[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

.github/ISSUE_TEMPLATE/bug_report.md

@@ -21,9 +21,9 @@ happen.
 
 **Desktop (please complete the following information):**
 
-- OS: \[e.g. iOS\]
-- Browser \[e.g. chrome, safari\]
-- Version \[e.g. 22\]
+- OS: [e.g. iOS]
+- Browser [e.g. chrome, safari]
+- Version [e.g. 22]
 
 **System parameters** Please run the following in your python kernel and copy
 the output below.

CI/functional_tests/test_molten_salts.py

@@ -25,6 +25,7 @@
 -------
 Perform a functional test on two molten salts.
 """
+
 from typing import Tuple
 
 import pytest
@@ -73,6 +74,7 @@ def mdsuite_project(traj_files, tmp_path) -> mds.Project:
     -------
     project: mdsuite.Project
             An MDSuite project to be tested.
+
     """
     project = mds.Project(storage_path=tmp_path.as_posix())
 
@@ -114,6 +116,7 @@ def test_analysis(mdsuite_project):
     -----
     See the link below for similar data for CNs for molten salts.
     https://link.springer.com/article/10.1007/s10800-018-1197-z
+
     """
     NaCl_experiment = mdsuite_project.experiments.NaCl
     KCl_experiment = mdsuite_project.experiments.KCl

CI/functional_tests/test_water_study.py

@@ -25,6 +25,7 @@
 -------
 Functional test for the analysis of a GROMACS water simulation.
 """
+
 from typing import List
 
 import pytest
@@ -65,6 +66,7 @@ def mdsuite_project(traj_files, tmp_path) -> mdsuite.Project:
     -------
     project: mdsuite.Project
             An MDSuite project to be tested.
+
     """
     gmx_units = Units(
         time=1e-12,
@@ -102,6 +104,7 @@ def test_water_analysis(mdsuite_project):
     -----
     The diffusion, angle, and eventually coordination data tested here are comparable
     with values taken from experiment and published studies.
+
     """
     water = mdsuite_project.experiments["water_sim"]
 

CI/integration_tests/calculators/__test_structure_factor.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import json
 import os
 from pathlib import Path

CI/integration_tests/calculators/_test_green_kubo_thermal_conductivity.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import json
 import os
 from pathlib import Path

CI/integration_tests/calculators/_test_green_kubo_viscosity.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import json
 import os
 from pathlib import Path

CI/integration_tests/calculators/_test_nernst_einstein_ionic_conductivity.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import json
 import os
 from pathlib import Path

CI/integration_tests/calculators/test_angular_distribution_function.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import pytest

CI/integration_tests/calculators/test_coordination_numbers.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import pytest

CI/integration_tests/calculators/test_einstein_diffusion_coefficients.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import dataclasses
 import os
 

CI/integration_tests/calculators/test_einstein_distinct_diffusion_coefficients.py

@@ -31,6 +31,7 @@
 values.
 
 """
+
 import os
 
 import pytest

CI/integration_tests/calculators/test_einstein_helfand_ionic_conductivity.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import pytest
@@ -61,6 +62,7 @@ def test_project(traj_file, true_values, tmp_path, desired_memory):
     Notes
     -----
     Test uncertainty is very high!
+
     """
     with mds.utils.helpers.change_memory_fraction(desired_memory=desired_memory):
         os.chdir(tmp_path)

CI/integration_tests/calculators/test_green_kubo_distinct_diffusion_coefficients.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import pytest

CI/integration_tests/calculators/test_green_kubo_ionic_conductivity.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import numpy as np

CI/integration_tests/calculators/test_green_kubo_self_diffusion_coefficients.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import dataclasses
 import os
 
@@ -103,9 +104,7 @@ def test_calculator(tmp_path, desired_memory):
         time_should_be = time_step * np.arange(0, vacf_range) * units.time
         thermal_vel_SI = np.sqrt(3 * kT / mass) * units.length / units.time
         relaxation_time_SI = relaxation_time * units.time
-        vacf_should_be = thermal_vel_SI**2 * np.exp(
-            -time_should_be / relaxation_time_SI
-        )
+        vacf_should_be = thermal_vel_SI**2 * np.exp(-time_should_be / relaxation_time_SI)
         diff_coeff_should_be = diff_coeff * units.length**2 / units.time
 
         np.testing.assert_allclose(res["time"], time_should_be, atol=1e-6)

CI/integration_tests/calculators/test_kirkwood_buff_integrals.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import pytest

CI/integration_tests/calculators/test_potential_of_mean_force.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import pytest

CI/integration_tests/calculators/test_radial_distribution_function.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 
 import pytest

CI/integration_tests/transformations/test_molecular_mapping_results.py

@@ -25,6 +25,7 @@
 -------
 Test the outcome of molecular mapping.
 """
+
 from typing import List, Tuple
 
 import pytest
@@ -73,6 +74,7 @@ def mdsuite_project(traj_files, tmp_path) -> mdsuite.Project:
     -------
     project: mdsuite.Project
             An MDSuite project to be tested.
+
     """
     water_files = traj_files[0]
     bmim_file = traj_files[1]
@@ -138,6 +140,7 @@ def test_water_molecule_smiles(self, mdsuite_project):
         -------
         Tests that the molecule groups detected are done so correctly and that the
         constructed trajectory is also correct.
+
         """
         reference_molecules = {
             "water": MoleculeInfo(
@@ -187,6 +190,7 @@ def test_water_molecule_reference_dict(self, mdsuite_project):
         -------
         Tests that the molecule groups detected are done so correctly and that the
         constructed trajectory is also correct.
+
         """
         mdsuite_project.experiments["ligand_water"].species["OW"].mass = [15.999]
         mdsuite_project.experiments["ligand_water"].species["HW1"].mass = [1.00784]

CI/integration_tests/transformations/test_transformation_run_options.py

@@ -45,6 +45,7 @@ def test_from_project(mdsuite_project):
     Notes
     -----
     Does not check actual values just runs the transformation.
+
     """
     mdsuite_project.run.CoordinateUnwrapper()
 
@@ -57,6 +58,7 @@ def test_from_project_twice(mdsuite_project):
     Notes
     -----
     Does not check actual values just runs the transformation.
+
     """
     mdsuite_project.run.CoordinateUnwrapper()
     mdsuite_project.run.CoordinateUnwrapper()
@@ -69,6 +71,7 @@ def test_from_experiment(mdsuite_project):
     Notes
     -----
     Does not check actual values just runs the transformation.
+
     """
     mdsuite_project.experiments.NaCl.run.CoordinateUnwrapper()
 
@@ -81,6 +84,7 @@ def test_from_experiment_twice(mdsuite_project):
     Notes
     -----
     Does not check actual values just runs the transformation.
+
     """
     mdsuite_project.experiments.NaCl.run.CoordinateUnwrapper()
     mdsuite_project.experiments.NaCl.run.CoordinateUnwrapper()

CI/integration_tests/visualizer/znvis_visualizer.py

@@ -25,6 +25,7 @@
 -------
 Test that the visualizer runs.
 """
+
 import os
 import tempfile
 import time
@@ -54,6 +55,7 @@ def test_run(self):
             test isn't prematurely closed and passes when it should have failed. For now
             120 seconds is more than enough time for this test but we can think of some
             improvements later.
+
         """
         process = MDSuiteProcess(target=self._run_app)
         process.start()

CI/unit_tests/database/test_experiment_database.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import dataclasses
 import os
 

CI/unit_tests/database/test_file_read.py

@@ -1,4 +1,5 @@
 """Test MDSuite file reading."""
+
 import numpy as np
 
 import mdsuite

CI/unit_tests/database/test_simulation_database.py

@@ -23,6 +23,7 @@
 -------
 Test for module for the simulation database.
 """
+
 import os
 import tempfile
 import unittest
@@ -43,6 +44,7 @@ def test_build_path_input(self):
         Returns
         -------
         Asserts that the correct path is generated for a given input.
+
         """
         temp_dir = tempfile.TemporaryDirectory()
         os.chdir(temp_dir.name)
@@ -70,6 +72,7 @@ def test_add_dataset(self):
         Returns
         -------
         Assert that a dataset of the correct size is built.
+
         """
         temp_dir = tempfile.TemporaryDirectory()
         os.chdir(temp_dir.name)
@@ -93,6 +96,7 @@ def test_resize_array(self):
         Returns
         -------
         Resizes a built dataset and checks that the size is now correct.
+
         """
         temp_dir = tempfile.TemporaryDirectory()
         os.chdir(temp_dir.name)
@@ -118,6 +122,7 @@ def test_database_exists(self):
         Returns
         -------
         Checks for a False and then True result.
+
         """
         temp_dir = tempfile.TemporaryDirectory()
         os.chdir(temp_dir.name)
@@ -135,6 +140,7 @@ def test_check_existence(self):
         Returns
         -------
         Checks for a True and False result.
+
         """
         temp_dir = tempfile.TemporaryDirectory()
         os.chdir(temp_dir.name)

CI/unit_tests/experiment/test_Experiment.py

@@ -1,4 +1,5 @@
 """Test MDSuite Experiment class."""
+
 import pytest
 
 from mdsuite.experiment.experiment import Experiment

CI/unit_tests/experiment/test_run_computation.py

@@ -9,6 +9,7 @@
 
 Description:
 """
+
 from unittest.mock import Mock
 
 from mdsuite.experiment.run import RunComputation

CI/unit_tests/graph_modules/test_molecular_graph.py

@@ -25,6 +25,7 @@
 -------
 Module to test the molecular graph module.
 """
+
 from dataclasses import dataclass
 from pathlib import Path
 
@@ -54,6 +55,7 @@ class SmilesTestData:
     species : dict
             A dictionary of species information for the test stating how many of each
             particle species is in the group e.g. {'C': 6, 'H': 14}
+
     """
 
     name: str
@@ -78,6 +80,7 @@ def test_apply_system_cutoff(self):
         Returns
         -------
         Checks whether or not the cutoff has been enforced.
+
         """
         zeros = np.array([0, 0, 0, 0, 0])
         cutoff_data = [
@@ -123,6 +126,7 @@ def test_build_smiles_graph(self):
         -------
         This test checks that the SMILES graphs built by the module return the correct
         molecule information for several scenarios.
+
         """
         emim = SmilesTestData(
             name="emim",