Migrate from os.path to pathlib (#3119)

examples/gallery/images/image.py

@@ -11,7 +11,7 @@
 """
 
 # %%
-import os
+from pathlib import Path
 
 import pygmt
 
@@ -28,6 +28,6 @@
 )
 
 # clean up the downloaded image in the current directory
-os.remove("gmt-logo.png")
+Path("gmt-logo.png").unlink()
 
 fig.show()

examples/tutorials/basics/text.py

@@ -7,7 +7,7 @@
 """
 
 # %%
-import os
+from pathlib import Path
 
 import pygmt
 
@@ -88,7 +88,7 @@
 fig.text(textfiles="examples.txt", angle=True, font=True, justify=True)
 
 # Cleanups
-os.remove("examples.txt")
+Path("examples.txt").unlink()
 
 fig.show()
 

pygmt/figure.py

@@ -67,10 +67,9 @@ class Figure:
     >>> fig.basemap(region=[0, 360, -90, 90], projection="W15c", frame=True)
     >>> fig.savefig("my-figure.png")
     >>> # Make sure the figure file is generated and clean it up
-    >>> import os
-    >>> os.path.exists("my-figure.png")
-    True
-    >>> os.remove("my-figure.png")
+    >>> from pathlib import Path
+    >>> assert Path("my-figure.png").exists()
+    >>> Path("my-figure.png").unlink()
 
     The plot region can be specified through ISO country codes (for example,
     ``"JP"`` for Japan):
@@ -380,8 +379,8 @@ def savefig(  # noqa: PLR0912
         # Remove the .pgw world file if exists
         # Not necessary after GMT 6.5.0.
         # See upstream fix https://github.com/GenericMappingTools/gmt/pull/7865
-        if ext == "tiff" and fname.with_suffix(".pgw").exists():
-            fname.with_suffix(".pgw").unlink()
+        if ext == "tiff":
+            fname.with_suffix(".pgw").unlink(missing_ok=True)
 
         # Rename if file extension doesn't match the input file suffix
         if ext != suffix[1:]:
@@ -495,7 +494,7 @@ def _preview(self, fmt, dpi, as_bytes=False, **kwargs):
             If ``as_bytes=False``, this is the file name of the preview image
             file. Else, it is the file content loaded as a bytes string.
         """
-        fname = os.path.join(self._preview_dir.name, f"{self._name}.{fmt}")
+        fname = Path(self._preview_dir.name) / f"{self._name}.{fmt}"
         self.savefig(fname, dpi=dpi, **kwargs)
         if as_bytes:
             with open(fname, "rb") as image:

pygmt/helpers/tempfile.py

@@ -2,9 +2,9 @@
 Utilities for dealing with temporary file management.
 """
 
-import os
 import uuid
 from contextlib import contextmanager
+from pathlib import Path
 from tempfile import NamedTemporaryFile
 
 import numpy as np
@@ -72,8 +72,7 @@ def __exit__(self, *args):
         """
         Remove the temporary file.
         """
-        if os.path.exists(self.name):
-            os.remove(self.name)
+        Path(self.name).unlink(missing_ok=True)
 
     def read(self, keep_tabs=False):
         """
@@ -133,7 +132,7 @@ def tempfile_from_geojson(geojson):
     with GMTTempFile(suffix=".gmt") as tmpfile:
         import geopandas as gpd
 
-        os.remove(tmpfile.name)  # ensure file is deleted first
+        Path(tmpfile.name).unlink()  # Ensure file is deleted first
         ogrgmt_kwargs = {"filename": tmpfile.name, "driver": "OGR_GMT", "mode": "w"}
         try:
             # OGR_GMT only supports 32-bit integers. We need to map int/int64
@@ -185,7 +184,7 @@ def tempfile_from_image(image):
         A temporary GeoTIFF file holding the image data. E.g. '1a2b3c4d5.tif'.
     """
     with GMTTempFile(suffix=".tif") as tmpfile:
-        os.remove(tmpfile.name)  # ensure file is deleted first
+        Path(tmpfile.name).unlink()  # Ensure file is deleted first
         try:
             image.rio.to_raster(raster_path=tmpfile.name)
         except AttributeError as e:  # object has no attribute 'rio'

pygmt/helpers/testing.py

@@ -4,8 +4,8 @@
 
 import importlib
 import inspect
-import os
 import string
+from pathlib import Path
 
 from pygmt.exceptions import GMTImageComparisonFailure
 from pygmt.io import load_dataarray
@@ -39,6 +39,7 @@ def check_figures_equal(*, extensions=("png",), tol=0.0, result_dir="result_imag
     >>> import pytest
     >>> import shutil
     >>> from pygmt import Figure
+    >>> from pathlib import Path
 
     >>> @check_figures_equal(result_dir="tmp_result_images")
     ... def test_check_figures_equal():
@@ -50,7 +51,7 @@ def check_figures_equal(*, extensions=("png",), tol=0.0, result_dir="result_imag
     ...     )
     ...     return fig_ref, fig_test
     >>> test_check_figures_equal()
-    >>> assert len(os.listdir("tmp_result_images")) == 0
+    >>> assert len(list(Path("tmp_result_images").iterdir())) == 0
     >>> shutil.rmtree(path="tmp_result_images")  # cleanup folder if tests pass
 
     >>> @check_figures_equal(result_dir="tmp_result_images")
@@ -63,12 +64,9 @@ def check_figures_equal(*, extensions=("png",), tol=0.0, result_dir="result_imag
     >>> with pytest.raises(GMTImageComparisonFailure):
     ...     test_check_figures_unequal()
     >>> for suffix in ["", "-expected", "-failed-diff"]:
-    ...     assert os.path.exists(
-    ...         os.path.join(
-    ...             "tmp_result_images",
-    ...             f"test_check_figures_unequal{suffix}.png",
-    ...         )
-    ...     )
+    ...     assert (
+    ...         Path("tmp_result_images") / f"test_check_figures_unequal{suffix}.png"
+    ...     ).exists()
     >>> shutil.rmtree(path="tmp_result_images")  # cleanup folder if tests pass
     """
     allowed_chars = set(string.digits + string.ascii_letters + "_-[]()")
@@ -78,7 +76,7 @@ def decorator(func):
         import pytest
         from matplotlib.testing.compare import compare_images
 
-        os.makedirs(result_dir, exist_ok=True)
+        Path(result_dir).mkdir(parents=True, exist_ok=True)
         old_sig = inspect.signature(func)
 
         @pytest.mark.parametrize("ext", extensions)
@@ -93,8 +91,8 @@ def wrapper(*args, ext="png", request=None, **kwargs):
                 file_name = func.__name__
             try:
                 fig_ref, fig_test = func(*args, **kwargs)
-                ref_image_path = os.path.join(result_dir, f"{file_name}-expected.{ext}")
-                test_image_path = os.path.join(result_dir, f"{file_name}.{ext}")
+                ref_image_path = Path(result_dir) / f"{file_name}-expected.{ext}"
+                test_image_path = Path(result_dir) / f"{file_name}.{ext}"
                 fig_ref.savefig(ref_image_path)
                 fig_test.savefig(test_image_path)
 
@@ -107,11 +105,11 @@ def wrapper(*args, ext="png", request=None, **kwargs):
                     in_decorator=True,
                 )
                 if err is None:  # Images are the same
-                    os.remove(ref_image_path)
-                    os.remove(test_image_path)
+                    ref_image_path.unlink()
+                    test_image_path.unlink()
                 else:  # Images are not the same
                     for key in ["actual", "expected", "diff"]:
-                        err[key] = os.path.relpath(err[key])
+                        err[key] = Path(err[key]).relative_to(".")
                     raise GMTImageComparisonFailure(
                         f"images not close (RMS {err['rms']:.3f}):\n"
                         f"\t{err['actual']}\n"

pygmt/src/grdfilter.py

@@ -114,7 +114,7 @@ def grdfilter(grid, **kwargs):
 
     Examples
     --------
-    >>> import os
+    >>> from pathlib import Path
     >>> import pygmt
     >>> # Apply a filter of 600 km (full width) to the @earth_relief_30m_g file
     >>> # and return a filtered field (saved as netCDF)
@@ -126,7 +126,7 @@ def grdfilter(grid, **kwargs):
     ...     spacing=0.5,
     ...     outgrid="filtered_pacific.nc",
     ... )
-    >>> os.remove("filtered_pacific.nc")  # Cleanup file
+    >>> Path("filtered_pacific.nc").unlink()  # Cleanup file
     >>> # Apply a Gaussian smoothing filter of 600 km to the input DataArray
     >>> # and return a filtered DataArray with the smoothed field
     >>> grid = pygmt.datasets.load_earth_relief()

pygmt/src/x2sys_cross.py

@@ -53,7 +53,7 @@ def tempfile_from_dftrack(track, suffix):
         )
         yield tmpfilename
     finally:
-        os.remove(tmpfilename)
+        Path(tmpfilename).unlink()
 
 
 @fmt_docstring

pygmt/tests/test_accessor.py

@@ -2,7 +2,6 @@
 Test the behaviour of the GMTDataArrayAccessor class.
 """
 
-import os
 import sys
 from pathlib import Path
 
@@ -101,7 +100,7 @@ def test_accessor_sliced_datacube():
         assert grid.gmt.registration == 0  # gridline registration
         assert grid.gmt.gtype == 1  # geographic coordinate type
     finally:
-        os.remove(fname)
+        Path(fname).unlink()
 
 
 def test_accessor_grid_source_file_not_exist():

pygmt/tests/test_clib.py

@@ -2,7 +2,6 @@
 Test the wrappers for the C API.
 """
 
-import os
 from contextlib import contextmanager
 from pathlib import Path
 
@@ -22,7 +21,7 @@
 )
 from pygmt.helpers import GMTTempFile
 
-TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
+POINTS_DATA = Path(__file__).parent / "data" / "points.txt"
 
 
 @contextmanager
@@ -136,11 +135,10 @@ def test_call_module():
     """
     Run a command to see if call_module works.
     """
-    data_fname = os.path.join(TEST_DATA_DIR, "points.txt")
     out_fname = "test_call_module.txt"
     with clib.Session() as lib:
         with GMTTempFile() as out_fname:
-            lib.call_module("info", f"{data_fname} -C ->{out_fname.name}")
+            lib.call_module("info", f"{POINTS_DATA} -C ->{out_fname.name}")
             assert Path(out_fname.name).stat().st_size > 0
             output = out_fname.read().strip()
             assert output == "11.5309 61.7074 -2.9289 7.8648 0.1412 0.9338"

pygmt/tests/test_clib_virtualfiles.py

@@ -2,9 +2,9 @@
 Test the C API functions related to virtual files.
 """
 
-import os
 from importlib.util import find_spec
 from itertools import product
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
@@ -15,8 +15,7 @@
 from pygmt.helpers import GMTTempFile
 from pygmt.tests.test_clib import mock
 
-TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
-POINTS_DATA = os.path.join(TEST_DATA_DIR, "points.txt")
+POINTS_DATA = Path(__file__).parent / "data" / "points.txt"
 
 
 @pytest.fixture(scope="module", name="data")

pygmt/tests/test_contour.py

@@ -2,16 +2,15 @@
 Test Figure.contour.
 """
 
-import os
+from pathlib import Path
 
 import numpy as np
 import pandas as pd
 import pytest
 import xarray as xr
 from pygmt import Figure
 
-TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
-POINTS_DATA = os.path.join(TEST_DATA_DIR, "points.txt")
+POINTS_DATA = Path(__file__).parent / "data" / "points.txt"
 
 
 @pytest.fixture(scope="module", name="data")

pygmt/tests/test_figure.py

@@ -5,7 +5,6 @@
 """
 
 import importlib
-import os
 from pathlib import Path
 
 import numpy as np
@@ -82,10 +81,8 @@ def test_figure_savefig_exists():
     fig.basemap(region="10/70/-300/800", projection="X3i/5i", frame="af")
     prefix = "test_figure_savefig_exists"
     for fmt in "bmp eps jpg jpeg pdf png ppm tif PNG JPG JPEG Png".split():
-        fname = f"{prefix}.{fmt}"
+        fname = Path(f"{prefix}.{fmt}")
         fig.savefig(fname)
-
-        fname = Path(fname)
         assert fname.exists()
         fname.unlink()
 
@@ -201,10 +198,10 @@ def test_figure_savefig_transparent():
         with pytest.raises(GMTInvalidInput):
             fig.savefig(fname, transparent=True)
     # png should not raise an error
-    fname = f"{prefix}.png"
+    fname = Path(f"{prefix}.png")
     fig.savefig(fname, transparent=True)
-    assert os.path.exists(fname)
-    os.remove(fname)
+    assert fname.exists()
+    fname.unlink()
 
 
 def test_figure_savefig_filename_with_spaces():
@@ -215,8 +212,9 @@ def test_figure_savefig_filename_with_spaces():
     fig.basemap(region=[0, 1, 0, 1], projection="X1c/1c", frame=True)
     with GMTTempFile(prefix="pygmt-filename with spaces", suffix=".png") as imgfile:
         fig.savefig(fname=imgfile.name)
-        assert r"\040" not in os.path.abspath(imgfile.name)
-        assert Path(imgfile.name).stat().st_size > 0
+        imgpath = Path(imgfile.name).resolve()
+        assert r"\040" not in str(imgpath)
+        assert imgpath.stat().st_size > 0
 
 
 def test_figure_savefig():

pygmt/tests/test_grd2cpt.py

@@ -2,7 +2,7 @@
 Test pygmt.grd2cpt.
 """
 
-import os
+from pathlib import Path
 
 import pytest
 from pygmt import Figure, grd2cpt
@@ -55,7 +55,7 @@ def test_grd2cpt_output_to_cpt_file(grid):
     """
     with GMTTempFile(suffix=".cpt") as cptfile:
         grd2cpt(grid=grid, output=cptfile.name)
-        assert os.path.getsize(cptfile.name) > 0
+        assert Path(cptfile.name).stat().st_size > 0
 
 
 def test_grd2cpt_unrecognized_data_type():

pygmt/tests/test_grdcontour.py

@@ -2,16 +2,15 @@
 Test Figure.grdcontour.
 """
 
-import os
+from pathlib import Path
 
 import numpy as np
 import pytest
 from pygmt import Figure
 from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers.testing import load_static_earth_relief
 
-TEST_DATA_DIR = os.path.join(os.path.dirname(__file__), "data")
-TEST_CONTOUR_FILE = os.path.join(TEST_DATA_DIR, "contours.txt")
+TEST_CONTOUR_FILE = Path(__file__).parent / "data" / "contours.txt"
 
 
 @pytest.fixture(scope="module", name="grid")