Drop support for Python 3.9 (#584)

Bump latest supported version of Python to 3.10. Run tests under
"latest" with Python 3.13. Python 3.9 reaches EOL by 31 Oct 2025. Bump
minimum required version of Numba to v0.56 and of sklearn to v1.1.
Address some small Ruff complains after bumping minimum supported
version of Python.

Author: santisoler

.github/workflows/test.yml

@@ -46,15 +46,15 @@ jobs:
           - optional
         include:
           - dependencies: oldest
-            python: "3.9"
+            python: "3.10"
           - dependencies: latest
-            python: "3.12"
+            python: "3.13"
           - dependencies: optional
-            python: "3.12"
+            python: "3.13"
           # test on macos-13 (x86) using oldest dependencies and python 3.8
           - os: macos-13
             dependencies: oldest
-            python: "3.9"
+            python: "3.10"
         exclude:
           # don't test on macos-latest (arm64) with oldest dependencies
           - os: macos-latest

harmonica/_equivalent_sources/gradient_boosted.py

@@ -368,7 +368,7 @@ def _create_windows(self, coordinates, shuffle=True):
         # Remove empty windows
         source_windows_nonempty = []
         data_windows_nonempty = []
-        for src, data in zip(source_windows, data_windows):
+        for src, data in zip(source_windows, data_windows, strict=True):
             if src.size > 0 and data.size > 0:
                 source_windows_nonempty.append(src)
                 data_windows_nonempty.append(data)

harmonica/_io/icgem_gdf.py

@@ -44,7 +44,7 @@ def load_icgem_gdf(fname, **kwargs):
     """
     rawdata, metadata = _read_gdf_file(fname, **kwargs)
     shape = (int(metadata["latitude_parallels"]), int(metadata["longitude_parallels"]))
-    data = dict(zip(metadata["attributes"], rawdata))
+    data = dict(zip(metadata["attributes"], rawdata, strict=True))
     coords = {
         "longitude": data["longitude"].reshape(shape)[0, :],
         "latitude": data["latitude"].reshape(shape)[:, 0][::-1],

harmonica/tests/test_prism_layer.py

@@ -430,7 +430,7 @@ def test_to_pyvista(dummy_layer, properties, drop_null_prisms):
     assert pv_grid.n_cells == 20
     assert pv_grid.n_points == 20 * 8
     # Check coordinates of prisms
-    for prism, cell in zip(layer.prism_layer._to_prisms(), pv_grid.cell):
+    for prism, cell in zip(layer.prism_layer._to_prisms(), pv_grid.cell, strict=True):
         npt.assert_allclose(prism, cell.bounds)
     # Check properties of the prisms
     if properties is None:

harmonica/tests/test_tesseroid.py

@@ -706,8 +706,8 @@ def test_spherical_shell_two_dim_adaptive_discret(
         # Define boundary coordinates of each tesseroid
         top = ellipsoid.mean_radius
         bottom = top - thickness
-        for w, e in zip(west, east):
-            for s, n in zip(south, north):
+        for w, e in zip(west, east, strict=True):
+            for s, n in zip(south, north, strict=False):
                 tesseroids.append([w, e, s, n, bottom, top])
         # Get analytical solutions
         analytical = spherical_shell_analytical(top, bottom, density, radius)
@@ -748,8 +748,8 @@ def test_spherical_shell_three_dim_adaptive_discret(thickness, field):
     latitude = np.linspace(-90, 90, shape[1] + 1)
     west, east = longitude[:-1], longitude[1:]
     south, north = latitude[:-1], latitude[1:]
-    for w, e in zip(west, east):
-        for s, n in zip(south, north):
+    for w, e in zip(west, east, strict=False):
+        for s, n in zip(south, north, strict=False):
             tesseroids.append([w, e, s, n, bottom, top])
     # Get analytical solutions
     analytical = spherical_shell_analytical(top, bottom, density, radius)

harmonica/tests/test_tesseroid_variable_density.py

@@ -237,8 +237,7 @@ def test_single_density_based_discretization(
     assert len(tesseroids) == 2
     # Check the horizontal coordinates of the tesseroids
     for tess in tesseroids:
-        for coord, original_coord in zip(tess[:4], tesseroid):
-            npt.assert_allclose(coord, original_coord)
+        npt.assert_allclose(tess[:4], tesseroid[:4])
 
     # Check the radial coordinates
     # ----------------------------
@@ -429,8 +428,8 @@ def build_spherical_shell(bottom, top, shape=(6, 12)):
     west, east = longitude[:-1], longitude[1:]
     south, north = latitude[:-1], latitude[1:]
     tesseroids = []
-    for w, e in zip(west, east):
-        for s, n in zip(south, north):
+    for w, e in zip(west, east, strict=False):
+        for s, n in zip(south, north, strict=False):
             tesseroids.append([w, e, s, n, bottom, top])
     return tesseroids
 

harmonica/tests/test_utils.py

@@ -36,7 +36,7 @@
 
 
 @pytest.mark.parametrize(
-    ("angles", "vector"), [(a, v) for a, v in zip(ANGLES, VECTORS)]
+    ("angles", "vector"), [(a, v) for a, v in zip(ANGLES, VECTORS, strict=True)]
 )
 def test_magnetic_ang_to_vec_float(angles, vector):
     """
@@ -53,7 +53,7 @@ def test_magnetic_ang_to_vec_float(angles, vector):
 
 @pytest.mark.parametrize("degrees", [False, True], ids=("radians", "degrees"))
 @pytest.mark.parametrize(
-    ("angles", "vector"), [(a, v) for a, v in zip(ANGLES, VECTORS)]
+    ("angles", "vector"), [(a, v) for a, v in zip(ANGLES, VECTORS, strict=False)]
 )
 def test_magnetic_vec_to_angles_float(angles, vector, degrees):
     """

harmonica/tests/test_visualizations.py

@@ -79,7 +79,7 @@ def test_prism_to_pyvista(prisms, density):
     assert pv_grid.n_cells == 4
     assert pv_grid.n_points == 32
     # Check coordinates of prisms
-    for prism, cell in zip(prisms, pv_grid.cell):
+    for prism, cell in zip(prisms, pv_grid.cell, strict=True):
         npt.assert_allclose(prism, cell.bounds)
     # Check properties of the prisms
     assert pv_grid.n_arrays == 1

pyproject.toml

@@ -22,18 +22,18 @@ classifiers = [
     "Topic :: Scientific/Engineering",
     "Topic :: Software Development :: Libraries",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "numpy >= 1.23",
     "pandas >= 1.4",
     "scipy >= 1.9",
-    "scikit-learn >= 1.0",
-    "numba >= 0.53",
+    "scikit-learn >= 1.1",
+    "numba >= 0.57",
     "xarray >= 2022.03",
     "verde >= 1.8.1",
     "xrft >= 1.0",