Merge pull request #376 from GeoStat-Framework/outsource_cython

Outsource Cython backend

Author: MuellerSeb

.github/workflows/main.yml

@@ -49,48 +49,20 @@ jobs:
         run: |
           python -m pylint src/gstools/
 
-      - name: cython-lint check
-        run: |
-          cython-lint src/gstools/
-
       - name: coveralls check
         run: |
           python -m pytest --cov gstools --cov-report term-missing -v tests/
           python -m coveralls --service=github
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-  build_wheels:
-    name: wheels for ${{ matrix.os }}
+  build:
+    name: test on ${{ matrix.os }} with py ${{ matrix.ver.py }} numpy${{ matrix.ver.np }} scipy${{ matrix.ver.sp }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        # macos-13 is an intel runner, macos-14 is apple silicon
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
-
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: "0"
-
-      - name: Build wheels
-        uses: pypa/cibuildwheel@v2.22.0
-        with:
-          output-dir: dist-wheel-${{ matrix.os }}
-
-      - uses: actions/upload-artifact@v4
-        with:
-          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 }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        os: [ubuntu-latest, ubuntu-24.04-arm, 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" }
@@ -101,6 +73,8 @@ jobs:
           - { py: "3.13", np: "==2.1.0", sp: "==1.14.1" }
           - { py: "3.13", np: ">=2.1.0", sp: ">=1.14.1" }
         exclude:
+          - os: ubuntu-24.04-arm
+            ver: { py: "3.8", np: "==1.20.0", sp: "==1.5.4" }
           - os: macos-14
             ver: { py: "3.8", np: "==1.20.0", sp: "==1.5.4" }
           - os: macos-14
@@ -123,8 +97,6 @@ jobs:
           pip install build
 
       - name: Install GSTools
-        env:
-          GSTOOLS_BUILD_PARALLEL: 1
         run: |
           pip install -v --editable .[test]
 
@@ -133,27 +105,25 @@ jobs:
           pip install "numpy${{ matrix.ver.np }}" "scipy${{ matrix.ver.sp }}"
           python -m pytest -v tests/
 
-      - name: Build sdist
+      - name: Build dist
         run: |
           # PEP 517 package builder from pypa
-          python -m build --sdist --outdir dist-sdist .
+          python -m build .
 
       - uses: actions/upload-artifact@v4
         if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.11'
         with:
-          name: dist-sdist
-          path: dist-sdist/*.tar.gz
+          name: dist
+          path: dist/*
 
   upload_to_pypi:
-    needs: [build_wheels, build_sdist]
+    needs: [build]
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/download-artifact@v4
         with:
-          pattern: dist-*
-          merge-multiple: true
-          path: dist
+          name: dist
 
       - name: Publish to Test PyPI
         # only if working on main

MANIFEST.in

@@ -88,38 +88,33 @@ When using conda, the parallel version of GSTools is installed per default.
 
 ***Parallelizing Cython***
 
-To enable the OpenMP support in Cython when using pip, you have to provide a C
-compiler and OpenMP. Parallel support is controlled by an environment variable
-``GSTOOLS_BUILD_PARALLEL``, that can be ``0`` or ``1`` (interpreted as ``0``
-if not present). GSTools then needs to be installed from source:
+For parallel support, the `GSTools-Cython <https://github.com/GeoStat-Framework/GSTools-Cython>`_
+backend needs to be compiled from source the following way:
 
 .. code-block:: none
 
     export GSTOOLS_BUILD_PARALLEL=1
-    pip install --no-binary=gstools gstools
+    pip install --no-binary=gstools-cython gstools
 
-Note, that the ``--no-binary=gstools`` option forces pip to not use a wheel
-for GSTools.
+You have to provide a C compiler and OpenMP to compile GSTools-Cython with parallel support.
+The feature is controlled by the environment variable
+``GSTOOLS_BUILD_PARALLEL``, that can be ``0`` or ``1`` (interpreted as ``0`` if not present).
+Note, that the ``--no-binary=gstools-cython`` option forces pip to not use a wheel
+for the GSTools-Cython backend.
 
 For the development version, you can do almost the same:
 
 .. code-block:: none
 
     export GSTOOLS_BUILD_PARALLEL=1
+    pip install git+git://github.com/GeoStat-Framework/GSTools-Cython.git@main
     pip install git+git://github.com/GeoStat-Framework/GSTools.git@main
 
 
 ***Using GSTools-Core for parallelization and even more speed***
 
 You can install the optional dependency `GSTools-Core <https://github.com/GeoStat-Framework/GSTools-Core>`_,
-which is a re-implementation of the algorithms used in GSTools. The new
-package uses the language Rust and it should be faster (in some cases by orders
-of magnitude), safer, and it will potentially completely replace the current
-standard implementation in Cython. Once the package GSTools-Core is available
-on your machine, it will be used by default. In case you want to switch back to
-the Cython implementation, you can set
-:code:`gstools.config.USE_GSTOOLS_CORE=False` in your code. This also works at
-runtime. You can install the optional dependency e.g. by
+which is a re-implementation of GSTools-Cython:
 
 .. code-block:: none
 
@@ -131,8 +126,12 @@ or by manually installing the package
 
     pip install gstools-core
 
-GSTools-Core will automatically run in parallel, without having to use provide
-OpenMP or a local C compiler.
+The new package uses the language Rust and it should be safer and faster (in some cases by orders of magnitude).
+Once the package GSTools-Core is available on your machine, it will be used by default.
+In case you want to switch back to the Cython implementation, you can set
+:code:`gstools.config.USE_GSTOOLS_CORE=False` in your code. This also works at runtime.
+
+GSTools-Core will automatically run in parallel, without having to provide OpenMP or a local C compiler.
 
 
 Citation

docs/source/index.rst

@@ -1,13 +1,11 @@
+
+
 [build-system]
 requires = [
-    "setuptools>=64",
-    "setuptools_scm>=7",
-    "numpy>=2.0.0rc1,<2.3; python_version >= '3.9'",
-    "oldest-supported-numpy; python_version < '3.9'",
-    "Cython>=3.0.10,<3.1.0",
-    "extension-helpers>=1",
+    "hatchling>=1.8.0",
+    "hatch-vcs",
 ]
-build-backend = "setuptools.build_meta"
+build-backend = "hatchling.build"
 
 [project]
 requires-python = ">=3.8"
@@ -17,7 +15,7 @@ authors = [
     {name = "Sebastian Müller, Lennart Schüler", email = "info@geostat-framework.org"},
 ]
 readme = "README.md"
-license = {text = "LGPL-3.0"}
+license = "LGPL-3.0"
 dynamic = ["version"]
 classifiers = [
     "Development Status :: 5 - Production/Stable",
@@ -47,6 +45,7 @@ classifiers = [
     "Topic :: Utilities",
 ]
 dependencies = [
+    "gstools-cython>=1,<2",
     "emcee>=3.0.0",
     "hankel>=1.0.0",
     "meshio>=5.1.0",
@@ -78,7 +77,6 @@ lint = [
     "black>=24",
     "pylint",
     "isort[colors]",
-    "cython-lint",
 ]
 
 [project.urls]
@@ -89,14 +87,25 @@ Homepage = "https://geostat-framework.org/#gstools"
 Source = "https://github.com/GeoStat-Framework/GSTools"
 Tracker = "https://github.com/GeoStat-Framework/GSTools/issues"
 
-[tool.setuptools]
-license-files = ["LICENSE"]
+[tool.hatch.version]
+source = "vcs"
+fallback_version = "0.0.0.dev0"
 
-[tool.setuptools_scm]
-write_to = "src/gstools/_version.py"
-write_to_template = "__version__ = '{version}'"
+[tool.hatch.version.raw-options]
 local_scheme = "no-local-version"
-fallback_version = "0.0.0.dev0"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/gstools/_version.py"
+template = "__version__ = '{version}'"
+
+[tool.hatch.build.targets.sdist]
+include = [
+  "/src",
+  "/tests",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/gstools"]
 
 [tool.isort]
 profile = "black"
@@ -160,12 +169,3 @@ target-version = [
     max-attributes = 30
     max-public-methods = 80
     max-positional-arguments=20
-
-[tool.cibuildwheel]
-# Switch to using build
-build-frontend = "build"
-# Disable building PyPy wheels on all platforms, 32bit for py3.10/11/12/13, 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"

pyproject.toml

@@ -20,12 +20,12 @@
 from copy import deepcopy as dcp
 
 import numpy as np
+from gstools_cython.field import summate as summate_c
+from gstools_cython.field import summate_fourier as summate_fourier_c
+from gstools_cython.field import summate_incompr as summate_incompr_c
 
 from gstools import config
 from gstools.covmodel.base import CovModel
-from gstools.field.summator import summate as summate_c
-from gstools.field.summator import summate_fourier as summate_fourier_c
-from gstools.field.summator import summate_incompr as summate_incompr_c
 from gstools.random.rng import RNG
 from gstools.tools.geometric import generate_grid