Merge pull request #290 from GeoStat-Framework/add_numpy2_support

Add numpy2 support

Author: MuellerSeb

.github/workflows/main.yml

@@ -20,17 +20,17 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install black 'isort[colors]<6'
+          pip install -v --editable .[lint]
 
       - name: black check
         run: |
@@ -40,63 +40,79 @@ jobs:
         run: |
           python -m isort --check --diff --color .
 
+      - name: cython-lint check
+        run: |
+          cython-lint src/pykrige/
+
   build_wheels:
-    name: wheels for ${{ matrix.cfg.os }} / ${{ matrix.cfg.arch }}
-    runs-on: ${{ matrix.cfg.os }}
+    name: wheels for ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        cfg:
-        - { os: ubuntu-latest, arch: x86_64 }
-        - { os: ubuntu-latest, arch: i686 }
-        - { os: windows-latest, arch: AMD64 }
-        - { os: windows-latest, arch: x86 }
-        - { os: macos-latest, arch: x86_64 }
-        - { os: macos-latest, arch: arm64 }
-        - { os: macos-latest, arch: universal2 }
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: '0'
 
       - name: Build wheels
-        uses: pypa/[email protected]
-        env:
-          CIBW_ARCHS: ${{ matrix.cfg.arch }}
+        uses: pypa/[email protected]
         with:
           output-dir: dist
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./dist/*.whl
 
   build_sdist:
-    name: sdist and coveralls
-    runs-on: ubuntu-latest
+    name: sdist on ${{ matrix.os }} with py ${{ matrix.ver.py }} numpy${{ matrix.ver.np }} scipy${{ matrix.ver.sp }}
+    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
+        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'}
+        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'}
+          - os: macos-14
+            ver: {py: '3.10', np: '==1.21.6', sp: '==1.7.2'}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: '0'
 
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+      - name: Set up Python ${{ matrix.ver.py }}
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: ${{ matrix.ver.py }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install build coveralls>=3.0.0
+          pip install build "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 }}" "scipy${{ matrix.ver.sp }}"
           python -m pytest --cov pykrige --cov-report term-missing -v tests/
           python -m coveralls --service=github
 
@@ -105,7 +121,8 @@ jobs:
           # PEP 517 package builder from pypa
           python -m build --sdist --outdir dist .
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
+        if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.9'
         with:
           path: dist/*.tar.gz
 

.readthedocs.yml

@@ -8,7 +8,7 @@ build:
 sphinx:
   configuration: docs/source/conf.py
 
-formats: all
+formats: [pdf]
 
 python:
   install:

CHANGELOG.md

@@ -2,6 +2,23 @@ Changelog
 =========
 
 
+Version 1.7.2
+-------------
+*May 27, 2024*
+
+**New features**
+
+* added support for numpy 2 ([#290](https://github.com/GeoStat-Framework/PyKrige/pull/290))
+
+**Changes**
+
+* remove universal2 wheels for macos (we already provide separate intel and arm64 wheels) ([#290](https://github.com/GeoStat-Framework/PyKrige/pull/290))
+
+**Bug fixes**
+
+* fixed cython long / longlong issue on windows ([#290](https://github.com/GeoStat-Framework/PyKrige/issues/290))
+
+
 Version 1.7.1
 -------------
 *October 14, 2023*

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2015-2022, PyKrige Developers
+Copyright (c) 2015-2024, PyKrige Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

pyproject.toml

@@ -2,9 +2,11 @@
 requires = [
     "setuptools>=64",
     "setuptools_scm>=7",
-    "oldest-supported-numpy",
-    "scipy>=1.1.0,<2",
-    "Cython>=0.28.3,<3.0",
+    "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",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -46,21 +48,21 @@ classifiers = [
     "Topic :: Utilities",
 ]
 dependencies = [
-    "numpy>=1.14.5,<2",
+    "numpy>=1.20.0",
     "scipy>=1.1.0,<2",
 ]
 
 [project.optional-dependencies]
 doc = [
-    "gstools>=1.3,<2",
+    "gstools>=1.4,<2",
     "pillow",
     "scikit-learn>=0.19",
     "m2r2>=0.2.8",
     "matplotlib>=3",
     "numpydoc>=1.1",
-    "sphinx>=4",
+    "sphinx>=7",
     "sphinx-gallery>=0.8",
-    "sphinx-rtd-theme>=1",
+    "sphinx-rtd-theme>=2",
 ]
 plot = ["matplotlib>=3,<4"]
 sklearn = ["scikit-learn>=0.19"]
@@ -69,6 +71,12 @@ test = [
     "scikit-learn>=0.19",
     "gstools>=1.4,<2",
 ]
+lint = [
+    "black>=23,<24",
+    "pylint",
+    "isort[colors]",
+    "cython-lint",
+]
 
 [project.urls]
 Changelog = "https://github.com/GeoStat-Framework/PyKrige/blob/main/CHANGELOG.md"
@@ -92,7 +100,16 @@ profile = "black"
 multi_line_output = 3
 
 [tool.black]
-target-version = ["py38"]
+target-version = [
+    "py38",
+    "py39",
+    "py310",
+    "py311",
+    "py312",
+]
+
+[tool.cython-lint]
+max-line-length = 100
 
 [tool.coverage]
     [tool.coverage.run]
@@ -121,6 +138,7 @@ target-version = ["py38"]
     [tool.pylint.message_control]
     disable = [
         "R0801",
+        "C0103",  # lots of invalid variable names
     ]
 
     [tool.pylint.reports]
@@ -137,12 +155,8 @@ target-version = ["py38"]
 [tool.cibuildwheel]
 # Switch to using build
 build-frontend = "build"
-# Disable building PyPy wheels on all platforms, 32bit for py3.10/11/12 and musllinux builds, py3.6/7
-skip = ["cp36-*", "cp37-*", "pp*", "cp31*-win32", "cp31*-manylinux_i686", "*-musllinux_*"]
+# Disable building PyPy wheels on all platforms, 32bit and musllinux builds, py3.6/7
+skip = ["cp36-*", "cp37-*", "pp*", "*-win32", "*-manylinux_i686", "*-musllinux_*"]
 # Run the package tests using `pytest`
 test-extras = "test"
 test-command = "pytest -v {package}/tests"
-# Skip trying to test arm64 builds on Intel Macs
-test-skip = "*-macosx_arm64 *-macosx_universal2:arm64"
-# no wheels for linux-32bit anymore for numpy>=1.22
-environment = "PIP_PREFER_BINARY=1"

src/pykrige/lib/__init__.py

@@ -1 +1 @@
-__all__ = ["cok", "lapack", "variogram_models"]
+__all__ = ["cok", "variogram_models"]