Remove legacy code

[PythonFZ]

I actually think several meta functions are now legacy and can be removed. I will leave this for a future PR.

Originally posted by @SamTov in #475 (comment)

[PythonFZ]

Using https://github.com/jendrikseipp/vulture I found (sorry for the long path):

C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\angular_distribution_function.py:212: unused attribute '_batch_size' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\calculator.py:46: unused attribute 'monitor_interval' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\coordination_number_calculation.py:111: unused attribute 'file_to_study' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\coordination_number_calculation.py:121: unused attribute 'post_generation' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\einstein_distinct_diffusion_coefficients.py:57: unused attribute 'monitor_interval' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\einstein_distinct_diffusion_coefficients.py:120: unused variable 'save' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\green_kubo_distinct_diffusion_coefficients.py:115: unused variable 'save' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\green_kubo_self_diffusion_coefficients.py:275: unused attribute 'extra_y_ranges' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\kirkwood_buff_integrals.py:97: unused attribute 'file_to_study' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\kirkwood_buff_integrals.py:98: unused attribute 'data_files' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\kirkwood_buff_integrals.py:109: unused attribute 'post_generation' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\nernst_einstein_ionic_conductivity.py:60: unused attribute 'post_generation' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\nernst_einstein_ionic_conductivity.py:76: unused variable 'save' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\nernst_einstein_ionic_conductivity.py:403: unused method 'run_post_generation_analysis' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\potential_of_mean_force.py:111: unused attribute 'file_to_study' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\potential_of_mean_force.py:124: unused attribute 'post_generation' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\potential_of_mean_force.py:152: unused attribute 'data_files' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\radial_distribution_function.py:145: unused variable 'save' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\spatial_distribution_function.py:74: unused class 'SpatialDistributionFunction' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\structure_factor.py:113: unused attribute 'file_to_study' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\structure_factor.py:114: unused attribute 'data_files' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\calculators\structure_factor.py:119: unused attribute 'post_generation' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\calculator_database.py:247: unused method 'update_database' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\calculator_database.py:247: unused variable 'delete_duplicate' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\calculator_database.py:247: unused variable 'parameters' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\database_base.py:58: unused attribute '_Session' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\experiment_database.py:87: unused variable 'property_groups' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\experiment_database.py:97: unused variable 'parameters' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\scheme.py:47: unused variable 'computation_results_id' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\scheme.py:50: unused variable 'experiment_species_id' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\scheme.py:89: unused variable 'experiment_attributes' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\scheme.py:328: unused variable 'computation_id' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\scheme.py:347: unused variable 'computation_id' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\simulation_database.py:136: unused variable 'sample_step' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\simulation_database.py:233: unused method '_update_indices' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\simulation_database.py:466: unused method '_add_group_structure' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\simulation_database.py:538: unused method 'change_key_names' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\simulation_database.py:595: unused method 'get_load_time' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\simulation_database.py:646: unused method 'get_database_summary' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\types.py:37: unused variable 'impl' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\types.py:39: unused method 'process_bind_param' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\types.py:39: unused variable 'dialect' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\types.py:48: unused method 'process_result_value' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\database\types.py:48: unused variable 'dialect' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\experiment\experiment.py:202: unused attribute 'property_groups' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\experiment\experiment.py:214: unused attribute 'analyse_time_series' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\experiment\experiment.py:430: unused method 'set_charge' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\experiment\experiment.py:446: unused method 'set_mass' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\experiment\experiment.py:553: unused attribute 'memory_requirements' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\experiment\experiment.py:558: unused method 'load_matrix' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\experiment\experiment.py:642: unused attribute 'property_groups' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\file_io\chemfiles_read.py:15: unused class 'ChemfilesRead' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\file_io\script_input.py:7: unused class 'ScriptInput' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\graph_modules\adjacency_matrix.py:29: unused class 'AdjacencyMatrix' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\graph_modules\molecular_graph.py:81: unused method '_perform_checks' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\graph_modules\molecular_graph.py:159: unused variable 'adjacency' (100% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\memory_management\memory_manager.py:226: unused method 'hdf5_load_time' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\memory_management\memory_manager.py:287: unused variable 'total_rows' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\memory_management\memory_manager.py:292: unused variable 'total_rows' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\project\project.py:154: unused method 'add_experiment' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\project\project.py:260: unused method 'disable_experiments' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\transformations\map_molecules.py:122: unused method '_update_type_dict' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\transformations\map_molecules.py:146: unused method '_update_species_type_dict' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\calculator_helper_methods.py:86: unused variable 'pcov' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\config.py:42: unused variable 'GPU' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\exceptions.py:29: unused class 'NoElementInDump' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\exceptions.py:37: unused class 'NoTempInData' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\exceptions.py:45: unused class 'NotApplicableToAnalysis' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\exceptions.py:77: unused class 'DatasetExists' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\exceptions.py:85: unused class 'RangeExceeded' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\exceptions.py:94: unused class 'DatabaseDoesNotExist' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\exceptions.py:105: unused class 'NotInDataFile' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\meta_functions.py:162: unused function 'line_counter' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\meta_functions.py:243: unused function 'linear_fitting_function' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\meta_functions.py:268: unused function 'simple_file_read' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\meta_functions.py:297: unused function 'timeit' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\meta_functions.py:447: unused function 'round_down' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\testing.py:89: unused property 'exception' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:29: unused variable 'standard_state_pressure' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:30: unused variable 'avogadro_constant' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:33: unused variable 'hyperfine_transition_frequency' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:36: unused variable 'luminous_efficacy' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:37: unused variable 'planck_constant' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:38: unused variable 'reduced_planck_constant' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:39: unused variable 'speed_of_light' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:40: unused variable 'gravity' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:41: unused variable 'atmosphere' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:54: unused variable 'NkTV2p' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:55: unused variable 'boltzmann' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:57: unused variable 'pressure' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\utils\units.py:58: unused variable 'avogadro' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\visualizer\d3_data_visualizer.py:70: unused attribute 'points' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\visualizer\d3_data_visualizer.py:71: unused attribute 'colors' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\visualizer\d3_data_visualizer.py:100: unused attribute 'show_settings' (60% confidence)
C:\Users\fabia\PycharmProjects\MDSuite\mdsuite\visualizer\znvis_visualizer.py:107: unused method '_prepare_species' (60% confidence)

[SamTov]

Funnily the constant 60% confident makes me less confident in all of them 😄

[PythonFZ]

Funnily the constant 60% confident makes me less confident in all of them 😄

I guess most of the lines mentioned here aren't unused code. But it might still be worth looking at them. If you are confident there is no legacy code we can also close this.

[SamTov]

No no I was just joking because all of them say 60% confidence which just makes me less confident. Some of this is definitely legacy code.