packaging: use pyproject.toml

.github/workflows/main.yml

@@ -14,8 +14,8 @@ on:
   workflow_dispatch:
 
 jobs:
-  format_check:
-    name: format check
+  source_check:
+    name: source check
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -35,7 +35,7 @@ jobs:
 
       - name: black check
         run: |
-          python -m black --check pykrige/ examples/ tests/
+          python -m black --check  --diff --color pykrige/ examples/ tests/
 
   build_sdist:
     name: sdist and coveralls
@@ -56,15 +56,8 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r requirements_setup.txt
-          pip install -r requirements.txt
-          pip install -r requirements_test.txt
-          pip install coveralls>=3.0.0
-
-      - name: Build sdist
-        run: |
-          python setup.py sdist -d dist
-          python setup.py build_ext --inplace
+          pip install build coveralls>=3.0.0
+          pip install --editable .[test]
 
       - name: Run tests
         env:
@@ -73,6 +66,11 @@ jobs:
           python -m pytest --cov pykrige --cov-report term-missing -v tests/
           python -m coveralls --service=github
 
+      - name: Build sdist
+        run: |
+          # PEP 517 package builder from pypa
+          python -m build --sdist --outdir dist .
+
       - uses: actions/upload-artifact@v2
         with:
           path: dist/*.tar.gz
@@ -91,11 +89,10 @@ jobs:
           fetch-depth: '0'
 
       - name: Build wheels
-        uses: joerick/cibuildwheel@v1.10.0
+        uses: pypa/cibuildwheel@v2.1.1
         env:
           CIBW_BUILD: cp36-* cp37-* cp38-* cp39-*
-          CIBW_BEFORE_BUILD: pip install numpy==1.19.* scipy==1.5.* cython==0.29.* setuptools
-          CIBW_TEST_REQUIRES: pytest scikit-learn
+          CIBW_TEST_EXTRAS: test
           CIBW_TEST_COMMAND: pytest -v {project}/tests
         with:
           output-dir: dist

.readthedocs.yml

@@ -0,0 +1,14 @@
+version: 2
+
+sphinx:
+  configuration: docs/source/conf.py
+
+formats: all
+
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

MANIFEST.in

@@ -1,7 +1,7 @@
-include README.md
-include MANIFEST.in
-include setup.py
-include setup.cfg
+prune *
+graft tests
 recursive-include pykrige *.py *.pyx *.pxd
-recursive-include tests *.py *.txt *.asc
-include LICENSE
+recursive-exclude pykrige *.c *.cpp
+include LICENSE README.md pyproject.toml setup.py setup.cfg
+exclude CHANGELOG.md
+global-exclude __pycache__ *.py[cod] .*

pyproject.toml

@@ -0,0 +1,63 @@
+[build-system]
+requires = [
+    "setuptools>=42",
+    "wheel",
+    "setuptools_scm[toml]>=3.5",
+    "oldest-supported-numpy",
+    "scipy>=1.1.0,<2",
+    "Cython>=0.28.3,<3.0",
+]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+write_to = "pykrige/_version.py"
+write_to_template = "__version__ = '{version}'"
+local_scheme = "no-local-version"
+fallback_version = "0.0.0.dev0"
+
+[tool.black]
+target-version = [
+    "py36",
+    "py37",
+    "py38",
+]
+
+[tool.coverage]
+    [tool.coverage.run]
+    source = ["pykrige"]
+    omit = [
+        "*docs*",
+        "*examples*",
+        "*tests*",
+    ]
+
+    [tool.coverage.report]
+    exclude_lines = [
+        "pragma: no cover",
+        "def __repr__",
+        "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.pylint.design]
+    max-args = 20
+    max-locals = 50
+    max-branches = 30
+    max-statements = 80
+    max-attributes = 25
+    max-public-methods = 75

setup.cfg

@@ -1,3 +1,82 @@
 [metadata]
-description-file = README.md
+name = PyKrige
+description = Kriging Toolkit for Python.
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://github.com/GeoStat-Framework/PyKrige
+author = Benjamin S. Murphy, Sebastian Müller
+author_email = info@geostat-framework.org
+maintainer = Sebastian Mueller, Roman Yurchak
+maintainer_email = info@geostat-framework.org
+license = BSD-3-Clause
 license_file = LICENSE
+platforms = any
+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 :: MacOS
+    Operating System :: MacOS :: MacOS X
+    Operating System :: Microsoft
+    Operating System :: Microsoft :: Windows
+    Operating System :: POSIX
+    Operating System :: Unix
+    Programming Language :: Python
+    Programming Language :: Python :: 3
+    Programming Language :: Python :: 3 :: Only
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
+    Programming Language :: Python :: 3.8
+    Programming Language :: Python :: 3.9
+    Topic :: Scientific/Engineering
+    Topic :: Scientific/Engineering :: GIS
+    Topic :: Utilities
+project_urls =
+    Documentation = https://pykrige.readthedocs.io
+    Source = https://github.com/GeoStat-Framework/PyKrige
+    Tracker = https://github.com/GeoStat-Framework/PyKrige/issues
+    Changelog = https://github.com/GeoStat-Framework/PyKrige/blob/main/CHANGELOG.md
+    Conda-Forge = https://anaconda.org/conda-forge/pykrige
+
+[options]
+packages = find:
+install_requires =
+    numpy>=1.14.5,<2
+    scipy>=1.1.0,<2
+python_requires = >=3.6
+include_package_data = True
+zip_safe = False
+
+[options.packages.find]
+exclude =
+    tests*
+    docs*
+
+[options.extras_require]
+doc =
+    gstools>=1.1.1,<2
+    pillow
+    scikit-learn>=0.19
+    m2r2>=0.2.8,<1
+    matplotlib>=3,<4
+    meshzoo>=0.7,<1
+    numpydoc>=1.1,<2
+    pykrige>=1.5,<2
+    pyvista>=0.31,<1
+    sphinx>=3,<4
+    sphinx-gallery>=0.8,<1
+    sphinx-rtd-theme>=0.5,<1
+    sphinxcontrib-napoleon
+plot =
+    matplotlib>=3,<4
+sklearn =
+    scikit-learn>=0.19
+test =
+    coverage[toml]>=5.2.1,<6
+    pytest>=6.0,<7
+    pytest-cov>=2.11.0,<3
+    gstools>=1.1.1,<2
+    scikit-learn>=0.19

setup.py

@@ -1,12 +1,10 @@
 # -*- coding: utf-8 -*-
 """Kriging Toolkit for Python."""
 import os
-from setuptools import setup, find_packages, Extension
+from setuptools import setup, Extension
 from Cython.Build import cythonize
 import numpy as np
 
-HERE = os.path.abspath(os.path.dirname(__file__))
-
 # cython extensions ###########################################################
 
 CY_MODULES = []
@@ -26,86 +24,10 @@
 )
 EXT_MODULES = cythonize(CY_MODULES)  # annotate=True
 
-# This is an important part. By setting this compiler directive, cython will
-# embed signature information in docstrings. Sphinx then knows how to extract
-# and use those signatures.
-# python setup.py build_ext --inplace --> then sphinx build
+# embed signatures for sphinx
 for ext_m in EXT_MODULES:
     ext_m.cython_directives = {"embedsignature": True}
 
 # setup #######################################################################
 
-with open(os.path.join(HERE, "README.md"), encoding="utf-8") as f:
-    README = f.read()
-with open(os.path.join(HERE, "requirements.txt"), encoding="utf-8") as f:
-    REQ = f.read().splitlines()
-with open(os.path.join(HERE, "requirements_setup.txt"), encoding="utf-8") as f:
-    REQ_SETUP = f.read().splitlines()
-with open(os.path.join(HERE, "requirements_test.txt"), encoding="utf-8") as f:
-    REQ_TEST = f.read().splitlines()
-with open(os.path.join(HERE, "docs", "requirements_doc.txt"), encoding="utf-8") as f:
-    REQ_DOC = f.read().splitlines()
-
-REQ_DEV = REQ_SETUP + REQ_TEST + REQ_DOC
-
-DOCLINE = __doc__.split("\n")[0]
-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 :: MacOS",
-    "Operating System :: MacOS :: MacOS X",
-    "Operating System :: Microsoft",
-    "Operating System :: Microsoft :: Windows",
-    "Operating System :: POSIX",
-    "Operating System :: Unix",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.6",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3 :: Only",
-    "Topic :: Scientific/Engineering",
-    "Topic :: Scientific/Engineering :: GIS",
-    "Topic :: Utilities",
-]
-
-setup(
-    name="PyKrige",
-    description=DOCLINE,
-    long_description=README,
-    long_description_content_type="text/markdown",
-    author="Benjamin S. Murphy",
-    author_email="bscott.murphy@gmail.com",
-    maintainer="Sebastian Mueller, Roman Yurchak",
-    maintainer_email="info@geostat-framework.org",
-    url="https://github.com/GeoStat-Framework/PyKrige",
-    license="BSD (3 clause)",
-    classifiers=CLASSIFIERS,
-    platforms=["Windows", "Linux", "Solaris", "Mac OS-X", "Unix"],
-    include_package_data=True,
-    python_requires=">=3.6",
-    use_scm_version={
-        "relative_to": __file__,
-        "write_to": "pykrige/_version.py",
-        "write_to_template": "__version__ = '{version}'",
-        "local_scheme": "no-local-version",
-        "fallback_version": "0.0.0.dev0",
-    },
-    setup_requires=REQ_SETUP,
-    install_requires=REQ,
-    extras_require={
-        "plot": ["matplotlib"],
-        "sklearn": ["scikit-learn>=0.19"],
-        "doc": REQ_DOC,
-        "test": REQ_TEST,
-        "dev": REQ_DEV,
-    },
-    packages=find_packages(exclude=["tests*", "docs*"]),
-    ext_modules=EXT_MODULES,
-    include_dirs=[np.get_include()],
-)
+setup(ext_modules=EXT_MODULES, include_dirs=[np.get_include()])