Clean up the CLIs

[weitse-hsu]

We should clean up the CLIs of the AEV-PLIG pipeline, which includes process_dataset.py, generate_graphs.py, and create_pytorch_data.py. For each CLI, here is a checklist to go through:

• Make sure all variable and function names make sense
• Make sure the docstrings are complete and straightforward
• Make sure the logging is useful and comprehensive
• Make sure the functionalities in the CLI is modularized
• Make sure the CLI is flexible and integrated all the old relevant CLIs
• Enforce PEP8 coding style

We use the following list to track the progress:

• process_dataset.py
• generate_graphs.py
• create_pytorch_data.py