Merge branch 'v4-dev' into swap_space_and_time_interpolation_order

Author: erikvansebille

docs/examples/example_moving_eddies.py

@@ -1,4 +1,3 @@
-import gc
 import math
 from argparse import ArgumentParser
 from datetime import timedelta
@@ -229,25 +228,25 @@ def fieldsetfile(mesh, tmpdir):
     return filename
 
 
-@pytest.mark.parametrize("mesh", ["flat", "spherical"])
-def test_moving_eddies_file(mesh, tmpdir):
-    gc.collect()
-    fieldset = parcels.FieldSet.from_parcels(
-        fieldsetfile(mesh, tmpdir), extra_fields={"P": "P"}
-    )
+def test_moving_eddies_file(tmpdir):
+    data_folder = parcels.download_example_dataset("MovingEddies_data")
+    filenames = {
+        "U": str(data_folder / "moving_eddiesU.nc"),
+        "V": str(data_folder / "moving_eddiesV.nc"),
+        "P": str(data_folder / "moving_eddiesP.nc"),
+    }
+    variables = {"U": "vozocrtx", "V": "vomecrty", "P": "P"}
+    dimensions = {"lon": "nav_lon", "lat": "nav_lat", "time": "time_counter"}
+    fieldset = parcels.FieldSet.from_netcdf(filenames, variables, dimensions)
     outfile = tmpdir.join("EddyParticle")
     pset = moving_eddies_example(fieldset, outfile, 2)
     # Also include last timestep
     for var in ["lon", "lat", "depth", "time"]:
         pset.particledata.setallvardata(
             f"{var}", pset.particledata.getvardata(f"{var}_nextloop")
         )
-    if mesh == "flat":
-        assert pset[0].lon < 2.2e5 and 1.1e5 < pset[0].lat < 1.2e5
-        assert pset[1].lon < 2.2e5 and 3.7e5 < pset[1].lat < 3.8e5
-    else:
-        assert pset[0].lon < 2.0 and 46.2 < pset[0].lat < 46.25
-        assert pset[1].lon < 2.0 and 48.8 < pset[1].lat < 48.85
+    assert pset[0].lon < 2.2e5 and 1.1e5 < pset[0].lat < 1.2e5
+    assert pset[1].lon < 2.2e5 and 3.7e5 < pset[1].lat < 3.8e5
 
 
 @pytest.mark.v4alpha

docs/examples/example_peninsula.py

@@ -1,4 +1,3 @@
-import gc
 import math  # NOQA
 from argparse import ArgumentParser
 from datetime import timedelta
@@ -216,14 +215,18 @@ def fieldsetfile(mesh, tmpdir):
     return filename
 
 
-@pytest.mark.parametrize("mesh", ["flat", "spherical"])
-def test_peninsula_file(mesh, tmpdir):
+def test_peninsula_file(tmpdir):
     """Open fieldset files and execute."""
-    gc.collect()
-    fieldset = parcels.FieldSet.from_parcels(
-        fieldsetfile(mesh, tmpdir),
-        extra_fields={"P": "P"},
-        allow_time_extrapolation=True,
+    data_folder = parcels.download_example_dataset("Peninsula_data")
+    filenames = {
+        "U": str(data_folder / "peninsulaU.nc"),
+        "V": str(data_folder / "peninsulaV.nc"),
+        "P": str(data_folder / "peninsulaP.nc"),
+    }
+    variables = {"U": "vozocrtx", "V": "vomecrty", "P": "P"}
+    dimensions = {"lon": "nav_lon", "lat": "nav_lat", "time": "time_counter"}
+    fieldset = parcels.FieldSet.from_netcdf(
+        filenames, variables, dimensions, allow_time_extrapolation=True
     )
     outfile = tmpdir.join("Peninsula")
     pset = peninsula_example(fieldset, outfile, 5, degree=1)
@@ -299,9 +302,17 @@ def main(args=None):
     fieldset.write(filename)
 
     # Open fieldset file set
-    fieldset = parcels.FieldSet.from_parcels(
-        "peninsula", extra_fields={"P": "P"}, allow_time_extrapolation=True
+    filenames = {
+        "U": f"{filename}U.nc",
+        "V": f"{filename}V.nc",
+        "P": f"{filename}P.nc",
+    }
+    variables = {"U": "vozocrtx", "V": "vomecrty", "P": "P"}
+    dimensions = {"lon": "nav_lon", "lat": "nav_lat", "time": "time_counter"}
+    fieldset = parcels.FieldSet.from_netcdf(
+        filenames, variables, dimensions, allow_time_extrapolation=True
     )
+
     outfile = "Peninsula"
 
     if args.profiling:

docs/examples/parcels_tutorial.ipynb

@@ -65,7 +65,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The first step to running particles with Parcels is to define a `FieldSet` object, which is simply a collection of hydrodynamic fields. In this first case, we use a simple flow of two idealised moving eddies. That field can be downloaded using the `download_example_dataset()` function that comes with Parcels. Since we know that the files are in what's called Parcels FieldSet format, we can call these files using the function `FieldSet.from_parcels()`.\n"
+    "The first step to running particles with Parcels is to define a `FieldSet` object, which is simply a collection of hydrodynamic fields. In this first case, we use a simple flow of two idealised moving eddies. That field can be downloaded using the `download_example_dataset()` function that comes with Parcels. Since we know that the files are in what's called Parcels FieldSet format, we can call these files using the function `FieldSet.from_netcdf()`.\n"
    ]
   },
   {
@@ -76,7 +76,13 @@
    "source": [
     "example_dataset_folder = parcels.download_example_dataset(\"MovingEddies_data\")\n",
     "\n",
-    "fieldset = parcels.FieldSet.from_parcels(f\"{example_dataset_folder}/moving_eddies\")\n",
+    "filenames = {\n",
+    "    \"U\": str(example_dataset_folder / \"moving_eddiesU.nc\"),\n",
+    "    \"V\": str(example_dataset_folder / \"moving_eddiesV.nc\"),\n",
+    "}\n",
+    "variables = {\"U\": \"vozocrtx\", \"V\": \"vomecrty\"}\n",
+    "dimensions = {\"lon\": \"nav_lon\", \"lat\": \"nav_lat\", \"time\": \"time_counter\"}\n",
+    "fieldset = parcels.FieldSet.from_netcdf(filenames, variables, dimensions)\n",
     "\n",
     "print(fieldset)"
    ]
@@ -666,10 +672,15 @@
    "outputs": [],
    "source": [
     "example_dataset_folder = parcels.download_example_dataset(\"Peninsula_data\")\n",
-    "fieldset = parcels.FieldSet.from_parcels(\n",
-    "    f\"{example_dataset_folder}/peninsula\",\n",
-    "    extra_fields={\"P\": \"P\"},\n",
-    "    allow_time_extrapolation=True,\n",
+    "filenames = {\n",
+    "    \"U\": str(example_dataset_folder / \"peninsulaU.nc\"),\n",
+    "    \"V\": str(example_dataset_folder / \"peninsulaV.nc\"),\n",
+    "    \"P\": str(example_dataset_folder / \"peninsulaP.nc\"),\n",
+    "}\n",
+    "variables = {\"U\": \"vozocrtx\", \"V\": \"vomecrty\", \"P\": \"P\"}\n",
+    "dimensions = {\"lon\": \"nav_lon\", \"lat\": \"nav_lat\", \"time\": \"time_counter\"}\n",
+    "fieldset = parcels.FieldSet.from_netcdf(\n",
+    "    filenames, variables, dimensions, allow_time_extrapolation=True\n",
     ")"
    ]
   },

docs/examples/tutorial_delaystart.ipynb

@@ -50,8 +50,14 @@
    "outputs": [],
    "source": [
     "example_dataset_folder = parcels.download_example_dataset(\"Peninsula_data\")\n",
-    "fieldset = parcels.FieldSet.from_parcels(\n",
-    "    f\"{example_dataset_folder}/peninsula\", allow_time_extrapolation=True\n",
+    "filenames = {\n",
+    "    \"U\": str(example_dataset_folder / \"peninsulaU.nc\"),\n",
+    "    \"V\": str(example_dataset_folder / \"peninsulaV.nc\"),\n",
+    "}\n",
+    "variables = {\"U\": \"vozocrtx\", \"V\": \"vomecrty\"}\n",
+    "dimensions = {\"lon\": \"nav_lon\", \"lat\": \"nav_lat\", \"time\": \"time_counter\"}\n",
+    "fieldset = parcels.FieldSet.from_netcdf(\n",
+    "    filenames, variables, dimensions, allow_time_extrapolation=True\n",
     ")"
    ]
   },

docs/examples/tutorial_output.ipynb

@@ -44,8 +44,15 @@
    "outputs": [],
    "source": [
     "example_dataset_folder = parcels.download_example_dataset(\"Peninsula_data\")\n",
-    "fieldset = parcels.FieldSet.from_parcels(\n",
-    "    f\"{example_dataset_folder}/peninsula\", allow_time_extrapolation=True\n",
+    "example_dataset_folder = parcels.download_example_dataset(\"Peninsula_data\")\n",
+    "filenames = {\n",
+    "    \"U\": str(example_dataset_folder / \"peninsulaU.nc\"),\n",
+    "    \"V\": str(example_dataset_folder / \"peninsulaV.nc\"),\n",
+    "}\n",
+    "variables = {\"U\": \"vozocrtx\", \"V\": \"vomecrty\"}\n",
+    "dimensions = {\"lon\": \"nav_lon\", \"lat\": \"nav_lat\", \"time\": \"time_counter\"}\n",
+    "fieldset = parcels.FieldSet.from_netcdf(\n",
+    "    filenames, variables, dimensions, allow_time_extrapolation=True\n",
     ")\n",
     "\n",
     "npart = 10  # number of particles to be released\n",

docs/examples/tutorial_periodic_boundaries.ipynb

@@ -86,8 +86,14 @@
    "outputs": [],
    "source": [
     "example_dataset_folder = parcels.download_example_dataset(\"Peninsula_data\")\n",
-    "fieldset = parcels.FieldSet.from_parcels(\n",
-    "    f\"{example_dataset_folder}/peninsula\", allow_time_extrapolation=True\n",
+    "filenames = {\n",
+    "    \"U\": str(example_dataset_folder / \"peninsulaU.nc\"),\n",
+    "    \"V\": str(example_dataset_folder / \"peninsulaV.nc\"),\n",
+    "}\n",
+    "variables = {\"U\": \"vozocrtx\", \"V\": \"vomecrty\"}\n",
+    "dimensions = {\"lon\": \"nav_lon\", \"lat\": \"nav_lat\", \"time\": \"time_counter\"}\n",
+    "fieldset = parcels.FieldSet.from_netcdf(\n",
+    "    filenames, variables, dimensions, allow_time_extrapolation=True\n",
     ")"
    ]
   },

docs/examples/tutorial_sampling.ipynb

@@ -67,10 +67,15 @@
    "source": [
     "# Velocity and temperature fields\n",
     "example_dataset_folder = parcels.download_example_dataset(\"Peninsula_data\")\n",
-    "fieldset = parcels.FieldSet.from_parcels(\n",
-    "    f\"{example_dataset_folder}/peninsula\",\n",
-    "    extra_fields={\"T\": \"T\"},\n",
-    "    allow_time_extrapolation=True,\n",
+    "filenames = {\n",
+    "    \"U\": str(example_dataset_folder / \"peninsulaU.nc\"),\n",
+    "    \"V\": str(example_dataset_folder / \"peninsulaV.nc\"),\n",
+    "    \"T\": str(example_dataset_folder / \"peninsulaT.nc\"),\n",
+    "}\n",
+    "variables = {\"U\": \"vozocrtx\", \"V\": \"vomecrty\", \"T\": \"T\"}\n",
+    "dimensions = {\"lon\": \"nav_lon\", \"lat\": \"nav_lat\", \"time\": \"time_counter\"}\n",
+    "fieldset = parcels.FieldSet.from_netcdf(\n",
+    "    filenames, variables, dimensions, allow_time_extrapolation=True\n",
     ")\n",
     "\n",
     "# Particle locations and initial time\n",

parcels/fieldset.py

@@ -2,7 +2,6 @@
 import os
 import sys
 import warnings
-from copy import deepcopy
 from glob import glob
 
 import numpy as np
@@ -894,57 +893,6 @@ def from_b_grid_dataset(
             **kwargs,
         )
 
-    @classmethod
-    def from_parcels(
-        cls,
-        basename,
-        uvar="vozocrtx",
-        vvar="vomecrty",
-        extra_fields=None,
-        allow_time_extrapolation: bool | None = None,
-        **kwargs,
-    ):
-        """Initialises FieldSet data from NetCDF files using the Parcels FieldSet.write() conventions.
-
-        Parameters
-        ----------
-        basename : str
-            Base name of the file(s); may contain
-            wildcards to indicate multiple files.
-        fieldtype :
-            Optional dictionary mapping fields to fieldtypes to be used for UnitConverter.
-            (either 'U', 'V', 'Kh_zonal', 'Kh_meridional' or None)
-        extra_fields :
-            Extra fields to read beyond U and V (Default value = None)
-        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
-        uvar :
-             (Default value = 'vozocrtx')
-        vvar :
-             (Default value = 'vomecrty')
-        **kwargs :
-            Keyword arguments passed to the :func:`Fieldset.from_netcdf` constructor.
-        """
-        if extra_fields is None:
-            extra_fields = {}
-
-        dimensions = {}
-        default_dims = {"lon": "nav_lon", "lat": "nav_lat", "depth": "depth", "time": "time_counter"}
-        extra_fields.update({"U": uvar, "V": vvar})
-        for vars in extra_fields:
-            dimensions[vars] = deepcopy(default_dims)
-            dimensions[vars]["depth"] = f"depth{vars.lower()}"
-        filenames = {v: str(f"{basename}{v}.nc") for v in extra_fields.keys()}
-        return cls.from_netcdf(
-            filenames,
-            variables=extra_fields,
-            dimensions=dimensions,
-            allow_time_extrapolation=allow_time_extrapolation,
-            **kwargs,
-        )
-
     @classmethod
     def from_xarray_dataset(cls, ds, variables, dimensions, mesh="spherical", allow_time_extrapolation=None, **kwargs):
         """Initialises FieldSet data from xarray Datasets.

tests/test_fieldset.py

@@ -143,21 +143,6 @@ def test_fieldset_from_data_different_dimensions(xdim, ydim):
     assert np.allclose(fieldset.P.data, 2.0, rtol=1e-12)
 
 
-@pytest.mark.parametrize("xdim", [100, 200])
-@pytest.mark.parametrize("ydim", [100, 200])
-def test_fieldset_from_parcels(xdim, ydim, tmpdir):
-    """Simple test for fieldset initialisation from Parcels FieldSet file format."""
-    filepath = tmpdir.join("test_parcels")
-    data, dimensions = generate_fieldset_data(xdim, ydim)
-    fieldset_out = FieldSet.from_data(data, dimensions)
-    fieldset_out.write(filepath)
-    fieldset = FieldSet.from_parcels(filepath)
-    assert len(fieldset.U.data.shape) == 3  # Will be 4 once we use depth
-    assert len(fieldset.V.data.shape) == 3
-    assert np.allclose(fieldset.U.data[0, :], data["U"], rtol=1e-12)
-    assert np.allclose(fieldset.V.data[0, :], data["V"], rtol=1e-12)
-
-
 def test_fieldset_from_modulefile():
     nemo_fname = str(TEST_DATA / "fieldset_nemo.py")
     nemo_error_fname = str(TEST_DATA / "fieldset_nemo_error.py")

tests/test_particlefile.py

@@ -402,7 +402,13 @@ def test_pset_execute_outputdt_backwards_fieldset_timevarying():
 
     # TODO: Not ideal using the `download_example_dataset` here, but I'm struggling to recreate this error using the test suite fieldsets we have
     example_dataset_folder = parcels.download_example_dataset("MovingEddies_data")
-    fieldset = parcels.FieldSet.from_parcels(f"{example_dataset_folder}/moving_eddies")
+    filenames = {
+        "U": str(example_dataset_folder / "moving_eddiesU.nc"),
+        "V": str(example_dataset_folder / "moving_eddiesV.nc"),
+    }
+    variables = {"U": "vozocrtx", "V": "vomecrty"}
+    dimensions = {"lon": "nav_lon", "lat": "nav_lat", "time": "time_counter"}
+    fieldset = parcels.FieldSet.from_netcdf(filenames, variables, dimensions)
 
     ds = setup_pset_execute(outputdt=outputdt, execute_kwargs=dict(runtime=runtime, dt=dt), fieldset=fieldset)
     file_outputdt = ds.isel(trajectory=0).time.diff(dim="obs").values