Enable ruff's pandas-vet (PD) rules (#2830)

* Enable ruff's pandas-vet (PD) rules
* Fix PD errors
* Ignore PD901

Co-authored-by: Wei Ji <[email protected]>

Author: seisman

pygmt/clib/conversion.py

@@ -92,7 +92,7 @@ def dataarray_to_matrix(grid):
     # grids, this would be North-South, East-West. GMT's region and inc are
     # East-West, North-South.
     for dim in grid.dims[::-1]:
-        coord = grid.coords[dim].values
+        coord = grid.coords[dim].to_numpy()
         coord_incs = coord[1:] - coord[0:-1]
         coord_inc = coord_incs[0]
         if not np.allclose(coord_incs, coord_inc):
@@ -120,7 +120,7 @@ def dataarray_to_matrix(grid):
         inc = [abs(i) for i in inc]
         grid = grid.sortby(variables=list(grid.dims), ascending=True)
 
-    matrix = as_c_contiguous(grid[::-1].values)
+    matrix = as_c_contiguous(grid[::-1].to_numpy())
     return matrix, region, inc
 
 

pygmt/tests/test_blockmedian.py

@@ -36,7 +36,7 @@ def test_blockmedian_input_table_matrix(dataframe):
     Run blockmedian using table input that is not a pandas.DataFrame but still
     a matrix.
     """
-    table = dataframe.values
+    table = dataframe.to_numpy()
     output = blockmedian(data=table, spacing="5m", region=[245, 255, 20, 30])
     assert isinstance(output, pd.DataFrame)
     assert output.shape == (5849, 3)

pygmt/tests/test_datasets_earth_vertical_gravity_gradient.py

@@ -21,7 +21,7 @@ def test_earth_vertical_gravity_gradient_01d():
     npt.assert_allclose(data.lon, np.arange(-180, 181, 1))
     npt.assert_allclose(data.min(), -137.125, atol=1 / 32)
     npt.assert_allclose(data.max(), 104.59375, atol=1 / 32)
-    assert data[1, 1].isnull()
+    assert data[1, 1].isnull()  # noqa: PD003  # ruff's bug
 
 
 def test_earth_vertical_gravity_gradient_01d_with_region():

pygmt/tests/test_datasets_samples.py

@@ -189,7 +189,7 @@ def test_earth_relief_holes():
     npt.assert_allclose(grid.max(), 1601)
     npt.assert_allclose(grid.min(), -4929.5)
     # Test for the NaN values in the remote file
-    assert grid[2, 21].isnull()
+    assert grid[2, 21].isnull()  # noqa: PD003  # ruff's bug
 
 
 def test_maunaloa_co2():

pygmt/tests/test_select.py

@@ -37,7 +37,7 @@ def test_select_input_table_matrix(dataframe):
 
     Also testing the reverse (I) alias.
     """
-    data = dataframe.values
+    data = dataframe.to_numpy()
     output = select(data=data, region=[245.5, 254.5, 20.5, 29.5], reverse="r")
     assert isinstance(output, pd.DataFrame)
     assert output.shape == (9177, 3)

pygmt/tests/test_surface.py

@@ -93,7 +93,7 @@ def test_surface_input_data_array(data, region, spacing, expected_grid):
     """
     Run surface by passing in a numpy array into data.
     """
-    data = data.values  # convert pandas.DataFrame to numpy.ndarray
+    data = data.to_numpy()  # convert pandas.DataFrame to numpy.ndarray
     output = surface(
         data=data,
         spacing=spacing,
@@ -132,7 +132,7 @@ def test_surface_with_outgrid_param(data, region, spacing, expected_grid):
     """
     Run surface with the -Goutputfile.nc parameter.
     """
-    data = data.values  # convert pandas.DataFrame to numpy.ndarray
+    data = data.to_numpy()  # convert pandas.DataFrame to numpy.ndarray
     with GMTTempFile(suffix=".nc") as tmpfile:
         output = surface(
             data=data,

pyproject.toml

@@ -100,12 +100,14 @@ select = [
     "F",    # pyflakes
     "I",    # isort
     "NPY",  # numpy
+    "PD",   # pandas-vet
     "PL",   # pylint
     "UP",   # pyupgrade
     "W",    # pycodestyle warnings
 ]
 ignore = [
     "E501", # Avoid enforcing line-length violations
+    "PD901",  # Allow using the generic variable name `df` for DataFrames
     "PLR2004",  # Allow any magic values
 ]