Merge pull request #15 from GeoStat-Framework/cythonize_laplace

MuellerSeb · web-flow · commit 9833866f1ab9 · 2025-10-16T15:51:46.000+02:00
Cythonize laplace
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -19,6 +19,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: "0"
 
       - name: Set up Python 3.11
         uses: actions/setup-python@v5
@@ -28,8 +30,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install --editable .[check,test]
-          pip install "coveralls>=3.0.0"
+          pip install -v --editable '.[check]'
 
       - name: black check
         run: |
@@ -43,64 +44,137 @@ jobs:
         run: |
           python -m isort --check --diff --color .
 
-      - name: pylint check
+      - name: ruff check
         run: |
-          python -m pylint src/anaflow/
+          python -m ruff check src/
 
-      - name: coveralls check
+      - name: cython-lint check
         run: |
-          python -m pytest --cov anaflow --cov-report term-missing -v tests/
-          python -m coveralls --service=github
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          cython-lint src/anaflow/
 
-  build_sdist:
-    name: sdist on ${{ matrix.os }} with py ${{ matrix.python-version }}
+  build_wheels:
+    name: wheels for ${{ matrix.os }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-13]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
+        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@v3.2.1
+        with:
+          output-dir: dist-wheel-${{ matrix.os }}
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-wheel-${{ matrix.os }}
+          path: ./dist-wheel-${{ matrix.os }}/*.whl
 
-      - name: Set up Python ${{ matrix.python-version }}
+  build_sdist:
+    name: sdist on ${{ matrix.os }} with py ${{ matrix.ver.py }} numpy${{ matrix.ver.np }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          [ubuntu-latest, ubuntu-24.04-arm, windows-latest, macos-14]
+        ver:
+          - { 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: "3.13", np: "==2.1.0", sp: "==1.14.1" }
+          - { py: "3.14", np: "==2.3.2", sp: "==1.16.1" }
+          - { py: "3.14", np: ">=2.3.2", sp: ">=1.16.1" }
+        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
+            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@v4
+        with:
+          fetch-depth: "0"
+
+      - name: Set up Python ${{ matrix.ver.py }}
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.ver.py }}
 
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
           pip install build
-          pip install --editable .[test]
+
+      - name: Install anaflow
+        run: |
+          pip install -v --editable .[test]
 
       - name: Run tests
         run: |
-          python -m pytest --cov anaflow --cov-report term-missing -v tests/
+          pip install "numpy${{ matrix.ver.np }}" "scipy${{ matrix.ver.sp }}"
+          python -m pytest -v tests/
 
       - name: Build sdist
         run: |
-          python -m build
+          # PEP 517 package builder from pypa
+          python -m build --sdist --outdir dist-sdist .
 
       - uses: actions/upload-artifact@v4
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
+        if: matrix.os == 'ubuntu-latest' && matrix.ver.py == '3.11'
         with:
-          name: dist
-          path: dist/*
+          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 anaflow
+        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 anaflow --cov-report term-missing -v tests/
+          python -m coveralls --service=github
 
   upload_to_pypi:
-    needs: [build_sdist]
+    needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/download-artifact@v4
         with:
-          name: dist
+          pattern: dist-*
+          merge-multiple: true
           path: dist
 
       - name: Publish to Test PyPI
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -0,0 +1,4 @@
+prune **
+recursive-include tests *.py
+recursive-include src/anaflow *.py *.pyx
+include LICENSE README.md pyproject.toml setup.py
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,24 +1,29 @@
 [build-system]
 requires = [
-    "hatchling>=1.8.0",
-    "hatch-vcs",
+    "setuptools>=77",
+    "wheel",
+    "Cython>=3",
+    "numpy>=2",
+    "scipy>=1.5.4",
+    "pentapy>=1.1.0,<2",
+    "setuptools_scm[toml]>=7",
 ]
-build-backend = "hatchling.build"
+build-backend = "setuptools.build_meta"
 
 [project]
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 name = "anaflow"
 authors = [{name = "Sebastian Mueller", email = "sebastian.mueller@ufz.de"}]
 readme = "README.md"
 license = "MIT"
+license-files = ["LICENSE"]
 dynamic = ["version"]
 description = "AnaFlow - analytical solutions for the groundwater-flow equation."
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Developers",
     "Intended Audience :: End Users/Desktop",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: MIT License",
     "Natural Language :: English",
     "Operating System :: MacOS",
     "Operating System :: MacOS :: MacOS X",
@@ -29,20 +34,20 @@ classifiers = [
     "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 :: Software Development",
     "Topic :: Utilities",
 ]
 dependencies = [
-    "numpy>=1.14.5",
+    "numpy>=1.20.0",
     "pentapy>=1.1.0,<2",
-    "scipy>=1.1.0",
+    "scipy>=1.5.4",
 ]
 
 [project.optional-dependencies]
@@ -58,7 +63,8 @@ test = ["pytest-cov>=3"]
 check = [
   "black>=25",
   "isort[colors]",
-  "pylint",
+  "ruff>=0.5.0",
+  "cython-lint",
 ]
 
 [project.urls]
@@ -69,33 +75,18 @@ Tracker = "https://github.com/GeoStat-Framework/anaflow/issues"
 Changelog = "https://github.com/GeoStat-Framework/anaflow/blob/main/CHANGELOG.md"
 Conda-Forge = "https://anaconda.org/conda-forge/anaflow"
 
-[tool.hatch.version]
-source = "vcs"
-fallback_version = "0.0.0.dev0"
-
-[tool.hatch.version.raw-options]
+[tool.setuptools_scm]
+write_to = "src/anaflow/_version.py"
+write_to_template = "__version__ = '{version}'"
 local_scheme = "no-local-version"
-
-[tool.hatch.build.hooks.vcs]
-version-file = "src/anaflow/_version.py"
-template = "__version__ = '{version}'"
-
-[tool.hatch.build.targets.sdist]
-include = [
-  "/src",
-  "/tests",
-]
-
-[tool.hatch.build.targets.wheel]
-packages = ["src/anaflow"]
+fallback_version = "0.0.0.dev0"
 
 [tool.isort]
 profile = "black"
 multi_line_output = 3
 
 [tool.black]
 target-version = [
-    "py38",
     "py39",
     "py310",
     "py311",
@@ -120,27 +111,27 @@ target-version = [
         "def __str__",
     ]
 
-[tool.pylint]
-    [tool.pylint.master]
-    extension-pkg-whitelist = [
-        "numpy",
-        "scipy",
-    ]
-    ignore = "_version.py"
-
-    [tool.pylint.message_control]
-    disable = [
-        "R0801",
-    ]
-
-    [tool.pylint.reports]
-    output-format = "colorized"
+[tool.ruff]
+line-length = 88
+target-version = "py39"
+exclude = ["_version.py"]
+
+[tool.ruff.lint]
+select = [
+    "E",
+    "F",
+    "W",
+    "I",
+]
 
-    [tool.pylint.design]
-    max-args = 25
-    max-locals = 50
-    max-branches = 30
-    max-statements = 80
-    max-attributes = 25
-    max-public-methods = 75
-    max-positional-arguments=25
+[tool.cibuildwheel]
+# Switch to using build
+build-frontend = "build"
+# 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"
diff --git a/setup.py b/setup.py
@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import numpy as np
+from Cython.Build import cythonize
+from setuptools import Extension, setup
+
+SRC_DIR = Path("src")
+MODULE_PATH = SRC_DIR / "anaflow" / "flow"
+MODULE_NAME = "anaflow.flow._laplace_accel"
+
+extensions = [
+    Extension(
+        MODULE_NAME,
+        [str(MODULE_PATH / "_laplace_accel.pyx")],
+        include_dirs=[np.get_include()],
+    )
+]
+
+extensions = cythonize(
+    extensions,
+    language_level=3,
+    compiler_directives={
+        "boundscheck": False,
+        "wraparound": False,
+        "initializedcheck": False,
+    },
+)
+
+setup(ext_modules=extensions, package_dir={"": "src"})
diff --git a/src/anaflow/flow/_laplace_accel.pyx b/src/anaflow/flow/_laplace_accel.pyx
diff --git a/src/anaflow/flow/laplace.py b/src/anaflow/flow/laplace.py
