Add Ruff rules for PEP naming

docs/user_guide/examples/tutorial_nemo_curvilinear.ipynb

@@ -152,7 +152,7 @@
    "outputs": [],
    "source": [
     "u, v = fieldset.UV.eval(\n",
-    "    np.array([0]), np.array([0]), np.array([20]), np.array([50]), applyConversion=False\n",
+    "    np.array([0]), np.array([0]), np.array([20]), np.array([50]), apply_conversion=False\n",
     ")  # do not convert m/s to deg/s\n",
     "print(f\"(u, v) = ({u[0]:.3f}, {v[0]:.3f})\")\n",
     "assert np.isclose(u, 1.0, atol=1e-3)"
@@ -298,7 +298,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "test-notebooks",
+   "display_name": "default",
    "language": "python",
    "name": "python3"
   },
@@ -312,7 +312,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.14.2"
   }
  },
  "nbformat": 4,

docs/user_guide/examples/tutorial_unitconverters.ipynb

@@ -159,7 +159,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that you can also interpolate the Field without a unit conversion, by using the `eval()` method and setting `applyConversion=False`, as below\n"
+    "Note that you can also interpolate the Field without a unit conversion, by using the `eval()` method and setting `apply_conversion=False`, as below\n"
    ]
   },
   {
@@ -174,7 +174,7 @@
     "        z,\n",
     "        lat,\n",
     "        lon,\n",
-    "        applyConversion=False,\n",
+    "        apply_conversion=False,\n",
     "    )\n",
     ")"
    ]

pyproject.toml

@@ -85,8 +85,15 @@ select = [
   "ISC001", # single-line-implicit-string-concatenation
   "TID", # flake8-tidy-imports
   "T100", # Checks for the presence of debugger calls and imports
+  "N", # pep8 naming conventions
+  "PGH004", # ensures no blanket noqa's are used
 ]
 
+exclude = [
+  "tests-v3/**",
+  'docs/user_guide/examples_v3/**',
+] # TODO v4: Remove once folders are gone
+
 ignore = [
   # line too long (82 > 79 characters)
   "E501",
@@ -104,6 +111,13 @@ ignore = [
   "RUF043",
   "RUF046", # Value being cast to `int` is already an integer
 
+  # Parcels specific deviations from PEP8 naming
+  'N802', # We use function names that are camelcased to denote functions
+  'N806', # We use capitalized variable names within functions in Parcels to denote fields, as well as multidimensional arrays
+  'N811', # Well, this just seems like a bad rule O_o
+  'N816', # TODO: Enable for `src` and consider disabling for notebooks
+  'N818', # Not all Parcels exceptions should have an "Error" suffix
+
   # TODO: Move this ignore so that it only applies in the tests folder. Do in conjunction with any doc related rules
   "RUF059", # Unpacked variable `coords` is never used
 

src/parcels/_core/field.py

@@ -201,7 +201,7 @@ def _check_velocitysampling(self):
                 stacklevel=2,
             )
 
-    def eval(self, time: datetime, z, y, x, particles=None, applyConversion=True):
+    def eval(self, time: datetime, z, y, x, particles=None, apply_conversion=True):
         """Interpolate field values in space and time.
 
         We interpolate linearly in time and apply implicit unit
@@ -222,7 +222,7 @@ def eval(self, time: datetime, z, y, x, particles=None, applyConversion=True):
 
         _update_particle_states_interp_value(particles, value)
 
-        if applyConversion:
+        if apply_conversion:
             value = self.units.to_target(value, z, y, x)
         return value
 
@@ -241,7 +241,12 @@ class VectorField:
     """VectorField class that holds vector field data needed to execute particles."""
 
     def __init__(
-        self, name: str, U: Field, V: Field, W: Field | None = None, vector_interp_method: Callable | None = None
+        self,
+        name: str,
+        U: Field,  # noqa: N803
+        V: Field,  # noqa: N803
+        W: Field | None = None,  # noqa: N803
+        vector_interp_method: Callable | None = None,
     ):
         _assert_str_and_python_varname(name)
 
@@ -287,7 +292,7 @@ def vector_interp_method(self, method: Callable):
         assert_same_function_signature(method, ref=ZeroInterpolator_Vector, context="Interpolation")
         self._vector_interp_method = method
 
-    def eval(self, time: datetime, z, y, x, particles=None, applyConversion=True):
+    def eval(self, time: datetime, z, y, x, particles=None, apply_conversion=True):
         """Interpolate field values in space and time.
 
         We interpolate linearly in time and apply implicit unit
@@ -314,7 +319,7 @@ def eval(self, time: datetime, z, y, x, particles=None, applyConversion=True):
         else:
             (u, v, w) = self._vector_interp_method(particle_positions, grid_positions, self)
 
-        if applyConversion:
+        if apply_conversion:
             u = self.U.units.to_target(u, z, y, x)
             v = self.V.units.to_target(v, z, y, x)
             if "3D" in self.vector_type:

src/parcels/_core/fieldset.py

@@ -182,7 +182,8 @@ def gridset(self) -> list[BaseGrid]:
                 grids.append(field.grid)
         return grids
 
-    def from_copernicusmarine(ds: xr.Dataset):
+    @classmethod
+    def from_copernicusmarine(cls, ds: xr.Dataset):
         """Create a FieldSet from a Copernicus Marine Service xarray.Dataset.
 
         Parameters
@@ -237,9 +238,10 @@ def from_copernicusmarine(ds: xr.Dataset):
                 vertical_dimensions=(sgrid.DimDimPadding("z_center", "depth", sgrid.Padding.LOW),),
             ).to_attrs(),
         )
-        return FieldSet.from_sgrid_conventions(ds, mesh="spherical")
+        return cls.from_sgrid_conventions(ds, mesh="spherical")
 
-    def from_fesom2(ds: ux.UxDataset):
+    @classmethod
+    def from_fesom2(cls, ds: ux.UxDataset):
         """Create a FieldSet from a FESOM2 uxarray.UxDataset.
 
         Parameters
@@ -275,10 +277,11 @@ def from_fesom2(ds: ux.UxDataset):
         for varname in set(ds.data_vars) - set(fields.keys()):
             fields[varname] = Field(varname, ds[varname], grid, _select_uxinterpolator(ds[varname]))
 
-        return FieldSet(list(fields.values()))
+        return cls(list(fields.values()))
 
+    @classmethod
     def from_sgrid_conventions(
-        ds: xr.Dataset, mesh: Mesh
+        cls, ds: xr.Dataset, mesh: Mesh
     ):  # TODO: Update mesh to be discovered from the dataset metadata
         """Create a FieldSet from a dataset using SGRID convention metadata.
 
@@ -360,7 +363,7 @@ def from_sgrid_conventions(
         for varname in set(ds.data_vars) - set(fields.keys()) - skip_vars:
             fields[varname] = Field(varname, ds[varname], grid, XLinear)
 
-        return FieldSet(list(fields.values()))
+        return cls(list(fields.values()))
 
 
 class CalendarError(Exception):  # TODO: Move to a parcels errors module

src/parcels/_core/index_search.py

@@ -276,7 +276,7 @@ def uxgrid_point_in_cell(grid, y: np.ndarray, x: np.ndarray, yi: np.ndarray, xi:
     return is_in_cell, coords
 
 
-def _triangle_area(A, B, C):
+def _triangle_area(A, B, C):  # noqa: N803
     """Compute the area of a triangle given by three points."""
     d1 = B - A
     d2 = C - A

src/parcels/_core/particlefile.py

@@ -130,7 +130,7 @@ def store(self):
     def create_new_zarrfile(self):
         return self._create_new_zarrfile
 
-    def _extend_zarr_dims(self, Z, store, dtype, axis):
+    def _extend_zarr_dims(self, Z, store, dtype, axis):  # noqa: N803
         if axis == 1:
             a = np.full((Z.shape[0], self.chunks[1]), _DATATYPES_TO_FILL_VALUES[dtype], dtype=dtype)
             obs = zarr.group(store=store, overwrite=False)["obs"]

src/parcels/_core/utils/sgrid.py

@@ -44,6 +44,8 @@ class Padding(enum.Enum):
 
 class AttrsSerializable(Protocol):
     def to_attrs(self) -> dict[str, str | int]: ...
+
+    @classmethod
     def from_attrs(cls, d: dict[str, Hashable]) -> Self: ...
 
 

src/parcels/interpolators.py

@@ -55,8 +55,8 @@ def _get_corner_data_Agrid(
     zi: int,
     yi: int,
     xi: int,
-    lenT: int,
-    lenZ: int,
+    lenT: int,  # noqa: N803
+    lenZ: int,  # noqa: N803
     npart: int,
     axis_dim: dict[str, str],
 ) -> np.ndarray:

src/parcels/kernels/advection.py

@@ -316,7 +316,7 @@ def AdvectionAnalytical(particles, fieldset):  # pragma: no cover
             V0 = V0 * (1 - tau) + tau * direction * fieldset.V.data[ti + 1, yi, xi + 1] * c1 * dz
             V1 = V1 * (1 - tau) + tau * direction * fieldset.V.data[ti + 1, yi + 1, xi + 1] * c3 * dz
 
-    def compute_ds(F0, F1, r, direction, tol):
+    def compute_ds(F0, F1, r, direction, tol):  # noqa: N803
         up = F0 * (1 - r) + F1 * r
         r_target = 1.0 if direction * up >= 0.0 else 0.0
         B = F0 - F1
@@ -358,7 +358,7 @@ def compute_ds(F0, F1, r, direction, tol):
     s_min = min(abs(ds_x), abs(ds_y), abs(ds_z), abs(ds_t / (dxdy * dz)))
 
     # calculate end position in time s_min
-    def compute_rs(r, B, delta, s_min):
+    def compute_rs(r, B, delta, s_min):  # noqa: N803
         if abs(B) < tol:
             return -delta * s_min + r
         else:

tests/test_advection.py

@@ -103,8 +103,8 @@ def test_horizontal_advection_in_3D_flow(npart=10):
 
 
 @pytest.mark.parametrize("direction", ["up", "down"])
-@pytest.mark.parametrize("wErrorThroughSurface", [True, False])
-def test_advection_3D_outofbounds(direction, wErrorThroughSurface):
+@pytest.mark.parametrize("resubmerge_particle", [True, False])
+def test_advection_3D_outofbounds(direction, resubmerge_particle):
     ds = simple_UV_dataset(mesh="flat")
     ds["W"] = ds["V"].copy()  # Just to have W field present
     ds["U"].data[:] = 0.01  # Set U to small value (to avoid horizontal out of bounds)
@@ -131,14 +131,14 @@ def SubmergeParticle(particles, fieldset):  # pragma: no cover
         particles[inds].state = StatusCode.Evaluate
 
     kernels = [AdvectionRK4_3D]
-    if wErrorThroughSurface:
+    if resubmerge_particle:
         kernels.append(SubmergeParticle)
     kernels.append(DeleteParticle)
 
     pset = ParticleSet(fieldset=fieldset, lon=0.5, lat=0.5, z=0.9)
     pset.execute(kernels, runtime=np.timedelta64(10, "s"), dt=np.timedelta64(1, "s"))
 
-    if direction == "up" and wErrorThroughSurface:
+    if direction == "up" and resubmerge_particle:
         np.testing.assert_allclose(pset.lon[0], 0.6, atol=1e-5)
         np.testing.assert_allclose(pset.z[0], 0, atol=1e-5)
     else:

tests/test_field.py

@@ -201,31 +201,31 @@ def test_field_unstructured_z_linear():
 
     # Test above first cell center - for piecewise constant, should return the depth of the first cell center
     assert np.isclose(
-        P.eval(time=[0], z=[10.0], y=[30.0], x=[30.0], applyConversion=False),
+        P.eval(time=[0], z=[10.0], y=[30.0], x=[30.0], apply_conversion=False),
         55.555557,
     )
     # Test below first cell center, but in the first layer  - for piecewise constant, should return the depth of the first cell center
     assert np.isclose(
-        P.eval(time=[0], z=[65.0], y=[30.0], x=[30.0], applyConversion=False),
+        P.eval(time=[0], z=[65.0], y=[30.0], x=[30.0], apply_conversion=False),
         55.555557,
     )
     # Test bottom layer  - for piecewise constant, should return the depth of the of the bottom layer cell center
     assert np.isclose(
-        P.eval(time=[0], z=[900.0], y=[30.0], x=[30.0], applyConversion=False),
+        P.eval(time=[0], z=[900.0], y=[30.0], x=[30.0], apply_conversion=False),
         944.44445801,
     )
 
     W = Field(name="W", data=ds.W, grid=grid, interp_method=UxPiecewiseLinearNode)
     assert np.isclose(
-        W.eval(time=[0], z=[10.0], y=[30.0], x=[30.0], applyConversion=False),
+        W.eval(time=[0], z=[10.0], y=[30.0], x=[30.0], apply_conversion=False),
         10.0,
     )
     assert np.isclose(
-        W.eval(time=[0], z=[65.0], y=[30.0], x=[30.0], applyConversion=False),
+        W.eval(time=[0], z=[65.0], y=[30.0], x=[30.0], apply_conversion=False),
         65.0,
     )
     assert np.isclose(
-        W.eval(time=[0], z=[900.0], y=[30.0], x=[30.0], applyConversion=False),
+        W.eval(time=[0], z=[900.0], y=[30.0], x=[30.0], apply_conversion=False),
         900.0,
     )
 
@@ -239,13 +239,13 @@ def test_field_constant_in_time():
 
     # Assert that the field can be evaluated at any time, and returns the same value
     time = np.datetime64("2000-01-01T00:00:00")
-    P1 = P.eval(time=time, z=[10.0], y=[30.0], x=[30.0], applyConversion=False)
+    P1 = P.eval(time=time, z=[10.0], y=[30.0], x=[30.0], apply_conversion=False)
     P2 = P.eval(
         time=time + np.timedelta64(1, "D"),
         z=[10.0],
         y=[30.0],
         x=[30.0],
-        applyConversion=False,
+        apply_conversion=False,
     )
     assert np.isclose(P1, P2)
 

tests/test_interpolation.py

@@ -179,7 +179,7 @@ def test_interpolation_mesh_type(mesh, npart=10):
     assert np.isclose(u, u_expected, atol=1e-7)
     assert v == 0.0
 
-    assert fieldset.U.eval(time, 0, lat, 0, applyConversion=False) == 1.0
+    assert fieldset.U.eval(time, 0, lat, 0, apply_conversion=False) == 1
 
 
 interp_methods = {

tests/test_uxarray_fieldset.py

@@ -123,25 +123,25 @@ def test_fesom2_square_delaunay_uniform_z_coordinate_eval():
     fieldset = FieldSet([UVW, P, UVW.U, UVW.V, UVW.W])
 
     assert np.isclose(
-        fieldset.U.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], applyConversion=False),
+        fieldset.U.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], apply_conversion=False),
         1.0,
         rtol=1e-3,
         atol=1e-6,
     )
     assert np.isclose(
-        fieldset.V.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], applyConversion=False),
+        fieldset.V.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], apply_conversion=False),
         1.0,
         rtol=1e-3,
         atol=1e-6,
     )
     assert np.isclose(
-        fieldset.W.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], applyConversion=False),
+        fieldset.W.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], apply_conversion=False),
         0.0,
         rtol=1e-3,
         atol=1e-6,
     )
     assert np.isclose(
-        fieldset.p.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], applyConversion=False),
+        fieldset.p.eval(time=[0.0], z=[1.0], y=[30.0], x=[30.0], apply_conversion=False),
         1.0,
         rtol=1e-3,
         atol=1e-6,
@@ -163,7 +163,7 @@ def test_fesom2_square_delaunay_antimeridian_eval():
     )
     fieldset = FieldSet([P])
 
-    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[-170.0], applyConversion=False), 1.0)
-    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[-180.0], applyConversion=False), 1.0)
-    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[180.0], applyConversion=False), 1.0)
-    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[170.0], applyConversion=False), 1.0)
+    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[-170.0], apply_conversion=False), 1.0)
+    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[-180.0], apply_conversion=False), 1.0)
+    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[180.0], apply_conversion=False), 1.0)
+    assert np.isclose(fieldset.p.eval(time=[0], z=[1.0], y=[30.0], x=[170.0], apply_conversion=False), 1.0)