[merge before other PRs] ruff updates

CI/functional_tests/test_molten_salts.py

@@ -35,9 +35,7 @@
 
 @pytest.fixture(scope="session")
 def traj_files(tmp_path_factory) -> Tuple[str, str]:
-    """
-    Download trajectory file into a temporary directory and keep it for all tests
-    """
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl_file = DataHub(

CI/functional_tests/test_water_study.py

@@ -37,7 +37,7 @@
 
 @pytest.fixture(scope="session")
 def traj_files(tmp_path_factory) -> List[str]:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     water = DataHub(
@@ -95,14 +95,13 @@ def mdsuite_project(traj_files, tmp_path) -> mdsuite.Project:
 
 def test_water_analysis(mdsuite_project):
     """
-    Run a functional test by performing a study on an MD simulation of water
+    Run a functional test by performing a study on an MD simulation of water.
 
     Notes
     -----
     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"]
 
     water_molecule = mds.Molecule(

CI/integration_tests/calculators/__test_structure_factor.py

@@ -37,7 +37,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -50,15 +50,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="StructureFactor.json")
 
 
 def test_structure_factor_project(traj_files, true_values, tmp_path):
-    """Test the structure_factor called from the project class"""
+    """Test the structure_factor called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(
@@ -85,7 +85,7 @@ def test_structure_factor_project(traj_files, true_values, tmp_path):
 
 
 def test_structure_factor_experiment(traj_files, true_values, tmp_path):
-    """Test the structure_factor called from the experiment class"""
+    """Test the structure_factor called from the experiment class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/_test_einstein_helfand_thermal_kinaci.py

@@ -38,7 +38,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -51,15 +51,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="EinsteinHelfandThermanKinaci.json")
 
 
 def test_project(traj_files, true_values, tmp_path):
-    """Test the einstein_helfand_thermal_kinaci called from the project class"""
+    """Test the einstein_helfand_thermal_kinaci called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(
@@ -81,7 +81,7 @@ def test_project(traj_files, true_values, tmp_path):
 
 
 def test_experiment(traj_files, true_values, tmp_path):
-    """Test the einstein_helfand_thermal_kinaci called from the experiment class"""
+    """Test the einstein_helfand_thermal_kinaci called from the experiment class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/_test_green_kubo_thermal_conductivity.py

@@ -37,7 +37,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -50,15 +50,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="GreenKuboThermalConductivity.json")
 
 
 def test_roject(traj_files, true_values, tmp_path):
-    """Test the green_kubo_thermal_conductivity called from the project class"""
+    """Test the green_kubo_thermal_conductivity called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(
@@ -80,7 +80,7 @@ def test_roject(traj_files, true_values, tmp_path):
 
 
 def test_experiment(traj_files, true_values, tmp_path):
-    """Test the green_kubo_thermal_conductivity called from the experiment class"""
+    """Test the green_kubo_thermal_conductivity called from the experiment class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/_test_green_kubo_viscosity.py

@@ -37,7 +37,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -50,15 +50,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="GreenKuboViscosity.json")
 
 
 def test_gkv_project(traj_files, true_values, tmp_path):
-    """Test the gkv called from the project class"""
+    """Test the gkv called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(
@@ -80,7 +80,7 @@ def test_gkv_project(traj_files, true_values, tmp_path):
 
 
 def test_gkv_experiment(traj_files, true_values, tmp_path):
-    """Test the gkv called from the experiment class"""
+    """Test the gkv called from the experiment class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/_test_green_kubo_viscosity_flux.py

@@ -38,7 +38,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -51,15 +51,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="GreenKuboViscosityFlux.json")
 
 
 def test_project(traj_files, true_values, tmp_path):
-    """Test the green_kubo_viscosity_flux called from the project class"""
+    """Test the green_kubo_viscosity_flux called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(
@@ -81,7 +81,7 @@ def test_project(traj_files, true_values, tmp_path):
 
 
 def test_experiment(traj_files, true_values, tmp_path):
-    """Test the green_kubo_viscosity_flux called from the experiment class"""
+    """Test the green_kubo_viscosity_flux called from the experiment class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/_test_nernst_einstein_ionic_conductivity.py

@@ -37,7 +37,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -50,15 +50,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="NernstEinsteinIonicConductivity.json")
 
 
 def test_neic_project(traj_files, true_values, tmp_path):
-    """Test the nernst_einstein_ionic_conductivity called from the project class"""
+    """Test the nernst_einstein_ionic_conductivity called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(
@@ -80,7 +80,7 @@ def test_neic_project(traj_files, true_values, tmp_path):
 
 
 def test_neic_experiment(traj_files, true_values, tmp_path):
-    """Test the nernst_einstein_ionic_conductivity called from the experiment class"""
+    """Test the nernst_einstein_ionic_conductivity called from the experiment class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/test_angular_distribution_function.py

@@ -35,7 +35,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -48,15 +48,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="AngularDistributionFunction.json")
 
 
 def test_project(traj_file, true_values, tmp_path):
-    """Test the ADF called from the project class"""
+    """Test the ADF called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/test_coordination_numbers.py

@@ -35,7 +35,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -48,15 +48,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.1"
     )
     return NaCl.get_analysis(analysis="CoordinationNumbers.json")
 
 
 def test_project(traj_file, true_values, tmp_path):
-    """Test the CN called from the project class"""
+    """Test the CN called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/test_einstein_distinct_diffusion_coefficients.py

@@ -40,7 +40,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -53,15 +53,15 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="RadialDistributionFunction.json")
 
 
 def test_eddc_project(traj_file, true_values, tmp_path):
-    """Test the EinsteinDistinctDiffusionCoefficients called from the project class"""
+    """Test the EinsteinDistinctDiffusionCoefficients called from the project class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(
@@ -88,9 +88,7 @@ def test_eddc_project(traj_file, true_values, tmp_path):
 
 
 def test_eddc_experiment(traj_file, true_values, tmp_path):
-    """
-    Test the EinsteinDistinctDiffusionCoefficients called from the experiment class
-    """
+    """Test the EinsteinDistinctDiffusionCoefficients called from the experiment class."""
     os.chdir(tmp_path)
     project = mds.Project()
     project.add_experiment(

CI/integration_tests/calculators/test_einstein_helfand_ionic_conductivity.py

@@ -34,7 +34,7 @@
 
 @pytest.fixture(scope="session")
 def traj_file(tmp_path_factory) -> str:
-    """Download trajectory file into a temporary directory and keep it for all tests"""
+    """Download trajectory file into a temporary directory and keep it for all tests."""
     temporary_path = tmp_path_factory.getbasetemp()
 
     NaCl = DataHub(
@@ -47,18 +47,18 @@ def traj_file(tmp_path_factory) -> str:
 
 @pytest.fixture(scope="session")
 def true_values() -> dict:
-    """Example fixture for downloading analysis results from github"""
+    """Example fixture for downloading analysis results from github."""
     NaCl = DataHub(
         url="https://github.com/zincware/DataHub/tree/main/NaCl_gk_i_q", tag="v0.1.0"
     )
     return NaCl.get_analysis(analysis="EinsteinHelfandIonicConductivity.json")
 
 
 def test_project(traj_file, true_values, tmp_path):
-    """Test the Einstein_Helfand_Ionic_Conductivity called from the project class
+    """Test the Einstein_Helfand_Ionic_Conductivity called from the project class.
 
     Notes
-    ------
+    -----
     Test uncertainty is very high!
     """
     os.chdir(tmp_path)