sparseqr 1.3__tar.gz → 1.4__tar.gz

sparseqr-1.4/.gitignore

@@ -0,0 +1,3 @@
+*.pyc
+*.pyo
+_spqr.*

sparseqr-1.4/CHANGELOG.md

@@ -0,0 +1,53 @@
+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [v1.4] - 2025-01-28
+### Fixed
+- Modernized the build system (`pyproject.toml`).
+- Changed the way suite-sparse is found to be more robust.
+
+## [v1.3] - 2025-01-09
+### Added
+- Bindings for `qr_factorize` and `qmult` (thanks to jkrokowski)
+
+### Fixed
+- Compatibility with more environments (more search paths, newer numpy, setuptools dependency)
+- Readme example uses `spsolve_triangular`.
+
+## [v1.2.1] - 2023-04-12
+### Fixed
+- Fixed a memory leak in `qr()` and `rz()`.
+### Changed
+- Bumped minimal Python version to 3.8.
+- `rz()` is called by the test script. Its output is ignored.
+
+## [v1.2] - 2022-05-27
+### Added
+- Added support for partial "economy" decompositions. (Christoph Hansknecht <c.hansknecht@tu-braunschweig.de>): 'The "economy" option can be used in SPQR to compute a QR factorization of a (m x n) matrix with m < n consisting of blocks Q_1, and Q_2, where Q_1 has as shape of (m x n) and Q_2 of (m x k - n). For k = n we get the reduced form, for k = m the full one. For k in between m and n, SPQR yields a block that spans part of the kernel of A. This patch adds this functionality to PySPQR.'
+- Added support for macOS on arm64.
+
+## [v1.1.2] - 2021-08-09
+### Added
+- Added rz recomposition (thanks to Ben Smith <bsmith@apl.washington.edu>)
+- Added support for "economy" decomposition. (Jeffrey Bouas <ignirtoq@gmail.com>)
+### Changed
+- Supports conda environments (thanks to Ben Smith <bsmith@apl.washington.edu> and Sterling Baird <sterling.baird@icloud.com>)
+
+## [v1.0.0] - 2017-08-31
+### Added
+ - Installation and packaging using `setuptools`
+### Changed
+ - Rename module `spqr` to `sparseqr`
+ - Clean up public API: `qr`, `solve`, `permutation_vector_to_matrix`
+
+## [v1.0.0] - 2017-08-31
+### Added
+ - Installation and packaging using `setuptools` (thanks to Juha Jeronen <juha.jeronen@tut.fi>)
+### Changed
+ - Rename module `spqr` to `sparseqr`
+ - Clean up public API: `qr`, `solve`, `permutation_vector_to_matrix`

sparseqr-1.4/PKG-INFO

@@ -0,0 +1,164 @@
+Metadata-Version: 2.3
+Name: sparseqr
+Version: 1.4
+Summary: Python wrapper for SuiteSparseQR
+Keywords: suitesparse,bindings,wrapper,scipy,numpy,qr-decomposition,qr-factorisation,sparse-matrix,sparse-linear-system,sparse-linear-solver
+Author-email: Yotam Gingold <yotam@yotamgingold.com>
+Requires-Python: >= 3.8
+Description-Content-Type: text/markdown
+Requires-Dist: numpy >1.2
+Requires-Dist: scipy >= 1.0
+Requires-Dist: cffi >= 1.0
+Requires-Dist: setuptools >35
+Project-URL: homepage, https://github.com/yig/PySPQR
+Project-URL: source, https://github.com/yig/PySPQR
+
+# Python wrapper for SuiteSparseQR
+
+This module wraps the [SuiteSparseQR](http://faculty.cse.tamu.edu/davis/suitesparse.html)
+decomposition function for use with [SciPy](http://www.scipy.org).
+This is Matlab's sparse `[Q,R,E] = qr()`.
+For some reason, no one ever wrapped that function of SuiteSparseQR for Python.
+
+Also wrapped are the SuiteSparseQR solvers for ``A x = b`` for the cases with sparse `A` and dense or sparse `b`.
+This is especially useful for solving sparse overdetermined linear systems in the least-squares sense.
+Here `A` is of size m-by-n and `b` is m-by-k (storing `k` different right-hand side vectors, each considered separately).
+
+# Usage
+
+```python
+import numpy
+import scipy.sparse.linalg
+import sparseqr
+
+# QR decompose a sparse matrix M such that  Q R = M E
+#
+M = scipy.sparse.rand( 10, 10, density = 0.1 )
+Q, R, E, rank = sparseqr.qr( M )
+print( "Should be approximately zero:", abs( Q*R - M*sparseqr.permutation_vector_to_matrix(E) ).sum() ) 
+
+# Solve many linear systems "M x = b for b in columns(B)"
+#
+B = scipy.sparse.rand( 10, 5, density = 0.1 )  # many RHS, sparse (could also have just one RHS with shape (10,))
+x = sparseqr.solve( M, B, tolerance = 0 )
+
+# Solve an overdetermined linear system  A x = b  in the least-squares sense
+#
+# The same routine also works for the usual non-overdetermined case.
+#
+A = scipy.sparse.rand( 20, 10, density = 0.1 )  # 20 equations, 10 unknowns
+b = numpy.random.random(20)  # one RHS, dense, but could also have many (in shape (20,k))
+x = sparseqr.solve( A, b, tolerance = 0 )
+## Call `rz()`:
+sparseqr.rz( A, b, tolerance = 0 )
+
+# Solve a linear system  M x = B  via QR decomposition
+#
+# This approach is slow due to the explicit construction of Q, but may be
+# useful if a large number of systems need to be solved with the same M.
+#
+M = scipy.sparse.rand( 10, 10, density = 0.1 )
+Q, R, E, rank = sparseqr.qr( M )
+r = rank  # r could be min(M.shape) if M is full-rank
+
+# The system is only solvable if the lower part of Q.T @ B is all zero:
+print( "System is solvable if this is zero (unlikely for a random matrix):", abs( (( Q.tocsc()[:,r:] ).T ).dot( B ) ).sum() )
+
+# Systems with large non-square matrices can benefit from "economy" decomposition.
+M = scipy.sparse.rand( 20, 5, density=0.1 )
+B = scipy.sparse.rand( 20, 5, density = 0.1 )
+Q, R, E, rank = sparseqr.qr( M )
+print("Q shape (should be 20x20):", Q.shape)
+print("R shape (should be 20x5):", R.shape)
+Q, R, E, rank = sparseqr.qr( M, economy=True )
+print("Q shape (should be 20x5):", Q.shape)
+print("R shape (should be 5x5):", R.shape)
+
+
+R = R.tocsr()[:r,:r] #for best performance, spsolve_triangular() wants the Matrix to be in CSR format.
+Q = Q.tocsc()[:,:r] # Use CSC format for fast indexing of columns.
+QB = (Q.T).dot(B).todense()  # spsolve_triangular() need the RHS in array format.
+result = scipy.sparse.linalg.spsolve_triangular(R, QB, lower=False)
+
+# Recover a solution (as a dense array):
+x = numpy.zeros( ( M.shape[1], B.shape[1] ), dtype = result.dtype )
+x[:r] = result
+x[E] = x.copy()
+
+# Recover a solution (as a sparse matrix):
+x = scipy.sparse.vstack( ( result, scipy.sparse.coo_matrix( ( M.shape[1] - rank, B.shape[1] ), dtype = result.dtype ) ) )
+x.row = E[ x.row ]
+```
+
+# Installation
+
+Before installing this module, you must first install [SuiteSparseQR](http://faculty.cse.tamu.edu/davis/suitesparse.html). You can do that via conda (`conda install suitesparse`) or your system's package manager (macOS: `brew install suitesparse`; debian/ubuntu linux: `apt-get install libsuitesparse-dev`).
+
+Now you are ready to install this module.
+
+## Via `pip`
+
+From PyPI:
+
+```bash
+pip install sparseqr
+```
+
+From GitHub:
+
+```bash
+pip install git+https://github.com/yig/PySPQR.git
+```
+
+## Directly
+
+Copy the three `sparseqr/*.py` files next to your source code,
+or leave them in their directory and call it as a module.
+
+
+# Deploy
+
+1. Change the version in:
+
+    ```
+    sparseqr/__init__.py
+    pyproject.toml
+    ```
+
+2. Update `CHANGELOG.md`
+
+3. Run:
+
+    ```
+    flit publish --format sdist
+    ```
+
+We don't publish binary wheels, because it must be compiled against suite-sparse as a system dependency. We could publish a `none-any` wheel, which would cause compilation to happen the first time the module is imported rather than when it is installed. Is there a point to that?
+
+# Known issues
+
+`pip uninstall sparseqr` won't remove the generated libraries. It will list them with a warning.
+
+# Tested on
+
+ - Python 3.9, 3.13.
+ - Conda and not conda.
+ - macOS, Ubuntu Linux, and Linux Mint.
+
+    PYTHONPATH='.:$PYTHONPATH' python3 test/test.py
+
+# Dependencies
+
+These are installed via pip:
+
+* [SciPy/NumPy](http://www.scipy.org)
+* [cffi](http://cffi.readthedocs.io/)
+
+These must be installed manually:
+
+* [SuiteSparseQR](http://faculty.cse.tamu.edu/davis/suitesparse.html) (macOS: `brew install suitesparse`; debian/ubuntu linux: `apt-get install libsuitesparse-dev`)
+
+# License
+
+Public Domain [CC0](http://creativecommons.org/publicdomain/zero/1.0/)
+

{sparseqr-1.3 → sparseqr-1.4}/README.md

@@ -77,6 +77,10 @@ x.row = E[ x.row ]
 
 # Installation
 
+Before installing this module, you must first install [SuiteSparseQR](http://faculty.cse.tamu.edu/davis/suitesparse.html). You can do that via conda (`conda install suitesparse`) or your system's package manager (macOS: `brew install suitesparse`; debian/ubuntu linux: `apt-get install libsuitesparse-dev`).
+
+Now you are ready to install this module.
+
 ## Via `pip`
 
 From PyPI:
@@ -91,22 +95,6 @@ From GitHub:
 pip install git+https://github.com/yig/PySPQR.git
 ```
 
-## Manually from GitHub
-
-As user:
-
-```bash
-git clone https://github.com/yig/PySPQR.git
-cd PySPQR
-python setup.py install --user
-```
-
-As admin, change the last command to
-
-```bash
-sudo python setup.py install
-```
-
 ## Directly
 
 Copy the three `sparseqr/*.py` files next to your source code,
@@ -119,7 +107,6 @@ or leave them in their directory and call it as a module.
 
     ```
     sparseqr/__init__.py
-    setup.py
     pyproject.toml
     ```
 
@@ -128,17 +115,18 @@ or leave them in their directory and call it as a module.
 3. Run:
 
     ```
-    poetry build -f sdist
-    poetry publish
+    flit publish --format sdist
     ```
 
+We don't publish binary wheels, because it must be compiled against suite-sparse as a system dependency. We could publish a `none-any` wheel, which would cause compilation to happen the first time the module is imported rather than when it is installed. Is there a point to that?
+
 # Known issues
 
 `pip uninstall sparseqr` won't remove the generated libraries. It will list them with a warning.
 
 # Tested on
 
- - Python 2.7, 3.4, 3.5, 3.9, 3.13.
+ - Python 3.9, 3.13.
  - Conda and not conda.
  - macOS, Ubuntu Linux, and Linux Mint.
 
@@ -146,10 +134,15 @@ or leave them in their directory and call it as a module.
 
 # Dependencies
 
+These are installed via pip:
+
 * [SciPy/NumPy](http://www.scipy.org)
-* [SuiteSparseQR](http://faculty.cse.tamu.edu/davis/suitesparse.html) (macOS: `brew install suitesparse`; debian/ubuntu linux: `apt-get install libsuitesparse-dev`)
 * [cffi](http://cffi.readthedocs.io/)
 
+These must be installed manually:
+
+* [SuiteSparseQR](http://faculty.cse.tamu.edu/davis/suitesparse.html) (macOS: `brew install suitesparse`; debian/ubuntu linux: `apt-get install libsuitesparse-dev`)
+
 # License
 
 Public Domain [CC0](http://creativecommons.org/publicdomain/zero/1.0/)

sparseqr-1.4/pyproject.toml

@@ -0,0 +1,29 @@
+[project]
+name = "sparseqr"
+version = "1.4"
+description = "Python wrapper for SuiteSparseQR"
+authors = [{name = "Yotam Gingold", email = "yotam@yotamgingold.com"}]
+license = {text = "Public Domain CC0"}
+readme = "README.md"
+keywords = ["suitesparse", "bindings", "wrapper", "scipy", "numpy", "qr-decomposition", "qr-factorisation", "sparse-matrix", "sparse-linear-system", "sparse-linear-solver"]
+
+requires-python = ">= 3.8"
+
+dependencies = [
+    "numpy >1.2",
+    "scipy >= 1.0",
+    "cffi >= 1.0",
+    "setuptools >35",
+]
+
+[project.urls]
+homepage = "https://github.com/yig/PySPQR"
+source = "https://github.com/yig/PySPQR"
+
+[build-system]
+requires = ["setuptools>=61"]
+build-backend = "setuptools.build_meta"
+
+#[tool.setuptools.packages.find]
+# include = ["test/*.py", "README.md", "LICENSE.md"]
+#exclude = ["sparseqr/_sparseqr*"]

sparseqr-1.4/setup.py

@@ -0,0 +1,15 @@
+# -*- coding: utf-8 -*-
+#
+from __future__ import division, print_function, absolute_import
+
+from setuptools import setup #, dist
+import os
+
+setup(
+    # See
+    #    http://setuptools.readthedocs.io/en/latest/setuptools.html
+    #
+    setup_requires = ["cffi>=1.0.0"],
+    cffi_modules = ["sparseqr/sparseqr_gen.py:ffibuilder"],
+    install_requires = ["cffi>=1.0.0"],
+)

{sparseqr-1.3 → sparseqr-1.4}/sparseqr/__init__.py

@@ -17,7 +17,7 @@ See the docstrings of the individual functions for details.
 
 from __future__ import absolute_import
 
-__version__ = '1.3'
+__version__ = '1.4'
 
 # import the important things into the package's top-level namespace.
 from .sparseqr import qr, rz, solve, permutation_vector_to_matrix, qr_factorize,qmult

{sparseqr-1.3 → sparseqr-1.4}/sparseqr/sparseqr_gen.py

@@ -4,9 +4,7 @@ License: Public Domain [CC0](http://creativecommons.org/publicdomain/zero/1.0/)
 Description: Wrapper for SuiteSparse qr() and solve() functions. Matlab and Julia have it, Python should have it, too.
 '''
 
-from __future__ import print_function, division, absolute_import
 import os
-from os.path import join, expanduser
 import platform
 
 from cffi import FFI
@@ -15,26 +13,21 @@ include_dirs = []
 library_dirs = []
 libraries = ['spqr']
 
-if platform.system() == 'Windows':
-    include_dirs.append( join('C:', 'Program Files', 'Python', 'suitesparse') )
+## If we're using conda, use the conda paths
+if 'CONDA_PREFIX' in os.environ:
+    include_dirs.append( os.path.join(os.environ['CONDA_PREFIX'], 'include', 'suitesparse') )
+    library_dirs.append( os.path.join(os.environ['CONDA_PREFIX'], 'lib') )
+
+## Otherwise, add common system-wide directories
 else:
-    include_dirs.append( '/usr/include/suitesparse' )
-    ## Homebrew on macOS arm64 puts headers and libraries
-    ## in `/opt/homebrew`. That's not on the default path, so add them:
-    include_dirs.append( '/opt/homebrew/include/suitesparse' )
-    # Does this work for anyone? At one point I thought it worked for me, but maybe I didn't test properly.
-    include_dirs.append( '/opt/homebrew/include' )
-    library_dirs.append( '/opt/homebrew/lib' )
-
-# for compatibility with conda envs
-if 'CONDA_DEFAULT_ENV' in os.environ:
-    homedir = expanduser("~")
-
-    for packager in ['anaconda3','miniconda3','condaforge','miniforge','mambaforge']:
-        for sub in ['','Library']:
-            thedir=join(homedir, packager, 'envs', os.environ['CONDA_DEFAULT_ENV'], sub, 'include', 'suitesparse')
-            if os.path.isdir(thedir):
-                include_dirs.append(thedir)
+    if platform.system() == 'Windows':
+        include_dirs.append( join('C:', 'Program Files', 'Python', 'suitesparse') )
+    else:
+        include_dirs.append( '/usr/include/suitesparse' )
+        ## Homebrew on macOS arm64 puts headers and libraries
+        ## in `/opt/homebrew`. That's not on the default path, so add them:
+        include_dirs.append( '/opt/homebrew/include/suitesparse' )
+        library_dirs.append( '/opt/homebrew/lib' )
 
 if platform.system() == 'Windows':
     # https://github.com/yig/PySPQR/issues/6
@@ -43,6 +36,11 @@ if platform.system() == 'Windows':
 
 ffibuilder = FFI()
 
+## Uncomment this and install with `pip install -v` to see the arguments to `set_source`.
+# print( "cffi include_dirs:", include_dirs )
+# print( "cffi library_dirs:", library_dirs )
+# print( "cffi libraries:", libraries )
+
 ffibuilder.set_source( "sparseqr._sparseqr",
     """#include <SuiteSparseQR_C.h>
 """,

sparseqr-1.3/PKG-INFO

@@ -1,20 +0,0 @@
-Metadata-Version: 2.1
-Name: sparseqr
-Version: 1.3
-Summary: Python wrapper for SuiteSparseQR
-License: Public Domain CC0
-Author: Yotam Gingold
-Author-email: yotam@yotamgingold.com
-Requires-Python: >=3.8,<4.0
-Classifier: License :: Other/Proprietary License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-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-Dist: cffi (>=1.0,<2.0)
-Requires-Dist: numpy (>1.2)
-Requires-Dist: scipy (>=1.0,<2.0)
-Requires-Dist: setuptools (>35)

sparseqr-1.3/pyproject.toml

@@ -1,22 +0,0 @@
-[tool.poetry]
-name = "sparseqr"
-version = "1.3"
-description = "Python wrapper for SuiteSparseQR"
-authors = ["Yotam Gingold <yotam@yotamgingold.com>"]
-license = "Public Domain CC0"
-
-include = ["test/*.py", "README.md", "LICENSE.md"]
-exclude = ["sparseqr/_sparseqr*"]
-
-[tool.poetry.dependencies]
-python = "^3.8"
-numpy = ">1.2"
-scipy = "^1.0"
-cffi = "^1.0"
-setuptools = ">35"
-
-[tool.poetry.dev-dependencies]
-
-[build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"