs.python.org/3/library/zipapp.html for details.

If the Bazel builtin flag --build_python_zip is set, then the zip output changes slightly: it is turned into a self-executable zip file by prepending some shell code to the zip file.

Having this part of py_binary itself is problematic for four main reasons:

1. It makes maintaining py_binary harder. The logic for creating the zip is subtle and introduces several branches on code that is otherwise straight forward.
2. A zipapp is just one of many ways to create a "distributable" py_binary. It doesn't make sense to bake one directly into py_binary.
3. A zipapp only works if it's pure-python code. If there are C library dependencies, then the zip must be extracted, which then breaks the logic for handling zipapp-based startup.
4. A zip file doesn't have native support for symlinks. This makes it incompatible with bootstrap=script and how it creates a venv with symlinks to the desired python interpreter. Working around this requires hacks being applied at runtime with their own problems.

What to do:

• Create a py_zipapp_binary and py_zipapp_test rule. As input, they take a py_binary As output, they produce a zipapp. An attribute decides if its executable or not.
• As part of the above: create a tool to generate zip files that contain symlinks. Use File.is_symlink to detect if inputs should be symlinks or not. For a python-based implementation, how to create a symlink: https://stackoverflow.com/questions/35782941/archiving-symlinks-with-python-zipfile . It doesn't necessairily have to be implemented in Python. Another language is fine, however, if it's a compiled language, then we'll need to update rules_python handle building and consuming prebuilt artifacts.
• Add windows support to py_zipapp_binary et al
• Add python_zip_file output group to py_zipapp for compatibility
• Add deprecation warning for py_binary zipapp usage
• Add entries to features.bzl
• Default windows to non-zip builds
• Disable and remove the --build_python_zip flag and python_zip_file output group.

I'll note that there are rule sets, e.g. rules_pkg that support somewhat arbitrary creation of zip files. Using one of those would also be fine.