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Modernize: use pyproject.toml for more things, add pre-commit; remove versioneer (#67)
* Modernize: use pyproject.toml for more things, add pre-commit; remove versioneer - Move metadata and config to `pyproject.toml` (and flake8 config to `.flake8`) - Use `setuptools-git-versioning` instead of `versioneer.py` - Add `.pre-commit-config.yaml` for git pre-commit hooks - Add GitHub Action to run pre-commit hooks to check linting
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‎.flake8‎

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

‎.gitattributes‎

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‎.github/workflows/lint.yml‎

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name: Lint via pre-commit
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on:
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pull_request:
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push:
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branches-ignore:
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- main
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permissions:
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contents: read
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jobs:
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pre-commit:
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name: pre-commit-hooks
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- uses: pre-commit/[email protected]

‎.github/workflows/test.yml‎

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

‎.pre-commit-config.yaml‎

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

‎MANIFEST.in‎

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

‎pyproject.toml‎

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

‎setup.cfg‎

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‎setup.py‎

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

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