update ms script

[stevenhwu]

• update get_data script
• Merge run_prediciton script
• updateing config and toml
• update pyproject, move to hatchling
• Remove duplicate -i/--input

[stevenhwu]

@yehzx Update for MS and release

Can you please double check
https://github.com/ComputationalAgronomy/biopathway-prediction/blob/86249c758f3a71258eaca7afa3821cc8cdd98e1f/biopathpred/cli.py#L317-L323

Duplicate code, with required=False, while True above
Generate error when you just run biopathpred without any parameter

Traceback (most recent call last):
  File "/home/steven/.conda/envs/biopathpred/bin/biopathpred", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/steven/.conda/envs/biopathpred/lib/python3.11/site-packages/biopathpred/cli.py", line 368, in main
    config = Configuration(args)
             ^^^^^^^^^^^^^^^^^^^
  File "/home/steven/.conda/envs/biopathpred/lib/python3.11/site-packages/biopathpred/modules/configuration.py", line 38, in __init__
    self.logger = self._config_logging()
                  ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/steven/.conda/envs/biopathpred/lib/python3.11/site-packages/biopathpred/modules/configuration.py", line 195, in _config_logging
    os.makedirs(self.args.output, exist_ok=True)
  File "<frozen os>", line 210, in makedirs
  File "<frozen posixpath>", line 103, in split
TypeError: expected str, bytes or os.PathLike object, not NoneType

[yehzx]

Duplicate code, with required=False, while True above
Generate error when you just run biopathpred without any parameter

Probably legacy code, I don't remember any specific purposes to put it there.
I removed the duplicated one.

[yehzx]

Feel free to merge this branch if you have finished the cleanup and checks.

One of the tests had some string sorting issues that seemed to occur only in the Github workflow but not on Windows or WSL.
I've added a sorting strategy in the source code and pushed it to the main branch. Merging this branch directly should be fine.