Refactor code into python module

[runck014]

project_name/
├── LICENSE
├── README.md
├── pyproject.toml
├── setup.py
├── setup.cfg
├── MANIFEST.in
├── .gitignore
├── docs/
│   ├── conf.py
│   ├── index.rst
│   └── ...
├── project_name/
│   ├── __init__.py
│   ├── module1.py
│   ├── module2.py
│   └── subpackage/
│       ├── __init__.py
│       └── ...
├── tests/
│   ├── __init__.py
│   ├── test_module1.py
│   ├── test_module2.py
│   └── ...
└── examples/
    ├── example1.py
    └── ...

[runck014]

Directory Structure for MPM Release

minimum_plant_model/
├── LICENSE
├── README.md
├── pyproject.toml
├── setup.py
├── .gitignore
├── docs/
│   ├── conf.py
│   ├── index.rst
│   └── scientific_background.md
├── tests/
│   ├── __init__.py
│   ├── test_main_model.py
│   ├── environment/               # Directory for environment-related tests
│   │   ├── __init__.py
│   │   ├── test_base_environment.py
│   │   ├── test_atmosphere.py
│   │   └── test_aboveground_environment.py
│   ├── plant/                     # Directory for plant-related tests
│   │   ├── __init__.py
│   │   ├── test_plant.py
│   │   ├── test_resource_pool.py
│   │   └── test_carbon_assimilation.py
│   └── data/
│       ├── test_drivers.csv
│       ├── test_parameters.csv
│       └── test_resource_pools.csv
├── minimum_plant_model/
│   ├── __init__.py
│   ├── main_model.py
│   ├── environment/                     # New directory for environment modules
│   │   ├── __init__.py
│   │   ├── base_environment.py          # Renamed from environment.py
│   │   ├── atmosphere.py                # Moved here from parent directory
│   │   └── aboveground_environment.py   # Extracted from base_environment.py
│   ├── plant/
│   │   ├── __init__.py
│   │   ├── resource_pool.py
│   │   └── carbon_assimilation.py
│   ├── utils.py
│   └── visualization.py
├── examples/
│   ├── __init__.py
│   ├── basic_simulation.py
│   ├── custom_environment.py
│   └── data/
│       ├── drivers_natural_all.csv
│       ├── parameters.csv
│       └── resource_pools_2RPs.csv

[runck014]

Questions:

How do you run the thing?
Might think of MPM as just the model. Anything that loads the model, invokes, processes output, etc. that should live outside of mpm. Have a command or utils sub-directory to separate concerns.
Add a main.py that will live at the top level of the whole repo to signal that this is what get's invoked. Makes it easier to show a command line tool example.
If there are different commandline tools, each one would invoke the model differently.
Think of this as a command line tool with flag parsing.
Python library
Structlog -- use this debugging. Set different levels. Have errors vs debug logs. Allows for setting a global flag. Add color.

[runck014]

Ensure the minimum viable test comparison to jupyter notebook: https://github.com/DRWang3/MPM_testing/blob/main/skeleton_drw.ipynb

For the basic examples:

Main with run a scenario file.
Examples could be structured in a way that they are scenarios files. These are end-to-end tests.

Don't do a yaml, just use commandline args.