[Numpy-discussion] ANN: Scipy 0.16.0 release candidate 1

Ralf Gommers ralf.gommers at gmail.com
Sat Jul 4 17:40:07 EDT 2015


I'm pleased to announce the availability of the first release candidate of
Scipy 0.16.0. Please try it out and report any issues on the Github issue
tracker or on the scipy-dev mailing list.

This first RC is a source-only release. Sources and release notes can be
found at https://github.com/scipy/scipy/releases/tag/v0.16.0rc1. Note that
this is a bit of an experiment - it's the first time we use the Github
Releases feature. Feedback welcome.

Thanks to everyone who contributed to this release!


SciPy 0.16.0 Release Notes

.. note:: Scipy 0.16.0 is not released yet!

.. contents::

SciPy 0.16.0 is the culmination of 6 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and
better documentation.  There have been a number of deprecations and
API changes in this release, which are documented below.  All users
are encouraged to upgrade to this release, as there are a large number
of bug-fixes and optimizations.  Moreover, our development attention
will now shift to bug-fix releases on the 0.15.x branch, and on adding
new features on the master branch.

This release requires Python 2.6, 2.7 or 3.2-3.4 and NumPy 1.6.2 or greater.

Highlights of this release include:

- A Cython API for BLAS/LAPACK in `scipy.linalg`
- A new benchmark suite.  It's now straightforward to add new benchmarks, and
  they're routinely included with performance enhancement PRs.
- Support for the second order sections (SOS) format in `scipy.signal`.

New features

Benchmark suite

The benchmark suite has switched to using `Airspeed Velocity
<http://spacetelescope.github.io/asv/>`__ for benchmarking. You can
run the suite locally via ``python runtests.py --bench``. For more
details, see ``benchmarks/README.rst``.

`scipy.linalg` improvements

A full set of Cython wrappers for BLAS and LAPACK has been added in the
modules `scipy.linalg.cython_blas` and `scipy.linalg.cython_lapack`.
In Cython, these wrappers can now be cimported from their corresponding
modules and used without linking directly against BLAS or LAPACK.

The functions `scipy.linalg.qr_delete`, `scipy.linalg.qr_insert` and
`scipy.linalg.qr_update` for updating QR decompositions were added.

The function `scipy.linalg.solve_circulant` solves a linear system with
a circulant coefficient matrix.

The function `scipy.linalg.invpascal` computes the inverse of a Pascal matrix.

The function `scipy.linalg.solve_toeplitz`, a Levinson-Durbin Toeplitz solver,
was added.

Added wrapper for potentially useful LAPACK function ``*lasd4``.  It computes
the square root of the i-th updated eigenvalue of a positive symmetric rank-one
modification to a positive diagonal matrix. See its LAPACK documentation and
unit tests for it to get more info.

Added two extra wrappers for LAPACK least-square solvers. Namely, they are
``*gelsd`` and ``*gelsy``.

Wrappers for the LAPACK ``*lange`` functions, which calculate various matrix
norms, were added.

Wrappers for ``*gtsv`` and ``*ptsv``, which solve ``A*X = B`` for tri-diagonal
matrix ``A``, were added.

`scipy.signal` improvements

Support for second order sections (SOS) as a format for IIR filters
was added.  The new functions are:

* `scipy.signal.sosfilt`
* `scipy.signal.sosfilt_zi`,
* `scipy.signal.sos2tf`
* `scipy.signal.sos2zpk`
* `scipy.signal.tf2sos`
* `scipy.signal.zpk2sos`.

Additionally, the filter design functions `iirdesign`, `iirfilter`, `butter`,
`cheby1`, `cheby2`, `ellip`, and `bessel` can return the filter in the SOS

The function `scipy.signal.place_poles`, which provides two methods to place
poles for linear systems, was added.

The option to use Gustafsson's method for choosing the initial conditions
of the forward and backward passes was added to `scipy.signal.filtfilt`.

New classes ``TransferFunction``, ``StateSpace`` and ``ZerosPolesGain`` were
added.  These classes are now returned when instantiating `scipy.signal.lti`.
Conversion between those classes can be done explicitly now.

An exponential (Poisson) window was added as `scipy.signal.exponential`, and a
Tukey window was added as `scipy.signal.tukey`.

The function for computing digital filter group delay was added as

The functionality for spectral analysis and spectral density estimation has
been significantly improved: `scipy.signal.welch` became ~8x faster and the
functions `scipy.signal.spectrogram`, `scipy.signal.coherence` and
`scipy.signal.csd` (cross-spectral density) were added.

`scipy.signal.lsim` was rewritten - all known issues are fixed, so this
function can now be used instead of ``lsim2``; ``lsim`` is orders of magnitude
faster than ``lsim2`` in most cases.

`scipy.sparse` improvements

The function `scipy.sparse.norm`, which computes sparse matrix norms, was

The function `scipy.sparse.random`, which allows to draw random variates from
an arbitrary distribution, was added.

`scipy.spatial` improvements

`scipy.spatial.cKDTree` has seen a major rewrite, which improved the
performance of the ``query`` method significantly, added support for parallel
queries, pickling, and options that affect the tree layout.  See pull request
4374 for more details.

The function `scipy.spatial.procrustes` for Procrustes analysis (statistical
shape analysis) was added.

`scipy.stats` improvements

The Wishart distribution and its inverse have been added, as
`scipy.stats.wishart` and `scipy.stats.invwishart`.

The Exponentially Modified Normal distribution has been
added as `scipy.stats.exponnorm`.

The Generalized Normal distribution has been added as `scipy.stats.gennorm`.

All distributions now contain a ``random_state`` property and allow specifying a
specific ``numpy.random.RandomState`` random number generator when generating
random variates.

Many statistical tests and other `scipy.stats` functions that have multiple
return values now return ``namedtuples``.  See pull request 4709 for details.

`scipy.optimize` improvements

A new derivative-free method DF-SANE has been added to the nonlinear equation
system solving function `scipy.optimize.root`.

Deprecated features

``scipy.stats.pdf_fromgamma`` is deprecated.  This function was undocumented,
untested and rarely used.  Statsmodels provides equivalent functionality
with ``statsmodels.distributions.ExpandedNormal``.

``scipy.stats.fastsort`` is deprecated.  This function is unnecessary,
``numpy.argsort`` can be used instead.

``scipy.stats.signaltonoise`` and ``scipy.stats.mstats.signaltonoise`` are
deprecated.  These functions did not belong in ``scipy.stats`` and are rarely
used.  See issue #609 for details.

``scipy.stats.histogram2`` is deprecated. This function is unnecessary,
``numpy.histogram2d`` can be used instead.

Backwards incompatible changes

The deprecated global optimizer ``scipy.optimize.anneal`` was removed.

The following deprecated modules have been removed: ``scipy.lib.blas``,
``scipy.lib.lapack``, ``scipy.linalg.cblas``, ``scipy.linalg.fblas``,
``scipy.linalg.clapack``, ``scipy.linalg.flapack``.  They had been deprecated
since Scipy 0.12.0, the functionality should be accessed as `scipy.linalg.blas`
and `scipy.linalg.lapack`.

The deprecated function ``scipy.special.all_mat`` has been removed.

The deprecated functions ``fprob``, ``ksprob``, ``zprob``, ``randwcdf``
and ``randwppf`` have been removed from `scipy.stats`.

Other changes

The version numbering for development builds has been updated to
comply with PEP 440.

Building with ``python setup.py develop`` is now supported.
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