Merge pull request #11 from GeoStat-Framework/add_py314

MuellerSeb · web-flow · commit 445af61a65cc · 2025-12-26T17:45:44.000+01:00
CI: add py314, remove py39, update cibw, cleanup
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -58,16 +58,16 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # macos-13 is an intel runner, macos-latest is apple silicon
-        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-13, macos-latest]
+        # macos-15-intel is an intel runner, macos-latest is apple silicon
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, windows-11-arm, macos-15-intel, macos-latest]
 
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: "0"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.22.0
+        uses: pypa/cibuildwheel@v3.3.0
         with:
           output-dir: dist-wheel-${{ matrix.os }}
 
@@ -82,19 +82,17 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        os: [ubuntu-latest, windows-latest, macos-15-intel, macos-latest]
         # https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
         ver:
-          - { py: "3.9", np: "==1.20.0" }
           - { py: "3.10", np: "==1.21.6" }
           - { py: "3.11", np: "==1.23.2" }
           - { py: "3.12", np: "==1.26.2" }
           - { py: "3.13", np: "==2.1.0" }
-          - { py: "3.13", np: ">=2.1.0" }
+          - { py: "3.14", np: "==2.3.2" }
+          - { py: "3.14", np: ">=2.3.2" }
         exclude:
-          - os: macos-14
-            ver: { py: "3.9", np: "==1.20.0" }
-          - os: macos-14
+          - os: macos-latest
             ver: { py: "3.10", np: "==1.21.6" }
     steps:
       - uses: actions/checkout@v4
@@ -155,14 +153,14 @@ jobs:
       - name: Install GSTools-Cython
         env:
           GSTOOLS_CY_COV: 1
+          GSTOOLS_BUILD_PARALLEL: 1
         run: |
           pip install -v --editable .[test]
 
       - name: Run tests
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          pip install "numpy${{ matrix.ver.np }}"
           python -m pytest --cov gstools_cython --cov-report term-missing -v tests/
           python -m coveralls --service=github
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,20 @@
 
 All notable changes to **GSTools-Cython** will be documented in this file.
 
+## [1.2.0] - 2025-12
+
+See [#11](https://github.com/GeoStat-Framework/GSTools-Cython/pull/11)
+
+### Changes
+
+- add support for Python 3.14 (incl. free-threaded support)
+- move pypy version to 3.11
+- add win arm64 wheels (without Python 3.10, since there are no numpy wheels prior to 3.11)
+- remove support for Python 3.9 (EOL)
+- fix bug in error message in variogram.pyx (undetected by cython<3.1)
+- update pyproject.toml and use setuptools>=77
+- increased coverage
+
 ## [1.1.0] - 2025-04
 
 See [#5](https://github.com/GeoStat-Framework/GSTools-Cython/pull/5)
@@ -23,6 +37,7 @@ First release of GSTools-Cython
 - moved Cython files into this separate package
 
 
-[Unreleased]: https://github.com/GeoStat-Framework/gstools-cython/compare/v1.1.0...HEAD
+[Unreleased]: https://github.com/GeoStat-Framework/gstools-cython/compare/v1.2.0...HEAD
+[1.2.0]: https://github.com/GeoStat-Framework/gstools-cython/compare/v1.1.0...v1.2.0
 [1.1.0]: https://github.com/GeoStat-Framework/gstools-cython/compare/v1.0.0...v1.1.0
 [1.0.0]: https://github.com/GeoStat-Framework/gstools-cython/releases/tag/v1.0.0
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -203,11 +203,13 @@ def setup(app):
 # latex_show_urls = 'footnote'
 # http://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-latex-output
 latex_elements = {
-    "preamble": r"""
+    "preamble": (
+        r"""
 \setcounter{secnumdepth}{1}
 \setcounter{tocdepth}{2}
 \pagestyle{fancy}
-""",
+"""
+    ),
     "pointsize": "10pt",
     "papersize": "a4paper",
     "fncychap": "\\usepackage[Glenn]{fncychap}",
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,43 +1,42 @@
 [build-system]
 requires = [
-    "setuptools>=64",
-    "setuptools<72.2; implementation_name == 'pypy'", # https://github.com/pypa/distutils/issues/283
+    "setuptools>=77",
     "setuptools_scm>=7",
-    "numpy>=2.0.0rc1",
-    "Cython>=3.0.10,<3.1.0",
+    "numpy>=2",
+    "Cython>=3",
     "extension-helpers>=1",
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 name = "gstools_cython"
 description = "Cython backend for GSTools."
 authors = [
     {name = "Sebastian Müller, Lennart Schüler", email = "info@geostat-framework.org"},
 ]
 readme = "README.md"
-license = {text = "LGPL-3.0"}
+license = "LGPL-3.0-or-later"
+license-files = ["LICENSE"]
 dynamic = ["version"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
     "Intended Audience :: End Users/Desktop",
     "Intended Audience :: Science/Research",
     "Intended Audience :: Education",
-    "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
     "Natural Language :: English",
     "Operating System :: Unix",
     "Operating System :: Microsoft",
     "Operating System :: MacOS",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
     "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",
+    "Programming Language :: Python :: 3.14",
     "Topic :: Scientific/Engineering",
     "Topic :: Scientific/Engineering :: GIS",
     "Topic :: Scientific/Engineering :: Hydrology",
@@ -58,7 +57,7 @@ doc = [
 ]
 test = [
     "pytest-cov>=3",
-     "Cython>=3.0.10,<3.1.0",
+     "Cython>=3",
 ]
 lint = [
     "black>=24",
@@ -75,9 +74,6 @@ Homepage = "https://geostat-framework.org/#gstools"
 Source = "https://github.com/GeoStat-Framework/GSTools-Cython"
 Tracker = "https://github.com/GeoStat-Framework/GSTools-Cython/issues"
 
-[tool.setuptools]
-license-files = ["LICENSE"]
-
 [tool.setuptools_scm]
 write_to = "src/gstools_cython/_version.py"
 write_to_template = "__version__ = '{version}'"
@@ -90,11 +86,11 @@ multi_line_output = 3
 
 [tool.black]
 target-version = [
-    "py39",
     "py310",
     "py311",
     "py312",
     "py313",
+    "py314",
 ]
 
 [tool.coverage]
@@ -145,8 +141,8 @@ target-version = [
 build-frontend = "build"
 # explicitly enable pypy
 enable = ["pypy"]
-# Disable building py3.6/7/8, pp3.8, 32bit linux
-skip = ["cp36-*", "cp37-*", "cp38-*", "pp38-*", "*_i686"]
+# Disable building py3.8/9, 32bit linux, and arm64 windows wheels for python 3.10 (no numpy support)
+skip = ["cp38-*", "cp39-*", "*_i686", "cp310-win_arm64"]
 # Run the package tests using `pytest`
 test-extras = "test"
 test-command = "pytest -v {package}/tests"
diff --git a/src/gstools_cython/variogram.pyx b/src/gstools_cython/variogram.pyx
@@ -253,7 +253,7 @@ def directional(
         counts of samples per bin and direciton
     """
     if pos.shape[1] != f.shape[1]:
-        raise ValueError(f'len(pos) = {pos.shape[1]} != len(f) = {f.shape[1])}')
+        raise ValueError(f'len(pos) = {pos.shape[1]} != len(f) = {f.shape[1]}')
 
     if bin_edges.shape[0] < 2:
         raise ValueError('len(bin_edges) too small')
@@ -359,7 +359,7 @@ def unstructured(
             raise ValueError(f'Haversine: dim = {dim} != 2')
 
     if pos.shape[1] != f.shape[1]:
-        raise ValueError(f'len(pos) = {pos.shape[1]} != len(f) = {f.shape[1])}')
+        raise ValueError(f'len(pos) = {pos.shape[1]} != len(f) = {f.shape[1]}')
 
     if bin_edges.shape[0] < 2:
         raise ValueError('len(bin_edges) too small')
diff --git a/tests/test_field.py b/tests/test_field.py
@@ -69,6 +69,8 @@ def test_summate(self):
         )
         summed = gs_cy.field.summate(cov_samples, z_1, z_2, pos)
         np.testing.assert_allclose(summed_modes, summed)
+        summed_threads = gs_cy.field.summate(cov_samples, z_1, z_2, pos, num_threads=2)
+        np.testing.assert_allclose(summed_modes, summed_threads)
 
     def test_summate_incompr(self):
         # x = y = np.linspace(0,1,3)
diff --git a/tests/test_krige.py b/tests/test_krige.py
@@ -44,6 +44,11 @@ def test_calc_field_krige_and_variance(self):
         )
         np.testing.assert_allclose(field, self.field_ref)
         np.testing.assert_allclose(error, self.error_ref)
+        field_threads, error_threads = gs_cy.krige.calc_field_krige_and_variance(
+            self.krig_mat, self.krig_vecs, self.cond, num_threads=2
+        )
+        np.testing.assert_allclose(field_threads, self.field_ref)
+        np.testing.assert_allclose(error_threads, self.error_ref)
 
     def test_calc_field_krige(self):
         field = gs_cy.krige.calc_field_krige(self.krig_mat, self.krig_vecs, self.cond)
diff --git a/tests/test_variogram.py b/tests/test_variogram.py
@@ -34,6 +34,58 @@ def test_directional(self):
         self.assertAlmostEqual(gamma[1, len(gamma[0]) // 2], var, places=2)
         self.assertAlmostEqual(gamma[1, -1], var, places=2)
 
+    def test_directional_separate_dirs(self):
+        pos = np.array(((0.0, 1.0), (0.0, 0.0)), dtype=np.double)
+        dirs = np.array(((1.0, 0.0), (1.0, 0.0)), dtype=np.double)
+        field = np.array(((1.0, 2.0),), dtype=np.double)
+        bins = np.array((0.0, 2.0), dtype=np.double)
+
+        _, counts = gs_cy.variogram.directional(
+            field, bins, pos, dirs, angles_tol=np.pi, separate_dirs=True
+        )
+
+        self.assertEqual(counts[0, 0], 1)
+        self.assertEqual(counts[1, 0], 0)
+
+    def test_directional_bandwidth_cressie(self):
+        pos = np.array(((0.0, 0.0, 1.0), (0.0, 1.0, 0.0)), dtype=np.double)
+        dirs = np.array(((1.0, 0.0),), dtype=np.double)
+        field = np.array(((1.0, 2.0, 5.0),), dtype=np.double)
+        bins = np.array((0.0, 2.0), dtype=np.double)
+
+        gamma, counts = gs_cy.variogram.directional(
+            field,
+            bins,
+            pos,
+            dirs,
+            angles_tol=np.pi,
+            bandwidth=0.5,
+            estimator_type="c",
+        )
+
+        self.assertEqual(counts[0, 0], 1)
+        f_diff = field[0, 2] - field[0, 0]
+        raw = np.sqrt(abs(f_diff))
+        expected = 0.5 * raw**4 / (0.457 + 0.494 + 0.045)
+        self.assertAlmostEqual(gamma[0, 0], expected, places=6)
+
+    def test_directional_error_checks(self):
+        pos = np.array(((0.0, 1.0), (0.0, 1.0)), dtype=np.double)
+        dirs = np.array(((1.0, 0.0),), dtype=np.double)
+        bins = np.array((0.0, 1.0), dtype=np.double)
+        field = np.array(((1.0, 2.0),), dtype=np.double)
+
+        with self.assertRaises(ValueError):
+            gs_cy.variogram.directional(field[:, :1], bins, pos, dirs)
+
+        with self.assertRaises(ValueError):
+            gs_cy.variogram.directional(
+                field, np.array((0.0,), dtype=np.double), pos, dirs
+            )
+
+        with self.assertRaises(ValueError):
+            gs_cy.variogram.directional(field, bins, pos, dirs, angles_tol=0.0)
+
     def test_unstructured(self):
         x = np.arange(1, 11, 1, dtype=np.double)
         z = np.array(
@@ -73,6 +125,46 @@ def test_unstructured(self):
         self.assertAlmostEqual(gamma[len(gamma) // 2], var, places=2)
         self.assertAlmostEqual(gamma[-1], var, places=2)
 
+    def test_unstructured_haversine(self):
+        pos = np.array(((0.0, 0.0), (0.0, 90.0)), dtype=np.double)
+        field = np.array(((1.0, 3.0),), dtype=np.double)
+        bins = np.array((0.0, 2.0), dtype=np.double)
+
+        gamma, counts = gs_cy.variogram.unstructured(
+            field, bins, pos, distance_type="h"
+        )
+
+        self.assertEqual(counts[0], 1)
+        self.assertAlmostEqual(gamma[0], 2.0, places=6)
+
+    def test_unstructured_num_threads(self):
+        pos = np.array(((0.0, 1.0, 2.0),), dtype=np.double)
+        field = np.array(((1.0, 3.0, 2.0),), dtype=np.double)
+        bins = np.array((0.0, 2.0), dtype=np.double)
+
+        gamma_default, counts_default = gs_cy.variogram.unstructured(field, bins, pos)
+        gamma_threads, counts_threads = gs_cy.variogram.unstructured(
+            field, bins, pos, num_threads=2
+        )
+
+        np.testing.assert_allclose(gamma_threads, gamma_default)
+        np.testing.assert_array_equal(counts_threads, counts_default)
+
+    def test_unstructured_error_checks(self):
+        pos = np.array(((0.0, 1.0), (0.0, 1.0)), dtype=np.double)
+        field = np.array(((1.0, 2.0),), dtype=np.double)
+        bins = np.array((0.0, 1.0), dtype=np.double)
+
+        with self.assertRaises(ValueError):
+            gs_cy.variogram.unstructured(field[:, :1], bins, pos)
+
+        with self.assertRaises(ValueError):
+            gs_cy.variogram.unstructured(field, np.array((0.0,), dtype=np.double), pos)
+
+        pos_bad = np.array(((0.0, 1.0), (0.0, 1.0), (0.0, 1.0)), dtype=np.double)
+        with self.assertRaises(ValueError):
+            gs_cy.variogram.unstructured(field, bins, pos_bad, distance_type="h")
+
     def test_structured(self):
         z = np.array(
             (41.2, 40.2, 39.7, 39.2, 40.1, 38.3, 39.1, 40.0, 41.1, 40.3),

Original file line number	Diff line number	Diff line change
`@@ -69,6 +69,8 @@ def test_summate(self):`
`69`	`69`	`)`
`70`	`70`	`summed = gs_cy.field.summate(cov_samples, z_1, z_2, pos)`
`71`	`71`	`np.testing.assert_allclose(summed_modes, summed)`
	`72`	`+ summed_threads = gs_cy.field.summate(cov_samples, z_1, z_2, pos, num_threads=2)`
	`73`	`+ np.testing.assert_allclose(summed_modes, summed_threads)`
`72`	`74`
`73`	`75`	`def test_summate_incompr(self):`
`74`	`76`	`# x = y = np.linspace(0,1,3)`