Refactored arguments.py to utilize argparse for command-line argument parsing.

[arncv]

Refactored arguments.py to utilize argparse for command-line argument parsing.

• Replaced manual argument parsing with argparse.
• Specified types and default values for each argument using argparse.
• Handled missing arguments by providing default values.

This refactoring aims to address the concerns raised in issue #138.

[nalbion]

There are a lot of other areas in the code with refer to project.args['some_key'] often they're not even mentioned in arguments.py

[LeonOstrez]

sorry @arncv I accidentally closed PR. As @nalbion mentioned there are multiple places in code where we are using args['some_key'] and that should be changed also