python project setup

General procedure for setting up a new Python project.

1. Create a new git repo and clone into a directory my_new_project

2. Add files .gitignore, LICENSE, README.md to my_new_project

3. Create a virtual environment under my_new_project/.venv

4. Activate the virtual environment, pip install any required packages, and add them to a requirements.txt file

5. Add a pyproject.toml to configure code formatting, etc. For example:

   [tool.isort]
   profile = "google"
   known_jax = ["numpy","jax"]
   known_jax_ecosystem = ["brax","flax","optax","tensorflow_probability"]
   sections=["FUTURE","STDLIB","THIRDPARTY","JAX","JAX_ECOSYSTEM","FIRSTPARTY","LOCALFOLDER"]
   
   [tool.yapf]
   style = "google"
   
   [tool.pyright]
   ignore = ["notebooks", "**ipynb"]

6. Create a subdir package_name containing __init__.py

7. To allow nonlocal imports, follow [https://stackoverflow.com/questions/714063/importing-modules-from-parent-folder/50194143#50194143](these directions):

   1. Add a minimal setup.py to the toplevel my_new_project directory.
   2. With the virtualenv activated, run pip install -e . from the my_new_project dir.

8. Now you can write code adding files under package_name. For each new file module.py:

   1. Add a corresponding import from package_name import module to __init__.py.
   2. Add any unit tests in module_test.py. These do not need to be imported in __init__.py.

9. Any subdirectories under package_name need their own __init__.py files containing imports for that subdirectory. Modules in that subdir can import modules from other subdirs as from package_name.other_subdir import other_module.