Merge pull request #37 from OceanParcels/adding_new_tests

Broadening the unit tests

Author: michaeldenes

.gitignore

@@ -2,7 +2,6 @@ input_data/
 **.code-workspace*
 **.DS_store**
 **.pyc**
-**.nc
 **.zarr
 docs/_build/*
 docs/_downloads

docs/examples/example_Croatian_fisheries_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

docs/examples/example_Greece_coast_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

docs/examples/example_Italy_coast_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

docs/examples/example_add_your_own_kernel_settings.json

@@ -59,10 +59,10 @@
             "lon": "nav_lon",
             "lat": "nav_lat"
         },
-        "mixing_variables": {
+        "vertical_mixing_variables": {
             "mixing_kz": "votkeavt"
         },
-        "mixing_dimensions": {
+        "vertical_mixing_dimensions": {
             "lon": "glamf",
             "lat": "gphif",
             "depth": "depthw",

tests/test_constructors.py

@@ -0,0 +1,156 @@
+import parcels.application_kernels
+import plasticparcels as pp
+import parcels
+from datetime import datetime, timedelta
+import pytest
+
+
+def make_simple_fieldset():
+    fieldset = parcels.FieldSet.from_data({'U': 0, 'V': 0},
+                                          {'lon': 0, 'lat': 0},
+                                          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),
+                           'outputdt': timedelta(hours=1),
+                           'dt': timedelta(minutes=20),
+                           }
+    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)
+                            'plastic_density': 1030.,    # Plastic particle density (kg/m^3)
+                            }
+    return plastictype_settings
+
+
+# Test the create_hydrodynamic_fieldset() function
+def test_create_hydrodynamic_fieldset():
+    settings_file = 'tests/test_data/test_settings.json'
+    settings = pp.utils.load_settings(settings_file)
+    settings['simulation'] = make_standard_simulation_settings()
+
+    fieldset = pp.constructors.create_hydrodynamic_fieldset(settings)
+
+    assert isinstance(fieldset, parcels.FieldSet)
+
+
+# Test the create_fieldset() function
+@pytest.mark.parametrize('use_3D', [True, False])
+@pytest.mark.parametrize('use_biofouling', [True, False])
+@pytest.mark.parametrize('use_stokes', [True, False])
+@pytest.mark.parametrize('use_wind', [True, False])
+@pytest.mark.parametrize('use_mixing', [True, False])
+def test_create_fieldset(use_3D, use_biofouling, use_stokes, use_wind, use_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['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):
+    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['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):
+    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['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])
+@pytest.mark.parametrize('use_stokes', [True, False])
+@pytest.mark.parametrize('use_wind', [True, False])
+@pytest.mark.parametrize('use_mixing', [True, False])
+def test_create_kernel(use_3D, use_biofouling, use_stokes, use_wind, use_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['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)
+    kernels = pp.constructors.create_kernel(fieldset)
+
+    if use_3D:
+        assert parcels.application_kernels.AdvectionRK4_3D in kernels
+        assert pp.kernels.checkThroughBathymetry in kernels
+        assert pp.kernels.checkErrorThroughSurface in kernels
+    else:
+        assert parcels.application_kernels.AdvectionRK4 in kernels
+
+    if use_3D and use_biofouling:
+        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