Merge pull request #308 from GeoStat-Framework/py314_support

support py313 and py314

Author: MuellerSeb

.github/workflows/main.yml

@@ -16,16 +16,16 @@ jobs:
   source_check:
     name: source check
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: "0"
 
-      - name: Set up Python 3.9
+      - name: Set up Python 3.11
         uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
 
       - name: Install dependencies
         run: |
@@ -34,7 +34,7 @@ jobs:
 
       - name: black check
         run: |
-          python -m black --check  --diff --color .
+          python -m black --check --diff --color .
 
       - name: isort check
         run: |
@@ -50,49 +50,48 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-15-intel, macos-latest] # windows-11-arm (no scipy)
 
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: '0'
+          fetch-depth: "0"
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.18.0
+        uses: pypa/cibuildwheel@v3.2.1
         with:
-          output-dir: dist
+          output-dir: dist-wheel-${{ matrix.os }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          path: ./dist/*.whl
+          name: dist-wheel-${{ matrix.os }}
+          path: ./dist-wheel-${{ matrix.os }}/*.whl
 
   build_sdist:
-    name: sdist on ${{ matrix.os }} with py ${{ matrix.ver.py }} numpy${{ matrix.ver.np }} scipy${{ matrix.ver.sp }}
+    name: sdist on ${{ matrix.os }} with py==${{ matrix.ver.py }} numpy${{ matrix.ver.np }} scipy${{ matrix.ver.sp }} sklearn${{ matrix.ver.sk }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
-        # https://github.com/scipy/oldest-supported-numpy/blob/main/setup.cfg
+        os:
+          [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-14]
         ver:
-          - {py: '3.8', np: '==1.20.0', sp: '==1.5.4'}
-          - {py: '3.9', np: '==1.20.0', sp: '==1.5.4'}
-          - {py: '3.10', np: '==1.21.6', sp: '==1.7.2'}
-          - {py: '3.11', np: '==1.23.2', sp: '==1.9.2'}
-          - {py: '3.12', np: '==1.26.2', sp: '==1.11.2'}
-          - {py: '3.12', np: '>=2.0.0rc1', sp: '>=1.13.0'}
+          - { py: "3.9", np: "==1.20.0", sp: "==1.5.4", sk: "==0.24.0" }
+          - { py: "3.10", np: "==1.21.6", sp: "==1.7.2", sk: "==1.0.2" }
+          - { py: "3.11", np: "==1.23.2", sp: "==1.9.2", sk: "==1.1.3" }
+          - { py: "3.12", np: "==1.26.2", sp: "==1.11.2", sk: "==1.3.1" }
+          - { py: "3.13", np: "==2.1.0", sp: "==1.14.1", sk: "==1.5.2" }
+          - { py: "3.14", np: "==2.3.2", sp: "==1.16.1", sk: "==1.7.2" }
+          - { py: "3.14", np: ">=2.3.2", sp: ">=1.16.1", sk: ">=1.7.2" }
         exclude:
           - os: macos-14
-            ver: {py: '3.8', np: '==1.20.0', sp: '==1.5.4'}
-          - os: macos-14
-            ver: {py: '3.9', np: '==1.20.0', sp: '==1.5.4'}
+            ver: { py: "3.9", np: "==1.20.0", sp: "==1.5.4", sk: "==0.24.0" }
           - os: macos-14
-            ver: {py: '3.10', np: '==1.21.6', sp: '==1.7.2'}
+            ver: { py: "3.10", np: "==1.21.6", sp: "==1.7.2", sk: "==1.0.2" }
     steps:
       - uses: actions/checkout@v4
         with:
-          fetch-depth: '0'
+          fetch-depth: "0"
 
       - name: Set up Python ${{ matrix.ver.py }}
         uses: actions/setup-python@v5
@@ -102,41 +101,74 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build "coveralls>=3.0.0"
+          pip install build
 
-      - name: Install PyKrige
+      - name: Install pykrige
         run: |
           pip install -v --editable .[test]
 
+      - name: Install pinned dependencies
+        run: |
+          pip install "numpy${{ matrix.ver.np }}" "scipy${{ matrix.ver.sp }}" "scikit-learn${{ matrix.ver.sk }}"
+
       - name: Run tests
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          pip install "numpy${{ matrix.ver.np }}" "scipy${{ matrix.ver.sp }}"
-          python -m pytest --cov pykrige --cov-report term-missing -v tests/
-          python -m coveralls --service=github
+          python -m pytest -v tests/
 
       - name: Build sdist
         run: |
           # PEP 517 package builder from pypa
-          python -m build --sdist --outdir dist .
+          python -m build --sdist --outdir dist-sdist .
 
-      - uses: actions/upload-artifact@v3
-        if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.9'
+      - uses: actions/upload-artifact@v4
+        if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.11'
         with:
-          path: dist/*.tar.gz
+          name: dist-sdist
+          path: dist-sdist/*.tar.gz
+
+  coverage:
+    name: coverage
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install "coveralls>=3.0.0"
+
+      - name: Install pykrige
+        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 pykrige --cov-report term-missing -v tests/
+          python -m coveralls --service=github
 
   upload_to_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/download-artifact@v2
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: dist-*
+          merge-multiple: true
           path: dist
 
       - name: Publish to Test PyPI
+        # only if working on main
         if: github.ref == 'refs/heads/main'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:

CHANGELOG.md

@@ -2,6 +2,23 @@ Changelog
 =========
 
 
+Version 1.7.3
+-------------
+*October 16, 2025*
+
+See [#308](https://github.com/GeoStat-Framework/PyKrige/pull/308)
+
+**Changes**
+
+* add wheels for Python 3.13 and 3.14 as well as for Linux aarch64
+* pin the earliest supported scikit-learn release alongside NumPy/SciPy in the sdist CI
+* allow the housing-based classification/regression tests to attempt loading the California housing dataset and skip cleanly when the download fails
+
+**Bug fixes**
+
+* prevent `ValueError` from NumPy when pseudo inverse kriging statistics encounter duplicate coordinates by keeping distance vectors 1-D
+
+
 Version 1.7.2
 -------------
 *May 27, 2024*

examples/05_kriging_1D.py

@@ -4,6 +4,7 @@
 
 An example of 1D kriging with PyKrige
 """
+
 import matplotlib.pyplot as plt
 import numpy as np
 

examples/06_exact_values_example_1D.py

@@ -4,7 +4,7 @@
 ============
 
 PyKrige demonstration and usage
-as a non-exact interpolator in 1D. 
+as a non-exact interpolator in 1D.
 """
 
 import matplotlib.pyplot as plt

pyproject.toml

@@ -1,17 +1,17 @@
 [build-system]
 requires = [
-    "setuptools>=64",
-    "setuptools_scm>=7",
-    "numpy>=2.0.0rc1,<2.3; python_version >= '3.9'",
-    "scipy>=1.13.0,<2; python_version >= '3.9'",
-    "oldest-supported-numpy; python_version < '3.9'",
-    "scipy>=1.3.2,<2; python_version < '3.9'",
-    "Cython>=3.0.10,<3.1.0",
+    "setuptools>=77",
+    "wheel",
+    "Cython>=3",
+    "numpy>=2",
+    "scipy>=1.5.4",
+    "pentapy>=1.1.0,<2",
+    "setuptools_scm[toml]>=7",
 ]
 build-backend = "setuptools.build_meta"
 
 [project]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 name = "PyKrige"
 description = "Kriging Toolkit for Python."
 authors = [
@@ -21,26 +21,27 @@ maintainers = [
     {name = "Sebastian Müller, Roman Yurchak", email = "[email protected]"},
 ]
 readme = "README.md"
-license = {text = "BSD-3-Clause"}
+license = "BSD-3-Clause"
+license-files = ["LICENSE"]
 dynamic = ["version"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
     "Intended Audience :: End Users/Desktop",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: BSD License",
     "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 :: 3.8",
     "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 :: Mathematics",
@@ -49,7 +50,7 @@ classifiers = [
 ]
 dependencies = [
     "numpy>=1.20.0",
-    "scipy>=1.1.0,<2",
+    "scipy>=1.5.4,<2",
 ]
 
 [project.optional-dependencies]
@@ -86,9 +87,6 @@ Homepage = "https://github.com/GeoStat-Framework/PyKrige"
 Source = "https://github.com/GeoStat-Framework/PyKrige"
 Tracker = "https://github.com/GeoStat-Framework/PyKrige/issues"
 
-[tool.setuptools]
-license-files = ["LICENSE"]
-
 [tool.setuptools_scm]
 write_to = "src/pykrige/_version.py"
 write_to_template = "__version__ = '{version}'"
@@ -155,8 +153,11 @@ max-line-length = 100
 [tool.cibuildwheel]
 # Switch to using build
 build-frontend = "build"
-# Disable building PyPy wheels on all platforms, 32bit and musllinux builds, py3.6/7
-skip = ["cp36-*", "cp37-*", "pp*", "*-win32", "*-manylinux_i686", "*-musllinux_*"]
+# Disable building py3.6/7/8, pp3.8, 32bit linux
+skip = ["*-win32", "*_i686", "*-musllinux_*", "cp31?t-*"]
 # Run the package tests using `pytest`
 test-extras = "test"
 test-command = "pytest -v {package}/tests"
+
+environment.PIP_ONLY_BINARY = "numpy,scipy"
+environment.PIP_PREFER_BINARY = "1"

src/pykrige/core.py

@@ -700,7 +700,7 @@ def _krige(
     # measurement points (X) and the kriging point (coords)
     if coordinates_type == "euclidean":
         d = squareform(pdist(X, metric="euclidean"))
-        bd = np.squeeze(cdist(X, coords[None, :], metric="euclidean"))
+        bd = np.asarray(cdist(X, coords[None, :], metric="euclidean")).ravel()
 
     # geographic coordinate distances still calculated in the old way...
     # assume X[:, 0] ('x') => lon, X[:, 1] ('y') => lat
@@ -709,12 +709,14 @@ def _krige(
         x1, x2 = np.meshgrid(X[:, 0], X[:, 0], sparse=True)
         y1, y2 = np.meshgrid(X[:, 1], X[:, 1], sparse=True)
         d = great_circle_distance(x1, y1, x2, y2)
-        bd = great_circle_distance(
-            X[:, 0],
-            X[:, 1],
-            coords[0] * np.ones(X.shape[0]),
-            coords[1] * np.ones(X.shape[0]),
-        )
+        bd = np.asarray(
+            great_circle_distance(
+                X[:, 0],
+                X[:, 1],
+                coords[0] * np.ones(X.shape[0]),
+                coords[1] * np.ones(X.shape[0]),
+            )
+        ).ravel()
 
     # this check is done when initializing variogram, but kept here anyways...
     else:
@@ -725,7 +727,7 @@ def _krige(
     # check if kriging point overlaps with measurement point
     if np.any(np.absolute(bd) <= 1e-10):
         zero_value = True
-        zero_index = np.where(bd <= 1e-10)[0][0]
+        zero_index = int(np.flatnonzero(bd <= 1e-10)[0])
 
     # set up kriging matrix
     n = X.shape[0]

tests/test_classification_krige.py

@@ -69,14 +69,13 @@ def test_krige_classification_housing():
 
     try:
         housing = fetch_california_housing()
-    except (ssl.SSLError, urllib.error.URLError):
-        ssl._create_default_https_context = ssl._create_unverified_context
-        try:
-            housing = fetch_california_housing()
-        except PermissionError:
-            # This can raise permission error on Appveyor
-            pytest.skip("Failed to load california housing dataset")
-        ssl._create_default_https_context = ssl.create_default_context
+    except (
+        ssl.SSLError,
+        urllib.error.URLError,
+        urllib.error.HTTPError,
+        PermissionError,
+    ):
+        pytest.skip("Failed to load california housing dataset")
 
     # take only first 1000
     p = housing["data"][:1000, :-2]

tests/test_core.py

@@ -2,6 +2,7 @@
 Testing code.
 Updated BSM February 2017
 """
+
 import os
 import sys