Code cleanups

docs/examples/example_dask_chunk_OCMs.py

@@ -273,7 +273,7 @@ def test_globcurrent_2D(mode, chunk_mode):
         # we removed the failsafe, so now if all chunksize dimensions are incorrect, there is nothing left to chunk,
         # which raises an error saying so. This is the expected behaviour
         if chunk_mode == 'failsafe':
-            return True
+            return
     # GlobCurrent sample file dimensions: time=UNLIMITED, lat=41, lon=81
     if chunk_mode != 'failsafe':  # chunking time but not lat
         assert (len(field_set.U.grid.load_chunk) == len(field_set.V.grid.load_chunk))
@@ -587,34 +587,6 @@ def test_diff_entry_chunksize_error_nemo_complex_nonconform_depth(mode):
     compute_nemo_particle_advection(fieldset, mode, lonp, latp)
 
 
-@pytest.mark.parametrize('mode', ['jit'])
-def test_erroneous_fieldset_init(mode):
-    data_folder = download_example_dataset('NemoNorthSeaORCA025-N006_data')
-    ufiles = sorted(glob(f'{data_folder}/ORCA*U.nc'))
-    vfiles = sorted(glob(f'{data_folder}/ORCA*V.nc'))
-    wfiles = sorted(glob(f'{data_folder}/ORCA*W.nc'))
-    mesh_mask = f'{data_folder}/coordinates.nc'
-
-    filenames = {'U': {'lon': mesh_mask, 'lat': mesh_mask, 'depth': wfiles[0], 'data': ufiles},
-                 'V': {'lon': mesh_mask, 'lat': mesh_mask, 'depth': wfiles[0], 'data': vfiles},
-                 'W': {'lon': mesh_mask, 'lat': mesh_mask, 'depth': wfiles[0], 'data': wfiles}}
-    variables = {'U': 'uo',
-                 'V': 'vo',
-                 'W': 'wo'}
-    dimensions = {'U': {'lon': 'glamf', 'lat': 'gphif', 'depth': 'depthw', 'time': 'time_counter'},
-                  'V': {'lon': 'glamf', 'lat': 'gphif', 'depth': 'depthw', 'time': 'time_counter'},
-                  'W': {'lon': 'glamf', 'lat': 'gphif', 'depth': 'depthw', 'time': 'time_counter'}}
-    chs = {'U': {'depth': ('depthu', 75), 'lat': ('y', 16), 'lon': ('x', 16)},
-           'V': {'depth': ('depthv', 75), 'lat': ('y', 16), 'lon': ('x', 16)},
-           'W': {'depth': ('depthw', 75), 'lat': ('y', 16), 'lon': ('x', 16)}}
-
-    try:
-        FieldSet.from_nemo(filenames, variables, dimensions, chunksize=chs)
-    except ValueError:
-        return True
-    return False
-
-
 @pytest.mark.parametrize('mode', ['jit'])
 def test_diff_entry_chunksize_correction_globcurrent(mode):
     data_folder = download_example_dataset("GlobCurrent_example_data")

docs/reference/misc.rst

@@ -29,9 +29,9 @@ parcels.tools.loggers module
     :members:
     :undoc-members:
 
-parcels.utils module
+parcels.tools.exampledata_utils module
 -----------------------------------
 
-.. automodule:: parcels.utils
+.. automodule:: parcels.tools.exampledata_utils
     :members:
     :undoc-members:

parcels/__init__.py

@@ -15,4 +15,3 @@
 from parcels.particlefile import *  # noqa
 from parcels.particleset import *  # noqa
 from parcels.tools import *  # noqa
-from parcels.utils import *  # noqa

parcels/interaction/neighborsearch/hashspherical.py

@@ -179,7 +179,7 @@ def all_neigh_depth(i_lat, i_lon, lat_sign):
                 neighbors.extend(
                     all_neigh_depth(new_i_lat, new_i_lon, new_lat_sign))
         else:
-            start_i_lon = int(np.floor(coor[2]/d_lon))
+            start_i_lon = int(np.floor(coor[2][0]/d_lon))
             for delta_lon in [-1, 0, 1]:
                 new_i_lon = (start_i_lon+delta_lon+n_new_lon) % n_new_lon
                 neighbors.extend(

parcels/tools/__init__.py

@@ -1,4 +1,5 @@
 from .converters import *  # noqa
+from .exampledata_utils import *  # noqa
 from .global_statics import *  # noqa
 from .interpolation_utils import *  # noqa
 from .loggers import *  # noqa

tests/test_advection.py

@@ -402,8 +402,8 @@ class RK45Particles(ptype[mode]):
     pset = ParticleSet(fieldset, pclass=pclass, lon=lon, lat=lat)
     pset.execute(kernel[method], dt=dt, endtime=endtime)
 
-    exp_lon = [truth_moving(x, y, pset.time)[0] for x, y, in zip(lon, lat)]
-    exp_lat = [truth_moving(x, y, pset.time)[1] for x, y, in zip(lon, lat)]
+    exp_lon = [truth_moving(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time)]
+    exp_lat = [truth_moving(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time)]
     assert np.allclose(pset.lon, exp_lon, rtol=rtol)
     assert np.allclose(pset.lat, exp_lat, rtol=rtol)
 
@@ -446,7 +446,7 @@ def test_decaying_eddy(fieldset_decaying, mode, method, rtol, diffField, npart=1
     fieldset = fieldset_decaying
     if method == 'AA':
         if mode == 'jit':
-            return True  # AnalyticalAdvection not implemented in JIT
+            return  # AnalyticalAdvection not implemented in JIT
         else:
             # needed for AnalyticalAdvection to work, but comes at expense of accuracy
             fieldset.U.interp_method = 'cgrid_velocity'
@@ -468,8 +468,8 @@ class RK45Particles(ptype[mode]):
     pset = ParticleSet(fieldset, pclass=pclass, lon=lon, lat=lat)
     pset.execute(kernel[method], dt=dt, endtime=endtime)
 
-    exp_lon = [truth_decaying(x, y, pset.time)[0] for x, y, in zip(lon, lat)]
-    exp_lat = [truth_decaying(x, y, pset.time)[1] for x, y, in zip(lon, lat)]
+    exp_lon = [truth_decaying(x, y, t)[0] for x, y, t in zip(lon, lat, pset.time)]
+    exp_lat = [truth_decaying(x, y, t)[1] for x, y, t in zip(lon, lat, pset.time)]
     assert np.allclose(pset.lon, exp_lon, rtol=rtol)
     assert np.allclose(pset.lat, exp_lat, rtol=rtol)