Modernize: use pyproject.toml for more things, add pre-commit; remove versioneer

.flake8

@@ -0,0 +1,8 @@
+[flake8]
+max-line-length = 100
+inline-quotes = "
+extend-ignore =
+    E203,
+# E203 whitespace before ':' (to be compatible with black)
+per-file-ignores =
+    suitesparse_graphblas/io/binary.py:C408

.github/workflows/lint.yml

@@ -0,0 +1,21 @@
+name: Lint via pre-commit
+
+on:
+  pull_request:
+  push:
+    branches-ignore:
+      - main
+
+permissions:
+  contents: read
+
+jobs:
+  pre-commit:
+    name: pre-commit-hooks
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - uses: pre-commit/action@v3.0.0

.github/workflows/test.yml

@@ -23,6 +23,8 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
     - name: Conda
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -57,18 +59,13 @@ jobs:
         popd
     - name: Build
       run: |
-        python setup.py build_ext --inplace
-        python setup.py develop
+        pip install -e . --no-deps
     - name: Test
       env:
         CYTHON_COVERAGE: true
       run: |
         coverage run --branch -m pytest
         coverage run -a --branch suitesparse_graphblas/tests/test_initialize.py
-    - name: Lint
-      run: |
-        black *py suitesparse_graphblas --check --diff
-        flake8 *py suitesparse_graphblas
     - name: create_headers.py check
       if: (! contains(matrix.os, 'windows'))
       run: |

.pre-commit-config.yaml

@@ -0,0 +1,69 @@
+# https://pre-commit.com/
+#
+# Before first use: `pre-commit install`
+# To run: `pre-commit run --all-files`
+# To update: `pre-commit autoupdate`
+#  - &flake8_dependencies below needs updated manually
+fail_fast: true
+default_language_version:
+    python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      # - id: trailing-whitespace
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.1
+    hooks:
+      - id: validate-pyproject
+        name: Validate pyproject.toml
+  - repo: https://github.com/myint/autoflake
+    rev: v2.0.1
+    hooks:
+      - id: autoflake
+        args: [--in-place]
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.3.1
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+  # - repo: https://github.com/MarcoGorelli/auto-walrus
+  #   rev: v0.2.2
+  #   hooks:
+  #     - id: auto-walrus
+  #       args: [--line-length, "100"]
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+      # - id: black-jupyter
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        additional_dependencies: &flake8_dependencies
+        # These versions need updated manually
+        - flake8==6.0.0
+        - flake8-comprehensions==3.10.1
+        - flake8-bugbear==23.1.20
+        # - flake8-simplify==0.19.3
+  - repo: https://github.com/asottile/yesqa
+    rev: v1.4.0
+    hooks:
+      - id: yesqa
+        additional_dependencies: *flake8_dependencies
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch  # no commit directly to main

MANIFEST.in

@@ -5,5 +5,4 @@ include suitesparse_graphblas/*.pxd
 include suitesparse_graphblas/*.pyx
 include suitesparse_graphblas/*.c
 include suitesparse_graphblas/*.h
-include versioneer.py
-include suitesparse_graphblas/_version.py
+include suitesparse_graphblas/tests/*.py

pyproject.toml

@@ -1,5 +1,106 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.19", "cython"]
+build-backend = "setuptools.build_meta"
+requires = [
+    "setuptools >=64",
+    "setuptools-git-versioning",
+    "wheel",
+    "cffi",
+    "cython",
+    "oldest-supported-numpy",
+]
+
+[project]
+name = "suitesparse-graphblas"
+dynamic = ["version"]
+description = "SuiteSparse:GraphBLAS Python bindings."
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+authors = [
+    {name = "Erik Welch"},
+    {name = "Jim Kitchen"},
+    {name = "Michel Pelletier"},
+]
+maintainers = [
+    {name = "Erik Welch", email = "erik.n.welch@gmail.com"},
+    {name = "Jim Kitchen", email = "jim22k@gmail.com"},
+    {name = "Michel Pelletier", email = "michel@graphegon.com"},
+]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "License :: OSI Approved :: Apache Software License",
+    "Operating System :: MacOS :: MacOS X",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3 :: Only",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Mathematics",
+]
+dependencies = [
+    # These are super-old; can/should we update them?
+    "cffi>=1.0.0",
+    "numpy>=1.19",
+]
+[project.urls]
+homepage = "https://github.com/GraphBLAS/python-suitesparse-graphblas"
+repository = "https://github.com/GraphBLAS/python-suitesparse-graphblas"
+changelog = "https://github.com/GraphBLAS/python-suitesparse-graphblas/releases"
+
+[project.optional-dependencies]
+test = [
+    "pytest",
+]
+
+[tool.setuptools]
+packages = [
+    'suitesparse_graphblas',
+    # 'suitesparse_graphblas.tests',
+    'suitesparse_graphblas.io',
+]
+
+[tool.setuptools-git-versioning]
+enabled = true
+dev_template = "{tag}+{ccount}.g{sha}"
+dirty_template = "{tag}+{ccount}.g{sha}.dirty"
 
 [tool.black]
 line-length = 100
+target-version = ["py38", "py39", "py310", "py311"]
+
+[tool.isort]
+sections = ["FUTURE", "STDLIB", "THIRDPARTY", "FIRSTPARTY", "LOCALFOLDER"]
+profile = "black"
+skip_gitignore = true
+float_to_top = true
+default_section = "THIRDPARTY"
+known_first_party = "suitesparse_graphblas"
+line_length = 100
+skip_glob = ["*.pxd", "*.pyx"]
+
+[tool.coverage.run]
+branch = true
+source = ["suitesparse_graphblas"]
+omit = []
+plugins = ["Cython.Coverage"]
+
+[tool.coverage.report]
+ignore_errors = false
+precision = 1
+fail_under = 0
+skip_covered = true
+skip_empty = true
+exclude_lines = [
+    "pragma: no cover",
+    "raise AssertionError",
+    "raise NotImplementedError",
+]
+
+[tool.pytest]
+testpaths = ["suitesparse_graphblas/tests"]

setup.py

@@ -1,12 +1,9 @@
-# Twiddle Dee (switch this between Dee and Dum to add meaningless git commits)
 import os
 import sys
 from glob import glob
 
 import numpy as np
-from setuptools import Extension, find_packages, setup
-
-import versioneer
+from setuptools import Extension, setup
 
 try:
     from Cython.Build import cythonize
@@ -16,8 +13,6 @@
 except ImportError:
     use_cython = False
 
-
-is_win = sys.platform.startswith("win")
 define_macros = [("NPY_NO_DEPRECATED_API", "NPY_1_7_API_VERSION")]
 
 if use_cython:
@@ -51,49 +46,7 @@
 if use_cython:
     ext_modules = cythonize(ext_modules, include_path=include_dirs)
 
-with open("README.md") as f:
-    long_description = f.read()
-
-package_data = {"suitesparse_graphblas": ["*.pyx", "*.pxd", "*.c", "*.h"]}
-if is_win:
-    package_data["suitesparse_graphblas"].append("*.dll")
-
 setup(
-    name="suitesparse-graphblas",
-    version=versioneer.get_version(),
-    cmdclass=versioneer.get_cmdclass(),
-    description="SuiteSparse:GraphBLAS Python bindings.",
-    long_description=long_description,
-    long_description_content_type="text/markdown",
-    packages=find_packages(),
-    author="Michel Pelletier, James Kitchen, Erik Welch",
-    author_email="michel@graphegon.com,jim22k@gmail.com,erik.n.welch@gmail.com",
-    url="https://github.com/GraphBLAS/python-suitesparse-graphblas",
     ext_modules=ext_modules,
     cffi_modules=["suitesparse_graphblas/build.py:ffibuilder"],
-    python_requires=">=3.8",
-    install_requires=["cffi>=1.0.0", "numpy>=1.19"],
-    setup_requires=["cffi>=1.0.0", "pytest-runner"],
-    tests_require=["pytest"],
-    license="Apache License 2.0",
-    package_data=package_data,
-    include_package_data=True,
-    classifiers=[
-        "Development Status :: 4 - Beta",
-        "License :: OSI Approved :: Apache Software License",
-        "Operating System :: MacOS :: MacOS X",
-        "Operating System :: POSIX :: Linux",
-        "Operating System :: Microsoft :: Windows",
-        "Programming Language :: Python",
-        "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3 :: Only",
-        "Intended Audience :: Science/Research",
-        "Topic :: Scientific/Engineering",
-        "Topic :: Scientific/Engineering :: Mathematics",
-    ],
-    zip_safe=False,
 )