Prepare for new release

Created by: StarPrecursor

Need to refactor and document the project for the first public release:

• Use a new name for the project
• Using logging as the log printer
• Move root/NumPy transfer function to an individual package
• Use pathlib to handle path
• Refactor
• Optimize memory use
• Test configurations and clean-up codes
• Update README for the new release

For the next releases:

• Flexible array size, (for example, you can specify use 10% of inputs for training or analyzing)
• Customized model class
• Unify NumPy array to use 2D array (don't allow (n, ) shape, use (n, 1) instead )*
• Set up formatter*
• Prepare the Wiki