Merge pull request #1661 from knutfrode/dev

[run-ex] Made fix and added test for export_variables. Thx to vincent…

Author: knutfrode

opendrift/models/basemodel/__init__.py

@@ -1892,10 +1892,19 @@ def run(self,
             # Forward simulation, start time has been set when seeding
             self.time = self.start_time
 
-        # Add the output variables which are always required
+        # Find variables and element properties for which previous value shall be stored
+        environment_previous = [vn for vn, v in self.required_variables.items()
+                                if v.get('store_previous', False) is True]
+        elements_previous = [vn for vn, v in self.elements.variables.items()
+                             if v.get('store_previous', False) is True]
+ 
+        # Add the output variables which are always required,
+        # as well as variables for which previous value is stored
         if export_variables is not None:
             export_variables = list(
-                set(export_variables + ['lon', 'lat', 'status']))
+                set(export_variables + ['lon', 'lat', 'status'] +
+                    environment_previous + elements_previous))
+
         self.export_variables = export_variables
 
         # Create Xarray Dataset to hold result
@@ -1977,11 +1986,6 @@ def run(self,
 
 
         # Make Xarray datasets to store environment variables and element properties from previous time step
-        environment_previous = [vn for vn, v in self.required_variables.items()
-                                if v.get('store_previous', False) is True]
-        elements_previous = [vn for vn, v in self.elements.variables.items()
-                             if v.get('store_previous', False) is True]
-        
         if len(environment_previous) > 0:
             self._environment_previous = self.result[[*environment_previous]].isel(time=0, drop=True).copy(deep=True)
         if len(elements_previous) > 0:

tests/models/test_io.py

@@ -35,6 +35,16 @@
 need_fastparquet = pytest.mark.skipif(has_fastparquet == False,
         reason = 'fastparquet must be installed to use fastparquet writer')
 
+def test_export_variables():
+    o = OceanDrift(loglevel=50)
+    o.set_config('drift:vertical_advection', True)  # Needs previous value of sea_surface_height
+    o.set_config('general:use_auto_landmask', False)
+    o.set_config('environment:constant:land_binary_mask', 0)
+    o.seed_elements(lon=3, lat=60, time=datetime.now())
+    o.run(steps=2, export_variables=['z'])
+    assert 'sea_surface_height' in o.result.var()
+    assert 'land_binary_mask' not in o.result.var()
+
 def test_custom_result(tmpdir):
     """Adding custom data to self.result during self.prepare_run()"""
 

tests/models/test_run.py

@@ -155,7 +155,6 @@ def test_config_suggestion(self):
             self.assertTrue('Did you mean' in str(e))
 
     def test_config_seed(self):
-        #o = Leeway(loglevel=20)
         o = OceanDrift(loglevel=20)
         o.list_configspec()
 
@@ -350,7 +349,7 @@ def test_vertical_mixing(self):
                          time=norkyst.start_time)
 
         o1.run(steps=20, time_step=300, time_step_output=1800,
-               export_buffer_length=10, outfile='verticalmixing.nc')
+               outfile='verticalmixing.nc')
         self.assertAlmostEqual(o1.result.z.min().values, -42.60, 1)
         self.assertAlmostEqual(o1.result.z.max().values, 0.0, 1)
         os.remove('verticalmixing.nc')