scikit-sparse 0.4.16__tar.gz → 0.5.0__tar.gz

{scikit_sparse-0.4.16 → scikit_sparse-0.5.0}/LICENSE.txt

@@ -1,4 +1,5 @@
-Copyright (c) 2009-2018, Joscha Reimer, Alex Grigorievskiy, Antony Lee, Yuri, Leon Barrett, Dag Sverre Seljebotn, Nathaniel Smith, David Cournapeau
+Copyright (C) 2009-2025, The scikit-sparse developers. All rights reserved.
+See pyproject.toml for complete list of contributors.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 

scikit_sparse-0.5.0/MANIFEST.in

@@ -0,0 +1,8 @@
+# MANIFEST.in
+# Files to be included in the source distribution (not in the wheel)
+include LICENSE.txt
+include README.rst
+recursive-include src/sksparse *.pyx *.pxd *.c *.cpp
+prune tests
+prune scripts *
+prune *.egg-info

scikit_sparse-0.5.0/PKG-INFO

@@ -0,0 +1,159 @@
+Metadata-Version: 2.4
+Name: scikit-sparse
+Version: 0.5.0
+Summary: Scikit-sparse is a Python wrapper for the SuiteSparse sparse matrix library.
+Author-email: David Cournapeau <cournape@gmail.com>, Nathaniel Smith <njs@pobox.com>, Dag Sverre Seljebotn <dagss@student.matnat.uio.no>, Leon Barrett <lbarrett@climate.com>, Yuri <yuri@tsoft.com>, Antony Lee <anntzer.lee@gmail.com>, Alex Grigorievskiy <alex.grigorievskiy@gmail.com>, Joscha Reimer <jor@informatik.uni-kiel.de>, Justin Ellis <justin.ellis18@gmail.com>, Aaron Johnson <aaron9035@gmail.com>, Bernard Roesler <bernard.roesler@gmail.com>
+Maintainer-email: Bernard Roesler <bernard.roesler@gmail.com>
+License-Expression: BSD-2-Clause
+Project-URL: Homepage, https://github.com/scikit-sparse/scikit-sparse
+Project-URL: Bug Tracker, https://github.com/scikit-sparse/scikit-sparse/issues
+Keywords: sparse,matrix,linear algebra,scipy,numpy
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Programming Language :: Cython
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE.txt
+Requires-Dist: numpy>2.0
+Requires-Dist: scipy>=1.14
+Requires-Dist: packaging
+Provides-Extra: dev
+Requires-Dist: build; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Requires-Dist: sphinx-copybutton; extra == "dev"
+Dynamic: license-file
+
+.. start-badges
+
+.. image:: https://img.shields.io/github/v/release/scikit-sparse/scikit-sparse
+   :target: https://github.com/scikit-sparse/scikit-sparse/releases/latest
+   :alt: Latest GitHub release
+
+.. image:: https://img.shields.io/pypi/v/scikit-sparse
+   :target: https://pypi.org/project/scikit-sparse/
+   :alt: Latest PyPI release
+
+.. image:: https://img.shields.io/conda/vn/conda-forge/scikit-sparse
+   :target: https://anaconda.org/conda-forge/scikit-sparse
+   :alt: Latest conda-forge release
+
+.. image:: https://github.com/scikit-sparse/scikit-sparse/actions/workflows/ci-dev.yml/badge.svg?branch=dev
+   :target: https://github.com/scikit-sparse/scikit-sparse/actions/workflows/ci-dev.yml
+   :alt: CI Status
+
+.. image:: https://readthedocs.org/projects/scikit-sparse/badge/?version=latest
+   :target: https://scikit-sparse.readthedocs.io/en/latest/
+
+.. end-badges
+
+========================
+Scikit-Sparse (sksparse)
+========================
+
+The ``scikit-sparse`` package is a companion to the `scipy.sparse
+<scipy_sparse_>`_ package for sparse matrix manipulation in Python. It provides
+routines that are not suitable for inclusion in `scipy.sparse <scipy_sparse_>`_
+proper, typically because they depend on external libraries with
+GPL licenses, such as `SuiteSparse <suitesparse_website_>`_.
+
+For more details on usage see `the docs <sksparse_docs_>`_.
+To upgrade from scikit-sparse v0.4.16 to v0.5.0, see `Upgrading to v0.5.0
+<sksparse_upgrading_>`_.
+
+.. _upstream_repo: https://github.com/scikit-sparse/scikit-sparse
+.. _upstream_docs: https://scikit-sparse.readthedocs.io
+.. _scipy_sparse: https://docs.scipy.org/doc/scipy/reference/sparse.html
+.. _suitesparse_website: https://people.engr.tamu.edu/davis/suitesparse.html
+.. _sksparse_docs: https://scikit-sparse.readthedocs.org
+.. _sksparse_upgrading: https://scikit-sparse.readthedocs.org/en/latest/changes.html#upgrading-from-v0-4-x
+   
+.. start-installation
+
+Requirements
+------------
+
+Installing ``scikit-sparse`` requires:
+
+* `Python <http://python.org/>`_ >= 3.10
+* `NumPy <http://numpy.org/>`_ >= 2.0
+* `SciPy <http://scipy.org/>`_ >= 1.14
+* `Cython <http://www.cython.org/>`_ >= 3.0
+* `SuiteSparse <suitesparse_website_>`_ >= 7.4.0
+
+Older versions may work but are untested.
+
+
+Installation
+------------
+
+Installing SuiteSparse
+++++++++++++++++++++++
+
+To install ``scikit-sparse``, you need to have the `SuiteSparse
+<suitesparse_website_>`_ library installed on your system.
+
+It is recommended that you install SuiteSparse and the scikit-sparse
+dependencies in a virtual environment, to avoid conflicts with other packages.
+We recommend using Anaconda::
+
+    $ conda create -n scikit-sparse python>=3.10 suitesparse
+    $ conda activate scikit-sparse
+
+If you are not using Anaconda, you can install SuiteSparse using your preferred
+package manager.
+
+On MacOS, you can use `Homebrew <http://brew.sh>`_::
+
+    $ brew install suite-sparse
+
+On Debian/Ubuntu systems, use the following command::
+
+    $ sudo apt-get install python-scipy libsuitesparse-dev
+
+On Arch Linux, run::
+
+    $ sudo pacman -S suitesparse
+
+
+Installing Scikit-Sparse
+++++++++++++++++++++++++
+
+Once you have SuiteSparse installed, you can install ``scikit-sparse`` with::
+
+    $ conda install -c conda-forge scikit-sparse
+
+or if you prefer to use pip, you can install it with::
+
+    $ pip install scikit-sparse
+
+Check if the installation was successful by running the following command::
+
+    $ python -c "import sksparse; print(sksparse.__version__)"
+
+
+.. end-installation
+
+See `Troubleshooting <docs_trouble_>`_ for more information on determining
+which SuiteSparse library is being used.
+
+.. _docs_trouble: https://scikit-sparse.readthedocs.io/en/latest/overview.html#troubleshooting
+
+
+----
+
+Copyright © 2009–2025, the `scikit-sparse developers <docs_dev_>`_.
+
+.. _docs_dev: https://scikit-sparse.readthedocs.io/en/latest/overview.html#developers

scikit_sparse-0.5.0/README.rst

@@ -0,0 +1,121 @@
+.. start-badges
+
+.. image:: https://img.shields.io/github/v/release/scikit-sparse/scikit-sparse
+   :target: https://github.com/scikit-sparse/scikit-sparse/releases/latest
+   :alt: Latest GitHub release
+
+.. image:: https://img.shields.io/pypi/v/scikit-sparse
+   :target: https://pypi.org/project/scikit-sparse/
+   :alt: Latest PyPI release
+
+.. image:: https://img.shields.io/conda/vn/conda-forge/scikit-sparse
+   :target: https://anaconda.org/conda-forge/scikit-sparse
+   :alt: Latest conda-forge release
+
+.. image:: https://github.com/scikit-sparse/scikit-sparse/actions/workflows/ci-dev.yml/badge.svg?branch=dev
+   :target: https://github.com/scikit-sparse/scikit-sparse/actions/workflows/ci-dev.yml
+   :alt: CI Status
+
+.. image:: https://readthedocs.org/projects/scikit-sparse/badge/?version=latest
+   :target: https://scikit-sparse.readthedocs.io/en/latest/
+
+.. end-badges
+
+========================
+Scikit-Sparse (sksparse)
+========================
+
+The ``scikit-sparse`` package is a companion to the `scipy.sparse
+<scipy_sparse_>`_ package for sparse matrix manipulation in Python. It provides
+routines that are not suitable for inclusion in `scipy.sparse <scipy_sparse_>`_
+proper, typically because they depend on external libraries with
+GPL licenses, such as `SuiteSparse <suitesparse_website_>`_.
+
+For more details on usage see `the docs <sksparse_docs_>`_.
+To upgrade from scikit-sparse v0.4.16 to v0.5.0, see `Upgrading to v0.5.0
+<sksparse_upgrading_>`_.
+
+.. _upstream_repo: https://github.com/scikit-sparse/scikit-sparse
+.. _upstream_docs: https://scikit-sparse.readthedocs.io
+.. _scipy_sparse: https://docs.scipy.org/doc/scipy/reference/sparse.html
+.. _suitesparse_website: https://people.engr.tamu.edu/davis/suitesparse.html
+.. _sksparse_docs: https://scikit-sparse.readthedocs.org
+.. _sksparse_upgrading: https://scikit-sparse.readthedocs.org/en/latest/changes.html#upgrading-from-v0-4-x
+   
+.. start-installation
+
+Requirements
+------------
+
+Installing ``scikit-sparse`` requires:
+
+* `Python <http://python.org/>`_ >= 3.10
+* `NumPy <http://numpy.org/>`_ >= 2.0
+* `SciPy <http://scipy.org/>`_ >= 1.14
+* `Cython <http://www.cython.org/>`_ >= 3.0
+* `SuiteSparse <suitesparse_website_>`_ >= 7.4.0
+
+Older versions may work but are untested.
+
+
+Installation
+------------
+
+Installing SuiteSparse
+++++++++++++++++++++++
+
+To install ``scikit-sparse``, you need to have the `SuiteSparse
+<suitesparse_website_>`_ library installed on your system.
+
+It is recommended that you install SuiteSparse and the scikit-sparse
+dependencies in a virtual environment, to avoid conflicts with other packages.
+We recommend using Anaconda::
+
+    $ conda create -n scikit-sparse python>=3.10 suitesparse
+    $ conda activate scikit-sparse
+
+If you are not using Anaconda, you can install SuiteSparse using your preferred
+package manager.
+
+On MacOS, you can use `Homebrew <http://brew.sh>`_::
+
+    $ brew install suite-sparse
+
+On Debian/Ubuntu systems, use the following command::
+
+    $ sudo apt-get install python-scipy libsuitesparse-dev
+
+On Arch Linux, run::
+
+    $ sudo pacman -S suitesparse
+
+
+Installing Scikit-Sparse
+++++++++++++++++++++++++
+
+Once you have SuiteSparse installed, you can install ``scikit-sparse`` with::
+
+    $ conda install -c conda-forge scikit-sparse
+
+or if you prefer to use pip, you can install it with::
+
+    $ pip install scikit-sparse
+
+Check if the installation was successful by running the following command::
+
+    $ python -c "import sksparse; print(sksparse.__version__)"
+
+
+.. end-installation
+
+See `Troubleshooting <docs_trouble_>`_ for more information on determining
+which SuiteSparse library is being used.
+
+.. _docs_trouble: https://scikit-sparse.readthedocs.io/en/latest/overview.html#troubleshooting
+
+
+----
+
+Copyright © 2009–2025, the `scikit-sparse developers <docs_dev_>`_.
+
+.. _docs_dev: https://scikit-sparse.readthedocs.io/en/latest/overview.html#developers

scikit_sparse-0.5.0/pyproject.toml

@@ -0,0 +1,125 @@
+[build-system]
+# setuptools>=61 for PEP 621 support
+requires = ["setuptools>=61.0", "wheel", "Cython>=3.0", "numpy>=2.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "scikit-sparse"
+version = "0.5.0"
+description = "Scikit-sparse is a Python wrapper for the SuiteSparse sparse matrix library."
+readme = "README.rst"
+requires-python = ">=3.10"
+license = "BSD-2-Clause"
+license-files = ["LICENSE.txt"]
+
+authors = [
+    { name = "David Cournapeau", email = "cournape@gmail.com" },
+    { name = "Nathaniel Smith", email = "njs@pobox.com" },
+    { name = "Dag Sverre Seljebotn", email = "dagss@student.matnat.uio.no" },
+    { name = "Leon Barrett", email = "lbarrett@climate.com" },
+    { name = "Yuri", email = "yuri@tsoft.com" },
+    { name = "Antony Lee", email = "anntzer.lee@gmail.com" },
+    { name = "Alex Grigorievskiy", email = "alex.grigorievskiy@gmail.com" },
+    { name = "Joscha Reimer", email = "jor@informatik.uni-kiel.de" },
+    { name = "Justin Ellis", email = "justin.ellis18@gmail.com" },
+    { name = "Aaron Johnson", email = "aaron9035@gmail.com" },
+    { name = "Bernard Roesler", email = "bernard.roesler@gmail.com" },
+]
+maintainers = [
+    { name = "Bernard Roesler", email = "bernard.roesler@gmail.com" },
+]
+
+keywords = ["sparse", "matrix", "linear algebra", "scipy", "numpy"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering",
+    "Topic :: Scientific/Engineering :: Mathematics",
+    "Programming Language :: Cython",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+
+dependencies = [
+    "numpy>2.0",
+    "scipy>=1.14",
+    "packaging",  # for version parsing
+]
+
+[project.optional-dependencies]
+dev = [
+    "build",
+    "pre-commit",
+    "pytest",
+    "ruff",
+    "sphinx",
+    "furo",
+    "sphinx-copybutton",
+]
+
+[project.urls]
+"Homepage" = "https://github.com/scikit-sparse/scikit-sparse"
+"Bug Tracker" = "https://github.com/scikit-sparse/scikit-sparse/issues"
+
+# This data is excluded from the wheel package, but not necessarily from the
+# sdist (for sdist, see: MANIFEST.in)
+[tool.setuptools.exclude-package-data]
+sksparse = ["*.c", "*.pyx"]
+
+[tool.cython]
+language_level = "3"
+
+[tool.ruff]
+line-length = 88
+target-version = "py310"
+
+[tool.ruff.lint]
+extend-select = [
+    'B',    # flake8-bugbear
+    'C4',   # flake8-comprehensions
+    'D',    # docstring errors
+    'E',    # pycodestyle errors
+    'F',    # pyflakes errors
+    'I',    # isort errors (import sorting)
+    'ISC',  # flake8-implicit-str-concat
+    'NPY',  # numpy-specific checks
+    'PD',   # pandas-vet
+    'PIE',  # flake8-pie
+    'PL',   # pylint errors
+    'PTH',  # use Path vs os
+    'UP',   # pyupgrade
+    'W',    # pycodestyle warnings (whitespace)
+]
+
+ignore = [
+    'B028',     # No explicit `stacklevel` keyword argument found
+    'B904',     # Within an `except` clause distinguish raised exceptions from errors in exception handling
+    'B905',     # `zip()` without an explicit `strict=` parameter
+    'D104',     # Missing docstring in __init__
+    'D105',     # Missing docstring in magic method
+    'D205',     # 1 blank line required between summary line and description
+    'E741',     # ambiguous variable name (l, O, I)
+    'PIE790',   # Unnecessary `pass` statement
+    'PLC2401',  # non-ASCII characters
+    'PLR0912',  # too many branches (max-branches)
+    'PLR0913',  # too many arguments (max-args)
+    'PLR0915',  # too many statements (max-statements)
+    'PLR2004',  # magic value used in comparison
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["sksparse"]
+
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ['D', 'I001', 'F403', 'F405']  # ignore import sorting, wildcard imports, and undefined names
+"test_*.py" = ['D101', 'D102', 'D103', 'E501']  # ignore docstring checks in test files
+"setup.py" = ['D100', 'D101', 'D102', 'D103', 'D104']  # ignore docstrings
+"benchmarks/*" = ['D100', 'D101', 'D102', 'D103', 'D104']  # ignore docstrings
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"

scikit_sparse-0.5.0/setup.py

@@ -0,0 +1,116 @@
+# Copyright (C) 2008-2025 The scikit-sparse developers:
+#
+# 2008        David Cournapeau        <cournape@gmail.com>
+# 2009-2015   Nathaniel Smith         <njs@pobox.com>
+# 2010        Dag Sverre Seljebotn    <dagss@student.matnat.uio.no>
+# 2014        Leon Barrett            <lbarrett@climate.com>
+# 2015        Yuri                    <yuri@tsoft.com>
+# 2016-2017   Antony Lee              <anntzer.lee@gmail.com>
+# 2016        Alex Grigorievskiy      <alex.grigorievskiy@gmail.com>
+# 2016-2017   Joscha Reimer           <jor@informatik.uni-kiel.de>
+# 2021-       Justin Ellis            <justin.ellis18@gmail.com>
+# 2022-       Aaron Johnson           <aaron9035@gmail.com>
+# 2025-       Bernard Roesler         <bernard.roesler@gmail.com>
+
+import os
+import subprocess
+import sys
+from pathlib import Path
+
+from setuptools import Extension, setup
+
+
+def get_numpy_include():
+    """Get the include directory for NumPy."""
+    try:
+        import numpy as np  # noqa: PLC0415
+
+        return np.get_include()
+    except ImportError:
+        return []
+
+
+INCLUDE_DIRS = []
+LIBRARY_DIRS = []
+
+numpy_include = get_numpy_include()
+if numpy_include:
+    INCLUDE_DIRS.append(numpy_include)
+
+# Check user SuiteSparse directories first
+user_include_dir = os.getenv("SUITESPARSE_INCLUDE_DIR")
+user_library_dir = os.getenv("SUITESPARSE_LIBRARY_DIR")
+
+if user_include_dir:
+    INCLUDE_DIRS.append(user_include_dir)
+
+if user_library_dir:
+    LIBRARY_DIRS.append(user_library_dir)
+
+# Check if suitesparse is installed via conda
+conda_prefix = os.getenv("CONDA_PREFIX")
+
+if conda_prefix:
+    if os.name == "nt":  # Windows
+        conda_include = Path(conda_prefix) / "Library" / "include" / "suitesparse"
+        conda_lib = Path(conda_prefix) / "Library" / "lib"
+    else:
+        conda_include = Path(conda_prefix) / "include" / "suitesparse"
+        conda_lib = Path(conda_prefix) / "lib"
+
+    if conda_include.is_dir():
+        INCLUDE_DIRS.append(str(conda_include))
+    if conda_lib.is_dir():
+        LIBRARY_DIRS.append(str(conda_lib))
+
+# Check if suitesparse is installed via homebrew
+try:
+    homebrew_prefix = (
+        subprocess.run(
+            "readlink -f $(brew --prefix suitesparse)",
+            shell=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.DEVNULL,
+            check=True,  # raise an error if command fails
+        )
+        .stdout.decode()
+        .strip()
+    )
+    brew_include = Path(homebrew_prefix) / "include" / "suitesparse"
+    brew_lib = Path(homebrew_prefix) / "lib"
+    if brew_include.is_dir():
+        INCLUDE_DIRS.append(str(brew_include))
+    if brew_lib.is_dir():
+        LIBRARY_DIRS.append(str(brew_lib))
+except Exception:
+    pass
+
+# Check system-wide directories
+INCLUDE_DIRS.append(str(Path(sys.prefix) / "include"))
+INCLUDE_DIRS.append("/usr/include/suitesparse")  # Linux default path
+
+extension_names = [
+    "cholmod",
+    "amd",
+    "btf",
+    "camd",
+    "colamd",
+    "ccolamd",
+    "klu",
+    "spqr",
+    "umfpack",
+]
+
+extensions = [
+    Extension(
+        f"sksparse.{name}",
+        [f"src/sksparse/{name}.pyx"],
+        include_dirs=INCLUDE_DIRS,
+        library_dirs=LIBRARY_DIRS,
+        libraries=[name] if name != "spqr" else ["cholmod", "spqr"],
+    )
+    for name in extension_names
+]
+
+# No need to call "cythonize" here. Rely on pyproject.toml.
+setup(ext_modules=extensions)