code-cov pmb.setup_lj_interaction

[1234somesh]

Partial fix to #58 and #115.

Added

• Helper method to delete entries from pmb.df

Fixed

• Warning handling and coverage in setup_lj_interaction

[pm-blanco]

Thank you for your work here @1234somesh!

There are a few minor points to consider before merging this to main:

• I think that delete_particle_entry actually is a more general function than its name suggests: it will actually delete any entry with the input name, regardless if that name is a particle, residue, molecule...
• There is now somewhat of a code redundancy between delete_particle_entry and destroy_pmb_object_in_system. The issue is that destroy_pmb_object_in_system is now both deleting molecules from the espresso system and deleting entries from the pyMBE, which makes pyMBE not very modular.

I suggest the following solution:

• Rename delete_particle_entry to delete_entries_in_df and particle_name to entry_name
• Adapt the docs of delete_entries_in_df to explain that it will delete all entries in pmb.df with name = entry_name
• Do a CI test that checks that delete_entries_in_df works as intended.
• Update the years of license in testsuite/lj_tests.py to include 2025 (date of last modification).

I would leave the refactoring of destroy_pmb_object_in_system to a separate PR because it requires of careful refactoring that implies more work than simply making it call your function.

[pm-blanco]

Looks good to me. Good job with the tests @1234somesh!