Merge pull request #1936 from OceanParcels/1844-data-full-zdim

Remove data_full_zdim from fieldfilebuffer

Author: VeckoTheGecko

.github/workflows/ci.yml

@@ -77,8 +77,9 @@ jobs:
           environment-file: environment.yml
       - name: Integration test
         # TODO v4: Re-enable `tutorial_periodic_boundaries`, `tutorial_timevaryingdepthdimensions` and `tutorial_croco_3D` notebooks
+        # TODO v4: Re-enable `tutorial_nemo_3D` notebook once 3D grids are implemented (https://github.com/OceanParcels/Parcels/pull/1936#issuecomment-2717666705)
         run: |
-          coverage run -m pytest -v -s --nbval-lax -k "not documentation and not tutorial_periodic_boundaries and not tutorial_timevaryingdepthdimensions and not tutorial_croco_3D" --html="${{ matrix.os }}_${{ matrix.python-version }}_integration_test_report.html" --self-contained-html docs/examples
+          coverage run -m pytest -v -s --nbval-lax -k "not documentation and not tutorial_periodic_boundaries and not tutorial_timevaryingdepthdimensions and not tutorial_croco_3D and not tutorial_nemo_3D" --html="${{ matrix.os }}_${{ matrix.python-version }}_integration_test_report.html" --self-contained-html docs/examples
           coverage xml
       - name: Codecov
         uses: codecov/codecov-action@v5.3.1

parcels/field.py

@@ -390,13 +390,9 @@ def from_netcdf(
             ) as filebuffer:
                 filebuffer.name = variable[1]
                 depth = filebuffer.depth
-                data_full_zdim = filebuffer.data_full_zdim
         else:
             indices["depth"] = np.array([0])
             depth = np.zeros(1)
-            data_full_zdim = 1
-
-        kwargs["data_full_zdim"] = data_full_zdim
 
         if len(data_filenames) > 1 and "time" not in dimensions:
             raise RuntimeError("Multiple files given but no time dimension specified")
@@ -421,7 +417,6 @@ def from_netcdf(
             dimensions,
             indices,
             interp_method=interp_method,
-            data_full_zdim=data_full_zdim,
         ) as filebuffer:
             # If Field.from_netcdf is called directly, it may not have a 'data' dimension
             # In that case, assume that 'name' is the data dimension

parcels/fieldfilebuffer.py

@@ -17,7 +17,6 @@ def __init__(
         indices,
         *,
         interp_method: InterpMethodOption = "linear",
-        data_full_zdim=None,
         gridindexingtype="nemo",
     ):
         self.filename: PathLike | list[PathLike] = filename
@@ -26,7 +25,6 @@ def __init__(
         self.dataset = None
         self.interp_method = interp_method
         self.gridindexingtype = gridindexingtype
-        self.data_full_zdim = data_full_zdim
 
     def __enter__(self):
         self.dataset = open_xarray_dataset(self.filename)
@@ -58,6 +56,8 @@ def ydim(self):
 
     @property
     def zdim(self):
+        if "depth" not in self.dimensions:
+            return 1
         depth = self.dataset[self.dimensions["depth"]]
         zdim = depth.size if len(depth.shape) == 1 else depth.shape[-3]
         if self.gridindexingtype in ["croco"]:
@@ -84,23 +84,14 @@ def latlon(self):
 
     @property
     def depth(self):
+        self.indices["depth"] = range(self.zdim)
         if "depth" in self.dimensions:
-            depth = self.dataset[self.dimensions["depth"]]
-            self.data_full_zdim = self.zdim
-            self.indices["depth"] = range(self.zdim)
-            return depth
-        else:
-            self.indices["depth"] = [0]
-            return np.zeros(1)
+            return self.dataset[self.dimensions["depth"]]
+        return np.zeros(1)
 
     @property
-    def depth_dimensions(self):
-        if "depth" in self.dimensions:
-            data = self.dataset[self.name]
-            depthsize = data.shape[-3]
-            self.data_full_zdim = depthsize
-            self.indices["depth"] = range(depthsize)
-            return np.empty((0, self.zdim) + data.shape[-2:])
+    def data_full_zdim(self):
+        return self.zdim
 
     def _check_extend_depth(self, data, dim):
         return (

pyproject.toml

@@ -46,7 +46,7 @@ platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
 
 [tool.pixi.tasks]
 tests = "pytest"
-tests-notebooks = "pytest -v -s --nbval-lax -k 'not documentation and not tutorial_periodic_boundaries and not tutorial_timevaryingdepthdimensions and not tutorial_croco_3D'" # TODO v4: Re-enable `tutorial_periodic_boundaries`, `tutorial_timevaryingdepthdimensions`, and `tutorial_croco_3D` notebooks
+tests-notebooks = "pytest -v -s --nbval-lax -k 'not documentation and not tutorial_periodic_boundaries and not tutorial_timevaryingdepthdimensions and not tutorial_croco_3D and not tutorial_nemo_3D'" # TODO v4: Re-enable `tutorial_periodic_boundaries`, `tutorial_timevaryingdepthdimensions`, `tutorial_croco_3D`, `tutorial_nemo_3D` notebooks
 coverage = "coverage run -m pytest && coverage html"
 typing = "mypy parcels"
 pre-commit = "pre-commit run --all-files"

tests/test_grids.py

@@ -873,7 +873,18 @@ def UpdateR(particle, fieldset, time):  # pragma: no cover
     assert np.allclose(pset.radius, pset.radius_start, atol=10)
 
 
-@pytest.mark.parametrize("gridindexingtype", ["mom5"])  # TODO v4: add pop in params?
+@pytest.mark.parametrize(
+    "gridindexingtype",
+    [
+        pytest.param(
+            "mom5",
+            marks=[
+                pytest.mark.v4alpha,
+                pytest.mark.xfail(reason="https://github.com/OceanParcels/Parcels/pull/1936#issuecomment-2717408483"),
+            ],
+        )
+    ],
+)  # TODO v4: add pop in params?
 @pytest.mark.parametrize("extrapolation", [True, False])
 def test_bgrid_interpolation(gridindexingtype, extrapolation):
     xi, yi = 3, 2