Fixed database typo and removed unnecessary class identifier.

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Batuhan Berk Başoğlu 2020-10-14 10:10:37 -04:00
parent 00ad49a143
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.. _hacking:
==================
Ways to Contribute
==================
This document aims to give an overview of the ways to contribute to SciPy. It
tries to answer commonly asked questions and provide some insight into how the
community process works in practice. Readers who are familiar with the SciPy
community and are experienced Python coders may want to jump straight to the
:ref:`contributor-toc`.
There are a lot of ways you can contribute:
- Contributing new code
- Fixing bugs, improving documentation, and other maintenance work
- Reviewing open pull requests
- Triaging issues
- Working on the `scipy.org`_ website
- Answering questions and participating on the scipy-dev and scipy-user
`mailing lists`_.
Contributing new code
=====================
If you have been working with the scientific Python toolstack for a while, you
probably have some code lying around of which you think "this could be useful
for others too". Perhaps it's a good idea then to contribute it to SciPy or
another open source project. The first question to ask is then, where does
this code belong? That question is hard to answer here, so we start with a
more specific one: *what code is suitable for putting into SciPy?*
Almost all of the new code added to SciPy has in common that it's potentially
useful in multiple scientific domains and it fits in the scope of existing
SciPy subpackages (see :ref:`deciding-on-new-features`). In principle new
subpackages can be added too, but this is far less common. For code that is
specific to a single application, there may be an existing project that can
use the code. Some SciKits (`scikit-learn`_, `scikit-image`_, `statsmodels`_,
etc.) are good examples here; they have a narrower focus and because of that
more domain-specific code than SciPy.
Now if you have code that you would like to see included in SciPy, how do you
go about it? After checking that your code can be distributed in SciPy under a
compatible license (see :ref:`license-considerations`), the first step is to
discuss on the scipy-dev mailing list. All new features, as well as changes to
existing code, are discussed and decided on there. You can, and probably
should, already start this discussion before your code is finished. Remember
that in order to be added to SciPy your code will need to be reviewed by
someone else, so try to find someone willing to review your work while you're
at it.
Assuming the outcome of the discussion on the mailing list is positive and you
have a function or piece of code that does what you need it to do, what next?
Before code is added to SciPy, it at least has to have good documentation, unit
tests, benchmarks, and correct code style.
1. Unit tests
In principle you should aim to create unit tests that exercise all the code
that you are adding. This gives some degree of confidence that your code
runs correctly, also on Python versions and hardware or OSes that you don't
have available yourself. An extensive description of how to write unit
tests is given in :doc:`numpy:reference/testing`, and :ref:`runtests`
documents how to run them.
2. Benchmarks
Unit tests check for correct functionality; benchmarks measure code
performance. Not all existing SciPy code has benchmarks, but it should:
as SciPy grows it is increasingly important to monitor execution times in
order to catch unexpected regressions. More information about writing
and running benchmarks is available in :ref:`benchmarking-with-asv`.
3. Documentation
Clear and complete documentation is essential in order for users to be able
to find and understand the code. Documentation for individual functions
and classes -- which includes at least a basic description, type and
meaning of all parameters and returns values, and usage examples in
`doctest`_ format -- is put in docstrings. Those docstrings can be read
within the interpreter, and are compiled into a reference guide in html and
pdf format. Higher-level documentation for key (areas of) functionality is
provided in tutorial format and/or in module docstrings. A guide on how to
write documentation is given in :ref:`numpy:howto-document`, and
:ref:`rendering-documentation` explains how to preview the documentation
as it will appear online.
4. Code style
Uniformity of style in which code is written is important to others trying
to understand the code. SciPy follows the standard Python guidelines for
code style, `PEP8`_. In order to check that your code conforms to PEP8,
you can use the `pep8 package`_ style checker. Most IDEs and text editors
have settings that can help you follow PEP8, for example by translating
tabs by four spaces. Using `pyflakes`_ to check your code is also a good
idea. More information is available in :ref:`pep8-scipy`.
A :ref:`checklist<pr-checklist>`, including these and other requirements, is
available at the end of the example :ref:`development-workflow`.
Another question you may have is: *where exactly do I put my code*? To answer
this, it is useful to understand how the SciPy public API (application
programming interface) is defined. For most modules the API is two levels
deep, which means your new function should appear as
``scipy.subpackage.my_new_func``. ``my_new_func`` can be put in an existing or
new file under ``/scipy/<subpackage>/``, its name is added to the ``__all__``
list in that file (which lists all public functions in the file), and those
public functions are then imported in ``/scipy/<subpackage>/__init__.py``. Any
private functions/classes should have a leading underscore (``_``) in their
name. A more detailed description of what the public API of SciPy is, is given
in :ref:`scipy-api`.
Once you think your code is ready for inclusion in SciPy, you can send a pull
request (PR) on Github. We won't go into the details of how to work with git
here, this is described well in :ref:`git-development`
and on the `Github help pages`_. When you send the PR for a new
feature, be sure to also mention this on the scipy-dev mailing list. This can
prompt interested people to help review your PR. Assuming that you already got
positive feedback before on the general idea of your code/feature, the purpose
of the code review is to ensure that the code is correct, efficient and meets
the requirements outlined above. In many cases the code review happens
relatively quickly, but it's possible that it stalls. If you have addressed
all feedback already given, it's perfectly fine to ask on the mailing list
again for review (after a reasonable amount of time, say a couple of weeks, has
passed). Once the review is completed, the PR is merged into the "master"
branch of SciPy.
The above describes the requirements and process for adding code to SciPy. It
doesn't yet answer the question though how decisions are made exactly. The
basic answer is: decisions are made by consensus, by everyone who chooses to
participate in the discussion on the mailing list. This includes developers,
other users and yourself. Aiming for consensus in the discussion is important
-- SciPy is a project by and for the scientific Python community. In those
rare cases that agreement cannot be reached, the maintainers of the module
in question can decide the issue.
.. _license-considerations:
License Considerations
----------------------
*I based my code on existing Matlab/R/... code I found online, is this OK?*
It depends. SciPy is distributed under a BSD license, so if the code that you
based your code on is also BSD licensed or has a BSD-compatible license (e.g.
MIT, PSF) then it's OK. Code which is GPL or Apache licensed, has no
clear license, requires citation or is free for academic use only can't be
included in SciPy. Therefore if you copied existing code with such a license
or made a direct translation to Python of it, your code can't be included.
If you're unsure, please ask on the scipy-dev `mailing list <mailing lists>`_.
*Why is SciPy under the BSD license and not, say, the GPL?*
Like Python, SciPy uses a "permissive" open source license, which allows
proprietary re-use. While this allows companies to use and modify the software
without giving anything back, it is felt that the larger user base results in
more contributions overall, and companies often publish their modifications
anyway, without being required to. See John Hunter's `BSD pitch`_.
For more information about SciPy's license, see :ref:`scipy-licensing`.
Maintaining existing code
=========================
The previous section talked specifically about adding new functionality to
SciPy. A large part of that discussion also applies to maintenance of existing
code. Maintenance means fixing bugs, improving code quality, documenting
existing functionality better, adding missing unit tests, adding performance
benchmarks, keeping build scripts up-to-date, etc. The SciPy `issue list`_
contains all reported bugs, build/documentation issues, etc. Fixing issues
helps improve the overall quality of SciPy, and is also a good way
of getting familiar with the project. You may also want to fix a bug because
you ran into it and need the function in question to work correctly.
The discussion on code style and unit testing above applies equally to bug
fixes. It is usually best to start by writing a unit test that shows the
problem, i.e. it should pass but doesn't. Once you have that, you can fix the
code so that the test does pass. That should be enough to send a PR for this
issue. Unlike when adding new code, discussing this on the mailing list may
not be necessary - if the old behavior of the code is clearly incorrect, no one
will object to having it fixed. It may be necessary to add some warning or
deprecation message for the changed behavior. This should be part of the
review process.
.. note::
Pull requests that *only* change code style, e.g. fixing some PEP8 issues in
a file, are discouraged. Such PRs are often not worth cluttering the git
annotate history, and take reviewer time that may be better spent in other ways.
Code style cleanups of code that is touched as part of a functional change
are fine however.
Reviewing pull requests
=======================
Reviewing open pull requests (PRs) is very welcome, and a valuable way to help
increase the speed at which the project moves forward. If you have specific
knowledge/experience in a particular area (say "optimization algorithms" or
"special functions") then reviewing PRs in that area is especially valuable -
sometimes PRs with technical code have to wait for a long time to get merged
due to a shortage of appropriate reviewers.
We encourage everyone to get involved in the review process; it's also a
great way to get familiar with the code base. Reviewers should ask
themselves some or all of the following questions:
- Was this change adequately discussed (relevant for new features and changes
in existing behavior)?
- Is the feature scientifically sound? Algorithms may be known to work based on
literature; otherwise, closer look at correctness is valuable.
- Is the intended behavior clear under all conditions (e.g. unexpected inputs
like empty arrays or nan/inf values)?
- Does the code meet the quality, test and documentation expectation outline
under `Contributing new code`_?
If we do not know you yet, consider introducing yourself.
Other ways to contribute
========================
There are many ways to contribute other than writing code.
Triaging issues (investigating bug reports for validity and possible actions to
take) is also a useful activity. SciPy has many hundreds of open issues;
closing invalid ones and correctly labeling valid ones (ideally with some first
thoughts in a comment) allows prioritizing maintenance work and finding related
issues easily when working on an existing function or subpackage.
Participating in discussions on the scipy-user and scipy-dev `mailing lists`_ is
a contribution in itself. Everyone who writes to those lists with a problem or
an idea would like to get responses, and writing such responses makes the
project and community function better and appear more welcoming.
The `scipy.org`_ website contains a lot of information on both SciPy the
project and SciPy the community, and it can always use a new pair of hands.
The sources for the website live in their own separate repo:
https://github.com/scipy/scipy.org
Getting started
===============
Thanks for your interest in contributing to SciPy! If you're interested in
contributing code, we hope you'll continue on to the :ref:`contributor-toc`
for details on how to set up your development environment, implement your
improvements, and submit your first PR!
.. _scikit-learn: http://scikit-learn.org
.. _scikit-image: http://scikit-image.org/
.. _statsmodels: https://www.statsmodels.org/
.. _testing guidelines: https://docs.scipy.org/doc/numpy/reference/testing.html
.. _formatted correctly: https://docs.scipy.org/doc/numpy/dev/gitwash/development_workflow.html#writing-the-commit-message
.. _bug report: https://scipy.org/bug-report.html
.. _PEP8: https://www.python.org/dev/peps/pep-0008/
.. _pep8 package: https://pypi.python.org/pypi/pep8
.. _pyflakes: https://pypi.python.org/pypi/pyflakes
.. _Github help pages: https://help.github.com/articles/set-up-git/
.. _issue list: https://github.com/scipy/scipy/issues
.. _Github: https://github.com/scipy/scipy
.. _scipy.org: https://scipy.org/
.. _scipy.github.com: https://scipy.github.com/
.. _scipy.org-new: https://github.com/scipy/scipy.org-new
.. _documentation wiki: https://docs.scipy.org/scipy/Front%20Page/
.. _SciPy Central: https://web.archive.org/web/20170520065729/http://central.scipy.org/
.. _doctest: https://pymotw.com/3/doctest/
.. _virtualenv: https://virtualenv.pypa.io/
.. _virtualenvwrapper: https://bitbucket.org/dhellmann/virtualenvwrapper/
.. _bsd pitch: http://nipy.sourceforge.net/nipy/stable/faq/johns_bsd_pitch.html
.. _Pytest: https://pytest.org/
.. _mailing lists: https://www.scipy.org/scipylib/mailing-lists.html
.. _Spyder: https://www.spyder-ide.org/
.. _Anaconda SciPy Dev Part I (macOS): https://youtu.be/1rPOSNd0ULI
.. _Anaconda SciPy Dev Part II (macOS): https://youtu.be/Faz29u5xIZc
.. _SciPy Development Workflow: https://youtu.be/HgU01gJbzMY

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Building and installing SciPy
+++++++++++++++++++++++++++++
See https://www.scipy.org/install.html
.. Contents::
INTRODUCTION
============
It is *strongly* recommended that you use either a complete scientific Python
distribution or binary packages on your platform if they are available, in
particular on Windows and Mac OS X. You should not attempt to build SciPy if
you are not familiar with compiling software from sources.
Recommended distributions are:
- Enthought Canopy (https://www.enthought.com/products/canopy/)
- Anaconda (https://www.anaconda.com)
- Python(x,y) (https://python-xy.github.io/)
- WinPython (https://winpython.github.io/)
The rest of this install documentation summarizes how to build Scipy. Note
that more extensive (and possibly more up-to-date) build instructions are
maintained at https://scipy.github.io/devdocs/building/
PREREQUISITES
=============
SciPy requires the following software installed for your platform:
1) Python__ >= 3.6
__ https://www.python.org
2) NumPy__ >= 1.14.5
__ https://www.numpy.org/
If building from source, SciPy also requires:
3) setuptools__
__ https://github.com/pypa/setuptools
4) pybind11__ >= 2.4.3
__ https://github.com/pybind/pybind11
5) If you want to build the documentation: Sphinx__ >= 1.2.1
__ http://www.sphinx-doc.org/
6) If you want to build SciPy master or other unreleased version from source
(Cython-generated C sources are included in official releases):
Cython__ >= 0.29.18
__ http://cython.org/
Windows
-------
Compilers
~~~~~~~~~
There are two ways to build SciPy on Windows:
1. Use Intel MKL, and Intel compilers or ifort + MSVC. This is what Anaconda
and Enthought Canopy use.
2. Use MSVC + GFortran with OpenBLAS. This is how the SciPy Windows wheels are
built.
Mac OS X
--------
It is recommended to use GCC or Clang, both work fine. Gcc is available for
free when installing Xcode, the developer toolsuite on Mac OS X. You also
need a Fortran compiler, which is not included with Xcode: you should use a
recent GFortran from an OS X package manager (like Homebrew).
Please do NOT use GFortran from `hpc.sourceforge.net <http://hpc.sourceforge.net>`_,
it is known to generate buggy SciPy binaries.
You should also use a BLAS/LAPACK library from an OS X package manager.
ATLAS, OpenBLAS, and MKL all work.
As of SciPy version 1.2.0, we do not support compiling against the system
Accelerate library for BLAS and LAPACK. It does not support a sufficiently
recent LAPACK interface.
Linux
-----
Most common distributions include all the dependencies. You will need to
install a BLAS/LAPACK (all of ATLAS, OpenBLAS, MKL work fine) including
development headers, as well as development headers for Python itself. Those
are typically packaged as python-dev.
INSTALLING SCIPY
================
For the latest information, see the website:
https://www.scipy.org
Development version from Git
----------------------------
Use the command::
git clone https://github.com/scipy/scipy.git
cd scipy
git clean -xdf
python setup.py install --user
Documentation
-------------
Type::
cd scipy/doc
make html
From tarballs
-------------
Unpack ``SciPy-<version>.tar.gz``, change to the ``SciPy-<version>/``
directory, and run::
pip install . -v --user
This may take several minutes to half an hour depending on the speed of your
computer.
TESTING
=======
To test SciPy after installation (highly recommended), execute in Python::
>>> import scipy
>>> scipy.test()
To run the full test suite use::
>>> scipy.test('full')
If you are upgrading from an older SciPy release, please test your code for any
deprecation warnings before and after upgrading to avoid surprises:
$ python -Wd -c my_code_that_shouldnt_break.py
Please note that you must have version 1.0 or later of the Pytest test
framework installed in order to run the tests. More information about Pytest is
available on the website__.
__ https://pytest.org/
COMPILER NOTES
==============
You can specify which Fortran compiler to use by using the following
install command::
python setup.py config_fc --fcompiler=<Vendor> install
To see a valid list of <Vendor> names, run::
python setup.py config_fc --help-fcompiler
IMPORTANT: It is highly recommended that all libraries that SciPy uses (e.g.
BLAS and ATLAS libraries) are built with the same Fortran compiler. In most
cases, if you mix compilers, you will not be able to import SciPy at best, and will have
crashes and random results at worst.
UNINSTALLING
============
When installing with ``python setup.py install`` or a variation on that, you do
not get proper uninstall behavior for an older already installed SciPy version.
In many cases that's not a problem, but if it turns out to be an issue, you
need to manually uninstall it first (remove from e.g. in
``/usr/lib/python3.4/site-packages/scipy`` or
``$HOME/lib/python3.4/site-packages/scipy``).
Alternatively, you can use ``pip install . --user`` instead of ``python
setup.py install --user`` in order to get reliable uninstall behavior.
The downside is that ``pip`` doesn't show you a build log and doesn't support
incremental rebuilds (it copies the whole source tree to a tempdir).
TROUBLESHOOTING
===============
If you experience problems when building/installing/testing SciPy, you
can ask help from scipy-user@python.org or scipy-dev@python.org mailing
lists. Please include the following information in your message:
NOTE: You can generate some of the following information (items 1-5,7)
in one command::
python -c 'from numpy.f2py.diagnose import run; run()'
1) Platform information::
python -c 'import os, sys; print(os.name, sys.platform)'
uname -a
OS, its distribution name and version information
etc.
2) Information about C, C++, Fortran compilers/linkers as reported by
the compilers when requesting their version information, e.g.,
the output of
::
gcc -v
g77 --version
3) Python version::
python -c 'import sys; print(sys.version)'
4) NumPy version::
python -c 'import numpy; print(numpy.__version__)'
5) ATLAS version, the locations of atlas and lapack libraries, building
information if any. If you have ATLAS version 3.3.6 or newer, then
give the output of the last command in
::
cd scipy/Lib/linalg
python setup_atlas_version.py build_ext --inplace --force
python -c 'import atlas_version'
7) The output of the following commands
::
python INSTALLDIR/numpy/distutils/system_info.py
where INSTALLDIR is, for example, /usr/lib/python3.4/site-packages/.
8) Feel free to add any other relevant information.
For example, the full output (both stdout and stderr) of the SciPy
installation command can be very helpful. Since this output can be
rather large, ask before sending it into the mailing list (or
better yet, to one of the developers, if asked).
9) In case of failing to import extension modules, the output of
::
ldd /path/to/ext_module.so
can be useful.

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Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
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2. Redistributions in binary form must reproduce the above
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Name: LAPACK
Files: extra-dll\libopenb*.dll
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Name: GCC runtime library
Files: extra-dll\*.dll
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Name: Microsoft Visual C++ Runtime Files
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atl90.dll
Microsoft.VC90.ATL.manifest
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----
Full text of license texts referred to above follows (that they are
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GCC RUNTIME LIBRARY EXCEPTION
Version 3.1, 31 March 2009
Copyright (C) 2009 Free Software Foundation, Inc. <http://fsf.org/>
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----
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Also add information on how to contact you by electronic and paper mail.
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The GNU General Public License does not permit incorporating your program
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may consider it more useful to permit linking proprietary applications with
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@ -0,0 +1,202 @@
The SciPy repository and source distributions bundle a number of libraries that
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Files: scipy/special/cephes/dd_*.[ch]
License: modified BSD license ("BSD-LBNL-License.doc")
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@ -0,0 +1,254 @@
SciPy is an open source library of routines for science and engineering
using Python. It is a community project sponsored by Enthought, Inc.
SciPy originated with code contributions by Travis Oliphant, Pearu
Peterson, and Eric Jones. Travis Oliphant and Eric Jones each contributed
about half the initial code. Pearu Peterson developed f2py, which is the
integral to wrapping the many Fortran libraries used in SciPy.
Since then many people have contributed to SciPy, both in code development,
suggestions, and financial support. Below is a partial list. If you've
been left off, please email the "SciPy Developers List" <scipy-dev@python.org>.
Please add names as needed so that we can keep up with all the contributors.
Kumar Appaiah for Dolph Chebyshev window.
Nathan Bell for sparsetools, help with scipy.sparse and scipy.splinalg.
Robert Cimrman for UMFpack wrapper for sparse matrix module, and implementing
the LOBPCG algorithm.
David M. Cooke for improvements to system_info, and LBFGSB wrapper.
Aric Hagberg for ARPACK wrappers, help with splinalg.eigen.
Chuck Harris for Zeros package in optimize (1d root-finding algorithms).
Prabhu Ramachandran for improvements to gui_thread.
Robert Kern for improvements to stats and bug-fixes.
Jean-Sebastien Roy for fmin_tnc code which he adapted from Stephen Nash's
original Fortran.
Ed Schofield for Maximum entropy and Monte Carlo modules, help with
sparse matrix module.
Travis Vaught for numerous contributions to annual conference and community
web-site and the initial work on stats module clean up.
Jeff Whitaker for Mac OS X support.
David Cournapeau for bug-fixes, refactoring of fftpack and cluster,
implementing the numscons and Bento build support, building Windows
binaries and adding single precision FFT.
Damian Eads for hierarchical clustering, dendrogram plotting,
distance functions in spatial package, vq documentation.
Anne Archibald for kd-trees and nearest neighbor in scipy.spatial.
Pauli Virtanen for Sphinx documentation generation, online documentation
framework and interpolation bugfixes.
Josef Perktold for major improvements to scipy.stats and its test suite and
fixes and tests to optimize.curve_fit and leastsq.
David Morrill for getting the scoreboard test system up and running.
Louis Luangkesorn for providing multiple tests for the stats module.
Jochen Kupper for the zoom feature in the now-deprecated plt plotting module.
Tiffany Kamm for working on the community web-site.
Mark Koudritsky for maintaining the web-site.
Andrew Straw for help with the web-page, documentation, packaging,
testing and work on the linalg module.
Stefan van der Walt for numerous bug-fixes, testing and documentation.
Jarrod Millman for release management, community coordination, and code
clean up.
Pierre Gerard-Marchant for statistical masked array functionality.
Alan McIntyre for updating SciPy tests to use the new NumPy test framework.
Matthew Brett for work on the Matlab file IO, bug-fixes, and improvements
to the testing framework.
Gary Strangman for the scipy.stats package.
Tiziano Zito for generalized symmetric and hermitian eigenvalue problem
solver.
Chris Burns for bug-fixes.
Per Brodtkorb for improvements to stats distributions.
Neilen Marais for testing and bug-fixing in the ARPACK wrappers.
Johannes Loehnert and Bart Vandereycken for fixes in the linalg
module.
David Huard for improvements to the interpolation interface.
David Warde-Farley for converting the ndimage docs to ReST.
Uwe Schmitt for wrapping non-negative least-squares.
Ondrej Certik for Debian packaging.
Paul Ivanov for porting Numeric-style C code to the new NumPy API.
Ariel Rokem for contributions on percentileofscore fixes and tests.
Yosef Meller for tests in the optimization module.
Ralf Gommers for release management, code clean up and improvements
to doc-string generation.
Bruce Southey for bug-fixes and improvements to scipy.stats.
Ernest Adrogué for the Skellam distribution.
Enzo Michelangeli for a fast kendall tau test.
David Simcha for a fisher exact test.
Warren Weckesser for bug-fixes, cleanups, and several new features.
Fabian Pedregosa for linear algebra bug-fixes, new features and refactoring.
Jake Vanderplas for wrapping ARPACK's generalized and shift-invert modes
and improving its tests.
Collin RM Stocks for wrapping pivoted QR decomposition.
Martin Teichmann for improving scipy.special.ellipk & agm accuracy,
and for linalg.qr_multiply.
Jeff Armstrong for discrete state-space and linear time-invariant functionality
in scipy.signal, and sylvester/riccati/lyapunov solvers in scipy.linalg.
Mark Wiebe for fixing type casting after changes in NumPy.
Andrey Smirnov for improvements to FIR filter design.
Anthony Scopatz for help with code review and merging.
Lars Buitinck for improvements to scipy.sparse and various other modules.
Scott Sinclair for documentation improvements and some bug fixes.
Gael Varoquaux for cleanups in scipy.sparse.
Skipper Seabold for a fix to special.gammainc.
Wes McKinney for a fix to special.gamma.
Thouis (Ray) Jones for bug fixes in ndimage.
Yaroslav Halchenko for a bug fix in ndimage.
Thomas Robitaille for the IDL 'save' reader.
Fazlul Shahriar for fixes to the NetCDF3 I/O.
Chris Jordan-Squire for bug fixes, documentation improvements and
scipy.special.logit & expit.
Christoph Gohlke for many bug fixes and help with Windows specific issues.
Jacob Silterra for cwt-based peak finding in scipy.signal.
Denis Laxalde for the unified interface to minimizers in scipy.optimize.
David Fong for the sparse LSMR solver.
Andreas Hilboll for adding several new interpolation methods.
Andrew Schein for improving the numerical precision of norm.logcdf().
Robert Gantner for improving expm() implementation.
Sebastian Werk for Halley's method in newton().
Bjorn Forsman for contributing signal.bode().
Tony S. Yu for ndimage improvements.
Jonathan J. Helmus for work on ndimage.
Alex Reinhart for documentation improvements.
Patrick Varilly for cKDTree improvements.
Sturla Molden for cKDTree improvements.
Nathan Crock for bug fixes.
Steven G. Johnson for Faddeeva W and erf* implementations.
Lorenzo Luengo for whosmat() in scipy.io.
Eric Moore for orthogonal polynomial recurrences in scipy.special.
Jacob Stevenson for the basinhopping optimization algorithm
Daniel Smith for sparse matrix functionality improvements
Gustav Larsson for a bug fix in convolve2d.
Alex Griffing for expm 2009, expm_multiply, expm_frechet,
trust region optimization methods, and sparse matrix onenormest
implementations, plus bugfixes.
Nils Werner for signal windowing and wavfile-writing improvements.
Kenneth L. Ho for the wrapper around the Interpolative Decomposition code.
Juan Luis Cano for refactorings in lti, sparse docs improvements and some
trivial fixes.
Pawel Chojnacki for simple documentation fixes.
Gert-Ludwig Ingold for contributions to special functions.
Joris Vankerschaver for multivariate Gaussian functionality.
Rob Falck for the SLSQP interface and linprog.
Jörg Dietrich for the k-sample Anderson Darling test.
Blake Griffith for improvements to scipy.sparse.
Andrew Nelson for scipy.optimize.differential_evolution.
Brian Newsom for work on ctypes multivariate integration.
Nathan Woods for work on multivariate integration.
Brianna Laugher for bug fixes.
Johannes Kulick for the Dirichlet distribution and the softmax function.
Bastian Venthur for bug fixes.
Alex Rothberg for stats.combine_pvalues.
Brandon Liu for stats.combine_pvalues.
Clark Fitzgerald for namedtuple outputs in scipy.stats.
Florian Wilhelm for usage of RandomState in scipy.stats distributions.
Robert T. McGibbon for Levinson-Durbin Toeplitz solver, Hessian information
from L-BFGS-B.
Alex Conley for the Exponentially Modified Normal distribution.
Abraham Escalante for contributions to scipy.stats
Johannes Ballé for the generalized normal distribution.
Irvin Probst (ENSTA Bretagne) for pole placement.
Ian Henriksen for Cython wrappers for BLAS and LAPACK
Fukumu Tsutsumi for bug fixes.
J.J. Green for interpolation bug fixes.
François Magimel for documentation improvements.
Josh Levy-Kramer for the log survival function of the hypergeometric distribution
Will Monroe for bug fixes.
Bernardo Sulzbach for bug fixes.
Alexander Grigorevskiy for adding extra LAPACK least-square solvers and
modifying linalg.lstsq function accordingly.
Sam Lewis for enhancements to the basinhopping module.
Tadeusz Pudlik for documentation and vectorizing spherical Bessel functions.
Philip DeBoer for wrapping random SO(N) and adding random O(N) and
correlation matrices in scipy.stats.
Tyler Reddy and Nikolai Nowaczyk for scipy.spatial.SphericalVoronoi
Bill Sacks for fixes to netcdf i/o.
Kolja Glogowski for a bug fix in scipy.special.
Surhud More for enhancing scipy.optimize.curve_fit to accept covariant errors
on data.
Antonio H. Ribeiro for implementing iirnotch, iirpeak functions and
trust-exact and trust-constr optimization methods.
Matt Haberland for improvements to scipy.optimize, scipy.linalg.lapack, and
developer documentation.
Ilhan Polat for bug fixes on Riccati solvers.
Sebastiano Vigna for code in the stats package related to Kendall's tau.
John Draper for bug fixes.
Alvaro Sanchez-Gonzalez for axis-dependent modes in multidimensional filters.
Alessandro Pietro Bardelli for improvements to pdist/cdist and to related tests.
Jonathan T. Siebert for bug fixes.
Thomas Keck for adding new scipy.stats distributions used in HEP
David Nicholson for bug fixes in spectral functions.
Roman Feldbauer for improvements in scipy.sparse
Dominic Antonacci for statistics documentation.
David Hagen for the object-oriented ODE solver interface.
Arno Onken for contributions to scipy.stats.
Cathy Douglass for bug fixes in ndimage.
Adam Cox for contributions to scipy.constants.
Charles Masson for the Wasserstein and the Cramér-von Mises statistical
distances.
Felix Lenders for implementing trust-trlib method.
Dezmond Goff for adding optional out parameter to pdist/cdist
Nick R. Papior for allowing a wider choice of solvers
Sean Quinn for the Moyal distribution
Lars Grüter for contributions to peak finding in scipy.signal
Jordan Heemskerk for exposing additional windowing functions in scipy.signal.
Michael Tartre (Two Sigma Investments) for contributions to weighted distance functions.
Shinya Suzuki for scipy.stats.brunnermunzel
Graham Clenaghan for bug fixes and optimizations in scipy.stats.
Konrad Griessinger for the small sample Kendall test
Tony Xiang for improvements in scipy.sparse
Roy Zywina for contributions to scipy.fftpack.
Christian H. Meyer for bug fixes in subspace_angles.
Kai Striega for improvements to the scipy.optimize.linprog simplex method.
Josua Sassen for improvements to scipy.interpolate.Rbf
Stiaan Gerber for a bug fix in scipy.optimize.
Nicolas Hug for the Yeo-Johnson transformation.
Idan David for improvements to the log survival function and log cumulative
distribution function of the hypergeometric distribution.
Petar Mlinarić for a bug fix in scipy.io.mmio.
Franz Forstmayr for documentation in scipy.signal
Vega Theil Carstensen for a bug fix in scipy.optimize.linesearch.
Jordi Montes for initial contribution of the Clarkson-Woodruff sketch.
William Conner DiPaolo for improvements to the Clarkson-Woodruff transform.
Forrest Collman for adding multi-target dijsktra to scipy.sparse.csgraph
Carlos Ramos Carreño for adding support for relational attributes in loadarff.
Jason M. Manley for documentation fixes.
Aidan Dang for block QR wrappers in scipy.linalg.lapack.
Clement Ng for modifying tests in scipy.stats.
Fletcher H. Easton for a bug fix in scipy.linalg.interpolative.
Christian Brueffer for improvements to code readability/style and documentation.
Sambit Panda for integration of multiscale_graphcorr into scipy.stats.
Timothy C. Willard for contributions to x-value requirements in scipy.interpolate.
Andrew Knyazev, the original author of LOBPCG, for advice on and maintenance of
sparse.linalg.lobpcg
Angeline G. Burrell for implementing nan_policy in the circular statistics
Michael Marien for contributing to scipy.stats.entropy
Joseph Weston for a bug fix in scipy.optimize.zeros.
Peyton Murray for a bug fix in scipy.optimize.curve_fit.
Leo P. Singer for bug fixes in scipy.optimize and scipy.interpolate and
contribution of the beta-binomial distribution to scipy.stats.
Domen Gorjup and Janko Slavič for continuous wavelet transform with complex
wavelets fix.
Søren Fuglede Jørgensen for improvements to scipy.sparse.csgraph
Grzegorz Mrukwa for a bug fix in rectangular_lsap.cpp
Milad Sadeghi.DM for adding khatri_rao matrix product to scipy.linalg.matfuncs.py
Santiago Hernandez for a bug fix in scipy.optimize._differentialevolution.py.
Dan Kleeman for implementing nan_policy in stats.zscores and winsorize
James Wright for simple documentation fixes
Paul van Mulbregt for stats (esp. Kolmogorov-Smirnov) and
optimize (toms748 root finder).
Sam Wallan for scipy.linalg.lapack enhancements
Richard Weiss for a bug fix in scipy.optimize._differentialevolution.py.
Luigi F. Cruz for adding time/frequency domain option to scipy.signal.resample.
Wesley Alves for improvements to scipy.stats.jarque_bera and scipy.stats.shapiro
Mark Borgerding for contributing linalg.convolution_matrix.
Institutions
------------
Enthought for providing resources and finances for development of SciPy.
Brigham Young University for providing resources for students to work on SciPy.
Agilent which gave a genereous donation for support of SciPy.
UC Berkeley for providing travel money and hosting numerous sprints.
The University of Stellenbosch for funding the development of
the SciKits portal.
Google Inc. for updating documentation of hypergeometric distribution.
Datadog Inc. for contributions to scipy.stats.
Urthecast Inc. for exposing additional windowing functions in scipy.signal.

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# This file is generated by numpy's setup.py
# It contains system_info results at the time of building this package.
__all__ = ["get_info","show"]
import os
import sys
extra_dll_dir = os.path.join(os.path.dirname(__file__), '.libs')
if sys.platform == 'win32' and os.path.isdir(extra_dll_dir):
if sys.version_info >= (3, 8):
os.add_dll_directory(extra_dll_dir)
else:
os.environ.setdefault('PATH', '')
os.environ['PATH'] += os.pathsep + extra_dll_dir
lapack_mkl_info={}
openblas_lapack_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_lapack_info'], 'libraries': ['openblas_lapack_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
lapack_opt_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_lapack_info'], 'libraries': ['openblas_lapack_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
blas_mkl_info={}
blis_info={}
openblas_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_info'], 'libraries': ['openblas_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
blas_opt_info={'library_dirs': ['C:\\projects\\scipy-wheels\\scipy\\build\\openblas_info'], 'libraries': ['openblas_info'], 'language': 'f77', 'define_macros': [('HAVE_CBLAS', None)]}
def get_info(name):
g = globals()
return g.get(name, g.get(name + "_info", {}))
def show():
"""
Show libraries in the system on which NumPy was built.
Print information about various resources (libraries, library
directories, include directories, etc.) in the system on which
NumPy was built.
See Also
--------
get_include : Returns the directory containing NumPy C
header files.
Notes
-----
Classes specifying the information to be printed are defined
in the `numpy.distutils.system_info` module.
Information may include:
* ``language``: language used to write the libraries (mostly
C or f77)
* ``libraries``: names of libraries found in the system
* ``library_dirs``: directories containing the libraries
* ``include_dirs``: directories containing library header files
* ``src_dirs``: directories containing library source files
* ``define_macros``: preprocessor macros used by
``distutils.setup``
Examples
--------
>>> np.show_config()
blas_opt_info:
language = c
define_macros = [('HAVE_CBLAS', None)]
libraries = ['openblas', 'openblas']
library_dirs = ['/usr/local/lib']
"""
for name,info_dict in globals().items():
if name[0] == "_" or type(info_dict) is not type({}): continue
print(name + ":")
if not info_dict:
print(" NOT AVAILABLE")
for k,v in info_dict.items():
v = str(v)
if k == "sources" and len(v) > 200:
v = v[:60] + " ...\n... " + v[-60:]
print(" %s = %s" % (k,v))

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"""
SciPy: A scientific computing package for Python
================================================
Documentation is available in the docstrings and
online at https://docs.scipy.org.
Contents
--------
SciPy imports all the functions from the NumPy namespace, and in
addition provides:
Subpackages
-----------
Using any of these subpackages requires an explicit import. For example,
``import scipy.cluster``.
::
cluster --- Vector Quantization / Kmeans
fft --- Discrete Fourier transforms
fftpack --- Legacy discrete Fourier transforms
integrate --- Integration routines
interpolate --- Interpolation Tools
io --- Data input and output
linalg --- Linear algebra routines
linalg.blas --- Wrappers to BLAS library
linalg.lapack --- Wrappers to LAPACK library
misc --- Various utilities that don't have
another home.
ndimage --- N-D image package
odr --- Orthogonal Distance Regression
optimize --- Optimization Tools
signal --- Signal Processing Tools
signal.windows --- Window functions
sparse --- Sparse Matrices
sparse.linalg --- Sparse Linear Algebra
sparse.linalg.dsolve --- Linear Solvers
sparse.linalg.dsolve.umfpack --- :Interface to the UMFPACK library:
Conjugate Gradient Method (LOBPCG)
sparse.linalg.eigen --- Sparse Eigenvalue Solvers
sparse.linalg.eigen.lobpcg --- Locally Optimal Block Preconditioned
Conjugate Gradient Method (LOBPCG)
spatial --- Spatial data structures and algorithms
special --- Special functions
stats --- Statistical Functions
Utility tools
-------------
::
test --- Run scipy unittests
show_config --- Show scipy build configuration
show_numpy_config --- Show numpy build configuration
__version__ --- SciPy version string
__numpy_version__ --- Numpy version string
"""
__all__ = ['test']
from numpy import show_config as show_numpy_config
if show_numpy_config is None:
raise ImportError(
"Cannot import SciPy when running from NumPy source directory.")
from numpy import __version__ as __numpy_version__
# Import numpy symbols to scipy name space (DEPRECATED)
from ._lib.deprecation import _deprecated
import numpy as _num
linalg = None
_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
'use numpy.{0} instead')
# deprecate callable objects, skipping classes
for _key in _num.__all__:
_fun = getattr(_num, _key)
if callable(_fun) and not isinstance(_fun, type):
_fun = _deprecated(_msg.format(_key))(_fun)
globals()[_key] = _fun
from numpy.random import rand, randn
_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
'use numpy.random.{0} instead')
rand = _deprecated(_msg.format('rand'))(rand)
randn = _deprecated(_msg.format('randn'))(randn)
from numpy.fft import fft, ifft
# fft is especially problematic, so we deprecate it with a shorter window
fft_msg = ('Using scipy.fft as a function is deprecated and will be '
'removed in SciPy 1.5.0, use scipy.fft.fft instead.')
# for wrapping in scipy.fft.__call__, so the stacklevel is one off from the
# usual (2)
_dep_fft = _deprecated(fft_msg, stacklevel=3)(fft)
fft = _deprecated(fft_msg)(fft)
ifft = _deprecated('scipy.ifft is deprecated and will be removed in SciPy '
'2.0.0, use scipy.fft.ifft instead')(ifft)
import numpy.lib.scimath as _sci
_msg = ('scipy.{0} is deprecated and will be removed in SciPy 2.0.0, '
'use numpy.lib.scimath.{0} instead')
for _key in _sci.__all__:
_fun = getattr(_sci, _key)
if callable(_fun):
_fun = _deprecated(_msg.format(_key))(_fun)
globals()[_key] = _fun
__all__ += _num.__all__
__all__ += ['randn', 'rand', 'fft', 'ifft']
del _num
# Remove the linalg imported from NumPy so that the scipy.linalg package can be
# imported.
del linalg
__all__.remove('linalg')
# We first need to detect if we're being called as part of the SciPy
# setup procedure itself in a reliable manner.
try:
__SCIPY_SETUP__
except NameError:
__SCIPY_SETUP__ = False
if __SCIPY_SETUP__:
import sys as _sys
_sys.stderr.write('Running from SciPy source directory.\n')
del _sys
else:
try:
from scipy.__config__ import show as show_config
except ImportError:
msg = """Error importing SciPy: you cannot import SciPy while
being in scipy source directory; please exit the SciPy source
tree first and relaunch your Python interpreter."""
raise ImportError(msg)
from scipy.version import version as __version__
# Allow distributors to run custom init code
from . import _distributor_init
from scipy._lib import _pep440
if _pep440.parse(__numpy_version__) < _pep440.Version('1.14.5'):
import warnings
warnings.warn("NumPy 1.14.5 or above is required for this version of "
"SciPy (detected version %s)" % __numpy_version__,
UserWarning)
del _pep440
from scipy._lib._ccallback import LowLevelCallable
from scipy._lib._testutils import PytestTester
test = PytestTester(__name__)
del PytestTester
# This makes "from scipy import fft" return scipy.fft, not np.fft
del fft
from . import fft

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import os
import numpy as np
from ._fortran import *
from .system_info import combine_dict
# Don't use the deprecated NumPy C API. Define this to a fixed version instead of
# NPY_API_VERSION in order not to break compilation for released SciPy versions
# when NumPy introduces a new deprecation. Use in setup.py::
#
# config.add_extension('_name', sources=['source_fname'], **numpy_nodepr_api)
#
numpy_nodepr_api = dict(define_macros=[("NPY_NO_DEPRECATED_API",
"NPY_1_9_API_VERSION")])
def uses_blas64():
return (os.environ.get("NPY_USE_BLAS_ILP64", "0") != "0")
from scipy._lib._testutils import PytestTester
test = PytestTester(__name__)
del PytestTester

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import re
import os
import sys
from distutils.util import get_platform
import numpy as np
from .system_info import combine_dict
__all__ = ['needs_g77_abi_wrapper', 'get_g77_abi_wrappers',
'gfortran_legacy_flag_hook', 'blas_ilp64_pre_build_hook',
'get_f2py_int64_options', 'generic_pre_build_hook',
'write_file_content', 'ilp64_pre_build_hook']
def get_fcompiler_ilp64_flags():
"""
Dictionary of compiler flags for switching to 8-byte default integer
size.
"""
flags = {
'absoft': ['-i8'], # Absoft
'compaq': ['-i8'], # Compaq Fortran
'compaqv': ['/integer_size:64'], # Compaq Visual Fortran
'g95': ['-i8'], # g95
'gnu95': ['-fdefault-integer-8'], # GNU gfortran
'ibm': ['-qintsize=8'], # IBM XL Fortran
'intel': ['-i8'], # Intel Fortran Compiler for 32-bit
'intele': ['-i8'], # Intel Fortran Compiler for Itanium
'intelem': ['-i8'], # Intel Fortran Compiler for 64-bit
'intelv': ['-i8'], # Intel Visual Fortran Compiler for 32-bit
'intelev': ['-i8'], # Intel Visual Fortran Compiler for Itanium
'intelvem': ['-i8'], # Intel Visual Fortran Compiler for 64-bit
'lahey': ['--long'], # Lahey/Fujitsu Fortran 95 Compiler
'mips': ['-i8'], # MIPSpro Fortran Compiler
'nag': ['-i8'], # NAGWare Fortran 95 compiler
'nagfor': ['-i8'], # NAG Fortran compiler
'pathf95': ['-i8'], # PathScale Fortran compiler
'pg': ['-i8'], # Portland Group Fortran Compiler
'flang': ['-i8'], # Portland Group Fortran LLVM Compiler
'sun': ['-i8'], # Sun or Forte Fortran 95 Compiler
}
# No support for this:
# - g77
# - hpux
# Unknown:
# - vast
return flags
def get_fcompiler_macro_include_flags(path):
"""
Dictionary of compiler flags for cpp-style preprocessing, with
an #include search path, and safety options necessary for macro
expansion.
"""
intel_opts = ['-fpp', '-I' + path]
nag_opts = ['-fpp', '-I' + path]
flags = {
'absoft': ['-W132', '-cpp', '-I' + path],
'gnu95': ['-cpp', '-ffree-line-length-none',
'-ffixed-line-length-none', '-I' + path],
'intel': intel_opts,
'intele': intel_opts,
'intelem': intel_opts,
'intelv': intel_opts,
'intelev': intel_opts,
'intelvem': intel_opts,
'lahey': ['-Cpp', '--wide', '-I' + path],
'mips': ['-col120', '-I' + path],
'nag': nag_opts,
'nagfor': nag_opts,
'pathf95': ['-ftpp', '-macro-expand', '-I' + path],
'flang': ['-Mpreprocess', '-Mextend', '-I' + path],
'sun': ['-fpp', '-I' + path],
}
# No support for this:
# - ibm (line length option turns on fixed format)
# TODO:
# - pg
return flags
def uses_mkl(info):
r_mkl = re.compile("mkl")
libraries = info.get('libraries', '')
for library in libraries:
if r_mkl.search(library):
return True
return False
def needs_g77_abi_wrapper(info):
"""Returns True if g77 ABI wrapper must be used."""
try:
needs_wrapper = int(os.environ["SCIPY_USE_G77_ABI_WRAPPER"]) != 0
except KeyError:
needs_wrapper = uses_mkl(info)
return needs_wrapper
def get_g77_abi_wrappers(info):
"""
Returns file names of source files containing Fortran ABI wrapper
routines.
"""
wrapper_sources = []
path = os.path.abspath(os.path.dirname(__file__))
if needs_g77_abi_wrapper(info):
wrapper_sources += [
os.path.join(path, 'src', 'wrap_g77_abi_f.f'),
os.path.join(path, 'src', 'wrap_g77_abi_c.c'),
]
else:
wrapper_sources += [
os.path.join(path, 'src', 'wrap_dummy_g77_abi.f'),
]
return wrapper_sources
def gfortran_legacy_flag_hook(cmd, ext):
"""
Pre-build hook to add dd gfortran legacy flag -fallow-argument-mismatch
"""
from .compiler_helper import try_add_flag
from distutils.version import LooseVersion
if isinstance(ext, dict):
# build_clib
compilers = ((cmd._f_compiler, ext.setdefault('extra_f77_compile_args', [])),
(cmd._f_compiler, ext.setdefault('extra_f90_compile_args', [])))
else:
# build_ext
compilers = ((cmd._f77_compiler, ext.extra_f77_compile_args),
(cmd._f90_compiler, ext.extra_f90_compile_args))
for compiler, args in compilers:
if compiler is None:
continue
if compiler.compiler_type == "gnu95" and compiler.version >= LooseVersion("10"):
try_add_flag(args, compiler, "-fallow-argument-mismatch")
def _get_build_src_dir():
plat_specifier = ".{}-{}.{}".format(get_platform(), *sys.version_info[:2])
return os.path.join('build', 'src' + plat_specifier)
def get_f2py_int64_options():
if np.dtype('i') == np.dtype(np.int64):
int64_name = 'int'
elif np.dtype('l') == np.dtype(np.int64):
int64_name = 'long'
elif np.dtype('q') == np.dtype(np.int64):
int64_name = 'long_long'
else:
raise RuntimeError("No 64-bit integer type available in f2py!")
f2cmap_fn = os.path.join(_get_build_src_dir(), 'int64.f2cmap')
text = "{'integer': {'': '%s'}, 'logical': {'': '%s'}}\n" % (
int64_name, int64_name)
write_file_content(f2cmap_fn, text)
return ['--f2cmap', f2cmap_fn]
def ilp64_pre_build_hook(cmd, ext):
"""
Pre-build hook for adding Fortran compiler flags that change
default integer size to 64-bit.
"""
fcompiler_flags = get_fcompiler_ilp64_flags()
return generic_pre_build_hook(cmd, ext, fcompiler_flags=fcompiler_flags)
def blas_ilp64_pre_build_hook(blas_info):
"""
Pre-build hook for adding ILP64 BLAS compilation flags, and
mangling Fortran source files to rename BLAS/LAPACK symbols when
there are symbol suffixes.
Examples
--------
::
from scipy._build_utils import blas_ilp64_pre_build_hook
ext = config.add_extension(...)
ext._pre_build_hook = blas_ilp64_pre_build_hook(blas_info)
"""
return lambda cmd, ext: _blas_ilp64_pre_build_hook(cmd, ext, blas_info)
def _blas_ilp64_pre_build_hook(cmd, ext, blas_info):
# Determine BLAS symbol suffix/prefix, if any
macros = dict(blas_info.get('define_macros', []))
prefix = macros.get('BLAS_SYMBOL_PREFIX', '')
suffix = macros.get('BLAS_SYMBOL_SUFFIX', '')
if suffix:
if not suffix.endswith('_'):
# Symbol suffix has to end with '_' to be Fortran-compatible
raise RuntimeError("BLAS/LAPACK has incompatible symbol suffix: "
"{!r}".format(suffix))
suffix = suffix[:-1]
# When symbol prefix/suffix is present, we have to patch sources
if prefix or suffix:
include_dir = os.path.join(_get_build_src_dir(), 'blas64-include')
fcompiler_flags = combine_dict(get_fcompiler_ilp64_flags(),
get_fcompiler_macro_include_flags(include_dir))
# Add the include dir for C code
if isinstance(ext, dict):
ext.setdefault('include_dirs', [])
ext['include_dirs'].append(include_dir)
else:
ext.include_dirs.append(include_dir)
# Create name-mapping include files
include_name_f = 'blas64-prefix-defines.inc'
include_name_c = 'blas64-prefix-defines.h'
include_fn_f = os.path.join(include_dir, include_name_f)
include_fn_c = os.path.join(include_dir, include_name_c)
text = ""
for symbol in get_blas_lapack_symbols():
text += '#define {} {}{}_{}\n'.format(symbol, prefix, symbol, suffix)
text += '#define {} {}{}_{}\n'.format(symbol.upper(), prefix, symbol, suffix)
# Code generation may give source codes with mixed-case names
for j in (1, 2):
s = symbol[:j].lower() + symbol[j:].upper()
text += '#define {} {}{}_{}\n'.format(s, prefix, symbol, suffix)
s = symbol[:j].upper() + symbol[j:].lower()
text += '#define {} {}{}_{}\n'.format(s, prefix, symbol, suffix)
write_file_content(include_fn_f, text)
ctext = re.sub(r'^#define (.*) (.*)$', r'#define \1_ \2_', text, flags=re.M)
write_file_content(include_fn_c, text + "\n" + ctext)
# Patch sources to include it
def patch_source(filename, old_text):
text = '#include "{}"\n'.format(include_name_f)
text += old_text
return text
else:
fcompiler_flags = get_fcompiler_ilp64_flags()
patch_source = None
return generic_pre_build_hook(cmd, ext,
fcompiler_flags=fcompiler_flags,
patch_source_func=patch_source,
source_fnpart="_blas64")
def generic_pre_build_hook(cmd, ext, fcompiler_flags, patch_source_func=None,
source_fnpart=None):
"""
Pre-build hook for adding compiler flags and patching sources.
Parameters
----------
cmd : distutils.core.Command
Hook input. Current distutils command (build_clib or build_ext).
ext : dict or numpy.distutils.extension.Extension
Hook input. Configuration information for library (dict, build_clib)
or extension (numpy.distutils.extension.Extension, build_ext).
fcompiler_flags : dict
Dictionary of ``{'compiler_name': ['-flag1', ...]}`` containing
compiler flags to set.
patch_source_func : callable, optional
Function patching sources, see `_generic_patch_sources` below.
source_fnpart : str, optional
String to append to the modified file basename before extension.
"""
is_clib = isinstance(ext, dict)
if is_clib:
build_info = ext
del ext
# build_clib doesn't have separate f77/f90 compilers
f77 = cmd._f_compiler
f90 = cmd._f_compiler
else:
f77 = cmd._f77_compiler
f90 = cmd._f90_compiler
# Add compiler flags
if is_clib:
f77_args = build_info.setdefault('extra_f77_compile_args', [])
f90_args = build_info.setdefault('extra_f90_compile_args', [])
compilers = [(f77, f77_args), (f90, f90_args)]
else:
compilers = [(f77, ext.extra_f77_compile_args),
(f90, ext.extra_f90_compile_args)]
for compiler, args in compilers:
if compiler is None:
continue
try:
flags = fcompiler_flags[compiler.compiler_type]
except KeyError:
raise RuntimeError("Compiler {!r} is not supported in this "
"configuration.".format(compiler.compiler_type))
args.extend(flag for flag in flags if flag not in args)
# Mangle sources
if patch_source_func is not None:
if is_clib:
build_info.setdefault('depends', []).extend(build_info['sources'])
new_sources = _generic_patch_sources(build_info['sources'], patch_source_func,
source_fnpart)
build_info['sources'][:] = new_sources
else:
ext.depends.extend(ext.sources)
new_sources = _generic_patch_sources(ext.sources, patch_source_func,
source_fnpart)
ext.sources[:] = new_sources
def _generic_patch_sources(filenames, patch_source_func, source_fnpart, root_dir=None):
"""
Patch Fortran sources, creating new source files.
Parameters
----------
filenames : list
List of Fortran source files to patch.
Files not ending in ``.f`` or ``.f90`` are left unaltered.
patch_source_func : callable(filename, old_contents) -> new_contents
Function to apply to file contents, returning new file contents
as a string.
source_fnpart : str
String to append to the modified file basename before extension.
root_dir : str, optional
Source root directory. Default: cwd
Returns
-------
new_filenames : list
List of names of the newly created patched sources.
"""
new_filenames = []
if root_dir is None:
root_dir = os.getcwd()
root_dir = os.path.abspath(root_dir)
src_dir = os.path.join(root_dir, _get_build_src_dir())
for src in filenames:
base, ext = os.path.splitext(os.path.basename(src))
if ext not in ('.f', '.f90'):
new_filenames.append(src)
continue
with open(src, 'r') as fsrc:
text = patch_source_func(src, fsrc.read())
# Generate useful target directory name under src_dir
src_path = os.path.abspath(os.path.dirname(src))
for basedir in [src_dir, root_dir]:
if os.path.commonpath([src_path, basedir]) == basedir:
rel_path = os.path.relpath(src_path, basedir)
break
else:
raise ValueError(f"{src!r} not under {root_dir!r}")
dst = os.path.join(src_dir, rel_path, base + source_fnpart + ext)
write_file_content(dst, text)
new_filenames.append(dst)
return new_filenames
def write_file_content(filename, content):
"""
Write content to file, but only if it differs from the current one.
"""
if os.path.isfile(filename):
with open(filename, 'r') as f:
old_content = f.read()
if old_content == content:
return
dirname = os.path.dirname(filename)
if not os.path.isdir(dirname):
os.makedirs(dirname)
with open(filename, 'w') as f:
f.write(content)
def get_blas_lapack_symbols():
cached = getattr(get_blas_lapack_symbols, 'cached', None)
if cached is not None:
return cached
# Obtain symbol list from Cython Blas/Lapack interface
srcdir = os.path.join(os.path.dirname(__file__), os.pardir, 'linalg')
symbols = []
# Get symbols from the generated files
for fn in ['cython_blas_signatures.txt', 'cython_lapack_signatures.txt']:
with open(os.path.join(srcdir, fn), 'r') as f:
for line in f:
m = re.match(r"^\s*[a-z]+\s+([a-z0-9]+)\(", line)
if m:
symbols.append(m.group(1))
# Get the rest from the generator script
# (we cannot import it directly here, so use exec)
sig_fn = os.path.join(srcdir, '_cython_signature_generator.py')
with open(sig_fn, 'r') as f:
code = f.read()
ns = {'__name__': '<module>'}
exec(code, ns)
symbols.extend(ns['blas_exclusions'])
symbols.extend(ns['lapack_exclusions'])
get_blas_lapack_symbols.cached = tuple(sorted(set(symbols)))
return get_blas_lapack_symbols.cached

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"""
Helpers for detection of compiler features
"""
import tempfile
import os
import sys
from numpy.distutils.system_info import dict_append
def try_compile(compiler, code=None, flags=[], ext=None):
"""Returns True if the compiler is able to compile the given code"""
from distutils.errors import CompileError
from numpy.distutils.fcompiler import FCompiler
if code is None:
if isinstance(compiler, FCompiler):
code = " program main\n return\n end"
else:
code = 'int main (int argc, char **argv) { return 0; }'
ext = ext or compiler.src_extensions[0]
with tempfile.TemporaryDirectory() as temp_dir:
fname = os.path.join(temp_dir, 'main'+ext)
with open(fname, 'w') as f:
f.write(code)
try:
compiler.compile([fname], output_dir=temp_dir, extra_postargs=flags)
except CompileError:
return False
return True
def has_flag(compiler, flag, ext=None):
"""Returns True if the compiler supports the given flag"""
return try_compile(compiler, flags=[flag], ext=ext)
def get_cxx_std_flag(compiler):
"""Detects compiler flag for c++14, c++11, or None if not detected"""
# GNU C compiler documentation uses single dash:
# https://gcc.gnu.org/onlinedocs/gcc/Standards.html
# but silently understands two dashes, like --std=c++11 too.
# Other GCC compatible compilers, like Intel C Compiler on Linux do not.
gnu_flags = ['-std=c++14', '-std=c++11']
flags_by_cc = {
'msvc': ['/std:c++14', None],
'intelw': ['/Qstd=c++14', '/Qstd=c++11'],
'intelem': ['-std=c++14', '-std=c++11']
}
flags = flags_by_cc.get(compiler.compiler_type, gnu_flags)
for flag in flags:
if flag is None:
return None
if has_flag(compiler, flag):
return flag
from numpy.distutils import log
log.warn('Could not detect c++ standard flag')
return None
def get_c_std_flag(compiler):
"""Detects compiler flag to enable C99"""
gnu_flag = '-std=c99'
flag_by_cc = {
'msvc': None,
'intelw': '/Qstd=c99',
'intelem': '-std=c99'
}
flag = flag_by_cc.get(compiler.compiler_type, gnu_flag)
if flag is None:
return None
if has_flag(compiler, flag):
return flag
from numpy.distutils import log
log.warn('Could not detect c99 standard flag')
return None
def try_add_flag(args, compiler, flag, ext=None):
"""Appends flag to the list of arguments if supported by the compiler"""
if try_compile(compiler, flags=args+[flag], ext=ext):
args.append(flag)
def set_c_flags_hook(build_ext, ext):
"""Sets basic compiler flags for compiling C99 code"""
std_flag = get_c_std_flag(build_ext.compiler)
if std_flag is not None:
ext.extra_compile_args.append(std_flag)
def set_cxx_flags_hook(build_ext, ext):
"""Sets basic compiler flags for compiling C++11 code"""
cc = build_ext._cxx_compiler
args = ext.extra_compile_args
std_flag = get_cxx_std_flag(cc)
if std_flag is not None:
args.append(std_flag)
if sys.platform == 'darwin':
# Set min macOS version
min_macos_flag = '-mmacosx-version-min=10.9'
if has_flag(cc, min_macos_flag):
args.append(min_macos_flag)
ext.extra_link_args.append(min_macos_flag)
def set_cxx_flags_clib_hook(build_clib, build_info):
cc = build_clib.compiler
new_args = []
new_link_args = []
std_flag = get_cxx_std_flag(cc)
if std_flag is not None:
new_args.append(std_flag)
if sys.platform == 'darwin':
# Set min macOS version
min_macos_flag = '-mmacosx-version-min=10.9'
if has_flag(cc, min_macos_flag):
new_args.append(min_macos_flag)
new_link_args.append(min_macos_flag)
dict_append(build_info, extra_compiler_args=new_args,
extra_link_args=new_link_args)

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def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_build_utils', parent_package, top_path)
config.add_data_dir('tests')
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())

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import warnings
import numpy as np
import numpy.distutils.system_info
from numpy.distutils.system_info import (system_info,
numpy_info,
NotFoundError,
BlasNotFoundError,
LapackNotFoundError,
AtlasNotFoundError,
LapackSrcNotFoundError,
BlasSrcNotFoundError,
dict_append,
get_info as old_get_info)
from scipy._lib import _pep440
def combine_dict(*dicts, **kw):
"""
Combine Numpy distutils style library configuration dictionaries.
Parameters
----------
*dicts
Dictionaries of keys. List-valued keys will be concatenated.
Otherwise, duplicate keys with different values result to
an error. The input arguments are not modified.
**kw
Keyword arguments are treated as an additional dictionary
(the first one, i.e., prepended).
Returns
-------
combined
Dictionary with combined values.
"""
new_dict = {}
for d in (kw,) + dicts:
for key, value in d.items():
if new_dict.get(key, None) is not None:
old_value = new_dict[key]
if isinstance(value, (list, tuple)):
if isinstance(old_value, (list, tuple)):
new_dict[key] = list(old_value) + list(value)
continue
elif value == old_value:
continue
raise ValueError("Conflicting configuration dicts: {!r} {!r}"
"".format(new_dict, d))
else:
new_dict[key] = value
return new_dict
if _pep440.parse(np.__version__) >= _pep440.Version("1.15.0.dev"):
# For new enough numpy.distutils, the ACCELERATE=None environment
# variable in the top-level setup.py is enough, so no need to
# customize BLAS detection.
get_info = old_get_info
else:
# For NumPy < 1.15.0, we need overrides.
def get_info(name, notfound_action=0):
# Special case our custom *_opt_info.
cls = {'lapack_opt': lapack_opt_info,
'blas_opt': blas_opt_info}.get(name.lower())
if cls is None:
return old_get_info(name, notfound_action)
return cls().get_info(notfound_action)
#
# The following is copypaste from numpy.distutils.system_info, with
# OSX Accelerate-related parts removed.
#
class lapack_opt_info(system_info):
notfounderror = LapackNotFoundError
def calc_info(self):
lapack_mkl_info = get_info('lapack_mkl')
if lapack_mkl_info:
self.set_info(**lapack_mkl_info)
return
openblas_info = get_info('openblas_lapack')
if openblas_info:
self.set_info(**openblas_info)
return
openblas_info = get_info('openblas_clapack')
if openblas_info:
self.set_info(**openblas_info)
return
atlas_info = get_info('atlas_3_10_threads')
if not atlas_info:
atlas_info = get_info('atlas_3_10')
if not atlas_info:
atlas_info = get_info('atlas_threads')
if not atlas_info:
atlas_info = get_info('atlas')
need_lapack = 0
need_blas = 0
info = {}
if atlas_info:
l = atlas_info.get('define_macros', [])
if ('ATLAS_WITH_LAPACK_ATLAS', None) in l \
or ('ATLAS_WITHOUT_LAPACK', None) in l:
need_lapack = 1
info = atlas_info
else:
warnings.warn(AtlasNotFoundError.__doc__, stacklevel=2)
need_blas = 1
need_lapack = 1
dict_append(info, define_macros=[('NO_ATLAS_INFO', 1)])
if need_lapack:
lapack_info = get_info('lapack')
#lapack_info = {} ## uncomment for testing
if lapack_info:
dict_append(info, **lapack_info)
else:
warnings.warn(LapackNotFoundError.__doc__, stacklevel=2)
lapack_src_info = get_info('lapack_src')
if not lapack_src_info:
warnings.warn(LapackSrcNotFoundError.__doc__, stacklevel=2)
return
dict_append(info, libraries=[('flapack_src', lapack_src_info)])
if need_blas:
blas_info = get_info('blas')
if blas_info:
dict_append(info, **blas_info)
else:
warnings.warn(BlasNotFoundError.__doc__, stacklevel=2)
blas_src_info = get_info('blas_src')
if not blas_src_info:
warnings.warn(BlasSrcNotFoundError.__doc__, stacklevel=2)
return
dict_append(info, libraries=[('fblas_src', blas_src_info)])
self.set_info(**info)
return
class blas_opt_info(system_info):
notfounderror = BlasNotFoundError
def calc_info(self):
blas_mkl_info = get_info('blas_mkl')
if blas_mkl_info:
self.set_info(**blas_mkl_info)
return
blis_info = get_info('blis')
if blis_info:
self.set_info(**blis_info)
return
openblas_info = get_info('openblas')
if openblas_info:
self.set_info(**openblas_info)
return
atlas_info = get_info('atlas_3_10_blas_threads')
if not atlas_info:
atlas_info = get_info('atlas_3_10_blas')
if not atlas_info:
atlas_info = get_info('atlas_blas_threads')
if not atlas_info:
atlas_info = get_info('atlas_blas')
need_blas = 0
info = {}
if atlas_info:
info = atlas_info
else:
warnings.warn(AtlasNotFoundError.__doc__, stacklevel=2)
need_blas = 1
dict_append(info, define_macros=[('NO_ATLAS_INFO', 1)])
if need_blas:
blas_info = get_info('blas')
if blas_info:
dict_append(info, **blas_info)
else:
warnings.warn(BlasNotFoundError.__doc__, stacklevel=2)
blas_src_info = get_info('blas_src')
if not blas_src_info:
warnings.warn(BlasSrcNotFoundError.__doc__, stacklevel=2)
return
dict_append(info, libraries=[('fblas_src', blas_src_info)])
self.set_info(**info)
return

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import sys
import subprocess
PUBLIC_SUBMODULES = [
'cluster',
'cluster.hierarchy',
'cluster.vq',
'constants',
'fft',
'fftpack',
'fftpack.convolve',
'integrate',
'interpolate',
'io',
'io.arff',
'io.wavfile',
'linalg',
'linalg.blas',
'linalg.lapack',
'linalg.interpolative',
'misc',
'ndimage',
'odr',
'optimize',
'signal',
'sparse',
'sparse.csgraph',
'sparse.linalg',
'spatial',
'spatial.distance',
'special',
'stats',
'stats.mstats',
]
def test_importing_submodules():
# Regression test for gh-6793.
for name in PUBLIC_SUBMODULES:
try:
cmd = [sys.executable, '-c', 'import scipy.{0}'.format(name)]
subprocess.check_output(cmd)
except subprocess.CalledProcessError:
raise AssertionError('Importing scipy.{0} failed'.format(name))

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import re
import scipy
from numpy.testing import assert_
def test_valid_scipy_version():
# Verify that the SciPy version is a valid one (no .post suffix or other
# nonsense). See NumPy issue gh-6431 for an issue caused by an invalid
# version.
version_pattern = r"^[0-9]+\.[0-9]+\.[0-9]+(|a[0-9]|b[0-9]|rc[0-9])"
dev_suffix = r"(\.dev0\+([0-9a-f]{7}|Unknown))"
if scipy.version.release:
res = re.match(version_pattern, scipy.__version__)
else:
res = re.match(version_pattern + dev_suffix, scipy.__version__)
assert_(res is not None, scipy.__version__)

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""" Distributor init file
Distributors: you can add custom code here to support particular distributions
of scipy.
For example, this is a good place to put any checks for hardware requirements.
The scipy standard source distribution will not put code in this file, so you
can safely replace this file with your own version.
"""
import os
# on Windows SciPy loads important DLLs
# and the code below aims to alleviate issues with DLL
# path resolution portability with an absolute path DLL load
if os.name == 'nt':
from ctypes import WinDLL
import glob
# convention for storing / loading the DLL from
# scipy/.libs/, if present
libs_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
'.libs'))
if os.path.isdir(libs_path):
# for Python >= 3.8, DLL resolution ignores the PATH variable
# and the current working directory; see release notes:
# https://docs.python.org/3/whatsnew/3.8.html#bpo-36085-whatsnew
# Only the system paths, the directory containing the DLL, and
# directories added with add_dll_directory() are searched for
# load-time dependencies with Python >= 3.8
# this module was originally added to support DLL resolution in
# Python 3.8 because of the changes described above--providing the
# absolute paths to the DLLs allowed for proper resolution/loading
# however, we also started to receive reports of problems with DLL
# resolution with Python 3.7 that were sometimes alleviated with
# inclusion of the _distributor_init.py module; see SciPy main
# repo gh-11826
# we noticed in scipy-wheels repo gh-70 that inclusion of
# _distributor_init.py in 32-bit wheels for Python 3.7 resulted
# in failures in DLL resolution (64-bit 3.7 did not)
# as a result, we decided to combine both the old (working directory)
# and new (absolute path to DLL location) DLL resolution mechanisms
# to improve the chances of resolving DLLs across a wider range of
# Python versions
# we did not experiment with manipulating the PATH environment variable
# to include libs_path; it is not immediately clear if this would have
# robustness or security advantages over changing working directories
# as done below
# we should remove the working directory shims when our minimum supported
# Python version is 3.8 and trust the improvements to secure DLL loading
# in the standard lib for Python >= 3.8
try:
owd = os.getcwd()
os.chdir(libs_path)
for filename in glob.glob(os.path.join(libs_path, '*dll')):
WinDLL(os.path.abspath(filename))
finally:
os.chdir(owd)

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"""
Module containing private utility functions
===========================================
The ``scipy._lib`` namespace is empty (for now). Tests for all
utilities in submodules of ``_lib`` can be run with::
from scipy import _lib
_lib.test()
"""
from scipy._lib._testutils import PytestTester
test = PytestTester(__name__)
del PytestTester

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from . import _ccallback_c
import ctypes
PyCFuncPtr = ctypes.CFUNCTYPE(ctypes.c_void_p).__bases__[0]
ffi = None
class CData(object):
pass
def _import_cffi():
global ffi, CData
if ffi is not None:
return
try:
import cffi
ffi = cffi.FFI()
CData = ffi.CData
except ImportError:
ffi = False
class LowLevelCallable(tuple):
"""
Low-level callback function.
Parameters
----------
function : {PyCapsule, ctypes function pointer, cffi function pointer}
Low-level callback function.
user_data : {PyCapsule, ctypes void pointer, cffi void pointer}
User data to pass on to the callback function.
signature : str, optional
Signature of the function. If omitted, determined from *function*,
if possible.
Attributes
----------
function
Callback function given.
user_data
User data given.
signature
Signature of the function.
Methods
-------
from_cython
Class method for constructing callables from Cython C-exported
functions.
Notes
-----
The argument ``function`` can be one of:
- PyCapsule, whose name contains the C function signature
- ctypes function pointer
- cffi function pointer
The signature of the low-level callback must match one of those expected
by the routine it is passed to.
If constructing low-level functions from a PyCapsule, the name of the
capsule must be the corresponding signature, in the format::
return_type (arg1_type, arg2_type, ...)
For example::
"void (double)"
"double (double, int *, void *)"
The context of a PyCapsule passed in as ``function`` is used as ``user_data``,
if an explicit value for ``user_data`` was not given.
"""
# Make the class immutable
__slots__ = ()
def __new__(cls, function, user_data=None, signature=None):
# We need to hold a reference to the function & user data,
# to prevent them going out of scope
item = cls._parse_callback(function, user_data, signature)
return tuple.__new__(cls, (item, function, user_data))
def __repr__(self):
return "LowLevelCallable({!r}, {!r})".format(self.function, self.user_data)
@property
def function(self):
return tuple.__getitem__(self, 1)
@property
def user_data(self):
return tuple.__getitem__(self, 2)
@property
def signature(self):
return _ccallback_c.get_capsule_signature(tuple.__getitem__(self, 0))
def __getitem__(self, idx):
raise ValueError()
@classmethod
def from_cython(cls, module, name, user_data=None, signature=None):
"""
Create a low-level callback function from an exported Cython function.
Parameters
----------
module : module
Cython module where the exported function resides
name : str
Name of the exported function
user_data : {PyCapsule, ctypes void pointer, cffi void pointer}, optional
User data to pass on to the callback function.
signature : str, optional
Signature of the function. If omitted, determined from *function*.
"""
try:
function = module.__pyx_capi__[name]
except AttributeError:
raise ValueError("Given module is not a Cython module with __pyx_capi__ attribute")
except KeyError:
raise ValueError("No function {!r} found in __pyx_capi__ of the module".format(name))
return cls(function, user_data, signature)
@classmethod
def _parse_callback(cls, obj, user_data=None, signature=None):
_import_cffi()
if isinstance(obj, LowLevelCallable):
func = tuple.__getitem__(obj, 0)
elif isinstance(obj, PyCFuncPtr):
func, signature = _get_ctypes_func(obj, signature)
elif isinstance(obj, CData):
func, signature = _get_cffi_func(obj, signature)
elif _ccallback_c.check_capsule(obj):
func = obj
else:
raise ValueError("Given input is not a callable or a low-level callable (pycapsule/ctypes/cffi)")
if isinstance(user_data, ctypes.c_void_p):
context = _get_ctypes_data(user_data)
elif isinstance(user_data, CData):
context = _get_cffi_data(user_data)
elif user_data is None:
context = 0
elif _ccallback_c.check_capsule(user_data):
context = user_data
else:
raise ValueError("Given user data is not a valid low-level void* pointer (pycapsule/ctypes/cffi)")
return _ccallback_c.get_raw_capsule(func, signature, context)
#
# ctypes helpers
#
def _get_ctypes_func(func, signature=None):
# Get function pointer
func_ptr = ctypes.cast(func, ctypes.c_void_p).value
# Construct function signature
if signature is None:
signature = _typename_from_ctypes(func.restype) + " ("
for j, arg in enumerate(func.argtypes):
if j == 0:
signature += _typename_from_ctypes(arg)
else:
signature += ", " + _typename_from_ctypes(arg)
signature += ")"
return func_ptr, signature
def _typename_from_ctypes(item):
if item is None:
return "void"
elif item is ctypes.c_void_p:
return "void *"
name = item.__name__
pointer_level = 0
while name.startswith("LP_"):
pointer_level += 1
name = name[3:]
if name.startswith('c_'):
name = name[2:]
if pointer_level > 0:
name += " " + "*"*pointer_level
return name
def _get_ctypes_data(data):
# Get voidp pointer
return ctypes.cast(data, ctypes.c_void_p).value
#
# CFFI helpers
#
def _get_cffi_func(func, signature=None):
# Get function pointer
func_ptr = ffi.cast('uintptr_t', func)
# Get signature
if signature is None:
signature = ffi.getctype(ffi.typeof(func)).replace('(*)', ' ')
return func_ptr, signature
def _get_cffi_data(data):
# Get pointer
return ffi.cast('uintptr_t', data)

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@ -0,0 +1,105 @@
"""
Module for testing automatic garbage collection of objects
.. autosummary::
:toctree: generated/
set_gc_state - enable or disable garbage collection
gc_state - context manager for given state of garbage collector
assert_deallocated - context manager to check for circular references on object
"""
import weakref
import gc
import sys
from contextlib import contextmanager
__all__ = ['set_gc_state', 'gc_state', 'assert_deallocated']
IS_PYPY = '__pypy__' in sys.modules
class ReferenceError(AssertionError):
pass
def set_gc_state(state):
""" Set status of garbage collector """
if gc.isenabled() == state:
return
if state:
gc.enable()
else:
gc.disable()
@contextmanager
def gc_state(state):
""" Context manager to set state of garbage collector to `state`
Parameters
----------
state : bool
True for gc enabled, False for disabled
Examples
--------
>>> with gc_state(False):
... assert not gc.isenabled()
>>> with gc_state(True):
... assert gc.isenabled()
"""
orig_state = gc.isenabled()
set_gc_state(state)
yield
set_gc_state(orig_state)
@contextmanager
def assert_deallocated(func, *args, **kwargs):
"""Context manager to check that object is deallocated
This is useful for checking that an object can be freed directly by
reference counting, without requiring gc to break reference cycles.
GC is disabled inside the context manager.
This check is not available on PyPy.
Parameters
----------
func : callable
Callable to create object to check
\\*args : sequence
positional arguments to `func` in order to create object to check
\\*\\*kwargs : dict
keyword arguments to `func` in order to create object to check
Examples
--------
>>> class C(object): pass
>>> with assert_deallocated(C) as c:
... # do something
... del c
>>> class C(object):
... def __init__(self):
... self._circular = self # Make circular reference
>>> with assert_deallocated(C) as c: #doctest: +IGNORE_EXCEPTION_DETAIL
... # do something
... del c
Traceback (most recent call last):
...
ReferenceError: Remaining reference(s) to object
"""
if IS_PYPY:
raise RuntimeError("assert_deallocated is unavailable on PyPy")
with gc_state(False):
obj = func(*args, **kwargs)
ref = weakref.ref(obj)
yield obj
del obj
if ref() is not None:
raise ReferenceError("Remaining reference(s) to object")

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"""Utility to compare pep440 compatible version strings.
The LooseVersion and StrictVersion classes that distutils provides don't
work; they don't recognize anything like alpha/beta/rc/dev versions.
"""
# Copyright (c) Donald Stufft and individual contributors.
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import collections
import itertools
import re
__all__ = [
"parse", "Version", "LegacyVersion", "InvalidVersion", "VERSION_PATTERN",
]
# BEGIN packaging/_structures.py
class Infinity(object):
def __repr__(self):
return "Infinity"
def __hash__(self):
return hash(repr(self))
def __lt__(self, other):
return False
def __le__(self, other):
return False
def __eq__(self, other):
return isinstance(other, self.__class__)
def __ne__(self, other):
return not isinstance(other, self.__class__)
def __gt__(self, other):
return True
def __ge__(self, other):
return True
def __neg__(self):
return NegativeInfinity
Infinity = Infinity()
class NegativeInfinity(object):
def __repr__(self):
return "-Infinity"
def __hash__(self):
return hash(repr(self))
def __lt__(self, other):
return True
def __le__(self, other):
return True
def __eq__(self, other):
return isinstance(other, self.__class__)
def __ne__(self, other):
return not isinstance(other, self.__class__)
def __gt__(self, other):
return False
def __ge__(self, other):
return False
def __neg__(self):
return Infinity
# BEGIN packaging/version.py
NegativeInfinity = NegativeInfinity()
_Version = collections.namedtuple(
"_Version",
["epoch", "release", "dev", "pre", "post", "local"],
)
def parse(version):
"""
Parse the given version string and return either a :class:`Version` object
or a :class:`LegacyVersion` object depending on if the given version is
a valid PEP 440 version or a legacy version.
"""
try:
return Version(version)
except InvalidVersion:
return LegacyVersion(version)
class InvalidVersion(ValueError):
"""
An invalid version was found, users should refer to PEP 440.
"""
class _BaseVersion(object):
def __hash__(self):
return hash(self._key)
def __lt__(self, other):
return self._compare(other, lambda s, o: s < o)
def __le__(self, other):
return self._compare(other, lambda s, o: s <= o)
def __eq__(self, other):
return self._compare(other, lambda s, o: s == o)
def __ge__(self, other):
return self._compare(other, lambda s, o: s >= o)
def __gt__(self, other):
return self._compare(other, lambda s, o: s > o)
def __ne__(self, other):
return self._compare(other, lambda s, o: s != o)
def _compare(self, other, method):
if not isinstance(other, _BaseVersion):
return NotImplemented
return method(self._key, other._key)
class LegacyVersion(_BaseVersion):
def __init__(self, version):
self._version = str(version)
self._key = _legacy_cmpkey(self._version)
def __str__(self):
return self._version
def __repr__(self):
return "<LegacyVersion({0})>".format(repr(str(self)))
@property
def public(self):
return self._version
@property
def base_version(self):
return self._version
@property
def local(self):
return None
@property
def is_prerelease(self):
return False
@property
def is_postrelease(self):
return False
_legacy_version_component_re = re.compile(
r"(\d+ | [a-z]+ | \.| -)", re.VERBOSE,
)
_legacy_version_replacement_map = {
"pre": "c", "preview": "c", "-": "final-", "rc": "c", "dev": "@",
}
def _parse_version_parts(s):
for part in _legacy_version_component_re.split(s):
part = _legacy_version_replacement_map.get(part, part)
if not part or part == ".":
continue
if part[:1] in "0123456789":
# pad for numeric comparison
yield part.zfill(8)
else:
yield "*" + part
# ensure that alpha/beta/candidate are before final
yield "*final"
def _legacy_cmpkey(version):
# We hardcode an epoch of -1 here. A PEP 440 version can only have an epoch
# greater than or equal to 0. This will effectively put the LegacyVersion,
# which uses the defacto standard originally implemented by setuptools,
# as before all PEP 440 versions.
epoch = -1
# This scheme is taken from pkg_resources.parse_version setuptools prior to
# its adoption of the packaging library.
parts = []
for part in _parse_version_parts(version.lower()):
if part.startswith("*"):
# remove "-" before a prerelease tag
if part < "*final":
while parts and parts[-1] == "*final-":
parts.pop()
# remove trailing zeros from each series of numeric parts
while parts and parts[-1] == "00000000":
parts.pop()
parts.append(part)
parts = tuple(parts)
return epoch, parts
# Deliberately not anchored to the start and end of the string, to make it
# easier for 3rd party code to reuse
VERSION_PATTERN = r"""
v?
(?:
(?:(?P<epoch>[0-9]+)!)? # epoch
(?P<release>[0-9]+(?:\.[0-9]+)*) # release segment
(?P<pre> # pre-release
[-_\.]?
(?P<pre_l>(a|b|c|rc|alpha|beta|pre|preview))
[-_\.]?
(?P<pre_n>[0-9]+)?
)?
(?P<post> # post release
(?:-(?P<post_n1>[0-9]+))
|
(?:
[-_\.]?
(?P<post_l>post|rev|r)
[-_\.]?
(?P<post_n2>[0-9]+)?
)
)?
(?P<dev> # dev release
[-_\.]?
(?P<dev_l>dev)
[-_\.]?
(?P<dev_n>[0-9]+)?
)?
)
(?:\+(?P<local>[a-z0-9]+(?:[-_\.][a-z0-9]+)*))? # local version
"""
class Version(_BaseVersion):
_regex = re.compile(
r"^\s*" + VERSION_PATTERN + r"\s*$",
re.VERBOSE | re.IGNORECASE,
)
def __init__(self, version):
# Validate the version and parse it into pieces
match = self._regex.search(version)
if not match:
raise InvalidVersion("Invalid version: '{0}'".format(version))
# Store the parsed out pieces of the version
self._version = _Version(
epoch=int(match.group("epoch")) if match.group("epoch") else 0,
release=tuple(int(i) for i in match.group("release").split(".")),
pre=_parse_letter_version(
match.group("pre_l"),
match.group("pre_n"),
),
post=_parse_letter_version(
match.group("post_l"),
match.group("post_n1") or match.group("post_n2"),
),
dev=_parse_letter_version(
match.group("dev_l"),
match.group("dev_n"),
),
local=_parse_local_version(match.group("local")),
)
# Generate a key which will be used for sorting
self._key = _cmpkey(
self._version.epoch,
self._version.release,
self._version.pre,
self._version.post,
self._version.dev,
self._version.local,
)
def __repr__(self):
return "<Version({0})>".format(repr(str(self)))
def __str__(self):
parts = []
# Epoch
if self._version.epoch != 0:
parts.append("{0}!".format(self._version.epoch))
# Release segment
parts.append(".".join(str(x) for x in self._version.release))
# Pre-release
if self._version.pre is not None:
parts.append("".join(str(x) for x in self._version.pre))
# Post-release
if self._version.post is not None:
parts.append(".post{0}".format(self._version.post[1]))
# Development release
if self._version.dev is not None:
parts.append(".dev{0}".format(self._version.dev[1]))
# Local version segment
if self._version.local is not None:
parts.append(
"+{0}".format(".".join(str(x) for x in self._version.local))
)
return "".join(parts)
@property
def public(self):
return str(self).split("+", 1)[0]
@property
def base_version(self):
parts = []
# Epoch
if self._version.epoch != 0:
parts.append("{0}!".format(self._version.epoch))
# Release segment
parts.append(".".join(str(x) for x in self._version.release))
return "".join(parts)
@property
def local(self):
version_string = str(self)
if "+" in version_string:
return version_string.split("+", 1)[1]
@property
def is_prerelease(self):
return bool(self._version.dev or self._version.pre)
@property
def is_postrelease(self):
return bool(self._version.post)
def _parse_letter_version(letter, number):
if letter:
# We assume there is an implicit 0 in a pre-release if there is
# no numeral associated with it.
if number is None:
number = 0
# We normalize any letters to their lower-case form
letter = letter.lower()
# We consider some words to be alternate spellings of other words and
# in those cases we want to normalize the spellings to our preferred
# spelling.
if letter == "alpha":
letter = "a"
elif letter == "beta":
letter = "b"
elif letter in ["c", "pre", "preview"]:
letter = "rc"
elif letter in ["rev", "r"]:
letter = "post"
return letter, int(number)
if not letter and number:
# We assume that if we are given a number but not given a letter,
# then this is using the implicit post release syntax (e.g., 1.0-1)
letter = "post"
return letter, int(number)
_local_version_seperators = re.compile(r"[\._-]")
def _parse_local_version(local):
"""
Takes a string like abc.1.twelve and turns it into ("abc", 1, "twelve").
"""
if local is not None:
return tuple(
part.lower() if not part.isdigit() else int(part)
for part in _local_version_seperators.split(local)
)
def _cmpkey(epoch, release, pre, post, dev, local):
# When we compare a release version, we want to compare it with all of the
# trailing zeros removed. So we'll use a reverse the list, drop all the now
# leading zeros until we come to something non-zero, then take the rest,
# re-reverse it back into the correct order, and make it a tuple and use
# that for our sorting key.
release = tuple(
reversed(list(
itertools.dropwhile(
lambda x: x == 0,
reversed(release),
)
))
)
# We need to "trick" the sorting algorithm to put 1.0.dev0 before 1.0a0.
# We'll do this by abusing the pre-segment, but we _only_ want to do this
# if there is no pre- or a post-segment. If we have one of those, then
# the normal sorting rules will handle this case correctly.
if pre is None and post is None and dev is not None:
pre = -Infinity
# Versions without a pre-release (except as noted above) should sort after
# those with one.
elif pre is None:
pre = Infinity
# Versions without a post-segment should sort before those with one.
if post is None:
post = -Infinity
# Versions without a development segment should sort after those with one.
if dev is None:
dev = Infinity
if local is None:
# Versions without a local segment should sort before those with one.
local = -Infinity
else:
# Versions with a local segment need that segment parsed to implement
# the sorting rules in PEP440.
# - Alphanumeric segments sort before numeric segments
# - Alphanumeric segments sort lexicographically
# - Numeric segments sort numerically
# - Shorter versions sort before longer versions when the prefixes
# match exactly
local = tuple(
(i, "") if isinstance(i, int) else (-Infinity, i)
for i in local
)
return epoch, release, pre, post, dev, local

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"""
Generic test utilities.
"""
import os
import re
import sys
__all__ = ['PytestTester', 'check_free_memory']
class FPUModeChangeWarning(RuntimeWarning):
"""Warning about FPU mode change"""
pass
class PytestTester(object):
"""
Pytest test runner entry point.
"""
def __init__(self, module_name):
self.module_name = module_name
def __call__(self, label="fast", verbose=1, extra_argv=None, doctests=False,
coverage=False, tests=None, parallel=None):
import pytest
module = sys.modules[self.module_name]
module_path = os.path.abspath(module.__path__[0])
pytest_args = ['--showlocals', '--tb=short']
if doctests:
raise ValueError("Doctests not supported")
if extra_argv:
pytest_args += list(extra_argv)
if verbose and int(verbose) > 1:
pytest_args += ["-" + "v"*(int(verbose)-1)]
if coverage:
pytest_args += ["--cov=" + module_path]
if label == "fast":
pytest_args += ["-m", "not slow"]
elif label != "full":
pytest_args += ["-m", label]
if tests is None:
tests = [self.module_name]
if parallel is not None and parallel > 1:
if _pytest_has_xdist():
pytest_args += ['-n', str(parallel)]
else:
import warnings
warnings.warn('Could not run tests in parallel because '
'pytest-xdist plugin is not available.')
pytest_args += ['--pyargs'] + list(tests)
try:
code = pytest.main(pytest_args)
except SystemExit as exc:
code = exc.code
return (code == 0)
def _pytest_has_xdist():
"""
Check if the pytest-xdist plugin is installed, providing parallel tests
"""
# Check xdist exists without importing, otherwise pytests emits warnings
from importlib.util import find_spec
return find_spec('xdist') is not None
def check_free_memory(free_mb):
"""
Check *free_mb* of memory is available, otherwise do pytest.skip
"""
import pytest
try:
mem_free = _parse_size(os.environ['SCIPY_AVAILABLE_MEM'])
msg = '{0} MB memory required, but environment SCIPY_AVAILABLE_MEM={1}'.format(
free_mb, os.environ['SCIPY_AVAILABLE_MEM'])
except KeyError:
mem_free = _get_mem_available()
if mem_free is None:
pytest.skip("Could not determine available memory; set SCIPY_AVAILABLE_MEM "
"variable to free memory in MB to run the test.")
msg = '{0} MB memory required, but {1} MB available'.format(
free_mb, mem_free/1e6)
if mem_free < free_mb * 1e6:
pytest.skip(msg)
def _parse_size(size_str):
suffixes = {'': 1e6,
'b': 1.0,
'k': 1e3, 'M': 1e6, 'G': 1e9, 'T': 1e12,
'kb': 1e3, 'Mb': 1e6, 'Gb': 1e9, 'Tb': 1e12,
'kib': 1024.0, 'Mib': 1024.0**2, 'Gib': 1024.0**3, 'Tib': 1024.0**4}
m = re.match(r'^\s*(\d+)\s*({0})\s*$'.format('|'.join(suffixes.keys())),
size_str,
re.I)
if not m or m.group(2) not in suffixes:
raise ValueError("Invalid size string")
return float(m.group(1)) * suffixes[m.group(2)]
def _get_mem_available():
"""
Get information about memory available, not counting swap.
"""
try:
import psutil
return psutil.virtual_memory().available
except (ImportError, AttributeError):
pass
if sys.platform.startswith('linux'):
info = {}
with open('/proc/meminfo', 'r') as f:
for line in f:
p = line.split()
info[p[0].strip(':').lower()] = float(p[1]) * 1e3
if 'memavailable' in info:
# Linux >= 3.14
return info['memavailable']
else:
return info['memfree'] + info['cached']
return None

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import threading
import scipy._lib.decorator
__all__ = ['ReentrancyError', 'ReentrancyLock', 'non_reentrant']
class ReentrancyError(RuntimeError):
pass
class ReentrancyLock(object):
"""
Threading lock that raises an exception for reentrant calls.
Calls from different threads are serialized, and nested calls from the
same thread result to an error.
The object can be used as a context manager or to decorate functions
via the decorate() method.
"""
def __init__(self, err_msg):
self._rlock = threading.RLock()
self._entered = False
self._err_msg = err_msg
def __enter__(self):
self._rlock.acquire()
if self._entered:
self._rlock.release()
raise ReentrancyError(self._err_msg)
self._entered = True
def __exit__(self, type, value, traceback):
self._entered = False
self._rlock.release()
def decorate(self, func):
def caller(func, *a, **kw):
with self:
return func(*a, **kw)
return scipy._lib.decorator.decorate(func, caller)
def non_reentrant(err_msg=None):
"""
Decorate a function with a threading lock and prevent reentrant calls.
"""
def decorator(func):
msg = err_msg
if msg is None:
msg = "%s is not re-entrant" % func.__name__
lock = ReentrancyLock(msg)
return lock.decorate(func)
return decorator

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''' Contexts for *with* statement providing temporary directories
'''
import os
from contextlib import contextmanager
from shutil import rmtree
from tempfile import mkdtemp
@contextmanager
def tempdir():
"""Create and return a temporary directory. This has the same
behavior as mkdtemp but can be used as a context manager.
Upon exiting the context, the directory and everything contained
in it are removed.
Examples
--------
>>> import os
>>> with tempdir() as tmpdir:
... fname = os.path.join(tmpdir, 'example_file.txt')
... with open(fname, 'wt') as fobj:
... _ = fobj.write('a string\\n')
>>> os.path.exists(tmpdir)
False
"""
d = mkdtemp()
yield d
rmtree(d)
@contextmanager
def in_tempdir():
''' Create, return, and change directory to a temporary directory
Examples
--------
>>> import os
>>> my_cwd = os.getcwd()
>>> with in_tempdir() as tmpdir:
... _ = open('test.txt', 'wt').write('some text')
... assert os.path.isfile('test.txt')
... assert os.path.isfile(os.path.join(tmpdir, 'test.txt'))
>>> os.path.exists(tmpdir)
False
>>> os.getcwd() == my_cwd
True
'''
pwd = os.getcwd()
d = mkdtemp()
os.chdir(d)
yield d
os.chdir(pwd)
rmtree(d)
@contextmanager
def in_dir(dir=None):
""" Change directory to given directory for duration of ``with`` block
Useful when you want to use `in_tempdir` for the final test, but
you are still debugging. For example, you may want to do this in the end:
>>> with in_tempdir() as tmpdir:
... # do something complicated which might break
... pass
But, indeed, the complicated thing does break, and meanwhile, the
``in_tempdir`` context manager wiped out the directory with the
temporary files that you wanted for debugging. So, while debugging, you
replace with something like:
>>> with in_dir() as tmpdir: # Use working directory by default
... # do something complicated which might break
... pass
You can then look at the temporary file outputs to debug what is happening,
fix, and finally replace ``in_dir`` with ``in_tempdir`` again.
"""
cwd = os.getcwd()
if dir is None:
yield cwd
return
os.chdir(dir)
yield dir
os.chdir(cwd)

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BSD 3-Clause License
Copyright (c) 2018, Quansight-Labs
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the copyright holder nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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@ -0,0 +1,117 @@
"""
.. note:
If you are looking for overrides for NumPy-specific methods, see the
documentation for :obj:`unumpy`. This page explains how to write
back-ends and multimethods.
``uarray`` is built around a back-end protocol and overridable multimethods.
It is necessary to define multimethods for back-ends to be able to override them.
See the documentation of :obj:`generate_multimethod` on how to write multimethods.
Let's start with the simplest:
``__ua_domain__`` defines the back-end *domain*. The domain consists of period-
separated string consisting of the modules you extend plus the submodule. For
example, if a submodule ``module2.submodule`` extends ``module1``
(i.e., it exposes dispatchables marked as types available in ``module1``),
then the domain string should be ``"module1.module2.submodule"``.
For the purpose of this demonstration, we'll be creating an object and setting
its attributes directly. However, note that you can use a module or your own type
as a backend as well.
>>> class Backend: pass
>>> be = Backend()
>>> be.__ua_domain__ = "ua_examples"
It might be useful at this point to sidetrack to the documentation of
:obj:`generate_multimethod` to find out how to generate a multimethod
overridable by :obj:`uarray`. Needless to say, writing a backend and
creating multimethods are mostly orthogonal activities, and knowing
one doesn't necessarily require knowledge of the other, although it
is certainly helpful. We expect core API designers/specifiers to write the
multimethods, and implementors to override them. But, as is often the case,
similar people write both.
Without further ado, here's an example multimethod:
>>> import uarray as ua
>>> from uarray import Dispatchable
>>> def override_me(a, b):
... return Dispatchable(a, int),
>>> def override_replacer(args, kwargs, dispatchables):
... return (dispatchables[0], args[1]), {}
>>> overridden_me = ua.generate_multimethod(
... override_me, override_replacer, "ua_examples"
... )
Next comes the part about overriding the multimethod. This requires
the ``__ua_function__`` protocol, and the ``__ua_convert__``
protocol. The ``__ua_function__`` protocol has the signature
``(method, args, kwargs)`` where ``method`` is the passed
multimethod, ``args``/``kwargs`` specify the arguments and ``dispatchables``
is the list of converted dispatchables passed in.
>>> def __ua_function__(method, args, kwargs):
... return method.__name__, args, kwargs
>>> be.__ua_function__ = __ua_function__
The other protocol of interest is the ``__ua_convert__`` protocol. It has the
signature ``(dispatchables, coerce)``. When ``coerce`` is ``False``, conversion
between the formats should ideally be an ``O(1)`` operation, but it means that
no memory copying should be involved, only views of the existing data.
>>> def __ua_convert__(dispatchables, coerce):
... for d in dispatchables:
... if d.type is int:
... if coerce and d.coercible:
... yield str(d.value)
... else:
... yield d.value
>>> be.__ua_convert__ = __ua_convert__
Now that we have defined the backend, the next thing to do is to call the multimethod.
>>> with ua.set_backend(be):
... overridden_me(1, "2")
('override_me', (1, '2'), {})
Note that the marked type has no effect on the actual type of the passed object.
We can also coerce the type of the input.
>>> with ua.set_backend(be, coerce=True):
... overridden_me(1, "2")
... overridden_me(1.0, "2")
('override_me', ('1', '2'), {})
('override_me', ('1.0', '2'), {})
Another feature is that if you remove ``__ua_convert__``, the arguments are not
converted at all and it's up to the backend to handle that.
>>> del be.__ua_convert__
>>> with ua.set_backend(be):
... overridden_me(1, "2")
('override_me', (1, '2'), {})
You also have the option to return ``NotImplemented``, in which case processing moves on
to the next back-end, which, in this case, doesn't exist. The same applies to
``__ua_convert__``.
>>> be.__ua_function__ = lambda *a, **kw: NotImplemented
>>> with ua.set_backend(be):
... overridden_me(1, "2")
Traceback (most recent call last):
...
uarray.backend.BackendNotImplementedError: ...
The last possibility is if we don't have ``__ua_convert__``, in which case the job is left
up to ``__ua_function__``, but putting things back into arrays after conversion will not be
possible.
"""
from ._backend import *
__version__ = '0.5.1+49.g4c3f1d7.scipy'

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@ -0,0 +1,426 @@
import typing
import inspect
import functools
from . import _uarray # type: ignore
import copyreg # type: ignore
import atexit
import pickle
ArgumentExtractorType = typing.Callable[..., typing.Tuple["Dispatchable", ...]]
ArgumentReplacerType = typing.Callable[
[typing.Tuple, typing.Dict, typing.Tuple], typing.Tuple[typing.Tuple, typing.Dict]
]
from ._uarray import ( # type: ignore
BackendNotImplementedError,
_Function,
_SkipBackendContext,
_SetBackendContext,
)
__all__ = [
"set_backend",
"set_global_backend",
"skip_backend",
"register_backend",
"clear_backends",
"create_multimethod",
"generate_multimethod",
"_Function",
"BackendNotImplementedError",
"Dispatchable",
"wrap_single_convertor",
"all_of_type",
"mark_as",
]
def unpickle_function(mod_name, qname):
import importlib
try:
module = importlib.import_module(mod_name)
func = getattr(module, qname)
return func
except (ImportError, AttributeError) as e:
from pickle import UnpicklingError
raise UnpicklingError from e
def pickle_function(func):
mod_name = getattr(func, "__module__", None)
qname = getattr(func, "__qualname__", None)
try:
test = unpickle_function(mod_name, qname)
except pickle.UnpicklingError:
test = None
if test is not func:
raise pickle.PicklingError(
"Can't pickle {}: it's not the same object as {}".format(func, test)
)
return unpickle_function, (mod_name, qname)
copyreg.pickle(_Function, pickle_function)
atexit.register(_uarray.clear_all_globals)
def create_multimethod(*args, **kwargs):
"""
Creates a decorator for generating multimethods.
This function creates a decorator that can be used with an argument
extractor in order to generate a multimethod. Other than for the
argument extractor, all arguments are passed on to
:obj:`generate_multimethod`.
See Also
--------
generate_multimethod
Generates a multimethod.
"""
def wrapper(a):
return generate_multimethod(a, *args, **kwargs)
return wrapper
def generate_multimethod(
argument_extractor: ArgumentExtractorType,
argument_replacer: ArgumentReplacerType,
domain: str,
default: typing.Optional[typing.Callable] = None,
):
"""
Generates a multimethod.
Parameters
----------
argument_extractor : ArgumentExtractorType
A callable which extracts the dispatchable arguments. Extracted arguments
should be marked by the :obj:`Dispatchable` class. It has the same signature
as the desired multimethod.
argument_replacer : ArgumentReplacerType
A callable with the signature (args, kwargs, dispatchables), which should also
return an (args, kwargs) pair with the dispatchables replaced inside the args/kwargs.
domain : str
A string value indicating the domain of this multimethod.
default: Optional[Callable], optional
The default implementation of this multimethod, where ``None`` (the default) specifies
there is no default implementation.
Examples
--------
In this example, ``a`` is to be dispatched over, so we return it, while marking it as an ``int``.
The trailing comma is needed because the args have to be returned as an iterable.
>>> def override_me(a, b):
... return Dispatchable(a, int),
Next, we define the argument replacer that replaces the dispatchables inside args/kwargs with the
supplied ones.
>>> def override_replacer(args, kwargs, dispatchables):
... return (dispatchables[0], args[1]), {}
Next, we define the multimethod.
>>> overridden_me = generate_multimethod(
... override_me, override_replacer, "ua_examples"
... )
Notice that there's no default implementation, unless you supply one.
>>> overridden_me(1, "a")
Traceback (most recent call last):
...
uarray.backend.BackendNotImplementedError: ...
>>> overridden_me2 = generate_multimethod(
... override_me, override_replacer, "ua_examples", default=lambda x, y: (x, y)
... )
>>> overridden_me2(1, "a")
(1, 'a')
See Also
--------
uarray
See the module documentation for how to override the method by creating backends.
"""
kw_defaults, arg_defaults, opts = get_defaults(argument_extractor)
ua_func = _Function(
argument_extractor,
argument_replacer,
domain,
arg_defaults,
kw_defaults,
default,
)
return functools.update_wrapper(ua_func, argument_extractor)
def set_backend(backend, coerce=False, only=False):
"""
A context manager that sets the preferred backend.
Parameters
----------
backend
The backend to set.
coerce
Whether or not to coerce to a specific backend's types. Implies ``only``.
only
Whether or not this should be the last backend to try.
See Also
--------
skip_backend: A context manager that allows skipping of backends.
set_global_backend: Set a single, global backend for a domain.
"""
try:
return backend.__ua_cache__["set", coerce, only]
except AttributeError:
backend.__ua_cache__ = {}
except KeyError:
pass
ctx = _SetBackendContext(backend, coerce, only)
backend.__ua_cache__["set", coerce, only] = ctx
return ctx
def skip_backend(backend):
"""
A context manager that allows one to skip a given backend from processing
entirely. This allows one to use another backend's code in a library that
is also a consumer of the same backend.
Parameters
----------
backend
The backend to skip.
See Also
--------
set_backend: A context manager that allows setting of backends.
set_global_backend: Set a single, global backend for a domain.
"""
try:
return backend.__ua_cache__["skip"]
except AttributeError:
backend.__ua_cache__ = {}
except KeyError:
pass
ctx = _SkipBackendContext(backend)
backend.__ua_cache__["skip"] = ctx
return ctx
def get_defaults(f):
sig = inspect.signature(f)
kw_defaults = {}
arg_defaults = []
opts = set()
for k, v in sig.parameters.items():
if v.default is not inspect.Parameter.empty:
kw_defaults[k] = v.default
if v.kind in (
inspect.Parameter.POSITIONAL_ONLY,
inspect.Parameter.POSITIONAL_OR_KEYWORD,
):
arg_defaults.append(v.default)
opts.add(k)
return kw_defaults, tuple(arg_defaults), opts
def set_global_backend(backend, coerce=False, only=False):
"""
This utility method replaces the default backend for permanent use. It
will be tried in the list of backends automatically, unless the
``only`` flag is set on a backend. This will be the first tried
backend outside the :obj:`set_backend` context manager.
Note that this method is not thread-safe.
.. warning::
We caution library authors against using this function in
their code. We do *not* support this use-case. This function
is meant to be used only by users themselves, or by a reference
implementation, if one exists.
Parameters
----------
backend
The backend to register.
See Also
--------
set_backend: A context manager that allows setting of backends.
skip_backend: A context manager that allows skipping of backends.
"""
_uarray.set_global_backend(backend, coerce, only)
def register_backend(backend):
"""
This utility method sets registers backend for permanent use. It
will be tried in the list of backends automatically, unless the
``only`` flag is set on a backend.
Note that this method is not thread-safe.
Parameters
----------
backend
The backend to register.
"""
_uarray.register_backend(backend)
def clear_backends(domain, registered=True, globals=False):
"""
This utility method clears registered backends.
.. warning::
We caution library authors against using this function in
their code. We do *not* support this use-case. This function
is meant to be used only by the users themselves.
.. warning::
Do NOT use this method inside a multimethod call, or the
program is likely to crash.
Parameters
----------
domain : Optional[str]
The domain for which to de-register backends. ``None`` means
de-register for all domains.
registered : bool
Whether or not to clear registered backends. See :obj:`register_backend`.
globals : bool
Whether or not to clear global backends. See :obj:`set_global_backend`.
See Also
--------
register_backend : Register a backend globally.
set_global_backend : Set a global backend.
"""
_uarray.clear_backends(domain, registered, globals)
class Dispatchable:
"""
A utility class which marks an argument with a specific dispatch type.
Attributes
----------
value
The value of the Dispatchable.
type
The type of the Dispatchable.
Examples
--------
>>> x = Dispatchable(1, str)
>>> x
<Dispatchable: type=<class 'str'>, value=1>
See Also
--------
all_of_type
Marks all unmarked parameters of a function.
mark_as
Allows one to create a utility function to mark as a given type.
"""
def __init__(self, value, dispatch_type, coercible=True):
self.value = value
self.type = dispatch_type
self.coercible = coercible
def __getitem__(self, index):
return (self.type, self.value)[index]
def __str__(self):
return "<{0}: type={1!r}, value={2!r}>".format(
type(self).__name__, self.type, self.value
)
__repr__ = __str__
def mark_as(dispatch_type):
"""
Creates a utility function to mark something as a specific type.
Examples
--------
>>> mark_int = mark_as(int)
>>> mark_int(1)
<Dispatchable: type=<class 'int'>, value=1>
"""
return functools.partial(Dispatchable, dispatch_type=dispatch_type)
def all_of_type(arg_type):
"""
Marks all unmarked arguments as a given type.
Examples
--------
>>> @all_of_type(str)
... def f(a, b):
... return a, Dispatchable(b, int)
>>> f('a', 1)
(<Dispatchable: type=<class 'str'>, value='a'>, <Dispatchable: type=<class 'int'>, value=1>)
"""
def outer(func):
@functools.wraps(func)
def inner(*args, **kwargs):
extracted_args = func(*args, **kwargs)
return tuple(
Dispatchable(arg, arg_type)
if not isinstance(arg, Dispatchable)
else arg
for arg in extracted_args
)
return inner
return outer
def wrap_single_convertor(convert_single):
"""
Wraps a ``__ua_convert__`` defined for a single element to all elements.
If any of them return ``NotImplemented``, the operation is assumed to be
undefined.
Accepts a signature of (value, type, coerce).
"""
@functools.wraps(convert_single)
def __ua_convert__(dispatchables, coerce):
converted = []
for d in dispatchables:
c = convert_single(d.value, d.type, coerce and d.coercible)
if c is NotImplemented:
return NotImplemented
converted.append(c)
return converted
return __ua_convert__

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@ -0,0 +1,30 @@
def pre_build_hook(build_ext, ext):
from scipy._build_utils.compiler_helper import (
set_cxx_flags_hook, try_add_flag)
cc = build_ext._cxx_compiler
args = ext.extra_compile_args
set_cxx_flags_hook(build_ext, ext)
if cc.compiler_type == 'msvc':
args.append('/EHsc')
else:
try_add_flag(args, cc, '-fvisibility=hidden')
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_uarray', parent_package, top_path)
config.add_data_files('LICENSE')
ext = config.add_extension('_uarray',
sources=['_uarray_dispatch.cxx'],
language='c++')
ext._pre_build_hook = pre_build_hook
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())

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@ -0,0 +1,482 @@
import functools
import operator
import sys
import warnings
import numbers
from collections import namedtuple
from multiprocessing import Pool
import inspect
import numpy as np
try:
from numpy.random import Generator as Generator
except ImportError:
class Generator(): # type: ignore[no-redef]
pass
def _valarray(shape, value=np.nan, typecode=None):
"""Return an array of all values.
"""
out = np.ones(shape, dtype=bool) * value
if typecode is not None:
out = out.astype(typecode)
if not isinstance(out, np.ndarray):
out = np.asarray(out)
return out
def _lazywhere(cond, arrays, f, fillvalue=None, f2=None):
"""
np.where(cond, x, fillvalue) always evaluates x even where cond is False.
This one only evaluates f(arr1[cond], arr2[cond], ...).
For example,
>>> a, b = np.array([1, 2, 3, 4]), np.array([5, 6, 7, 8])
>>> def f(a, b):
return a*b
>>> _lazywhere(a > 2, (a, b), f, np.nan)
array([ nan, nan, 21., 32.])
Notice, it assumes that all `arrays` are of the same shape, or can be
broadcasted together.
"""
if fillvalue is None:
if f2 is None:
raise ValueError("One of (fillvalue, f2) must be given.")
else:
fillvalue = np.nan
else:
if f2 is not None:
raise ValueError("Only one of (fillvalue, f2) can be given.")
arrays = np.broadcast_arrays(*arrays)
temp = tuple(np.extract(cond, arr) for arr in arrays)
tcode = np.mintypecode([a.dtype.char for a in arrays])
out = _valarray(np.shape(arrays[0]), value=fillvalue, typecode=tcode)
np.place(out, cond, f(*temp))
if f2 is not None:
temp = tuple(np.extract(~cond, arr) for arr in arrays)
np.place(out, ~cond, f2(*temp))
return out
def _lazyselect(condlist, choicelist, arrays, default=0):
"""
Mimic `np.select(condlist, choicelist)`.
Notice, it assumes that all `arrays` are of the same shape or can be
broadcasted together.
All functions in `choicelist` must accept array arguments in the order
given in `arrays` and must return an array of the same shape as broadcasted
`arrays`.
Examples
--------
>>> x = np.arange(6)
>>> np.select([x <3, x > 3], [x**2, x**3], default=0)
array([ 0, 1, 4, 0, 64, 125])
>>> _lazyselect([x < 3, x > 3], [lambda x: x**2, lambda x: x**3], (x,))
array([ 0., 1., 4., 0., 64., 125.])
>>> a = -np.ones_like(x)
>>> _lazyselect([x < 3, x > 3],
... [lambda x, a: x**2, lambda x, a: a * x**3],
... (x, a), default=np.nan)
array([ 0., 1., 4., nan, -64., -125.])
"""
arrays = np.broadcast_arrays(*arrays)
tcode = np.mintypecode([a.dtype.char for a in arrays])
out = _valarray(np.shape(arrays[0]), value=default, typecode=tcode)
for index in range(len(condlist)):
func, cond = choicelist[index], condlist[index]
if np.all(cond is False):
continue
cond, _ = np.broadcast_arrays(cond, arrays[0])
temp = tuple(np.extract(cond, arr) for arr in arrays)
np.place(out, cond, func(*temp))
return out
def _aligned_zeros(shape, dtype=float, order="C", align=None):
"""Allocate a new ndarray with aligned memory.
Primary use case for this currently is working around a f2py issue
in NumPy 1.9.1, where dtype.alignment is such that np.zeros() does
not necessarily create arrays aligned up to it.
"""
dtype = np.dtype(dtype)
if align is None:
align = dtype.alignment
if not hasattr(shape, '__len__'):
shape = (shape,)
size = functools.reduce(operator.mul, shape) * dtype.itemsize
buf = np.empty(size + align + 1, np.uint8)
offset = buf.__array_interface__['data'][0] % align
if offset != 0:
offset = align - offset
# Note: slices producing 0-size arrays do not necessarily change
# data pointer --- so we use and allocate size+1
buf = buf[offset:offset+size+1][:-1]
data = np.ndarray(shape, dtype, buf, order=order)
data.fill(0)
return data
def _prune_array(array):
"""Return an array equivalent to the input array. If the input
array is a view of a much larger array, copy its contents to a
newly allocated array. Otherwise, return the input unchanged.
"""
if array.base is not None and array.size < array.base.size // 2:
return array.copy()
return array
def prod(iterable):
"""
Product of a sequence of numbers.
Faster than np.prod for short lists like array shapes, and does
not overflow if using Python integers.
"""
product = 1
for x in iterable:
product *= x
return product
class DeprecatedImport(object):
"""
Deprecated import with redirection and warning.
Examples
--------
Suppose you previously had in some module::
from foo import spam
If this has to be deprecated, do::
spam = DeprecatedImport("foo.spam", "baz")
to redirect users to use "baz" module instead.
"""
def __init__(self, old_module_name, new_module_name):
self._old_name = old_module_name
self._new_name = new_module_name
__import__(self._new_name)
self._mod = sys.modules[self._new_name]
def __dir__(self):
return dir(self._mod)
def __getattr__(self, name):
warnings.warn("Module %s is deprecated, use %s instead"
% (self._old_name, self._new_name),
DeprecationWarning)
return getattr(self._mod, name)
# copy-pasted from scikit-learn utils/validation.py
def check_random_state(seed):
"""Turn seed into a np.random.RandomState instance
If seed is None (or np.random), return the RandomState singleton used
by np.random.
If seed is an int, return a new RandomState instance seeded with seed.
If seed is already a RandomState instance, return it.
If seed is a new-style np.random.Generator, return it.
Otherwise, raise ValueError.
"""
if seed is None or seed is np.random:
return np.random.mtrand._rand
if isinstance(seed, (numbers.Integral, np.integer)):
return np.random.RandomState(seed)
if isinstance(seed, np.random.RandomState):
return seed
try:
# Generator is only available in numpy >= 1.17
if isinstance(seed, np.random.Generator):
return seed
except AttributeError:
pass
raise ValueError('%r cannot be used to seed a numpy.random.RandomState'
' instance' % seed)
def _asarray_validated(a, check_finite=True,
sparse_ok=False, objects_ok=False, mask_ok=False,
as_inexact=False):
"""
Helper function for SciPy argument validation.
Many SciPy linear algebra functions do support arbitrary array-like
input arguments. Examples of commonly unsupported inputs include
matrices containing inf/nan, sparse matrix representations, and
matrices with complicated elements.
Parameters
----------
a : array_like
The array-like input.
check_finite : bool, optional
Whether to check that the input matrices contain only finite numbers.
Disabling may give a performance gain, but may result in problems
(crashes, non-termination) if the inputs do contain infinities or NaNs.
Default: True
sparse_ok : bool, optional
True if scipy sparse matrices are allowed.
objects_ok : bool, optional
True if arrays with dype('O') are allowed.
mask_ok : bool, optional
True if masked arrays are allowed.
as_inexact : bool, optional
True to convert the input array to a np.inexact dtype.
Returns
-------
ret : ndarray
The converted validated array.
"""
if not sparse_ok:
import scipy.sparse
if scipy.sparse.issparse(a):
msg = ('Sparse matrices are not supported by this function. '
'Perhaps one of the scipy.sparse.linalg functions '
'would work instead.')
raise ValueError(msg)
if not mask_ok:
if np.ma.isMaskedArray(a):
raise ValueError('masked arrays are not supported')
toarray = np.asarray_chkfinite if check_finite else np.asarray
a = toarray(a)
if not objects_ok:
if a.dtype is np.dtype('O'):
raise ValueError('object arrays are not supported')
if as_inexact:
if not np.issubdtype(a.dtype, np.inexact):
a = toarray(a, dtype=np.float_)
return a
# Add a replacement for inspect.getfullargspec()/
# The version below is borrowed from Django,
# https://github.com/django/django/pull/4846.
# Note an inconsistency between inspect.getfullargspec(func) and
# inspect.signature(func). If `func` is a bound method, the latter does *not*
# list `self` as a first argument, while the former *does*.
# Hence, cook up a common ground replacement: `getfullargspec_no_self` which
# mimics `inspect.getfullargspec` but does not list `self`.
#
# This way, the caller code does not need to know whether it uses a legacy
# .getfullargspec or a bright and shiny .signature.
FullArgSpec = namedtuple('FullArgSpec',
['args', 'varargs', 'varkw', 'defaults',
'kwonlyargs', 'kwonlydefaults', 'annotations'])
def getfullargspec_no_self(func):
"""inspect.getfullargspec replacement using inspect.signature.
If func is a bound method, do not list the 'self' parameter.
Parameters
----------
func : callable
A callable to inspect
Returns
-------
fullargspec : FullArgSpec(args, varargs, varkw, defaults, kwonlyargs,
kwonlydefaults, annotations)
NOTE: if the first argument of `func` is self, it is *not*, I repeat
*not*, included in fullargspec.args.
This is done for consistency between inspect.getargspec() under
Python 2.x, and inspect.signature() under Python 3.x.
"""
sig = inspect.signature(func)
args = [
p.name for p in sig.parameters.values()
if p.kind in [inspect.Parameter.POSITIONAL_OR_KEYWORD,
inspect.Parameter.POSITIONAL_ONLY]
]
varargs = [
p.name for p in sig.parameters.values()
if p.kind == inspect.Parameter.VAR_POSITIONAL
]
varargs = varargs[0] if varargs else None
varkw = [
p.name for p in sig.parameters.values()
if p.kind == inspect.Parameter.VAR_KEYWORD
]
varkw = varkw[0] if varkw else None
defaults = tuple(
p.default for p in sig.parameters.values()
if (p.kind == inspect.Parameter.POSITIONAL_OR_KEYWORD and
p.default is not p.empty)
) or None
kwonlyargs = [
p.name for p in sig.parameters.values()
if p.kind == inspect.Parameter.KEYWORD_ONLY
]
kwdefaults = {p.name: p.default for p in sig.parameters.values()
if p.kind == inspect.Parameter.KEYWORD_ONLY and
p.default is not p.empty}
annotations = {p.name: p.annotation for p in sig.parameters.values()
if p.annotation is not p.empty}
return FullArgSpec(args, varargs, varkw, defaults, kwonlyargs,
kwdefaults or None, annotations)
class MapWrapper(object):
"""
Parallelisation wrapper for working with map-like callables, such as
`multiprocessing.Pool.map`.
Parameters
----------
pool : int or map-like callable
If `pool` is an integer, then it specifies the number of threads to
use for parallelization. If ``int(pool) == 1``, then no parallel
processing is used and the map builtin is used.
If ``pool == -1``, then the pool will utilize all available CPUs.
If `pool` is a map-like callable that follows the same
calling sequence as the built-in map function, then this callable is
used for parallelization.
"""
def __init__(self, pool=1):
self.pool = None
self._mapfunc = map
self._own_pool = False
if callable(pool):
self.pool = pool
self._mapfunc = self.pool
else:
# user supplies a number
if int(pool) == -1:
# use as many processors as possible
self.pool = Pool()
self._mapfunc = self.pool.map
self._own_pool = True
elif int(pool) == 1:
pass
elif int(pool) > 1:
# use the number of processors requested
self.pool = Pool(processes=int(pool))
self._mapfunc = self.pool.map
self._own_pool = True
else:
raise RuntimeError("Number of workers specified must be -1,"
" an int >= 1, or an object with a 'map' method")
def __enter__(self):
return self
def __del__(self):
self.close()
self.terminate()
def terminate(self):
if self._own_pool:
self.pool.terminate()
def join(self):
if self._own_pool:
self.pool.join()
def close(self):
if self._own_pool:
self.pool.close()
def __exit__(self, exc_type, exc_value, traceback):
if self._own_pool:
self.pool.close()
self.pool.terminate()
def __call__(self, func, iterable):
# only accept one iterable because that's all Pool.map accepts
try:
return self._mapfunc(func, iterable)
except TypeError:
# wrong number of arguments
raise TypeError("The map-like callable must be of the"
" form f(func, iterable)")
def rng_integers(gen, low, high=None, size=None, dtype='int64',
endpoint=False):
"""
Return random integers from low (inclusive) to high (exclusive), or if
endpoint=True, low (inclusive) to high (inclusive). Replaces
`RandomState.randint` (with endpoint=False) and
`RandomState.random_integers` (with endpoint=True).
Return random integers from the "discrete uniform" distribution of the
specified dtype. If high is None (the default), then results are from
0 to low.
Parameters
----------
gen: {None, np.random.RandomState, np.random.Generator}
Random number generator. If None, then the np.random.RandomState
singleton is used.
low: int or array-like of ints
Lowest (signed) integers to be drawn from the distribution (unless
high=None, in which case this parameter is 0 and this value is used
for high).
high: int or array-like of ints
If provided, one above the largest (signed) integer to be drawn from
the distribution (see above for behavior if high=None). If array-like,
must contain integer values.
size: None
Output shape. If the given shape is, e.g., (m, n, k), then m * n * k
samples are drawn. Default is None, in which case a single value is
returned.
dtype: {str, dtype}, optional
Desired dtype of the result. All dtypes are determined by their name,
i.e., 'int64', 'int', etc, so byteorder is not available and a specific
precision may have different C types depending on the platform.
The default value is np.int_.
endpoint: bool, optional
If True, sample from the interval [low, high] instead of the default
[low, high) Defaults to False.
Returns
-------
out: int or ndarray of ints
size-shaped array of random integers from the appropriate distribution,
or a single such random int if size not provided.
"""
if isinstance(gen, Generator):
return gen.integers(low, high=high, size=size, dtype=dtype,
endpoint=endpoint)
else:
if gen is None:
# default is RandomState singleton used by np.random.
gen = np.random.mtrand._rand
if endpoint:
# inclusive of endpoint
# remember that low and high can be arrays, so don't modify in
# place
if high is None:
return gen.randint(low + 1, size=size, dtype=dtype)
if high is not None:
return gen.randint(low, high=high + 1, size=size, dtype=dtype)
# exclusive
return gen.randint(low, high=high, size=size, dtype=dtype)

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@ -0,0 +1,422 @@
# ######################### LICENSE ############################ #
# Copyright (c) 2005-2015, Michele Simionato
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
# Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# Redistributions in bytecode form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in
# the documentation and/or other materials provided with the
# distribution.
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
# OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
# TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
# USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
# DAMAGE.
"""
Decorator module, see https://pypi.python.org/pypi/decorator
for the documentation.
"""
import re
import sys
import inspect
import operator
import itertools
import collections
__version__ = '4.0.5'
if sys.version >= '3':
from inspect import getfullargspec
def get_init(cls):
return cls.__init__
else:
class getfullargspec(object):
"A quick and dirty replacement for getfullargspec for Python 2.x"
def __init__(self, f):
self.args, self.varargs, self.varkw, self.defaults = \
inspect.getargspec(f)
self.kwonlyargs = []
self.kwonlydefaults = None
def __iter__(self):
yield self.args
yield self.varargs
yield self.varkw
yield self.defaults
getargspec = inspect.getargspec
def get_init(cls):
return cls.__init__.__func__
# getargspec has been deprecated in Python 3.5
ArgSpec = collections.namedtuple(
'ArgSpec', 'args varargs varkw defaults')
def getargspec(f):
"""A replacement for inspect.getargspec"""
spec = getfullargspec(f)
return ArgSpec(spec.args, spec.varargs, spec.varkw, spec.defaults)
DEF = re.compile(r'\s*def\s*([_\w][_\w\d]*)\s*\(')
# basic functionality
class FunctionMaker(object):
"""
An object with the ability to create functions with a given signature.
It has attributes name, doc, module, signature, defaults, dict, and
methods update and make.
"""
# Atomic get-and-increment provided by the GIL
_compile_count = itertools.count()
def __init__(self, func=None, name=None, signature=None,
defaults=None, doc=None, module=None, funcdict=None):
self.shortsignature = signature
if func:
# func can be a class or a callable, but not an instance method
self.name = func.__name__
if self.name == '<lambda>': # small hack for lambda functions
self.name = '_lambda_'
self.doc = func.__doc__
self.module = func.__module__
if inspect.isfunction(func):
argspec = getfullargspec(func)
self.annotations = getattr(func, '__annotations__', {})
for a in ('args', 'varargs', 'varkw', 'defaults', 'kwonlyargs',
'kwonlydefaults'):
setattr(self, a, getattr(argspec, a))
for i, arg in enumerate(self.args):
setattr(self, 'arg%d' % i, arg)
if sys.version < '3': # easy way
self.shortsignature = self.signature = (
inspect.formatargspec(
formatvalue=lambda val: "", *argspec)[1:-1])
else: # Python 3 way
allargs = list(self.args)
allshortargs = list(self.args)
if self.varargs:
allargs.append('*' + self.varargs)
allshortargs.append('*' + self.varargs)
elif self.kwonlyargs:
allargs.append('*') # single star syntax
for a in self.kwonlyargs:
allargs.append('%s=None' % a)
allshortargs.append('%s=%s' % (a, a))
if self.varkw:
allargs.append('**' + self.varkw)
allshortargs.append('**' + self.varkw)
self.signature = ', '.join(allargs)
self.shortsignature = ', '.join(allshortargs)
self.dict = func.__dict__.copy()
# func=None happens when decorating a caller
if name:
self.name = name
if signature is not None:
self.signature = signature
if defaults:
self.defaults = defaults
if doc:
self.doc = doc
if module:
self.module = module
if funcdict:
self.dict = funcdict
# check existence required attributes
assert hasattr(self, 'name')
if not hasattr(self, 'signature'):
raise TypeError('You are decorating a non-function: %s' % func)
def update(self, func, **kw):
"Update the signature of func with the data in self"
func.__name__ = self.name
func.__doc__ = getattr(self, 'doc', None)
func.__dict__ = getattr(self, 'dict', {})
func.__defaults__ = getattr(self, 'defaults', ())
func.__kwdefaults__ = getattr(self, 'kwonlydefaults', None)
func.__annotations__ = getattr(self, 'annotations', None)
try:
frame = sys._getframe(3)
except AttributeError: # for IronPython and similar implementations
callermodule = '?'
else:
callermodule = frame.f_globals.get('__name__', '?')
func.__module__ = getattr(self, 'module', callermodule)
func.__dict__.update(kw)
def make(self, src_templ, evaldict=None, addsource=False, **attrs):
"Make a new function from a given template and update the signature"
src = src_templ % vars(self) # expand name and signature
evaldict = evaldict or {}
mo = DEF.match(src)
if mo is None:
raise SyntaxError('not a valid function template\n%s' % src)
name = mo.group(1) # extract the function name
names = set([name] + [arg.strip(' *') for arg in
self.shortsignature.split(',')])
for n in names:
if n in ('_func_', '_call_'):
raise NameError('%s is overridden in\n%s' % (n, src))
if not src.endswith('\n'): # add a newline just for safety
src += '\n' # this is needed in old versions of Python
# Ensure each generated function has a unique filename for profilers
# (such as cProfile) that depend on the tuple of (<filename>,
# <definition line>, <function name>) being unique.
filename = '<decorator-gen-%d>' % (next(self._compile_count),)
try:
code = compile(src, filename, 'single')
exec(code, evaldict)
except: # noqa: E722
print('Error in generated code:', file=sys.stderr)
print(src, file=sys.stderr)
raise
func = evaldict[name]
if addsource:
attrs['__source__'] = src
self.update(func, **attrs)
return func
@classmethod
def create(cls, obj, body, evaldict, defaults=None,
doc=None, module=None, addsource=True, **attrs):
"""
Create a function from the strings name, signature, and body.
evaldict is the evaluation dictionary. If addsource is true, an
attribute __source__ is added to the result. The attributes attrs
are added, if any.
"""
if isinstance(obj, str): # "name(signature)"
name, rest = obj.strip().split('(', 1)
signature = rest[:-1] # strip a right parens
func = None
else: # a function
name = None
signature = None
func = obj
self = cls(func, name, signature, defaults, doc, module)
ibody = '\n'.join(' ' + line for line in body.splitlines())
return self.make('def %(name)s(%(signature)s):\n' + ibody,
evaldict, addsource, **attrs)
def decorate(func, caller):
"""
decorate(func, caller) decorates a function using a caller.
"""
evaldict = func.__globals__.copy()
evaldict['_call_'] = caller
evaldict['_func_'] = func
fun = FunctionMaker.create(
func, "return _call_(_func_, %(shortsignature)s)",
evaldict, __wrapped__=func)
if hasattr(func, '__qualname__'):
fun.__qualname__ = func.__qualname__
return fun
def decorator(caller, _func=None):
"""decorator(caller) converts a caller function into a decorator"""
if _func is not None: # return a decorated function
# this is obsolete behavior; you should use decorate instead
return decorate(_func, caller)
# else return a decorator function
if inspect.isclass(caller):
name = caller.__name__.lower()
callerfunc = get_init(caller)
doc = 'decorator(%s) converts functions/generators into ' \
'factories of %s objects' % (caller.__name__, caller.__name__)
elif inspect.isfunction(caller):
if caller.__name__ == '<lambda>':
name = '_lambda_'
else:
name = caller.__name__
callerfunc = caller
doc = caller.__doc__
else: # assume caller is an object with a __call__ method
name = caller.__class__.__name__.lower()
callerfunc = caller.__call__.__func__
doc = caller.__call__.__doc__
evaldict = callerfunc.__globals__.copy()
evaldict['_call_'] = caller
evaldict['_decorate_'] = decorate
return FunctionMaker.create(
'%s(func)' % name, 'return _decorate_(func, _call_)',
evaldict, doc=doc, module=caller.__module__,
__wrapped__=caller)
# ####################### contextmanager ####################### #
try: # Python >= 3.2
from contextlib import _GeneratorContextManager
except ImportError: # Python >= 2.5
from contextlib import GeneratorContextManager as _GeneratorContextManager
class ContextManager(_GeneratorContextManager):
def __call__(self, func):
"""Context manager decorator"""
return FunctionMaker.create(
func, "with _self_: return _func_(%(shortsignature)s)",
dict(_self_=self, _func_=func), __wrapped__=func)
init = getfullargspec(_GeneratorContextManager.__init__)
n_args = len(init.args)
if n_args == 2 and not init.varargs: # (self, genobj) Python 2.7
def __init__(self, g, *a, **k):
return _GeneratorContextManager.__init__(self, g(*a, **k))
ContextManager.__init__ = __init__
elif n_args == 2 and init.varargs: # (self, gen, *a, **k) Python 3.4
pass
elif n_args == 4: # (self, gen, args, kwds) Python 3.5
def __init__(self, g, *a, **k):
return _GeneratorContextManager.__init__(self, g, a, k)
ContextManager.__init__ = __init__
contextmanager = decorator(ContextManager)
# ############################ dispatch_on ############################ #
def append(a, vancestors):
"""
Append ``a`` to the list of the virtual ancestors, unless it is already
included.
"""
add = True
for j, va in enumerate(vancestors):
if issubclass(va, a):
add = False
break
if issubclass(a, va):
vancestors[j] = a
add = False
if add:
vancestors.append(a)
# inspired from simplegeneric by P.J. Eby and functools.singledispatch
def dispatch_on(*dispatch_args):
"""
Factory of decorators turning a function into a generic function
dispatching on the given arguments.
"""
assert dispatch_args, 'No dispatch args passed'
dispatch_str = '(%s,)' % ', '.join(dispatch_args)
def check(arguments, wrong=operator.ne, msg=''):
"""Make sure one passes the expected number of arguments"""
if wrong(len(arguments), len(dispatch_args)):
raise TypeError('Expected %d arguments, got %d%s' %
(len(dispatch_args), len(arguments), msg))
def gen_func_dec(func):
"""Decorator turning a function into a generic function"""
# first check the dispatch arguments
argset = set(getfullargspec(func).args)
if not set(dispatch_args) <= argset:
raise NameError('Unknown dispatch arguments %s' % dispatch_str)
typemap = {}
def vancestors(*types):
"""
Get a list of sets of virtual ancestors for the given types
"""
check(types)
ras = [[] for _ in range(len(dispatch_args))]
for types_ in typemap:
for t, type_, ra in zip(types, types_, ras):
if issubclass(t, type_) and type_ not in t.__mro__:
append(type_, ra)
return [set(ra) for ra in ras]
def ancestors(*types):
"""
Get a list of virtual MROs, one for each type
"""
check(types)
lists = []
for t, vas in zip(types, vancestors(*types)):
n_vas = len(vas)
if n_vas > 1:
raise RuntimeError(
'Ambiguous dispatch for %s: %s' % (t, vas))
elif n_vas == 1:
va, = vas
mro = type('t', (t, va), {}).__mro__[1:]
else:
mro = t.__mro__
lists.append(mro[:-1]) # discard t and object
return lists
def register(*types):
"""
Decorator to register an implementation for the given types
"""
check(types)
def dec(f):
check(getfullargspec(f).args, operator.lt, ' in ' + f.__name__)
typemap[types] = f
return f
return dec
def dispatch_info(*types):
"""
An utility to introspect the dispatch algorithm
"""
check(types)
lst = [tuple(a.__name__ for a in anc)
for anc in itertools.product(*ancestors(*types))]
return lst
def _dispatch(dispatch_args, *args, **kw):
types = tuple(type(arg) for arg in dispatch_args)
try: # fast path
f = typemap[types]
except KeyError:
pass
else:
return f(*args, **kw)
combinations = itertools.product(*ancestors(*types))
next(combinations) # the first one has been already tried
for types_ in combinations:
f = typemap.get(types_)
if f is not None:
return f(*args, **kw)
# else call the default implementation
return func(*args, **kw)
return FunctionMaker.create(
func, 'return _f_(%s, %%(shortsignature)s)' % dispatch_str,
dict(_f_=_dispatch), register=register, default=func,
typemap=typemap, vancestors=vancestors, ancestors=ancestors,
dispatch_info=dispatch_info, __wrapped__=func)
gen_func_dec.__name__ = 'dispatch_on' + dispatch_str
return gen_func_dec

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@ -0,0 +1,107 @@
import functools
import warnings
__all__ = ["_deprecated"]
def _deprecated(msg, stacklevel=2):
"""Deprecate a function by emitting a warning on use."""
def wrap(fun):
if isinstance(fun, type):
warnings.warn(
"Trying to deprecate class {!r}".format(fun),
category=RuntimeWarning, stacklevel=2)
return fun
@functools.wraps(fun)
def call(*args, **kwargs):
warnings.warn(msg, category=DeprecationWarning,
stacklevel=stacklevel)
return fun(*args, **kwargs)
call.__doc__ = msg
return call
return wrap
class _DeprecationHelperStr(object):
"""
Helper class used by deprecate_cython_api
"""
def __init__(self, content, message):
self._content = content
self._message = message
def __hash__(self):
return hash(self._content)
def __eq__(self, other):
res = (self._content == other)
if res:
warnings.warn(self._message, category=DeprecationWarning,
stacklevel=2)
return res
def deprecate_cython_api(module, routine_name, new_name=None, message=None):
"""
Deprecate an exported cdef function in a public Cython API module.
Only functions can be deprecated; typedefs etc. cannot.
Parameters
----------
module : module
Public Cython API module (e.g. scipy.linalg.cython_blas).
routine_name : str
Name of the routine to deprecate. May also be a fused-type
routine (in which case its all specializations are deprecated).
new_name : str
New name to include in the deprecation warning message
message : str
Additional text in the deprecation warning message
Examples
--------
Usually, this function would be used in the top-level of the
module ``.pyx`` file:
>>> from scipy._lib.deprecation import deprecate_cython_api
>>> import scipy.linalg.cython_blas as mod
>>> deprecate_cython_api(mod, "dgemm", "dgemm_new",
... message="Deprecated in Scipy 1.5.0")
>>> del deprecate_cython_api, mod
After this, Cython modules that use the deprecated function emit a
deprecation warning when they are imported.
"""
old_name = "{}.{}".format(module.__name__, routine_name)
if new_name is None:
depdoc = "`%s` is deprecated!" % old_name
else:
depdoc = "`%s` is deprecated, use `%s` instead!" % \
(old_name, new_name)
if message is not None:
depdoc += "\n" + message
d = module.__pyx_capi__
# Check if the function is a fused-type function with a mangled name
j = 0
has_fused = False
while True:
fused_name = "__pyx_fuse_{}{}".format(j, routine_name)
if fused_name in d:
has_fused = True
d[_DeprecationHelperStr(fused_name, depdoc)] = d.pop(fused_name)
j += 1
else:
break
# If not, apply deprecation to the named routine
if not has_fused:
d[_DeprecationHelperStr(routine_name, depdoc)] = d.pop(routine_name)

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@ -0,0 +1,272 @@
''' Utilities to allow inserting docstring fragments for common
parameters into function and method docstrings'''
import sys
__all__ = ['docformat', 'inherit_docstring_from', 'indentcount_lines',
'filldoc', 'unindent_dict', 'unindent_string', 'doc_replace']
def docformat(docstring, docdict=None):
''' Fill a function docstring from variables in dictionary
Adapt the indent of the inserted docs
Parameters
----------
docstring : string
docstring from function, possibly with dict formatting strings
docdict : dict, optional
dictionary with keys that match the dict formatting strings
and values that are docstring fragments to be inserted. The
indentation of the inserted docstrings is set to match the
minimum indentation of the ``docstring`` by adding this
indentation to all lines of the inserted string, except the
first.
Returns
-------
outstring : string
string with requested ``docdict`` strings inserted
Examples
--------
>>> docformat(' Test string with %(value)s', {'value':'inserted value'})
' Test string with inserted value'
>>> docstring = 'First line\\n Second line\\n %(value)s'
>>> inserted_string = "indented\\nstring"
>>> docdict = {'value': inserted_string}
>>> docformat(docstring, docdict)
'First line\\n Second line\\n indented\\n string'
'''
if not docstring:
return docstring
if docdict is None:
docdict = {}
if not docdict:
return docstring
lines = docstring.expandtabs().splitlines()
# Find the minimum indent of the main docstring, after first line
if len(lines) < 2:
icount = 0
else:
icount = indentcount_lines(lines[1:])
indent = ' ' * icount
# Insert this indent to dictionary docstrings
indented = {}
for name, dstr in docdict.items():
lines = dstr.expandtabs().splitlines()
try:
newlines = [lines[0]]
for line in lines[1:]:
newlines.append(indent+line)
indented[name] = '\n'.join(newlines)
except IndexError:
indented[name] = dstr
return docstring % indented
def inherit_docstring_from(cls):
"""
This decorator modifies the decorated function's docstring by
replacing occurrences of '%(super)s' with the docstring of the
method of the same name from the class `cls`.
If the decorated method has no docstring, it is simply given the
docstring of `cls`s method.
Parameters
----------
cls : Python class or instance
A class with a method with the same name as the decorated method.
The docstring of the method in this class replaces '%(super)s' in the
docstring of the decorated method.
Returns
-------
f : function
The decorator function that modifies the __doc__ attribute
of its argument.
Examples
--------
In the following, the docstring for Bar.func created using the
docstring of `Foo.func`.
>>> class Foo(object):
... def func(self):
... '''Do something useful.'''
... return
...
>>> class Bar(Foo):
... @inherit_docstring_from(Foo)
... def func(self):
... '''%(super)s
... Do it fast.
... '''
... return
...
>>> b = Bar()
>>> b.func.__doc__
'Do something useful.\n Do it fast.\n '
"""
def _doc(func):
cls_docstring = getattr(cls, func.__name__).__doc__
func_docstring = func.__doc__
if func_docstring is None:
func.__doc__ = cls_docstring
else:
new_docstring = func_docstring % dict(super=cls_docstring)
func.__doc__ = new_docstring
return func
return _doc
def extend_notes_in_docstring(cls, notes):
"""
This decorator replaces the decorated function's docstring
with the docstring from corresponding method in `cls`.
It extends the 'Notes' section of that docstring to include
the given `notes`.
"""
def _doc(func):
cls_docstring = getattr(cls, func.__name__).__doc__
# If python is called with -OO option,
# there is no docstring
if cls_docstring is None:
return func
end_of_notes = cls_docstring.find(' References\n')
if end_of_notes == -1:
end_of_notes = cls_docstring.find(' Examples\n')
if end_of_notes == -1:
end_of_notes = len(cls_docstring)
func.__doc__ = (cls_docstring[:end_of_notes] + notes +
cls_docstring[end_of_notes:])
return func
return _doc
def replace_notes_in_docstring(cls, notes):
"""
This decorator replaces the decorated function's docstring
with the docstring from corresponding method in `cls`.
It replaces the 'Notes' section of that docstring with
the given `notes`.
"""
def _doc(func):
cls_docstring = getattr(cls, func.__name__).__doc__
notes_header = ' Notes\n -----\n'
# If python is called with -OO option,
# there is no docstring
if cls_docstring is None:
return func
start_of_notes = cls_docstring.find(notes_header)
end_of_notes = cls_docstring.find(' References\n')
if end_of_notes == -1:
end_of_notes = cls_docstring.find(' Examples\n')
if end_of_notes == -1:
end_of_notes = len(cls_docstring)
func.__doc__ = (cls_docstring[:start_of_notes + len(notes_header)] +
notes +
cls_docstring[end_of_notes:])
return func
return _doc
def indentcount_lines(lines):
''' Minimum indent for all lines in line list
>>> lines = [' one', ' two', ' three']
>>> indentcount_lines(lines)
1
>>> lines = []
>>> indentcount_lines(lines)
0
>>> lines = [' one']
>>> indentcount_lines(lines)
1
>>> indentcount_lines([' '])
0
'''
indentno = sys.maxsize
for line in lines:
stripped = line.lstrip()
if stripped:
indentno = min(indentno, len(line) - len(stripped))
if indentno == sys.maxsize:
return 0
return indentno
def filldoc(docdict, unindent_params=True):
''' Return docstring decorator using docdict variable dictionary
Parameters
----------
docdict : dictionary
dictionary containing name, docstring fragment pairs
unindent_params : {False, True}, boolean, optional
If True, strip common indentation from all parameters in
docdict
Returns
-------
decfunc : function
decorator that applies dictionary to input function docstring
'''
if unindent_params:
docdict = unindent_dict(docdict)
def decorate(f):
f.__doc__ = docformat(f.__doc__, docdict)
return f
return decorate
def unindent_dict(docdict):
''' Unindent all strings in a docdict '''
can_dict = {}
for name, dstr in docdict.items():
can_dict[name] = unindent_string(dstr)
return can_dict
def unindent_string(docstring):
''' Set docstring to minimum indent for all lines, including first
>>> unindent_string(' two')
'two'
>>> unindent_string(' two\\n three')
'two\\n three'
'''
lines = docstring.expandtabs().splitlines()
icount = indentcount_lines(lines)
if icount == 0:
return docstring
return '\n'.join([line[icount:] for line in lines])
def doc_replace(obj, oldval, newval):
"""Decorator to take the docstring from obj, with oldval replaced by newval
Equivalent to ``func.__doc__ = obj.__doc__.replace(oldval, newval)``
Parameters
----------
obj: object
The object to take the docstring from.
oldval: string
The string to replace from the original docstring.
newval: string
The string to replace ``oldval`` with.
"""
# __doc__ may be None for optimized Python (-OO)
doc = (obj.__doc__ or '').replace(oldval, newval)
def inner(func):
func.__doc__ = doc
return func
return inner

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@ -0,0 +1,60 @@
import os
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_lib', parent_package, top_path)
config.add_data_files('tests/*.py')
include_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), 'src'))
depends = [os.path.join(include_dir, 'ccallback.h')]
config.add_extension("_ccallback_c",
sources=["_ccallback_c.c"],
depends=depends,
include_dirs=[include_dir])
config.add_extension("_test_ccallback",
sources=["src/_test_ccallback.c"],
depends=depends,
include_dirs=[include_dir])
config.add_extension("_fpumode",
sources=["_fpumode.c"])
def get_messagestream_config(ext, build_dir):
# Generate a header file containing defines
config_cmd = config.get_config_cmd()
defines = []
if config_cmd.check_func('open_memstream', decl=True, call=True):
defines.append(('HAVE_OPEN_MEMSTREAM', '1'))
target = os.path.join(os.path.dirname(__file__), 'src',
'messagestream_config.h')
with open(target, 'w') as f:
for name, value in defines:
f.write('#define {0} {1}\n'.format(name, value))
depends = [os.path.join(include_dir, 'messagestream.h')]
config.add_extension("messagestream",
sources=["messagestream.c"] + [get_messagestream_config],
depends=depends,
include_dirs=[include_dir])
config.add_extension("_test_deprecation_call",
sources=["_test_deprecation_call.c"],
include_dirs=[include_dir])
config.add_extension("_test_deprecation_def",
sources=["_test_deprecation_def.c"],
include_dirs=[include_dir])
config.add_subpackage('_uarray')
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configuration(top_path='').todict())

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