Bump to ruff>=0.12.0 and fix violations (#3980)

* pandas-df-variable-name (PD901) is deprecated
* Silent some PLC0415 violations
* Fix PT031 violations
Reference: https://docs.pytest.org/en/stable/how-to/capture-warnings.html#recwarn
* Bump to ruff>=0.12.0

Author: seisman

environment.yml

@@ -26,7 +26,7 @@ dependencies:
     # Dev dependencies (style checks)
     - codespell
     - pre-commit
-    - ruff>=0.10.0
+    - ruff>=0.12.0
     # Dev dependencies (unit testing)
     - matplotlib-base
     - pytest>=6.0

pygmt/figure.py

@@ -419,7 +419,7 @@ def _repr_html_(self) -> str:
         html = '<img src="data:image/png;base64,{image}" width="{width}px">'
         return html.format(image=base64_png.decode("utf-8"), width=500)
 
-    from pygmt.src import (  # type: ignore[misc]
+    from pygmt.src import (  # type: ignore[misc] # noqa: PLC0415
         basemap,
         coast,
         colorbar,

pygmt/helpers/tempfile.py

@@ -132,7 +132,7 @@ def tempfile_from_geojson(geojson):
         E.g. '1a2b3c4d5e6.gmt'.
     """
     with GMTTempFile(suffix=".gmt") as tmpfile:
-        import geopandas as gpd
+        import geopandas as gpd  # noqa: PLC0415
 
         Path(tmpfile.name).unlink()  # Ensure file is deleted first
         ogrgmt_kwargs = {"filename": tmpfile.name, "driver": "OGR_GMT", "mode": "w"}
@@ -157,7 +157,7 @@ def tempfile_from_geojson(geojson):
             geojson.to_file(**ogrgmt_kwargs)
         except AttributeError:
             # Other 'geo' formats which implement __geo_interface__
-            import json
+            import json  # noqa: PLC0415
 
             jsontext = json.dumps(geojson.__geo_interface__)
             gpd.read_file(filename=io.StringIO(jsontext)).to_file(**ogrgmt_kwargs)

pygmt/helpers/testing.py

@@ -72,8 +72,8 @@ def check_figures_equal(*, extensions=("png",), tol=0.0, result_dir="result_imag
     keyword_only = inspect.Parameter.KEYWORD_ONLY
 
     def decorator(func):
-        import pytest
-        from matplotlib.testing.compare import compare_images
+        import pytest  #  noqa: PLC0415
+        from matplotlib.testing.compare import compare_images  # noqa: PLC0415
 
         Path(result_dir).mkdir(parents=True, exist_ok=True)
         old_sig = inspect.signature(func)
@@ -188,7 +188,7 @@ def skip_if_no(package):
         A pytest.mark.skipif to use as either a test decorator or a
         parametrization mark.
     """
-    import pytest
+    import pytest  # noqa: PLC0415
 
     try:
         _ = importlib.import_module(name=package)

pygmt/tests/test_clib.py

@@ -2,6 +2,7 @@
 Test the wrappers for the C API.
 """
 
+import importlib
 from contextlib import contextmanager
 
 import pytest
@@ -241,8 +242,6 @@ def test_fails_for_wrong_version(monkeypatch):
     """
     Make sure that importing clib raise an exception if GMT is too old.
     """
-    import importlib
-
     with monkeypatch.context() as mpatch:
         # Make sure the current GMT major version is 6.
         assert clib.__gmt_version__.split(".")[0] == "6"

pygmt/tests/test_clib_dataarray_to_matrix.py

@@ -96,7 +96,7 @@ def test_dataarray_to_matrix_irregular_inc_warning():
     grid = xr.DataArray(data, coords=[("y", y), ("x", x)])
     with pytest.warns(expected_warning=RuntimeWarning) as record:
         dataarray_to_matrix(grid)
-        assert len(record) == 1
+    assert len(record) == 1
 
 
 def test_dataarray_to_matrix_zero_inc_fails():

pygmt/tests/test_datatypes_dataset.py

@@ -161,6 +161,6 @@ def test_dataset_to_strings_with_none_values():
             Path(path).unlink()
         with pytest.warns(expected_warning=RuntimeWarning) as record:
             paths = which(fname=tiles, download="a")
-            assert len(record) == 1
+        assert len(record) == 1
         assert len(paths) == 2
         assert "" in paths

pygmt/tests/test_figure.py

@@ -124,9 +124,9 @@ def test_figure_savefig_geotiff():
 
     # Check if a TIFF is georeferenced or not
     if _HAS_RIOXARRAY:
-        import rioxarray
-        from rasterio.errors import NotGeoreferencedWarning
-        from rasterio.transform import Affine
+        import rioxarray  # noqa: PLC0415
+        from rasterio.errors import NotGeoreferencedWarning  # noqa: PLC0415
+        from rasterio.transform import Affine  # noqa: PLC0415
 
         # GeoTIFF
         with rioxarray.open_rasterio(geofname) as xds:
@@ -152,15 +152,17 @@ def test_figure_savefig_geotiff():
         # TIFF
         with pytest.warns(expected_warning=NotGeoreferencedWarning) as record:
             with rioxarray.open_rasterio(fname) as xds:
-                assert xds.rio.crs is None
-                npt.assert_allclose(
-                    actual=xds.rio.bounds(), desired=(0.0, 0.0, 1331.0, 1257.0)
-                )
-                assert xds.rio.shape == (1257, 1331)
-                assert xds.rio.transform() == Affine(
-                    a=1.0, b=0.0, c=0.0, d=0.0, e=1.0, f=0.0
-                )
-            assert len(record) == 1
+                pass
+        assert len(record) == 1
+        with rioxarray.open_rasterio(fname) as xds:
+            assert xds.rio.crs is None
+            npt.assert_allclose(
+                actual=xds.rio.bounds(), desired=(0.0, 0.0, 1331.0, 1257.0)
+            )
+            assert xds.rio.shape == (1257, 1331)
+            assert xds.rio.transform() == Affine(
+                a=1.0, b=0.0, c=0.0, d=0.0, e=1.0, f=0.0
+            )
     geofname.unlink()
     fname.unlink()
 

pygmt/tests/test_grdclip.py

@@ -88,7 +88,7 @@ def test_grdclip_replace():
     # TODO(PyGMT>=0.19.0): Remove this test below for the 'new' parameter
     with pytest.warns(FutureWarning):
         grid = grdclip(grid=grid, new=[1, 3])  # Replace 1 with 3
-        npt.assert_array_equal(np.unique(grid), [2, 3])
+    npt.assert_array_equal(np.unique(grid), [2, 3])
 
 
 def test_grdclip_between_repeated():

pygmt/tests/test_grdfill.py

@@ -147,4 +147,4 @@ def test_grdfill_deprecated_mode(grid, expected_grid):
     """
     with pytest.warns(FutureWarning):
         result = grdfill(grid=grid, mode="c20")
-        xr.testing.assert_allclose(a=result, b=expected_grid)
+    xr.testing.assert_allclose(a=result, b=expected_grid)