Removing FieldSet.from_pop()

As it uses som field data manipulation that will have to be done by the user in xarray in v4

Author: erikvansebille

docs/examples/documentation_indexing.ipynb

@@ -239,7 +239,7 @@
     "\n",
     "Interpolation for Arakawa B-grids is detailed in [Section 2.1.3 of Delandmeter and Van Sebille (2019)](https://www.geosci-model-dev.net/12/3571/2019/gmd-12-3571-2019.html). Again, the dimensions that need to be provided are those of the barycentric cell edges `(i, j, k)`.\n",
     "\n",
-    "To load B-grid data, you can use the method `FieldSet.from_b_grid_dataset`, or specifically in the case of POP-model data `FieldSet.from_pop`.\n"
+    "To load B-grid data, you can use the method `FieldSet.from_b_grid_dataset`.\n"
    ]
   },
   {

parcels/fieldset.py

@@ -754,113 +754,6 @@ def from_c_grid_dataset(
             **kwargs,
         )
 
-    @classmethod
-    def from_pop(
-        cls,
-        filenames,
-        variables,
-        dimensions,
-        mesh: Mesh = "spherical",
-        allow_time_extrapolation: bool | None = None,
-        tracer_interp_method: InterpMethodOption = "bgrid_tracer",
-        depth_units="m",
-        **kwargs,
-    ):
-        """Initialises FieldSet object from NetCDF files of POP fields.
-            It is assumed that the velocities in the POP fields is in cm/s.
-
-        Parameters
-        ----------
-        filenames :
-            Dictionary mapping variables to file(s). The
-            filepath may contain wildcards to indicate multiple files,
-            or be a list of file.
-            filenames can be a list ``[files]``, a dictionary ``{var:[files]}``,
-            a dictionary ``{dim:[files]}`` (if lon, lat, depth and/or data not stored in same files as data),
-            or a dictionary of dictionaries ``{var:{dim:[files]}}``
-            time values are in ``filenames[data]``
-        variables : dict
-            Dictionary mapping variables to variable names in the netCDF file(s).
-            Note that the built-in Advection kernels assume that U and V are in m/s
-        dimensions : dict
-            Dictionary mapping data dimensions (lon,
-            lat, depth, time, data) to dimensions in the netCF file(s).
-            Note that dimensions can also be a dictionary of dictionaries if
-            dimension names are different for each variable.
-            Watch out: POP is discretised on a B-grid:
-            U and V velocity nodes are not located as W velocity and T tracer nodes (see http://www2.cesm.ucar.edu/models/cesm1.0/pop2/doc/sci/POPRefManual.pdf ). ::
-
-                +-----------------------------+-----------------------------+-----------------------------+
-                |U[k,j+1,i],V[k,j+1,i]        |                             |U[k,j+1,i+1],V[k,j+1,i+1]    |
-                +-----------------------------+-----------------------------+-----------------------------+
-                |                             |W[k:k+2,j+1,i+1],T[k,j+1,i+1]|                             |
-                +-----------------------------+-----------------------------+-----------------------------+
-                |U[k,j,i],V[k,j,i]            |                             |U[k,j,i+1],V[k,j,i+1]        |
-                +-----------------------------+-----------------------------+-----------------------------+
-
-            In 2D: U and V nodes are on the cell vertices and interpolated bilinearly as a A-grid.
-            T node is at the cell centre and interpolated constant per cell as a C-grid.
-            In 3D: U and V nodes are at the middle of the cell vertical edges,
-            They are interpolated bilinearly (independently of z) in the cell.
-            W nodes are at the centre of the horizontal interfaces.
-            They are interpolated linearly (as a function of z) in the cell.
-            T node is at the cell centre, and constant per cell.
-            Note that Parcels assumes that the length of the depth dimension (at the W-points)
-            is one larger than the size of the velocity and tracer fields in the depth dimension.
-        fieldtype :
-            Optional dictionary mapping fields to fieldtypes to be used for UnitConverter.
-            (either 'U', 'V', 'Kh_zonal', 'Kh_meridional' or None)
-        mesh : str
-            String indicating the type of mesh coordinates and
-            units used during velocity interpolation, see also `this tutorial <../examples/tutorial_unitconverters.ipynb>`__:
-
-            1. spherical (default): Lat and lon in degree, with a
-               correction for zonal velocity U near the poles.
-            2. flat: No conversion, lat/lon are assumed to be in m.
-        allow_time_extrapolation : bool
-            boolean whether to allow for extrapolation
-            (i.e. beyond the last available time snapshot)
-            Default is False if dimensions includes time, else True
-        tracer_interp_method : str
-            Method for interpolation of tracer fields. It is recommended to use 'bgrid_tracer' (default)
-            Note that in the case of from_pop() and from_b_grid_dataset(), the velocity fields are default to 'bgrid_velocity'
-        depth_units :
-            The units of the vertical dimension. Default in Parcels is 'm',
-            but many POP outputs are in 'cm'
-        **kwargs :
-            Keyword arguments passed to the :func:`Fieldset.from_b_grid_dataset` constructor.
-
-        """
-        if "creation_log" not in kwargs.keys():
-            kwargs["creation_log"] = "from_pop"
-        fieldset = cls.from_b_grid_dataset(
-            filenames,
-            variables,
-            dimensions,
-            mesh=mesh,
-            allow_time_extrapolation=allow_time_extrapolation,
-            tracer_interp_method=tracer_interp_method,
-            gridindexingtype="pop",
-            **kwargs,
-        )
-        if hasattr(fieldset, "U"):
-            fieldset.U.set_scaling_factor(0.01)  # cm/s to m/s
-        if hasattr(fieldset, "V"):
-            fieldset.V.set_scaling_factor(0.01)  # cm/s to m/s
-        if hasattr(fieldset, "W"):
-            if depth_units == "m":
-                fieldset.W.set_scaling_factor(-0.01)  # cm/s to m/s and change the W direction
-                warnings.warn(
-                    "Parcels assumes depth in POP output to be in 'm'. Use depth_units='cm' if the output depth is in 'cm'.",
-                    FieldSetWarning,
-                    stacklevel=2,
-                )
-            elif depth_units == "cm":
-                fieldset.W.set_scaling_factor(-1.0)  # change the W direction but keep W in cm/s because depth is in cm
-            else:
-                raise SyntaxError("'depth_units' has to be 'm' or 'cm'")
-        return fieldset
-
     @classmethod
     def from_mom5(
         cls,

tests/test_fieldset.py

@@ -659,6 +659,8 @@ def generate_dataset(xdim, ydim, zdim=1, tdim=1):
         assert np.allclose(pset.lon_nextloop[0], 5.0) and np.allclose(pset.lat_nextloop[0], 10)
 
 
+@pytest.mark.v4alpha
+@pytest.mark.xfail(reason="From_pop is not supported during v4-alpha development. This will be reconsidered in v4.")
 def test_fieldset_frompop():
     filenames = str(TEST_DATA / "POPtestdata_time.nc")
     variables = {"U": "U", "V": "V", "W": "W", "T": "T"}

tests/test_grids.py

@@ -575,6 +575,8 @@ def sampleVel(particle, fieldset, time):  # pragma: no cover
     assert abs(pset[0].vertical - 1) < 1e-3
 
 
+@pytest.mark.v4alpha
+@pytest.mark.xfail(reason="From_pop is not supported during v4-alpha development. This will be reconsidered in v4.")
 @pytest.mark.parametrize("vert_discretisation", ["zlevel", "slevel", "slevel2"])
 def test_popgrid(vert_discretisation):
     if vert_discretisation == "zlevel":
@@ -868,7 +870,7 @@ def UpdateR(particle, fieldset, time):  # pragma: no cover
     assert np.allclose(pset.radius, pset.radius_start, atol=10)
 
 
-@pytest.mark.parametrize("gridindexingtype", ["pop", "mom5"])
+@pytest.mark.parametrize("gridindexingtype", ["mom5"])  # TODO add pop in v4?
 @pytest.mark.parametrize("extrapolation", [True, False])
 def test_bgrid_interpolation(gridindexingtype, extrapolation):
     xi, yi = 3, 2

tests/tools/test_warnings.py

@@ -17,6 +17,8 @@
 from tests.utils import TEST_DATA
 
 
+@pytest.mark.v4alpha
+@pytest.mark.xfail(reason="From_pop is not supported during v4-alpha development. This will be reconsidered in v4.")
 def test_fieldset_warning_pop():
     filenames = str(TEST_DATA / "POPtestdata_time.nc")
     variables = {"U": "U", "V": "V", "W": "W", "T": "T"}