code and unit test for salt bridge tool

[brittyscience]

A fair warning, this branch failed commit, I told it to ignore the pre commit hooks so I can get the code pushed to git hub. This tool is still a work in progress.

[qcampbel]

Just some more feedback for your salt bridge tool. Let me know if you have questions!

[qcampbel]

this branch has some conflicts -- can you resolve it? (see "Resolve conflicts" below). I think it's from merging main after we organize tools in alphabetical order.

[brittyscience]

I initially thought it was a conflict due to alphabetic order, fixed that and passed the local pytest. It seems like there is a conflict due to these errors. I do not think I have touched those files, so I am uncertain how to resolve this yet. Ill look into this and see what I can do.

FAILED tests/test_preprocess/test_packing.py::test_packmol_validate_input_missing_info - UnboundLocalError: cannot access local variable 'mol_name' where it is not associated with a value
FAILED tests/test_preprocess/test_pdb_tools.py::test_small_molecule_pdb - UnboundLocalError: cannot access local variable 'mol_name' where it is not associated with a value
FAILED tests/test_preprocess/test_pdb_tools.py::test_packmol_pdb_download_only - UnboundLocalError: cannot access local variable 'mol_name' where it is not associated with a value
FAILED tests/test_preprocess/test_pdb_tools.py::test_packmol_download_only_once - UnboundLocalError: cannot access local variable 'mol_name' where it is not associated with a value
FAILED tests/test_preprocess/test_pdb_tools.py::test_packmol_sm_download_called - UnboundLocalError: cannot access local variable 'mol_name' where it is not associated with a value
FAILED tests/test_preprocess/test_pdb_tools.py::test_packmol_download_only[small_molecule0] - UnboundLocalError: cannot access local variable 'mol_name' where it is not associated with a value
FAILED tests/test_preprocess/test_pdb_tools.py::test_packmol_download_only[small_molecule1] - UnboundLocalError: cannot access local variable 'mol_name' where it is not associated with a value

[brittyscience]

It is ready and fixed after some polishing ups. Can someone please review it so I can see my very first tool officially joining the club? 🥇

[SamCox822]

@brittyscience is this ready for review?

[SamCox822]

this function might be easier to test if you break it up into some sub-functions