Use ruff to lint

.pre-commit-config.yaml

@@ -1,15 +1,10 @@
 repos:
-  - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.1.5
     hooks:
-      - id: isort
-
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
-    hooks:
-      - id: flake8
+      # Run the linter.
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      # Run the formatter.
+      - id: ruff-format

docs/conf.py

@@ -14,8 +14,6 @@
 #
 import pkg_resources
 
-import xugrid
-
 # -- Project information -----------------------------------------------------
 
 project = "Xugrid"

examples/connectivity.py

@@ -89,7 +89,7 @@
     xr.full_like(ds["face_z"].ugrid.obj, False, dtype=bool),
     ds.grids[0],
 )
-uda.values[0] = True
+uda[0] = True
 uda.ugrid.plot()
 
 # %%

examples/overlap_regridder.py

@@ -28,9 +28,7 @@
 
 
 def create_grid(bounds, nx, ny):
-    """
-    Create a simple grid of triangles covering a rectangle.
-    """
+    """Create a simple grid of triangles covering a rectangle."""
     import numpy as np
     from matplotlib.tri import Triangulation
 

examples/regridder_overview.py

@@ -37,9 +37,7 @@
 
 
 def create_grid(bounds, nx, ny):
-    """
-    Create a simple grid of triangles covering a rectangle.
-    """
+    """Create a simple grid of triangles covering a rectangle."""
     import numpy as np
     from matplotlib.tri import Triangulation
 

ruff.toml

@@ -0,0 +1,19 @@
+# See https://docs.astral.sh/ruff/rules/
+select = ["C4", "D2", "D3", "D4", "E", "F", "I", "NPY", "PD"]
+ignore = [
+    "D202",
+    "D205",
+    "D206",
+    "D400",
+    "D404",
+    "E402",
+    "E501",
+    "E703",
+    "PD002",
+    "PD901",
+]
+fixable = ["I"]
+ignore-init-module-imports = true
+
+[pydocstyle]
+convention = "numpy"

tests/__init__.py

@@ -1,6 +1,4 @@
 # __init__.py for pytest-cov
-import importlib
-
 import pytest
 
 

tests/conftest.py

@@ -30,3 +30,36 @@
     quads_1,
     quads_structured,
 )
+
+__all__ = (
+    "disk",
+    "disk_layered",
+    "expected_results_centroid",
+    "expected_results_linear",
+    "expected_results_overlap",
+    "grid_data_a",
+    "grid_data_a_1d",
+    "grid_data_a_2d",
+    "grid_data_a_layered",
+    "grid_data_a_layered_1d",
+    "grid_data_a_layered_2d",
+    "grid_data_b",
+    "grid_data_b_1d",
+    "grid_data_b_2d",
+    "grid_data_b_flipped_1d",
+    "grid_data_c",
+    "grid_data_c_1d",
+    "grid_data_c_2d",
+    "grid_data_d",
+    "grid_data_d_1d",
+    "grid_data_dask_expected",
+    "grid_data_dask_expected_layered",
+    "grid_data_dask_source",
+    "grid_data_dask_source_layered",
+    "grid_data_dask_target",
+    "grid_data_e",
+    "grid_data_e_1d",
+    "quads_0_25",
+    "quads_1",
+    "quads_structured",
+)

tests/test_core_utils.py

@@ -13,13 +13,13 @@
 
 
 def test_either_dict_or_kwargs():
-    result = either_dict_or_kwargs(dict(a=1), None, "foo")
-    expected = dict(a=1)
+    result = either_dict_or_kwargs({"a": 1}, None, "foo")
+    expected = {"a": 1}
     assert result == expected
 
-    result = either_dict_or_kwargs(None, dict(a=1), "foo")
-    expected = dict(a=1)
+    result = either_dict_or_kwargs(None, {"a": 1}, "foo")
+    expected = {"a": 1}
     assert result == expected
 
     with pytest.raises(ValueError, match=r"foo"):
-        result = either_dict_or_kwargs(dict(a=1), dict(a=1), "foo")
+        result = either_dict_or_kwargs({"a": 1}, {"a": 1}, "foo")

tests/test_plot_utils.py

@@ -59,7 +59,7 @@ def _importorskip(
 
 @contextlib.contextmanager
 def figure_context(*args, **kwargs):
-    """context manager which autocloses a figure (even if the test failed)"""
+    """Context manager which autocloses a figure (even if the test failed)"""
 
     try:
         yield None
@@ -395,5 +395,5 @@ def test_label_from_attrs(self) -> None:
 
         # Latex strings can be longer without needing a new line:
         long_latex_name = r"$Ra_s = \mathrm{mean}(\epsilon_k) / \mu M^2_\infty$"
-        da.attrs = dict(long_name=long_latex_name)
+        da.attrs = {"long_name": long_latex_name}
         assert label_from_attrs(da) == long_latex_name

tests/test_regrid/test_regridder.py

@@ -67,7 +67,7 @@ def test_centroid_locator_regridder(disk, quads_1):
     regridder = CentroidLocatorRegridder(source=disk, target=square)
     result = regridder.regrid(disk)
     assert isinstance(result, xu.UgridDataArray)
-    assert result.notnull().any()
+    assert result.notna().any()
     assert result.min() >= disk.min()
     assert result.max() <= disk.max()
     assert result.grid.n_face == square.grid.n_face
@@ -76,7 +76,7 @@ def test_centroid_locator_regridder(disk, quads_1):
     regridder = CentroidLocatorRegridder(source=result, target=disk)
     back = regridder.regrid(result)
     assert isinstance(back, xu.UgridDataArray)
-    assert back.notnull().any()
+    assert back.notna().any()
     assert back.min() >= disk.min()
     assert back.max() <= disk.max()
     assert back.grid.n_face == disk.grid.n_face
@@ -108,7 +108,7 @@ def test_overlap_regridder(disk, quads_1):
     square = quads_1
     regridder = OverlapRegridder(disk, square, method="mean")
     result = regridder.regrid(disk)
-    assert result.notnull().any()
+    assert result.notna().any()
     assert result.min() >= disk.min()
     assert result.max() <= disk.max()
 
@@ -142,7 +142,7 @@ def test_barycentric_interpolator(disk, quads_0_25):
     square = quads_0_25
     regridder = BarycentricInterpolator(source=disk, target=square)
     result = regridder.regrid(disk)
-    assert result.notnull().any()
+    assert result.notna().any()
     assert result.min() >= disk.min()
     assert result.max() <= disk.max()
 

tests/test_snap.py

@@ -154,6 +154,6 @@ def test_snap_to_grid_with_data():
     assert isinstance(uds, xu.UgridDataset)
     assert isinstance(gdf, gpd.GeoDataFrame)
     assert uds["a"].dims == (uds.ugrid.grid.edge_dimension,)
-    assert uds["a"].notnull().sum() == 8
-    assert uds["line_index"].notnull().sum() == 8
+    assert uds["a"].notna().sum() == 8
+    assert uds["line_index"].notna().sum() == 8
     assert uds["line_index"].sum() == 0  # all values should be 0

tests/test_ugrid_dataset.py

@@ -144,7 +144,7 @@ def test_getattr(self):
         assert self.uda.dims == self.uda.ugrid.obj.dims
         assert isinstance(self.uda.data, np.ndarray)
         # So are functions
-        assert isinstance(self.uda.isnull(), xugrid.UgridDataArray)
+        assert isinstance(self.uda.isna(), xugrid.UgridDataArray)
         # obj should be accessible
         assert isinstance(self.uda.obj, xr.DataArray)
 
@@ -489,7 +489,7 @@ def test_setitem(self):
     def test_getattr(self):
         assert tuple(self.uds.dims) == ("mesh2d_nFaces",)
         assert isinstance(self.uds.a, xugrid.UgridDataArray)
-        assert isinstance(self.uds.notnull(), xugrid.UgridDataset)
+        assert isinstance(self.uds.notna(), xugrid.UgridDataset)
         # obj should be accessible
         assert isinstance(self.uds.obj, xr.Dataset)
 
@@ -944,11 +944,14 @@ def test_merge():
 
 def get_ugrid_fillvaluem999_startindex1():
     """
-    this is a very minimal but comparable dataset to Grevelingen_0002_map.nc (FM output)
-    It contains triangles and squares
-    the fillvalue of the connectivity arrays is -999
-    the start_index of the connectivity arrays is 1
+    Return a minimal dataset with a specific fill value.
 
+    This is a very minimal but comparable dataset to Grevelingen_0002_map.nc
+    (FM output).
+
+    * It contains both triangles and squares.
+    * The fillvalue of the connectivity arrays is -999
+    * The start_index of the connectivity arrays is 1
     """
 
     ds2 = xr.Dataset()
@@ -1113,7 +1116,9 @@ def get_ugrid_fillvaluem999_startindex1():
 
 def test_fm_fillvalue_startindex_isel():
     """
-    FM data has 1-based starting index and _FillValue -999, this raises several issues. Since it is not possible to generate a Ugrid2d with these attributes, we are testing with raw data
+    FM data has 1-based starting index and _FillValue -999, this raises several
+    issues. Since it is not possible to generate a Ugrid2d with these
+    attributes, we are testing with raw data
     """
 
     # xugrid 0.5.0 warns "RuntimeWarning: invalid value encountered in cast: cast = data.astype(dtype, copy=True)"
@@ -1125,7 +1130,9 @@ def test_fm_fillvalue_startindex_isel():
 
 def test_fm_facenodeconnectivity_fillvalue():
     """
-    FM data has 1-based starting index and _FillValue -999, this raises several issues. Since it is not possible to generate a Ugrid2d with these attributes, we are testing with raw data
+    FM data has 1-based starting index and _FillValue -999, this raises several
+    issues. Since it is not possible to generate a Ugrid2d with these
+    attributes, we are testing with raw data
     """
 
     # xugrid 0.5.0 warns "RuntimeWarning: invalid value encountered in cast: cast = data.astype(dtype, copy=True)"

tox.ini

@@ -12,30 +12,6 @@ isolated_build = True
 setenv =
     CONDA_EXE=mamba
 
-[testenv:format]
-skip_install = True
-basepython = python3.9
-commands =
-    isort .
-    black .
-    blacken-docs README.rst
-deps =
-    black
-    blacken-docs
-    isort
-
-[testenv:lint]
-skip_install = True
-basepython = python3.9
-commands =
-    isort --check .
-    black --check .
-    flake8 .
-deps =
-    black
-    flake8
-    isort
-
 [testenv:build]
 description = run pytest and build docs
 basepython = python3.9

xugrid/__init__.py

@@ -35,3 +35,33 @@
 except pkg_resources.DistributionNotFound:
     # package is not installed
     pass
+
+
+__all__ = (
+    "data",
+    "concat",
+    "full_like",
+    "merge",
+    "ones_like",
+    "open_dataarray",
+    "open_dataset",
+    "open_mfdataset",
+    "open_zarr",
+    "zeros_like",
+    "UgridDataArrayAccessor",
+    "UgridDatasetAccessor",
+    "UgridDataArray",
+    "UgridDataset",
+    "plot",
+    "BarycentricInterpolator",
+    "CentroidLocatorRegridder",
+    "OverlapRegridder",
+    "RelativeOverlapRegridder",
+    "burn_vector_geometry",
+    "UgridRolesAccessor",
+    "merge_partitions",
+    "polygonize",
+    "snap_to_grid",
+    "Ugrid1d",
+    "Ugrid2d",
+)

xugrid/constants.py

@@ -43,9 +43,7 @@ class Vector(NamedTuple):
 
 
 class MissingOptionalModule:
-    """
-    Presents a clear error for optional modules.
-    """
+    """Presents a clear error for optional modules."""
 
     def __init__(self, name):
         self.name = name

xugrid/conversion.py

@@ -117,7 +117,7 @@ def _scalar_spacing(coords, spacing):
     diff = coords.diff(dim)
     spacing_value = abs(spacing.item())
     if not np.allclose(
-        abs(diff.values), spacing_value, atol=abs(1.0e-4 * spacing.item())
+        abs(diff.to_numpy()), spacing_value, atol=abs(1.0e-4 * spacing.item())
     ):
         raise ValueError(
             f"spacing of {coords.name} does not match value of {spacing.name}"
@@ -140,7 +140,7 @@ def _implicit_spacing(coords):
             f"Cannot derive spacing of 1-sized coordinate: {coords.name} \n"
             f"Set bounds yourself or assign a d{coords.name} variable with spacing"
         )
-    halfdiff = 0.5 * abs(coords.diff(dim)).values
+    halfdiff = 0.5 * abs(coords.diff(dim)).to_numpy()
     return np.insert(halfdiff, 0, halfdiff[0])