diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
index db9fd1a6..8777dc93 100644
--- a/.github/workflows/deploy.yaml
+++ b/.github/workflows/deploy.yaml
@@ -66,9 +66,9 @@ jobs:
           platforms: all
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.2
+        uses: pypa/cibuildwheel@v2.20.0
         env:
-          CIBW_SKIP: "cp36-* cp37-* cp38-* pp* *i686 *-musllinux*"
+          CIBW_SKIP: "cp36-* cp37-* cp38-* cp313-* pp* *i686 *-musllinux*"
           CIBW_ARCHS: "${{ matrix.cibw_archs }}"
           CIBW_TEST_COMMAND: "python -c \"import pyresample; assert 'unknown' not in pyresample.__version__, 'incorrect version found'\""
           CIBW_TEST_SKIP: "*_arm64 *_universal2:arm64"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 89f920f0..f7ce0c87 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,14 +2,9 @@ exclude: '^$'
 fail_fast: false
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: 'v0.5.6'
+  rev: 'v0.6.2'
   hooks:
   - id: ruff
-# once https://github.com/astral-sh/ruff/issues/2402 is fully resolved then we can get rid of flake8:
-- repo: https://github.com/pycqa/flake8
-  rev: 7.1.1
-  hooks:
-  - id: flake8
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.6.0
   hooks:
diff --git a/pyproject.toml b/pyproject.toml
index d4269128..242b2a8b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=2.0.0rc1,<2.3", "Cython>=3", "versioneer"]
+requires = ["setuptools", "wheel", "numpy>=2.0.0rc1,<2.3", "Cython>=3", "versioneer[toml]"]
 build-backend = "setuptools.build_meta"
 
 [tool.ruff]
@@ -36,3 +36,22 @@ warn_redundant_casts = true
 warn_unused_ignores = true
 warn_unreachable = true
 warn_unused_configs = true
+
+[tool.versioneer]
+VCS = "git"
+style = "pep440"
+versionfile_source = "pyresample/version.py"
+versionfile_build = "pyresample/version.py"
+tag_prefix = "v"
+
+[tool.isort]
+sections = ["FUTURE", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]
+profile = "black"
+skip_gitignore = true
+default_section = "THIRDPARTY"
+known_first_party = "pyresample"
+line_length = 120
+
+[tool.coverage.run]
+relative_files = true
+omit = ["pyresample/version.py", "versioneer.py"]
diff --git a/pyresample/bilinear/__init__.py b/pyresample/bilinear/__init__.py
index 28901973..b64a0cd8 100644
--- a/pyresample/bilinear/__init__.py
+++ b/pyresample/bilinear/__init__.py
@@ -41,11 +41,7 @@
 )
 
 try:
-    from .xarr import (  # noqa: F401
-        CACHE_INDICES,
-        XArrayBilinearResampler,
-        XArrayResamplerBilinear,
-    )
+    from .xarr import CACHE_INDICES, XArrayBilinearResampler, XArrayResamplerBilinear  # noqa: F401
 except ImportError:
     warnings.warn("XArray, dask, and/or zarr not found, XArrayBilinearResampler won't be available.", stacklevel=2)
     XArrayBilinearResampler = None  # type: ignore
diff --git a/pyresample/boundary/__init__.py b/pyresample/boundary/__init__.py
index 258952af..69b228b2 100644
--- a/pyresample/boundary/__init__.py
+++ b/pyresample/boundary/__init__.py
@@ -17,9 +17,4 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 """The Boundary classes."""
 
-from pyresample.boundary.legacy_boundary import (  # noqa
-    AreaBoundary,
-    AreaDefBoundary,
-    Boundary,
-    SimpleBoundary,
-)
+from pyresample.boundary.legacy_boundary import AreaBoundary, AreaDefBoundary, Boundary, SimpleBoundary  # noqa
diff --git a/pyresample/ewa/dask_ewa.py b/pyresample/ewa/dask_ewa.py
index 6bc57ec7..e41291d0 100644
--- a/pyresample/ewa/dask_ewa.py
+++ b/pyresample/ewa/dask_ewa.py
@@ -39,10 +39,7 @@
 from dask.highlevelgraph import HighLevelGraph
 
 from pyresample.ewa import ll2cr
-from pyresample.ewa._fornav import (
-    fornav_weights_and_sums_wrapper,
-    write_grid_image_single,
-)
+from pyresample.ewa._fornav import fornav_weights_and_sums_wrapper, write_grid_image_single
 from pyresample.geometry import SwathDefinition
 from pyresample.resampler import BaseResampler
 
diff --git a/pyresample/future/__init__.py b/pyresample/future/__init__.py
index a2e45daf..47834f1f 100644
--- a/pyresample/future/__init__.py
+++ b/pyresample/future/__init__.py
@@ -18,9 +18,4 @@
 """Future features that are backwards incompatible with current functionality."""
 
 from .resamplers import Resampler  # noqa
-from .resamplers import (  # noqa
-    create_resampler,
-    list_resamplers,
-    register_resampler,
-    unregister_resampler,
-)
+from .resamplers import create_resampler, list_resamplers, register_resampler, unregister_resampler  # noqa
diff --git a/pyresample/future/resamplers/__init__.py b/pyresample/future/resamplers/__init__.py
index 35c8f1a5..e41d7362 100644
--- a/pyresample/future/resamplers/__init__.py
+++ b/pyresample/future/resamplers/__init__.py
@@ -20,10 +20,5 @@
 from __future__ import annotations
 
 from .nearest import KDTreeNearestXarrayResampler  # noqa
-from .registry import (  # noqa
-    create_resampler,
-    list_resamplers,
-    register_resampler,
-    unregister_resampler,
-)
+from .registry import create_resampler, list_resamplers, register_resampler, unregister_resampler  # noqa
 from .resampler import Resampler  # noqa
diff --git a/pyresample/gradient/__init__.py b/pyresample/gradient/__init__.py
index d53231cc..4e2aa3b8 100644
--- a/pyresample/gradient/__init__.py
+++ b/pyresample/gradient/__init__.py
@@ -36,15 +36,8 @@
 from shapely.geometry import Polygon
 
 from pyresample import CHUNK_SIZE
-from pyresample.geometry import (
-    AreaDefinition,
-    SwathDefinition,
-    get_geostationary_bounding_box_in_lonlats,
-)
-from pyresample.gradient._gradient_search import (
-    one_step_gradient_indices,
-    one_step_gradient_search,
-)
+from pyresample.geometry import AreaDefinition, SwathDefinition, get_geostationary_bounding_box_in_lonlats
+from pyresample.gradient._gradient_search import one_step_gradient_indices, one_step_gradient_search
 from pyresample.resampler import BaseResampler, resample_blocks
 
 logger = logging.getLogger(__name__)
diff --git a/pyresample/resampler.py b/pyresample/resampler.py
index 2a12c48c..6a5ff3e8 100644
--- a/pyresample/resampler.py
+++ b/pyresample/resampler.py
@@ -40,12 +40,7 @@
 except ImportError:
     xr = None
 
-from pyresample.geometry import (
-    AreaDefinition,
-    CoordinateDefinition,
-    IncompatibleAreas,
-    SwathDefinition,
-)
+from pyresample.geometry import AreaDefinition, CoordinateDefinition, IncompatibleAreas, SwathDefinition
 
 from .future.resamplers.resampler import hash_dict
 
diff --git a/pyresample/slicer.py b/pyresample/slicer.py
index 5306818d..579fd58a 100644
--- a/pyresample/slicer.py
+++ b/pyresample/slicer.py
@@ -27,11 +27,7 @@
 from pyproj.enums import TransformDirection
 
 from pyresample import AreaDefinition, SwathDefinition
-from pyresample.geometry import (
-    IncompatibleAreas,
-    InvalidArea,
-    get_geostationary_bounding_box_in_proj_coords,
-)
+from pyresample.geometry import IncompatibleAreas, InvalidArea, get_geostationary_bounding_box_in_proj_coords
 
 try:
     import dask.array as da
diff --git a/pyresample/test/conftest.py b/pyresample/test/conftest.py
index 04df36fc..0bce5f63 100644
--- a/pyresample/test/conftest.py
+++ b/pyresample/test/conftest.py
@@ -25,11 +25,7 @@
 
 import pyresample
 from pyresample import LegacyAreaDefinition, LegacySwathDefinition
-from pyresample.future.geometry import (
-    AreaDefinition,
-    CoordinateDefinition,
-    SwathDefinition,
-)
+from pyresample.future.geometry import AreaDefinition, CoordinateDefinition, SwathDefinition
 from pyresample.test.utils import create_test_latitude, create_test_longitude
 
 SRC_SWATH_2D_SHAPE = (50, 10)
diff --git a/pyresample/test/test_bilinear.py b/pyresample/test/test_bilinear.py
index 7c008c46..fa6c979d 100644
--- a/pyresample/test/test_bilinear.py
+++ b/pyresample/test/test_bilinear.py
@@ -156,9 +156,7 @@ def test_get_fractional_distances_irregular(self):
 
     def test_get_fractional_distances_uprights_parallel(self):
         """Test calculation when uprights are parallel."""
-        from pyresample.bilinear._base import (
-            _get_fractional_distances_uprights_parallel,
-        )
+        from pyresample.bilinear._base import _get_fractional_distances_uprights_parallel
 
         res = _get_fractional_distances_uprights_parallel(self.pts_vert_parallel, 0., 0.)
         self.assertEqual(res[0], 0.5)
@@ -237,11 +235,7 @@ def test_get_input_xy(self):
 
     def test_get_four_closest_corners(self):
         """Test calculation of bounding corners."""
-        from pyresample.bilinear._base import (
-            _get_four_closest_corners,
-            _get_input_xy,
-            _get_output_xy,
-        )
+        from pyresample.bilinear._base import _get_four_closest_corners, _get_input_xy, _get_output_xy
 
         proj = Proj(self.target_def.proj_str)
         out_x, out_y = _get_output_xy(self.target_def)
@@ -1040,9 +1034,7 @@ def test_get_fractional_distances_irregular(self):
 
     def test_get_fractional_distances_uprights_parallel(self):
         """Test calculation when uprights are parallel."""
-        from pyresample.bilinear._base import (
-            _get_fractional_distances_uprights_parallel,
-        )
+        from pyresample.bilinear._base import _get_fractional_distances_uprights_parallel
 
         res = _get_fractional_distances_uprights_parallel(self.pts_vert_parallel, 0., 0.)
         self.assertEqual(res[0], 0.5)
diff --git a/pyresample/test/test_formatting.py b/pyresample/test/test_formatting.py
index de7cb587..b2193bde 100644
--- a/pyresample/test/test_formatting.py
+++ b/pyresample/test/test_formatting.py
@@ -22,11 +22,7 @@
 import pytest
 
 import pyresample
-from pyresample._formatting_html import (
-    area_repr,
-    plot_area_def,
-    swath_area_attrs_section,
-)
+from pyresample._formatting_html import area_repr, plot_area_def, swath_area_attrs_section
 
 from .test_geometry.test_swath import _gen_swath_def_numpy, _gen_swath_def_xarray_dask
 
diff --git a/pyresample/test/test_geometry_legacy.py b/pyresample/test/test_geometry_legacy.py
index 34e42455..440bd12a 100644
--- a/pyresample/test/test_geometry_legacy.py
+++ b/pyresample/test/test_geometry_legacy.py
@@ -31,11 +31,7 @@
 import xarray as xr
 
 from pyresample import geometry
-from pyresample.geometry import (
-    IncompatibleAreas,
-    combine_area_extents_vertical,
-    concatenate_area_defs,
-)
+from pyresample.geometry import IncompatibleAreas, combine_area_extents_vertical, concatenate_area_defs
 from pyresample.test.utils import catch_warnings
 
 
diff --git a/pyresample/test/test_plot.py b/pyresample/test/test_plot.py
index 47fb7a37..e186754a 100644
--- a/pyresample/test/test_plot.py
+++ b/pyresample/test/test_plot.py
@@ -120,10 +120,7 @@ def test_add_gridlines(self, axes, fx_locator):
 
     def test_translate_coast_res(self):
         """Test the translation of coast resolution arguments from old basemap notation to cartopy."""
-        from pyresample.plot import (
-            BASEMAP_NOT_CARTOPY,
-            _translate_coast_resolution_to_cartopy,
-        )
+        from pyresample.plot import BASEMAP_NOT_CARTOPY, _translate_coast_resolution_to_cartopy
 
         with self.assertRaises(KeyError) as raises:
             if sys.version_info > (3,):
diff --git a/pyresample/test/test_resample_blocks.py b/pyresample/test/test_resample_blocks.py
index 6d56e14c..5d472f8f 100644
--- a/pyresample/test/test_resample_blocks.py
+++ b/pyresample/test/test_resample_blocks.py
@@ -211,10 +211,7 @@ def fun(data, block_info=None, **kwargs):
 
     def test_resample_blocks_can_generate_gradient_indices(self):
         """Test resample blocks can generate gradient indices."""
-        from pyresample.gradient import (
-            gradient_resampler_indices,
-            gradient_resampler_indices_block,
-        )
+        from pyresample.gradient import gradient_resampler_indices, gradient_resampler_indices_block
         from pyresample.resampler import resample_blocks
 
         chunks = 40
diff --git a/pyresample/test/test_resamplers/test_nearest.py b/pyresample/test/test_resamplers/test_nearest.py
index 543459f0..a4a16db5 100644
--- a/pyresample/test/test_resamplers/test_nearest.py
+++ b/pyresample/test/test_resamplers/test_nearest.py
@@ -28,11 +28,7 @@
 
 from pyresample.future.geometry import AreaDefinition, SwathDefinition
 from pyresample.future.resamplers import KDTreeNearestXarrayResampler
-from pyresample.test.utils import (
-    assert_maximum_dask_computes,
-    assert_warnings_contain,
-    catch_warnings,
-)
+from pyresample.test.utils import assert_maximum_dask_computes, assert_warnings_contain, catch_warnings
 from pyresample.utils.errors import PerformanceWarning
 
 
diff --git a/pyresample/test/test_resamplers/test_resampler_registry.py b/pyresample/test/test_resamplers/test_resampler_registry.py
index 0738a33d..c6bb0f18 100644
--- a/pyresample/test/test_resamplers/test_resampler_registry.py
+++ b/pyresample/test/test_resamplers/test_resampler_registry.py
@@ -25,12 +25,7 @@
 
 import pytest
 
-from pyresample.future import (
-    Resampler,
-    list_resamplers,
-    register_resampler,
-    unregister_resampler,
-)
+from pyresample.future import Resampler, list_resamplers, register_resampler, unregister_resampler
 from pyresample.test.utils import assert_warnings_contain
 
 
diff --git a/pyresample/test/test_utils.py b/pyresample/test/test_utils.py
index 7f7197be..712346f7 100644
--- a/pyresample/test/test_utils.py
+++ b/pyresample/test/test_utils.py
@@ -29,12 +29,7 @@
 from pyproj import CRS
 
 import pyresample
-from pyresample.test.utils import (
-    TEST_FILES_PATH,
-    assert_future_geometry,
-    create_test_latitude,
-    create_test_longitude,
-)
+from pyresample.test.utils import TEST_FILES_PATH, assert_future_geometry, create_test_latitude, create_test_longitude
 from pyresample.utils import load_cf_area
 from pyresample.utils.row_appendable_array import RowAppendableArray
 
@@ -620,10 +615,7 @@ def test_cf_guess_axis_varname(self):
                           self.nc_handles['nh10km'], 'doesNotExist', 'x', 'polar_stereographic')
 
     def test_cf_is_valid_coordinate_standardname(self):
-        from pyresample.utils.cf import (
-            _is_valid_coordinate_standardname,
-            _valid_cf_type_of_grid_mapping,
-        )
+        from pyresample.utils.cf import _is_valid_coordinate_standardname, _valid_cf_type_of_grid_mapping
 
         # nominal
         for proj_type in _valid_cf_type_of_grid_mapping:
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 3f58ba27..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,32 +0,0 @@
-[bdist_rpm]
-requires=python3-numpy pykdtree python3-numexpr python3-pyproj python3-configobj python3-shapely
-release=1
-doc_files = docs/Makefile docs/source/*.rst
-
-[flake8]
-max-line-length = 120
-exclude = versioneer.py,version.py
-ignore = D107,W504
-per-file-ignores =
-    pyresample/test/*.py:D102
-
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = pyresample/version.py
-versionfile_build = pyresample/version.py
-tag_prefix = v
-
-[coverage:run]
-relative_files = True
-omit =
-    pyresample/version.py
-    versioneer.py
-
-[isort]
-sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
-profile = black
-skip_gitignore = true
-force_to_top = true
-default_section = THIRDPARTY
-known_first_party = pyresample