Merge branch 'v4-dev' into adding_unity_unitconverter

Author: erikvansebille

src/parcels/_core/fieldset.py

@@ -10,7 +10,6 @@
 import xarray as xr
 import xgcm
 
-from parcels._core.converters import Geographic, GeographicPolar
 from parcels._core.field import Field, VectorField
 from parcels._core.utils.string import _assert_str_and_python_varname
 from parcels._core.utils.time import get_datetime_type_calendar
@@ -277,15 +276,13 @@ def from_fesom2(ds: ux.UxDataset):
             raise ValueError(
                 f"Dataset missing one of the required dimensions 'time', 'nz', or 'nz1'. Found dimensions {ds_dims}"
             )
-        grid = UxGrid(ds.uxgrid, z=ds.coords["nz"])
+        grid = UxGrid(ds.uxgrid, z=ds.coords["nz"], mesh="spherical")
         ds = _discover_fesom2_U_and_V(ds)
 
         fields = {}
         if "U" in ds.data_vars and "V" in ds.data_vars:
             fields["U"] = Field("U", ds["U"], grid, _select_uxinterpolator(ds["U"]))
             fields["V"] = Field("V", ds["V"], grid, _select_uxinterpolator(ds["U"]))
-            fields["U"].units = GeographicPolar()
-            fields["V"].units = Geographic()
 
             if "W" in ds.data_vars:
                 fields["W"] = Field("W", ds["W"], grid, _select_uxinterpolator(ds["U"]))

src/parcels/_core/uxgrid.py

@@ -18,7 +18,7 @@ class UxGrid(BaseGrid):
     for interpolation on unstructured grids.
     """
 
-    def __init__(self, grid: ux.grid.Grid, z: ux.UxDataArray, mesh="flat") -> UxGrid:
+    def __init__(self, grid: ux.grid.Grid, z: ux.UxDataArray, mesh) -> UxGrid:
         """
         Initializes the UxGrid with a uxarray grid and vertical coordinate array.
 
@@ -30,8 +30,8 @@ def __init__(self, grid: ux.grid.Grid, z: ux.UxDataArray, mesh="flat") -> UxGrid
             A 1D array of vertical coordinates (depths) associated with the layer interface heights (not the mid-layer depths).
             While uxarray allows nz to be spatially and temporally varying, the parcels.UxGrid class considers the case where
             the vertical coordinate is constant in time and space. This implies flat bottom topography and no moving ALE vertical grid.
-        mesh : str, optional
-            The type of mesh used for the grid. Either "flat" (default) or "spherical".
+        mesh : str
+            The type of mesh used for the grid. Either "flat" or "spherical".
         """
         self.uxgrid = grid
         if not isinstance(z, ux.UxDataArray):

src/parcels/_core/xgrid.py

@@ -102,7 +102,7 @@ class XGrid(BaseGrid):
 
     """
 
-    def __init__(self, grid: xgcm.Grid, mesh="flat"):
+    def __init__(self, grid: xgcm.Grid, mesh):
         self.xgcm_grid = grid
         self._mesh = mesh
         self._spatialhash = None
@@ -124,7 +124,7 @@ def __init__(self, grid: xgcm.Grid, mesh="flat"):
         self._ds = ds
 
     @classmethod
-    def from_dataset(cls, ds: xr.Dataset, mesh="flat", xgcm_kwargs=None):
+    def from_dataset(cls, ds: xr.Dataset, mesh, xgcm_kwargs=None):
         """WARNING: unstable API, subject to change in future versions."""  # TODO v4: make private or remove warning on v4 release
         if xgcm_kwargs is None:
             xgcm_kwargs = {}

tests/test_advection.py

@@ -84,7 +84,7 @@ def test_advection_zonal_periodic():
     halo.XG.values = ds.XG.values[1] + 2
     ds = xr.concat([ds, halo], dim="XG")
 
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     V = Field("V", ds["V"], grid, interp_method=XLinear)
     UV = VectorField("UV", U, V)
@@ -103,7 +103,7 @@ def test_horizontal_advection_in_3D_flow(npart=10):
     """Flat 2D zonal flow that increases linearly with z from 0 m/s to 1 m/s."""
     ds = simple_UV_dataset(mesh="flat")
     ds["U"].data[:] = 1.0
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     U.data[:, 0, :, :] = 0.0  # Set U to 0 at the surface
     V = Field("V", ds["V"], grid, interp_method=XLinear)
@@ -121,7 +121,7 @@ def test_horizontal_advection_in_3D_flow(npart=10):
 @pytest.mark.parametrize("wErrorThroughSurface", [True, False])
 def test_advection_3D_outofbounds(direction, wErrorThroughSurface):
     ds = simple_UV_dataset(mesh="flat")
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     U.data[:] = 0.01  # Set U to small value (to avoid horizontal out of bounds)
     V = Field("V", ds["V"], grid, interp_method=XLinear)
@@ -202,7 +202,7 @@ def test_length1dimensions(u, v, w):  # TODO: Refactor this test to be more read
     if w:
         ds["W"] = (["time", "depth", "YG", "XG"], W)
 
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     V = Field("V", ds["V"], grid, interp_method=XLinear)
     fields = [U, V, VectorField("UV", U, V)]
@@ -263,7 +263,7 @@ def test_radialrotation(npart=10):
 )
 def test_moving_eddy(kernel, rtol):
     ds = moving_eddy_dataset()
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     V = Field("V", ds["V"], grid, interp_method=XLinear)
     if kernel in [AdvectionRK2_3D, AdvectionRK4_3D]:
@@ -315,7 +315,7 @@ def truth_moving(x_0, y_0, t):
 )
 def test_decaying_moving_eddy(kernel, rtol):
     ds = decaying_moving_eddy_dataset()
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     V = Field("V", ds["V"], grid, interp_method=XLinear)
     UV = VectorField("UV", U, V)
@@ -363,7 +363,7 @@ def truth_moving(x_0, y_0, t):
 def test_stommelgyre_fieldset(kernel, rtol, grid_type):
     npart = 2
     ds = stommel_gyre_dataset(grid_type=grid_type)
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     vector_interp_method = None if grid_type == "A" else CGrid_Velocity
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     V = Field("V", ds["V"], grid, interp_method=XLinear)
@@ -404,7 +404,7 @@ def UpdateP(particles, fieldset):  # pragma: no cover
 def test_peninsula_fieldset(kernel, rtol, grid_type):
     npart = 2
     ds = peninsula_dataset(grid_type=grid_type)
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U"], grid, interp_method=XLinear)
     V = Field("V", ds["V"], grid, interp_method=XLinear)
     P = Field("P", ds["P"], grid, interp_method=XLinear)

tests/test_field.py

@@ -14,7 +14,7 @@
 
 def test_field_init_param_types():
     data = datasets_structured["ds_2d_left"]
-    grid = XGrid.from_dataset(data)
+    grid = XGrid.from_dataset(data, mesh="flat")
 
     with pytest.raises(TypeError, match="Expected a string for variable name, got int instead."):
         Field(name=123, data=data["data_g"], grid=grid, interp_method=XLinear)
@@ -47,14 +47,15 @@ def test_field_init_param_types():
     [
         pytest.param(
             ux.UxDataArray(),
-            XGrid.from_dataset(datasets_structured["ds_2d_left"]),
+            XGrid.from_dataset(datasets_structured["ds_2d_left"], mesh="flat"),
             id="uxdata-grid",
         ),
         pytest.param(
             xr.DataArray(),
             UxGrid(
                 datasets_unstructured["stommel_gyre_delaunay"].uxgrid,
                 z=datasets_unstructured["stommel_gyre_delaunay"].coords["nz"],
+                mesh="flat",
             ),
             id="xarray-uxgrid",
         ),
@@ -75,7 +76,7 @@ def test_field_incompatible_combination(data, grid):
     [
         pytest.param(
             datasets_structured["ds_2d_left"]["data_g"],
-            XGrid.from_dataset(datasets_structured["ds_2d_left"]),
+            XGrid.from_dataset(datasets_structured["ds_2d_left"], mesh="flat"),
             id="ds_2d_left",
         ),  # TODO: Perhaps this test should be expanded to cover more datasets?
     ],
@@ -106,7 +107,7 @@ def test_field_init_fail_on_float_time_dim():
     )
 
     data = ds["data_g"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     with pytest.raises(
         ValueError,
         match="Error getting time interval.*. Are you sure that the time dimension on the xarray dataset is stored as timedelta, datetime or cftime datetime objects\?",
@@ -124,7 +125,7 @@ def test_field_init_fail_on_float_time_dim():
     [
         pytest.param(
             datasets_structured["ds_2d_left"]["data_g"],
-            XGrid.from_dataset(datasets_structured["ds_2d_left"]),
+            XGrid.from_dataset(datasets_structured["ds_2d_left"], mesh="flat"),
             id="ds_2d_left",
         ),
     ],
@@ -143,7 +144,7 @@ def test_vectorfield_init_different_time_intervals():
 
 def test_field_invalid_interpolator():
     ds = datasets_structured["ds_2d_left"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
 
     def invalid_interpolator_wrong_signature(particle_positions, grid_positions, invalid):
         return 0.0
@@ -160,7 +161,7 @@ def invalid_interpolator_wrong_signature(particle_positions, grid_positions, inv
 
 def test_vectorfield_invalid_interpolator():
     ds = datasets_structured["ds_2d_left"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
 
     def invalid_interpolator_wrong_signature(particle_positions, grid_positions, invalid):
         return 0.0
@@ -194,7 +195,7 @@ def test_field_unstructured_z_linear():
     for k, z in enumerate(ds.coords["nz"]):
         ds["W"].values[:, k, :] = z
 
-    grid = UxGrid(ds.uxgrid, z=ds.coords["nz"])
+    grid = UxGrid(ds.uxgrid, z=ds.coords["nz"], mesh="flat")
     # Note that the vertical coordinate is required to be the position of the layer interfaces ("nz"), not the mid-layers ("nz1")
     P = Field(name="p", data=ds.p, grid=grid, interp_method=UXPiecewiseConstantFace)
 
@@ -232,7 +233,7 @@ def test_field_unstructured_z_linear():
 def test_field_constant_in_time():
     """Tests field evaluation for a field with no time interval (i.e., constant in time)."""
     ds = datasets_unstructured["stommel_gyre_delaunay"]
-    grid = UxGrid(ds.uxgrid, z=ds.coords["nz"])
+    grid = UxGrid(ds.uxgrid, z=ds.coords["nz"], mesh="flat")
     # Note that the vertical coordinate is required to be the position of the layer interfaces ("nz"), not the mid-layers ("nz1")
     P = Field(name="p", data=ds.p, grid=grid, interp_method=UXPiecewiseConstantFace)
 

tests/test_index_search.py

@@ -13,7 +13,7 @@
 @pytest.fixture
 def field_cone():
     ds = datasets["2d_left_unrolled_cone"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     field = Field(
         name="test_field",
         data=ds["data_g"],

tests/test_interpolation.py

@@ -52,7 +52,7 @@ def field():
             "y": (["y"], [0.5, 1.5, 2.5, 3.5], {"axis": "Y"}),
         },
     )
-    return Field("U", ds["U"], XGrid.from_dataset(ds), interp_method=XLinear)
+    return Field("U", ds["U"], XGrid.from_dataset(ds, mesh="flat"), interp_method=XLinear)
 
 
 @pytest.mark.parametrize(

tests/test_particlefile.py

@@ -32,7 +32,7 @@
 def fieldset() -> FieldSet:  # TODO v4: Move into a `conftest.py` file and remove duplicates
     """Fixture to create a FieldSet object for testing."""
     ds = datasets["ds_2d_left"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     U = Field("U", ds["U_A_grid"], grid, XLinear)
     V = Field("V", ds["V_A_grid"], grid, XLinear)
     UV = VectorField("UV", U, V)
@@ -73,7 +73,7 @@ def test_pfile_array_write_zarr_memorystore(fieldset):
 def test_write_fieldset_without_time(tmp_zarrfile):
     ds = peninsula_dataset()  # DataSet without time
     assert "time" not in ds.dims
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     fieldset = FieldSet([Field("U", ds["U"], grid, XLinear)])
 
     pset = ParticleSet(fieldset, pclass=Particle, lon=0, lat=0)

tests/test_spatialhash.py

@@ -6,14 +6,14 @@
 
 def test_spatialhash_init():
     ds = datasets["2d_left_rotated"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     spatialhash = grid.get_spatial_hash()
     assert spatialhash is not None
 
 
 def test_invalid_positions():
     ds = datasets["2d_left_rotated"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
 
     j, i, coords = grid.get_spatial_hash().query([np.nan, np.inf], [np.nan, np.inf])
     assert np.all(j == -3)
@@ -22,7 +22,7 @@ def test_invalid_positions():
 
 def test_mixed_positions():
     ds = datasets["2d_left_rotated"]
-    grid = XGrid.from_dataset(ds)
+    grid = XGrid.from_dataset(ds, mesh="flat")
     lat = grid.lat.mean()
     lon = grid.lon.mean()
     y = [lat, np.nan]

tests/test_uxarray_fieldset.py

@@ -38,13 +38,13 @@ def uv_fesom_channel(ds_fesom_channel) -> VectorField:
         U=Field(
             name="U",
             data=ds_fesom_channel.U,
-            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"]),
+            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"], mesh="flat"),
             interp_method=UXPiecewiseConstantFace,
         ),
         V=Field(
             name="V",
             data=ds_fesom_channel.V,
-            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"]),
+            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"], mesh="flat"),
             interp_method=UXPiecewiseConstantFace,
         ),
     )
@@ -58,19 +58,19 @@ def uvw_fesom_channel(ds_fesom_channel) -> VectorField:
         U=Field(
             name="U",
             data=ds_fesom_channel.U,
-            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"]),
+            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"], mesh="flat"),
             interp_method=UXPiecewiseConstantFace,
         ),
         V=Field(
             name="V",
             data=ds_fesom_channel.V,
-            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"]),
+            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"], mesh="flat"),
             interp_method=UXPiecewiseConstantFace,
         ),
         W=Field(
             name="W",
             data=ds_fesom_channel.W,
-            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"]),
+            grid=UxGrid(ds_fesom_channel.uxgrid, z=ds_fesom_channel.coords["nz"], mesh="flat"),
             interp_method=UXPiecewiseLinearNode,
         ),
     )
@@ -112,13 +112,14 @@ def test_fesom2_square_delaunay_uniform_z_coordinate_eval():
     Since the underlying data is constant, we can check that the values are as expected.
     """
     ds = datasets_unstructured["fesom2_square_delaunay_uniform_z_coordinate"]
+    grid = UxGrid(ds.uxgrid, z=ds.coords["nz"], mesh="flat")
     UVW = VectorField(
         name="UVW",
-        U=Field(name="U", data=ds.U, grid=UxGrid(ds.uxgrid, z=ds.coords["nz"]), interp_method=UXPiecewiseConstantFace),
-        V=Field(name="V", data=ds.V, grid=UxGrid(ds.uxgrid, z=ds.coords["nz"]), interp_method=UXPiecewiseConstantFace),
-        W=Field(name="W", data=ds.W, grid=UxGrid(ds.uxgrid, z=ds.coords["nz"]), interp_method=UXPiecewiseLinearNode),
+        U=Field(name="U", data=ds.U, grid=grid, interp_method=UXPiecewiseConstantFace),
+        V=Field(name="V", data=ds.V, grid=grid, interp_method=UXPiecewiseConstantFace),
+        W=Field(name="W", data=ds.W, grid=grid, interp_method=UXPiecewiseLinearNode),
     )
-    P = Field(name="p", data=ds.p, grid=UxGrid(ds.uxgrid, z=ds.coords["nz"]), interp_method=UXPiecewiseLinearNode)
+    P = Field(name="p", data=ds.p, grid=grid, interp_method=UXPiecewiseLinearNode)
     fieldset = FieldSet([UVW, P, UVW.U, UVW.V, UVW.W])
 
     assert fieldset.U.eval(time=ds.time[0].values, z=[1.0], y=[30.0], x=[30.0], applyConversion=False) == 1.0