Merge branch 'develop' into 'master'

Develop

See merge request gnome/pygnome!68

py_gnome/gnome/array_types.py

@@ -276,6 +276,8 @@ def split_element(self, num, value, l_frac=None):
                    # fractional water content in emulsion
                    'frac_water': ((), np.float64, 'frac_water', 0),
                    'interfacial_area': ((), np.float64, 'interfacial_area', 0),
+                   # internal factor for biodegradation
+                   'yield_factor': ((), np.float64, 'yield_factor', 0),
                    # use negative as a not yet set flag
                    'bulltime': ((), np.float64, 'bulltime', -1.),
                    'frac_lost': ((), np.float64, 'frac_lost', 0),

py_gnome/gnome/outputters/netcdf.py

@@ -94,6 +94,7 @@
     'frac_coverage': {},
     'bulltime': {},
     'evap_decay_constant': {},
+    'yield_factor': {},
     'partition_coeff': {},
     'droplet_avg_size': {},
     'init_mass': {'long_name': 'initial mass',
@@ -260,6 +261,7 @@ class NetCDFOutput(Outputter, OutputterFilenameMixin):
                               'bulltime',
                               'partition_coeff',
                               'evap_decay_constant',
+                              'yield_factor',
                               ]
 
     _schema = NetCDFOutputSchema

py_gnome/gnome/weatherers/bio_degradation.py

@@ -56,6 +56,7 @@ def __init__(self, waves=None, **kwargs):
                                  'mass_components': gat('mass_components'),
                                  'droplet_avg_size': gat('droplet_avg_size'),
                                  'positions': gat('positions'),
+                                 'yield_factor': gat('yield_factor'),
                                  })
 
         #
@@ -202,11 +203,13 @@ def weather_elements(self, sc, time_step, model_time):
                 continue
 
             # get the substance index
-            indx = sc._substances_spills.substances.index(substance)
+            #indx = sc._substances_spills.substances.index(substance)
 
             # get pseudocomponent boiling point and its type
-            assert 'boiling_point' in substance._sara.dtype.names
-            type_bp = substance._sara[['type','boiling_point']]
+            #assert 'boiling_point' in substance._sara.dtype.names
+            assert hasattr(substance,'boiling_point')
+            #type_bp = substance._sara[['type','boiling_point']]
+            type_bp = zip(substance.sara_type, substance.boiling_point)
 
             # get bio degradation rate coefficient array for this substance
             K_comp_rates = np.asarray(map(self.get_K_comp_rates, type_bp))
@@ -215,19 +218,20 @@ def weather_elements(self, sc, time_step, model_time):
             # so we need recalculate ones for the time step interval
             K_comp_rates = K_comp_rates / (60 * 60 * 24) * time_step
 
+            self.previous_yield_factor = data['yield_factor']
             # calculate yield factor (specific surace)
             if np.any(data['droplet_avg_size']):
-                yield_factor = 1.0 / (data['droplet_avg_size'] * data['density'])
+                data['yield_factor'] = 1.0 / (data['droplet_avg_size'] * data['density'])
             else:
-                yield_factor = 0.0
+                data['yield_factor'] = 0.0
 
             # calculate the mass over time step
-            bio_deg = self.bio_degradate_oil(K_comp_rates, data, yield_factor)
+            bio_deg = self.bio_degradate_oil(K_comp_rates, data, data['yield_factor'])
 
             # update yield factor for the next time step
-            self.prev_yield_factor = yield_factor
+            #self.prev_yield_factor = yield_factor
 
-            # calculate mass ballance for bio degradation process - mass loss
+            # calculate mass balance for bio degradation process - mass loss
             sc.mass_balance['bio_degradation'] += data['mass'].sum() - bio_deg.sum()
 
             # update masses
@@ -243,29 +247,3 @@ def weather_elements(self, sc, time_step, model_time):
         sc.update_from_fatedataview()
 
 
-    def serialize(self, json_='webapi'):
-
-        toserial = self.to_serialize(json_)
-        schema = self.__class__._schema()
-        serial = schema.serialize(toserial)
-
-        if json_ == 'webapi':
-            if self.waves:
-                serial['waves'] = self.waves.serialize(json_)
-
-        return serial
-
-    @classmethod
-    def deserialize(cls, json_):
-
-        if not cls.is_sparse(json_):
-            schema = cls._schema()
-            dict_ = schema.deserialize(json_)
-
-            if 'waves' in json_:
-                obj = json_['waves']['obj_type']
-                dict_['waves'] = (eval(obj).deserialize(json_['waves']))
-
-            return dict_
-        else:
-            return json_

py_gnome/tests/unit_tests/test_weatherers/test_bio_degradation.py

@@ -21,17 +21,13 @@
                               Biodegradation,
                               weatherer_sort)
 
-from .conftest import weathering_data_arrays
+from .conftest import weathering_data_arrays, test_oil
 
 
 from ..conftest import (sample_model_weathering2)
 
 from pprint import PrettyPrinter
 
-pytestmark = pytest.mark.skipif(True,
-                                reason="Biodeg tests all need to be updated")
-
-
 pp = PrettyPrinter(indent=2, width=120)
 
 wind = constant_wind(15., 270, 'knots')
@@ -55,9 +51,10 @@ def test_sort_order():
     waves = Waves(wind, Water())
     bio_deg = Biodegradation(waves)
 
-    assert weatherer_sort(bio_deg) == 9
+    assert weatherer_sort(bio_deg) == 11
 
 
+@pytest.mark.skipif(reason="serialization for weatherers overall needs review")
 def test_serialize_deseriailize():
     'test serialize/deserialize for webapi'
 
@@ -83,12 +80,10 @@ def test_serialize_deseriailize():
 
 def test_prepare_for_model_run():
 
-    et = floating(substance='ABU SAFAH')
     bio_deg = Biodegradation(waves)
 
     (sc, time_step) = weathering_data_arrays(bio_deg.array_types,
-                                             water,
-                                             element_type=et)[:2]
+                                             water)[:2]
 
     assert 'bio_degradation' not in sc.mass_balance
 
@@ -98,19 +93,17 @@ def test_prepare_for_model_run():
 
 
 @pytest.mark.parametrize(('oil', 'temp', 'num_elems', 'expected_mb', 'on'),
-                         [('ABU SAFAH', 311.15, 3, 0.0, True),
-                          ('BAHIA', 311.15, 3, 0.0, True),
-                          ('ALASKA NORTH SLOPE (MIDDLE PIPELINE)', 311.15, 3,
-                           np.nan, False)])
+                         [('oil_ans_mp', 311.15, 3, 0.0, True),
+                          #('ABU SAFAH', 311.15, 3, 0.0, True),
+                          ('oil_bahia', 311.15, 3, 0.0, True),
+                          ('oil_ans_mp', 311.15, 3, np.nan, False)])
 def test_bio_degradation_mass_balance(oil, temp, num_elems, expected_mb, on):
 
-    et = floating(substance=oil)
     bio_deg = Biodegradation(waves)
     (sc, time_step) = weathering_data_arrays(bio_deg.array_types,
                                              water,
-                                             element_type=et,
                                              num_elements=num_elems)[:2]
-    model_time = (sc.spills[0].get('release_time') +
+    model_time = (sc.spills[0].release_time +
                   timedelta(seconds=time_step))
 
     bio_deg.on = on
@@ -128,14 +121,12 @@ def test_bio_degradation_mass_balance(oil, temp, num_elems, expected_mb, on):
 
 @pytest.mark.parametrize(('oil', 'temp', 'expected_balance'),
     # TODO - expected ballance values:
-                         [('ABU SAFAH', 288.7, -1),
-                          ('ALASKA NORTH SLOPE (MIDDLE PIPELINE)', 288.7,
-                           -1),
-                          ('ALASKA NORTH SLOPE, OIL & GAS', 279.261,
-                           -1),
-                          ('BAHIA', 288.7, -1),
-                          ]
-                         )
+                         [(test_oil, 288.7, -1),
+                          #('ABU SAFAH', 288.7, -1),
+                          ('oil_ans_mp', 288.7, -1),
+                          #('ALASKA NORTH SLOPE, OIL & GAS', 279.261,
+                           #-1),
+                          ('oil_bahia', 288.7, -1)])
 def test_bio_degradation_full_run(sample_model_fcn2,
                                   oil, temp, expected_balance):
     '''

py_gnome/tests/unit_tests/test_weatherers/test_dispersion.py

@@ -100,12 +100,12 @@ def test_dispersion_not_active(oil, temp, num_elems):
 @pytest.mark.xfail
 # the test oils don't match the data base, using so tests don't depend on db
 @pytest.mark.parametrize(('oil', 'temp', 'dispersed'),
-                         [('ABU SAFAH', 288.7, 63.076),
+                         [('oil_bahia', 288.7, 133.784),
+                         #('ABU SAFAH', 288.7, 63.076),
                           # ('ALASKA NORTH SLOPE (MIDDLE PIPELINE)',
                           ('oil_ans_mp',
                            288.7, 592.887),
                           # ('BAHIA', 288.7, 14.472)
-                          ('oil_bahia', 288.7, 133.784)
                           ]
                          )
 def test_full_run(sample_model_fcn2, oil, temp, dispersed):

py_gnome/tests/unit_tests/test_weatherers/test_dissolution.py

@@ -353,7 +353,7 @@ def test_full_run(sample_model_fcn2, oil, temp, expected_balance):
 @pytest.mark.xfail
 @pytest.mark.parametrize(('oil', 'temp', 'expected_balance'),
                          # [(_sample_oils['benzene'], 288.7, 2.98716)
-                         [('benzene', 288.15, 9731.05479)])
+                         [('oil_benzene', 288.15, 9731.05479)])
 def test_full_run_no_evap(sample_model_fcn2, oil, temp, expected_balance):
     '''
     test dissolution outputs post step for a full run of model. Dump json