Editable install fails due to multiple top-level modules (setuptools discovery issue)

[tsd10]

Description

When attempting to install the repository in editable mode:

uv pip install -e .

or

pip install -e .

the installation fails with the following error:

error: Multiple top-level modules discovered in a flat-layout: ['train', 'prepare'].

This appears to be due to setuptools being unable to automatically determine which modules to include in a flat project layout.

Current Behavior

Editable install fails using both pip and uv pip
Error originates from setuptools package discovery
Expected Behavior

The project should install successfully in editable mode without requiring manual changes to pyproject.toml.

Temporary Fix

Adding the following resolves the issue:

[tool.setuptools]
py-modules = ["train", "prepare"]

Suggested Fixes

One of the following could resolve the issue permanently:

Explicitly define modules in pyproject.toml:

[tool.setuptools]
py-modules = ["train", "prepare"]

Convert to a package structure (recommended):

autoresearch/
init.py
Move to a src/ layout for better packaging practices

Environment

Python: 3.10
Installer: uv (also reproducible with pip)
OS: Linux (HPC cluster)

Additional Context

This issue may affect users trying to extend or modify the project locally using editable installs.

[wu-xiaochen]

This is a common issue with flat-layout projects. The recommended fix is to convert to a src/ layout, or add to pyproject.toml:

[tool.setuptools]
py-modules = ["train", "prepare"]

The src/ layout is cleaner and follows modern Python packaging best practices.