[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

parcels/__init__.py

@@ -5,7 +5,6 @@
 from parcels.application_kernels import *
 from parcels.field import *
 from parcels.fieldset import *
-from parcels.uxfieldset import *
 from parcels.grid import *
 from parcels.gridset import *
 from parcels.interaction import *
@@ -14,3 +13,4 @@
 from parcels.particlefile import *
 from parcels.particleset import *
 from parcels.tools import *
+from parcels.uxfieldset import *

parcels/application_kernels/advection.py

@@ -14,13 +14,16 @@
     "AdvectionRK45",
 ]
 
-def UxAdvectionEuler(particle,fieldset:UXFieldSet,time):
+
+def UxAdvectionEuler(particle, fieldset: UXFieldSet, time):
     """Advection of particles using Explicit Euler (aka Euler Forward) integration.
-    on an unstructured grid."""
-    vel = fieldset.eval(["u","v"],time,particle.depth,particle.lat,particle.lon,particle)
+    on an unstructured grid.
+    """
+    vel = fieldset.eval(["u", "v"], time, particle.depth, particle.lat, particle.lon, particle)
     particle.lon += vel["u"] * particle.dt
     particle.lat += vel["v"] * particle.dt
 
+
 def AdvectionRK4(particle, fieldset, time):  # pragma: no cover
     """Advection of particles using fourth-order Runge-Kutta integration."""
     (u1, v1) = fieldset.UV[particle]

parcels/particleset.py

@@ -9,7 +9,6 @@
 import xarray as xr
 from scipy.spatial import KDTree
 from tqdm import tqdm
-import uxarray as ux
 
 from parcels._compat import MPI
 from parcels.application_kernels.advection import AdvectionRK4
@@ -32,6 +31,7 @@
 from parcels.tools.statuscodes import StatusCode
 from parcels.tools.warnings import ParticleSetWarning
 from parcels.uxfieldset import UXFieldSet
+
 __all__ = ["ParticleSet"]
 
 
@@ -169,7 +169,7 @@ def ArrayClass_init(self, *args, **kwargs):
         assert lon.size == time.size, "time and positions (lon, lat, depth) do not have the same lengths."
 
         if type(fieldset) == UXFieldSet:
-            lonlatdepth_dtype = np.float32 # To do : get precision from fieldset
+            lonlatdepth_dtype = np.float32  # To do : get precision from fieldset
         else:
             if isinstance(fieldset.U, Field) and (not fieldset.U.allow_time_extrapolation):
                 _warn_particle_times_outside_fieldset_time_bounds(time, fieldset.U.grid.time_full)

parcels/uxfieldset.py

@@ -1,46 +1,28 @@
-import importlib.util
-import os
-import sys
-import warnings
-from copy import deepcopy
-from glob import glob
-
-import dask.array as da
+import cftime
 import numpy as np
 import uxarray as ux
 from uxarray.neighbors import _barycentric_coordinates
-import cftime
-
-from parcels._compat import MPI
-from parcels._typing import GridIndexingType, InterpMethodOption, Mesh
-from parcels.field import DeferredArray, Field, NestedField, VectorField
-from parcels.grid import Grid
-from parcels.gridset import GridSet
-from parcels.particlefile import ParticleFile
-from parcels.tools._helpers import fieldset_repr
-from parcels.tools.converters import TimeConverter, convert_xarray_time_units
-from parcels.tools.loggers import logger
-from parcels.tools.statuscodes import TimeExtrapolationError
-from parcels.tools.warnings import FieldSetWarning
 
 __all__ = ["UXFieldSet"]
 
 _inside_tol = 1e-6
+
+
 class UXFieldSet:
     """A FieldSet class that holds hydrodynamic data needed to execute particles
-    in a UXArray.Dataset"""
+    in a UXArray.Dataset
+    """
 
     def __init__(self, uxds: ux.UxDataset, time_origin: float | np.datetime64 | np.timedelta64 | cftime.datetime = 0):
-
-        # Ensure that dataset provides a grid, and the u and v velocity 
+        # Ensure that dataset provides a grid, and the u and v velocity
         # components at a minimum
         if not hasattr(uxds, "uxgrid"):
             raise ValueError("The UXArray dataset does not provide a grid")
         if not hasattr(uxds, "u"):
             raise ValueError("The UXArray dataset does not provide u velocity data")
         if not hasattr(uxds, "v"):
             raise ValueError("The UXArray dataset does not provide v velocity data")
-        
+
         self.time_origin = time_origin
         self.uxds = uxds
         self._spatialhash = self.uxds.get_spatialhash()
@@ -52,16 +34,15 @@ def _check_complete(self):
         assert self.uxds.uxgrid is not None, "UXFieldSet does not provide a grid"
 
     def _face_interp(self, field, time, z, y, x, particle=None):
-
-        #ti, zi, fi = self.unravel_index(particle.ei) # Get the time, z, and face index of the particle
+        # ti, zi, fi = self.unravel_index(particle.ei) # Get the time, z, and face index of the particle
         ti = 0
         zi = 0
         fi = particle.ei
-        return field[ti,zi,fi]
+        return field[ti, zi, fi]
 
     def _node_interp(self, field, time, z, y, x, particle=None):
         """Performs barycentric interpolation of a field at a given location."""
-        #ti, zi, fi = self.unravel_index(particle.ei) # Get the time, z, and face index of the particle
+        # ti, zi, fi = self.unravel_index(particle.ei) # Get the time, z, and face index of the particle
         ti = 0
         zi = 0
         fi = particle.ei
@@ -77,13 +58,12 @@ def _node_interp(self, field, time, z, y, x, particle=None):
 
         coord = np.deg2rad([x, y])
         bcoord = _barycentric_coordinates(nodes, coord)
-        return np.sum(bcoord * field[ti,zi,node_ids].flatten(), axis=0) 
+        return np.sum(bcoord * field[ti, zi, node_ids].flatten(), axis=0)
 
     def eval(self, field_names: list(str), time, z, y, x, particle=None, applyConversion=True):
-        
         res = {}
         if particle:
-            #ti, zi, fi = self.unravel_index(particle.ei) # Get the time, z, and face index of the particle
+            # ti, zi, fi = self.unravel_index(particle.ei) # Get the time, z, and face index of the particle
             fi = particle.ei
             # Check if particle is in the same face, otherwise search again.
             n_nodes = self.uxds.uxgrid.n_nodes_per_face[fi].to_numpy()
@@ -104,12 +84,12 @@ def eval(self, field_names: list(str), time, z, y, x, particle=None, applyConver
             # To do : Get the vertical and time indices for the particle
 
             if (not is_inside) or (err > _inside_tol):
-                fi = self._spatialhash.query([particle.x,particle.y]) # Get the face id for the particle   
-                particle.ei = fi 
+                fi = self._spatialhash.query([particle.x, particle.y])  # Get the face id for the particle
+                particle.ei = fi
 
         for f in field_names:
             field = getattr(self, f)
-            face_registered = ("n_face" in field.dims)
+            face_registered = "n_face" in field.dims
             if face_registered:
                 if particle:
                     r = self._face_interp(field, particle.time, particle.z, particle.y, particle.x, particle)
@@ -125,9 +105,9 @@ def eval(self, field_names: list(str), time, z, y, x, particle=None, applyConver
                 res[f] = self.units.to_target(r, z, y, x)
             else:
                 res[f] = r
-            
+
         return res
-            
+
         # if self.U.interp_method not in ["cgrid_velocity", "partialslip", "freeslip"]:
         #     u = self.U.eval(time, z, y, x, particle=particle, applyConversion=False)
         #     v = self.V.eval(time, z, y, x, particle=particle, applyConversion=False)

tests/test_uxfieldset.py

@@ -1,37 +1,33 @@
-from datetime import timedelta
-
-import numpy as np
-import pytest
 import uxarray as ux
 
-from parcels import (
-    UXFieldSet,
-    ParticleSet,
-    Particle
-)
-
+from parcels import Particle, ParticleSet, UXFieldSet
 from tests.utils import TEST_DATA
 
 
 def test_fesom_fieldset():
     # Load a FESOM dataset
-    grid_path=f"{TEST_DATA}/fesom_channel.nc"
-    data_path=[f"{TEST_DATA}/u.fesom_channel.nc",
-               f"{TEST_DATA}/v.fesom_channel.nc",
-               f"{TEST_DATA}/w.fesom_channel.nc"]
-    ds = ux.open_mfdataset(grid_path,data_path)
+    grid_path = f"{TEST_DATA}/fesom_channel.nc"
+    data_path = [
+        f"{TEST_DATA}/u.fesom_channel.nc",
+        f"{TEST_DATA}/v.fesom_channel.nc",
+        f"{TEST_DATA}/w.fesom_channel.nc",
+    ]
+    ds = ux.open_mfdataset(grid_path, data_path)
     fieldset = UXFieldSet(ds)
     fieldset._check_complete()
     # Check that the fieldset has the expected properties
     assert fieldset.uxds == ds
 
+
 def test_fesom_in_particleset():
-        # Load a FESOM dataset
-    grid_path=f"{TEST_DATA}/fesom_channel.nc"
-    data_path=[f"{TEST_DATA}/u.fesom_channel.nc",
-               f"{TEST_DATA}/v.fesom_channel.nc",
-               f"{TEST_DATA}/w.fesom_channel.nc"]
-    ds = ux.open_mfdataset(grid_path,data_path)
+    # Load a FESOM dataset
+    grid_path = f"{TEST_DATA}/fesom_channel.nc"
+    data_path = [
+        f"{TEST_DATA}/u.fesom_channel.nc",
+        f"{TEST_DATA}/v.fesom_channel.nc",
+        f"{TEST_DATA}/w.fesom_channel.nc",
+    ]
+    ds = ux.open_mfdataset(grid_path, data_path)
     fieldset = UXFieldSet(ds)
     print(type(fieldset))
-    pset = ParticleSet(fieldset, pclass=Particle)
+    pset = ParticleSet(fieldset, pclass=Particle)