Making files flake8 compliant

Author: michaeldenes

tests/test_constructors.py

@@ -11,6 +11,7 @@ def make_simple_fieldset():
                                           mesh='spherical')
     return fieldset
 
+
 def make_standard_simulation_settings():
     simulation_settings = {'startdate': datetime.strptime('2020-01-04-00:00:00', '%Y-%m-%d-%H:%M:%S'),
                                 'runtime': timedelta(days=2),
@@ -19,6 +20,7 @@ def make_standard_simulation_settings():
                                 }
     return simulation_settings
 
+
 def make_standard_plastictype_settings():
     plastictype_settings = {'wind_coefficient' : 0.01,  # Percentage of wind to apply to particles
                                 'plastic_diameter' : 0.01, # Plastic particle diameter (m)
@@ -37,6 +39,7 @@ def test_create_hydrodynamic_fieldset():
 
     assert isinstance(fieldset, parcels.FieldSet)
 
+
 # Test the create_fieldset() function
 @pytest.mark.parametrize('use_3D', [True, False])
 @pytest.mark.parametrize('use_biofouling', [True, False])
@@ -49,17 +52,18 @@ def test_create_fieldset(use_3D, use_biofouling, use_stokes, use_wind, use_mixin
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
-    
+
     settings['use_3D'] = use_3D
     settings['use_biofouling'] = use_biofouling
     settings['use_stokes'] = use_stokes
     settings['use_wind'] = use_wind
     settings['use_mixing'] = use_mixing
-    
+
     fieldset = pp.constructors.create_fieldset(settings)
 
     assert isinstance(fieldset, parcels.FieldSet)
 
+
 # Test three different initialisation maps
 @pytest.mark.parametrize('initialisation_map', ['coastal', 'fisheries', 'rivers'])
 def test_create_particleset_from_map(initialisation_map):
@@ -68,18 +72,19 @@ def test_create_particleset_from_map(initialisation_map):
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
- 
+
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     settings['release'] = {'initialisation_type': initialisation_map,
                             'country': 'Italy',
                             }
-    
+
     fieldset = make_simple_fieldset()
     pset = pp.constructors.create_particleset_from_map(fieldset, settings)
 
     assert isinstance(pset, parcels.ParticleSet)
 
+
 # Test the two global concentration release map types
 @pytest.mark.parametrize('concentration_type', ['Beach', 'Ocean'])
 def test_create_particleset_from_map_concentrations(concentration_type):
@@ -88,18 +93,19 @@ def test_create_particleset_from_map_concentrations(concentration_type):
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
- 
+
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     settings['release'] = {'initialisation_type': 'global_concentrations',
                             'concentration_type': concentration_type,
                             }
-    
+
     fieldset = make_simple_fieldset()
     pset = pp.constructors.create_particleset_from_map(fieldset, settings)
 
     assert isinstance(pset, parcels.ParticleSet)
 
+
 # Test three different initialisation maps
 @pytest.mark.parametrize('use_3D', [True, False])
 @pytest.mark.parametrize('use_biofouling', [True, False])
@@ -118,7 +124,7 @@ def test_create_kernel(use_3D, use_biofouling, use_stokes, use_wind, use_mixing)
     settings['use_stokes'] = use_stokes
     settings['use_wind'] = use_wind
     settings['use_mixing'] = use_mixing
-    
+
     fieldset = pp.constructors.create_fieldset(settings)
     kernels = pp.constructors.create_kernel(fieldset)
 
@@ -133,18 +139,18 @@ def test_create_kernel(use_3D, use_biofouling, use_stokes, use_wind, use_mixing)
         assert pp.kernels.Biofouling in kernels
     elif use_3D and not use_biofouling:
         assert pp.kernels.SettlingVelocity in kernels
-    
+
     if use_mixing:
         assert pp.kernels.VerticalMixing in kernels
 
     if use_stokes:
         assert pp.kernels.StokesDrift in kernels
         assert pp.kernels.unbeaching in kernels
-    
+
     if use_wind:
         assert pp.kernels.WindageDrift in kernels
         assert pp.kernels.unbeaching in kernels
-    
+
     assert pp.kernels.deleteParticle in kernels
     assert pp.kernels.periodicBC in kernels
-    assert pp.kernels.PolyTEOS10_bsq in kernels
+    assert pp.kernels.PolyTEOS10_bsq in kernels

tests/test_kernels.py

@@ -14,6 +14,7 @@ def make_standard_simulation_settings():
                                 }
     return simulation_settings
 
+
 def make_standard_plastictype_settings():
     #Use tiny wind percentage because test data set is not large and wind speeds are quick!
     plastictype_settings = {'wind_coefficient' : 0.0001,  # Percentage of wind to apply to particles
@@ -22,6 +23,7 @@ def make_standard_plastictype_settings():
                                 }
     return plastictype_settings
 
+
 def make_standard_particleset(fieldset, settings):
     # Generate a particleset that has particles in the test domain
     settings['release'] = {'initialisation_type': 'fisheries', 'country': 'Malta'}
@@ -30,9 +32,10 @@ def make_standard_particleset(fieldset, settings):
     # Only keep particles in the test domain
     keep_particles = (pset.lon >17) & (pset.lon <20) & (pset.lat < 36) & (pset.lat > 34) 
     pset.remove_booleanvector(~keep_particles)
-    
+
     return pset
 
+
 @pytest.mark.parametrize('use_3D', [True, False])
 def test_advection_only(use_3D):
     settings_file = 'tests/test_data/test_settings.json'
@@ -41,7 +44,7 @@ def test_advection_only(use_3D):
 
     settings['simulation'] = make_standard_simulation_settings()
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     # Turn on/off 3D advection
     settings['use_3D'] = use_3D
 
@@ -67,14 +70,15 @@ def test_advection_only(use_3D):
     # Assert that the particles move from their initial location
     assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.)
 
+
 def test_settling_velocity():
     settings_file = 'tests/test_data/test_settings.json'
     settings = pp.utils.load_settings(settings_file)
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     # Turn on 3D advection
     settings['use_3D'] = True
 
@@ -85,7 +89,7 @@ def test_settling_velocity():
     settings['use_mixing'] = False
 
     fieldset = pp.constructors.create_fieldset(settings)
-    
+
     kernels = pp.constructors.create_kernel(fieldset)
 
     pset = make_standard_particleset(fieldset, settings)
@@ -99,14 +103,15 @@ def test_settling_velocity():
     # Assert that the particles move from their initial location
     assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.) & (np.sum(np.abs(pset.depth - start_depths)) > 0.)
 
+
 def test_biofouling():
     settings_file = 'tests/test_data/test_settings.json'
     settings = pp.utils.load_settings(settings_file)
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     # Turn on biofouling
     settings['use_biofouling'] = True
 
@@ -117,7 +122,7 @@ def test_biofouling():
     settings['use_mixing'] = False
 
     fieldset = pp.constructors.create_fieldset(settings)
-    
+
     kernels = [pp.kernels.PolyTEOS10_bsq, pp.kernels.Biofouling,
                pp.kernels.checkThroughBathymetry, pp.kernels.checkErrorThroughSurface,
                pp.kernels.deleteParticle]
@@ -131,25 +136,26 @@ def test_biofouling():
     # Assert that the particles move from their initial location
     assert (np.sum(np.abs(pset.depth - start_depths)) > 0.)
 
+
 def test_Stokes():
     settings_file = 'tests/test_data/test_settings.json'
     settings = pp.utils.load_settings(settings_file)
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     # Turn on Stokes Drift
     settings['use_stokes'] = True
-    
+
     # Turn off all other processes
     settings['use_3D'] = False
     settings['use_biofouling'] = False
     settings['use_wind'] = False
     settings['use_mixing'] = False
 
     fieldset = pp.constructors.create_fieldset(settings)
-    
+
     kernels = [pp.kernels.StokesDrift, pp.kernels.deleteParticle]
 
     pset = make_standard_particleset(fieldset, settings)
@@ -162,29 +168,30 @@ def test_Stokes():
     # Assert that the particles move from their initial location
     assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.)
 
+
 def test_wind():
     settings_file = 'tests/test_data/test_settings.json'
     settings = pp.utils.load_settings(settings_file)
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     # Turn on Stokes Drift
     settings['use_wind'] = True
-    
+
     # Turn off all other processes
     settings['use_3D'] = False
     settings['use_biofouling'] = False
     settings['use_stokes'] = False
     settings['use_mixing'] = False
 
     fieldset = pp.constructors.create_fieldset(settings)
-    
+
     kernels = [pp.kernels.WindageDrift, pp.kernels.unbeaching, pp.kernels.periodicBC, pp.kernels.deleteParticle]
 
     pset = make_standard_particleset(fieldset, settings)
-    
+
     start_lons = pset.lon.copy()
     start_lats = pset.lat.copy()
 
@@ -193,17 +200,18 @@ def test_wind():
     # Assert that the particles move from their initial location
     assert (np.sum(np.abs(pset.lon - start_lons)) > 0.) & (np.sum(np.abs(pset.lat - start_lats)) > 0.)
 
+
 def test_mixing():
     settings_file = 'tests/test_data/test_settings.json'
     settings = pp.utils.load_settings(settings_file)
     settings = pp.utils.download_plasticparcels_dataset('NEMO0083', settings, 'input_data')
 
     settings['simulation'] = make_standard_simulation_settings()
     settings['plastictype'] = make_standard_plastictype_settings()
-    
+
     settings['use_3D'] = True
     settings['use_mixing'] = True
-    
+
     # Turn off all other processes
     settings['use_wind'] = False
     settings['use_biofouling'] = False
@@ -212,7 +220,7 @@ def test_mixing():
     fieldset = pp.constructors.create_fieldset(settings)
     kernels = [parcels.application_kernels.AdvectionRK4_3D, pp.kernels.checkThroughBathymetry,
                pp.kernels.checkErrorThroughSurface, pp.kernels.deleteParticle]
-    
+
     kernels_mixing = [parcels.application_kernels.AdvectionRK4_3D, pp.kernels.VerticalMixing,
                pp.kernels.checkThroughBathymetry, pp.kernels.checkErrorThroughSurface,
                pp.kernels.deleteParticle]

tests/test_settings.py

@@ -1,5 +1,6 @@
 import plasticparcels as pp
 
+
 def test_settings():
     settings = pp.utils.load_settings('tests/test_data/test_settings.json')
     assert settings is not None
@@ -8,4 +9,4 @@ def test_settings():
 def test_download_script(tmpdir):
     settings = pp.utils.load_settings('tests/test_data/test_settings.json')
     pp.utils.download_plasticparcels_dataset("NEMO0083", settings=settings, data_home=tmpdir)
-    assert True
+    assert True