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

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

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

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

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

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

CI/integration_tests/visualizer/znvis_visualizer.py

@@ -25,6 +25,7 @@
 -------
 Test that the visualizer runs.
 """
+
 import os
 import tempfile
 import time

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
@@ -52,13 +53,11 @@ def test_build_path_input(self):
             "Pressure": (5000, 6),
             "Temperature": (5000, 1),
         }
-        architecture = database._build_path_input(
-            {
-                "Na": {"Forces": (200, 5000, 3)},
-                "Pressure": (5000, 6),
-                "Temperature": (5000, 1),
-            }
-        )
+        architecture = database._build_path_input({
+            "Na": {"Forces": (200, 5000, 3)},
+            "Pressure": (5000, 6),
+            "Temperature": (5000, 1),
+        })
         self.assertDictEqual(assertion, architecture)
         os.chdir("..")
         temp_dir.cleanup()

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
 
@@ -90,15 +91,13 @@ def test_apply_system_cutoff(self):
         cutoff_tensor = tf.constant(cutoff_data, dtype=tf.float32)
 
         # Middle range cutoff
-        target = tf.constant(
-            [
-                [0, 0, 0, 0, 1],
-                [0, 0, 1, 1, 1],
-                [0, 0, 0, 1, 1],
-                [0, 0, 0, 0, 0],
-                [1, 0, 1, 1, 0],
-            ]
-        )
+        target = tf.constant([
+            [0, 0, 0, 0, 1],
+            [0, 0, 1, 1, 1],
+            [0, 0, 0, 1, 1],
+            [0, 0, 0, 0, 0],
+            [1, 0, 1, 1, 0],
+        ])
         mask = _apply_system_cutoff(cutoff_tensor, cutoff=5)
         np.testing.assert_array_equal(np.diagonal(mask), zeros)
         np.testing.assert_array_equal(mask, target)

CI/unit_tests/memory_manager/test_memory_manager.py

@@ -19,6 +19,7 @@
 -------
 Test for the memory manager module.
 """
+
 import unittest
 
 import numpy as np

CI/unit_tests/project/test_project_add_experiment.py

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

CI/unit_tests/project/test_project_database.py

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

CI/unit_tests/project/test_project_instantiation.py

@@ -9,6 +9,7 @@
 
 Description:
 """
+
 import pathlib
 
 import mdsuite

CI/unit_tests/project/test_project_load_experiments.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import os
 from tempfile import TemporaryDirectory
 

CI/unit_tests/transformations/test_transformations.py

@@ -153,9 +153,9 @@ def test_unwrap_coordinates():
     # x stays in box 0
     # y jumps 0 -> -1 -> -1 -> 0
     # z jumps 0 -> 1 -> 1 -> 2
-    pos = np.array(
-        [[[0.5, 0.1, 3.2]], [[0.6, 2.1, 0.9]], [[0.6, 2.1, 2.1]], [[0.6, 0.1, 0.1]]]
-    )
+    pos = np.array([
+        [[0.5, 0.1, 3.2]], [[0.6, 2.1, 0.9]], [[0.6, 2.1, 2.1]], [[0.6, 0.1, 0.1]]
+    ])
     pos = np.swapaxes(pos, 0, 1)
     print(np.shape(pos))
 
@@ -172,14 +172,12 @@ def test_unwrap_coordinates():
 
     output, carryover = trafo.transform_batch(input, carryover=last_carryover)
 
-    output_should_be = np.array(
-        [
-            [[4 * 1.1 + 0.5, 0.1, 3.2]],
-            [[4 * 1.1 + 0.6, -0.1, 4.2]],
-            [[4 * 1.1 + 0.6, -0.1, 5.4]],
-            [[4 * 1.1 + 0.6, 0.1, 6.7]],
-        ]
-    )
+    output_should_be = np.array([
+        [[4 * 1.1 + 0.5, 0.1, 3.2]],
+        [[4 * 1.1 + 0.6, -0.1, 4.2]],
+        [[4 * 1.1 + 0.6, -0.1, 5.4]],
+        [[4 * 1.1 + 0.6, 0.1, 6.7]],
+    ])
     output_should_be = np.swapaxes(output_should_be, 0, 1)
     carryover_should_be = {"last_pos": [[0.6, 0.1, 0.1]], "last_image_box": [[4, 0, 2]]}
     assertDeepAlmostEqual(output.numpy(), output_should_be)

CI/unit_tests/transformations/test_transformator_parent.py

@@ -21,6 +21,7 @@
 --------
 If you use this module please cite us with:
 """
+
 import os
 
 import numpy as np

CI/unit_tests/utils/test_calculator_helper_methods.py

@@ -25,6 +25,7 @@
 -------
 Module for testing the calculator helper methods.
 """
+
 import numpy as np
 import pytest
 from numpy.testing import assert_array_equal, assert_raises

CI/unit_tests/utils/test_constants.py

@@ -1,4 +1,5 @@
 """Test for MDSuite utils.constants."""
+
 import dataclasses
 
 import pytest

CI/unit_tests/utils/test_meta_functions.py

@@ -25,6 +25,7 @@
 -------
 Test the meta functions module.
 """
+
 import os
 
 import numpy as np

CI/unit_tests/utils/test_molecule_class.py

@@ -25,6 +25,7 @@
 -------
 Unit tests for the molecule data class.
 """
+
 import pytest
 
 import mdsuite

CI/unit_tests/utils/test_scaling_functions.py

@@ -20,6 +20,7 @@
 -------
 Unit tests for the scaling functions module.
 """
+
 import unittest
 
 import numpy as np

CI/unit_tests/utils/test_testing.py

@@ -25,6 +25,7 @@
 -------
 Test the mdsuite testing modules.
 """
+
 import time
 import unittest
 

CI/unit_tests/utils/test_units.py

@@ -1,4 +1,5 @@
 """Test MDSuite units."""
+
 import mdsuite as mds
 
 

docs/source/conf.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 import sys
 
 import sphinx_rtd_theme

mdsuite/__init__.py

@@ -24,6 +24,7 @@
 Summary
 -------
 """
+
 try:
     from importlib import metadata
 except ImportError:  # for Python<3.8