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zincware / MDSuite

A post-processing engine for particle simulations
https://mdsuite.readthedocs.io/
Eclipse Public License 2.0
36 stars 7 forks source link

Remove legacy code #487

Open PythonFZ opened 2 years ago

PythonFZ commented 2 years ago

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 https://github.com/zincware/MDSuite/pull/475#discussion_r795618398_

PythonFZ commented 2 years ago

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 commented 2 years ago

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

PythonFZ commented 2 years ago

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 commented 2 years ago

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.