Remove FieldSet.from_nemo

Update tests

Author: VeckoTheGecko

src/parcels/_core/fieldset.py

@@ -10,7 +10,6 @@
 import xarray as xr
 import xgcm
 
-from parcels import convert
 from parcels._core.converters import Geographic, GeographicPolar
 from parcels._core.field import Field, VectorField
 from parcels._core.utils import sgrid
@@ -248,31 +247,6 @@ def from_copernicusmarine(ds: xr.Dataset):
         )
         return FieldSet.from_sgrid_conventions(ds, mesh="spherical")
 
-    def from_nemo(ds: xr.Dataset):
-        """Create a FieldSet from a xarray.Dataset from NEMO netcdf files.
-
-        Parameters
-        ----------
-        ds : xarray.Dataset
-            xarray.Dataset as obtained from a set of NEMO netcdf files.
-
-        Returns
-        -------
-        FieldSet
-            FieldSet object containing the fields from the dataset that can be used for a Parcels simulation.
-
-        Notes
-        -----
-        The NEMO model (https://www.nemo-ocean.eu/) is used by a variety of oceanographic institutions around the world.
-        Output from these models may differ subtly in terms of variable names and metadata conventions.
-        This function attempts to standardize these differences to create a Parcels FieldSet.
-        If you encounter issues with your specific NEMO dataset, please open an issue on the Parcels GitHub repository with details about your dataset.
-
-        """
-        ds = convert.nemo_to_sgrid(ds)
-        fieldset = FieldSet.from_sgrid_conventions(ds)
-        return fieldset
-
     def from_fesom2(ds: ux.UxDataset):
         """Create a FieldSet from a FESOM2 uxarray.UxDataset.
 
@@ -571,7 +545,7 @@ def _get_mesh_type_from_sgrid_dataset(ds_sgrid: xr.Dataset) -> Mesh:
 
     sgrid_metadata = sgrid.parse_grid_attrs(grid_da.attrs)
 
-    fpoint_x, fpoint_y = sgrid_metadata.node_dimensions
+    fpoint_x, fpoint_y = sgrid_metadata.node_coordinates
 
     if _is_coordinate_in_degrees(ds_sgrid[fpoint_x]) ^ _is_coordinate_in_degrees(ds_sgrid[fpoint_x]):
         msg = (
@@ -588,7 +562,7 @@ def _is_coordinate_in_degrees(da: xr.DataArray) -> bool:
     match da.attrs.get("units"):
         case None:
             raise ValueError(
-                f"Coordinate {da.name} of your dataset has no 'units' attribute - we don't know what the spatial units are."
+                f"Coordinate {da.name!r} of your dataset has no 'units' attribute - we don't know what the spatial units are."
             )
         case "degrees":
             return True

src/parcels/convert.py

@@ -163,14 +163,37 @@ def _discover_U_and_V(ds: xr.Dataset, cf_standard_names_fallbacks) -> xr.Dataset
     return ds
 
 
-def nemo_to_sgrid(*, coords: xr.Dataset, **fields: dict[str, xr.Dataset]):
+def nemo_to_sgrid(*, coords: xr.Dataset, **fields: dict[str, xr.Dataset | xr.DataArray]):
+    # TODO: Update docstring
+    """Create a FieldSet from a xarray.Dataset from NEMO netcdf files.
+
+    Parameters
+    ----------
+    ds : xarray.Dataset
+        xarray.Dataset as obtained from a set of NEMO netcdf files.
+
+    Returns
+    -------
+    xarray.Dataset
+        Dataset object following SGRID conventions to be (optionally) modified and passed to a FieldSet constructor.
+
+    Notes
+    -----
+    The NEMO model (https://www.nemo-ocean.eu/) is used by a variety of oceanographic institutions around the world.
+    Output from these models may differ subtly in terms of variable names and metadata conventions.
+    This function attempts to standardize these differences to create a Parcels FieldSet.
+    If you encounter issues with your specific NEMO dataset, please open an issue on the Parcels GitHub repository with details about your dataset.
+
+    """
     fields = fields.copy()
     coords = coords[["gphif", "glamf"]]
 
     for name, field_da in fields.items():
         if isinstance(field_da, xr.Dataset):
             field_da = field_da[name]
             # TODO: logging message, warn if multiple fields are in this dataset
+        else:
+            field_da = field_da.rename(name)
 
         match name:
             case "U":
@@ -179,7 +202,7 @@ def nemo_to_sgrid(*, coords: xr.Dataset, **fields: dict[str, xr.Dataset]):
                 field_da = field_da.rename({"x": "x_center"})
             case _:
                 pass
-
+        field_da = field_da.reset_coords(drop=True)
         fields[name] = field_da
 
     if "time" in coords.dims:

tests/test_advection.py

@@ -437,14 +437,13 @@ def UpdateP(particles, fieldset):  # pragma: no cover
 
 def test_nemo_curvilinear_fieldset():
     data_folder = parcels.download_example_dataset("NemoCurvilinear_data")
-    ds_fields = xr.open_mfdataset(
-        data_folder.glob("*.nc4"),
-        data_vars="minimal",
-        coords="minimal",
-        compat="override",
-    )
-    ds_fields = ds_fields.isel(time=0, z_a=0, z=0, drop=True)
-    fieldset = parcels.FieldSet.from_nemo(ds_fields)
+    U = xr.open_mfdataset(data_folder.glob("*U.nc4"))
+    V = xr.open_mfdataset(data_folder.glob("*V.nc4"))
+    coords = xr.open_dataset(data_folder / "mesh_mask.nc4")
+
+    ds = parcels.convert.nemo_to_sgrid(U=U, V=V, coords=coords)
+
+    fieldset = parcels.FieldSet.from_sgrid_conventions(ds)
 
     npart = 20
     lonp = 30 * np.ones(npart)
@@ -470,16 +469,14 @@ def test_nemo_curvilinear_fieldset():
 )
 def test_nemo_3D_curvilinear_fieldset(kernel):
     data_folder = parcels.download_example_dataset("NemoNorthSeaORCA025-N006_data")
-    ds_fields = xr.open_mfdataset(
-        data_folder.glob("ORCA*.nc"),
-        data_vars="minimal",
-        coords="minimal",
-        compat="override",
-    )
-    ds_coords = xr.open_dataset(data_folder / "coordinates.nc", decode_times=False)
-    ds_coords = ds_coords.isel(time=0, drop=True)
-    ds = xr.merge([ds_fields, ds_coords[["glamf", "gphif"]]])
-    fieldset = parcels.FieldSet.from_nemo(ds)
+    U = xr.open_mfdataset(data_folder.glob("*U.nc"))
+    V = xr.open_mfdataset(data_folder.glob("*V.nc"))
+    W = xr.open_mfdataset(data_folder.glob("*W.nc"))
+    coords = xr.open_dataset(data_folder / "coordinates.nc", decode_times=False)
+
+    ds = parcels.convert.nemo_to_sgrid(U=U["uo"], V=V["vo"], W=W["wo"], coords=coords)
+
+    fieldset = parcels.FieldSet.from_sgrid_conventions(ds)
 
     npart = 10
     lons_initial = np.linspace(1.9, 3.4, npart)