Improve the code coverage of pyMBE

[pm-blanco]

Here is the list of the features that require our attention:

• pymbe_library.destroy_pmb_object_in_system()
• pymbe_library.parse_sequence_from_file()
• pymbe_library.search_particles_in_residue()
• pymbe_library.setup_lj_interactions() (missing some corner cases)
• determine_reservoir_concentrations

Ideally we also should add coverage for lib.handy_functions

• @kosovan :

• lib.analysis.get_dt()
• lib.analysis.get_params_from_file_name()
• lib.analysis.block_analyze()

• @davidbbeyer :

• pymbe.get_charge_map()
• pymbe_library.generate_coordinates_outside_sphere()
• pymbe_library.generate_random_points_in_a_sphere() for the case inside the sphere
• pymbe_library.determine_reservoir_concentrations()
• pymbe_library.setup_cpH()
• pymbe_library.setup_gcmc()
• pymbe_library.setup_grxmc_reactions()
• pymbe_library.setup_grxmc_unified()

• @paobtorres

• pymbe_library.create_protein()
• pymbe_library.enable_motion_of_rigid_object()
• pymbe_library.protein_sequence_parser() for non-standard cases
• pymbe_library.define_protein()
• pymbe_library.read_protein_vtf_in_df()

• @pm-blanco

• pymbe_library.calculate_net_charge()
• pymbe_library.create_added_salt()
• pymbe_library.create_counterions()
• pymbe_library.create_residue() for residue types
• pymbe_library.load_interaction_parameters() for a FENE bond
• pymbe_library.check_aminoacid_key()
• pymbe_library.check_if_metal_ion()
• pymbe_library.get_metal_ions_charge_map()
• pymbe_library.define_particles()
• lib.analysis.split_dataframe_in_equal_blocks()
• lib.analysis.split_dataframe()
• lib.analysis.add_data_to_df()
• lib.analysis.analyze_time_series()

• @pinedaps

• pymbe_library.get_particle_id_map()
• pymbe_library.get_radius_map()
• pymbe_library.assign_molecule_id() for the empty residue name edge case
• pymbe_library.calculate_HH() for the case where a molecule has no sequence

• @jngrad

• pymbe_library.NumpyEncoder.default()
• pymbe_library.print_reduced_units()
• lib.analysis.built_output_name()
• lib.analysis.get_params_from_dir_name()

[jngrad]

Outcome of the pyMBE online meeting: address the assigned tasks in a best effort manner by June 1, 2024. If you don't get all tasks done by then, open the PR anyway with the unit tests you already have. The goal is to have about 80% code coverage, so that we can be confident we are not breaking any feature while doing the big refactoring (#13) in June.

Later this year, we might organize a pyMBE coding day to take care of the remaining unit tests.

[jngrad]

To everyone: code coverage is now available on the main branch. Be sure to start your work on top of the most recent commit of the main branch to reduce the risk of introducing merge conflicts. You can use np.testing.assert_allclose() or pd.testing.assert_frame_equal() checks, or use unittest assertions to make the unit tests more structured and expressive (testsuite/serialization_test.py can be used as template).