==========================
SciPy 0.13.0 Release Notes
==========================

.. contents::

SciPy 0.13.0 is the culmination of 7 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 0.13.x branch, and on adding
new features on the master branch.

This release requires Python 2.6, 2.7 or 3.1-3.3 and NumPy 1.5.1 or greater.
Highlights of this release are:

  - support for fancy indexing and boolean comparisons with sparse matrices
  - interpolative decompositions and matrix functions in the linalg module
  - two new trust-region solvers for unconstrained minimization


New features
============

``scipy.integrate`` improvements
--------------------------------

N-dimensional numerical integration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

A new function `scipy.integrate.nquad`, which provides N-dimensional
integration functionality with a more flexible interface than ``dblquad`` and
``tplquad``, has been added.

``dopri*`` improvements
^^^^^^^^^^^^^^^^^^^^^^^

The intermediate results from the ``dopri`` family of ODE solvers can now be
accessed by a *solout* callback function.


``scipy.linalg`` improvements
-----------------------------

Interpolative decompositions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Scipy now includes a new module `scipy.linalg.interpolative`
containing routines for computing interpolative matrix decompositions
(ID). This feature is based on the ID software package by
P.G. Martinsson, V. Rokhlin, Y. Shkolnisky, and M. Tygert, previously
adapted for Python in the PymatrixId package by K.L. Ho.

Polar decomposition
^^^^^^^^^^^^^^^^^^^

A new function `scipy.linalg.polar`, to compute the polar decomposition 
of a matrix, was added.

BLAS level 3 functions
^^^^^^^^^^^^^^^^^^^^^^

The BLAS functions ``symm``, ``syrk``, ``syr2k``, ``hemm``, ``herk`` and
``her2k`` are now wrapped in `scipy.linalg`.

Matrix functions
^^^^^^^^^^^^^^^^

Several matrix function algorithms have been implemented or updated following
detailed descriptions in recent papers of Nick Higham and his co-authors.
These include the matrix square root (``sqrtm``), the matrix logarithm
(``logm``), the matrix exponential (``expm``) and its Frechet derivative
(``expm_frechet``), and fractional matrix powers (``fractional_matrix_power``).


``scipy.optimize`` improvements
-------------------------------

Trust-region unconstrained minimization algorithms
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The ``minimize`` function gained two trust-region solvers for unconstrained
minimization: ``dogleg`` and ``trust-ncg``.


``scipy.sparse`` improvements
-----------------------------

Boolean comparisons and sparse matrices
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

All sparse matrix types now support boolean data, and boolean operations.  Two
sparse matrices `A` and `B` can be compared in all the expected ways `A < B`,
`A >= B`, `A != B`, producing similar results as dense Numpy arrays.
Comparisons with dense matrices and scalars are also supported. 

CSR and CSC fancy indexing
^^^^^^^^^^^^^^^^^^^^^^^^^^

Compressed sparse row and column sparse matrix types now support fancy indexing
with boolean matrices, slices, and lists. So where A is a (CSC or CSR) sparse
matrix, you can do things like::

    >>> A[A > 0.5] = 1  # since Boolean sparse matrices work
    >>> A[:2, :3] = 2
    >>> A[[1,2], 2] = 3


``scipy.sparse.linalg`` improvements
------------------------------------

The new function ``onenormest`` provides a lower bound of the 1-norm of a
linear operator and has been implemented according to Higham and Tisseur
(2000).  This function is not only useful for sparse matrices, but can also be
used to estimate the norm of products or powers of dense matrices without
explicitly building the intermediate matrix.

The multiplicative action of the matrix exponential of a linear operator
(``expm_multiply``) has been implemented following the description in Al-Mohy
and Higham (2011).

Abstract linear operators (`scipy.sparse.linalg.LinearOperator`) can now be
multiplied, added to each other, and exponentiated, producing new linear
operators. This enables easier construction of composite linear operations.


``scipy.spatial`` improvements
------------------------------

The vertices of a `ConvexHull` can now be accessed via the `vertices` attribute,
which gives proper orientation in 2-D.


``scipy.signal`` improvements
-----------------------------

The cosine window function `scipy.signal.cosine` was added.


``scipy.special`` improvements
------------------------------

New functions `scipy.special.xlogy` and `scipy.special.xlog1py` were added.
These functions can simplify and speed up code that has to calculate 
``x * log(y)`` and give 0 when ``x == 0``.


``scipy.io`` improvements
-------------------------

Unformatted Fortran file reader
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The new class `scipy.io.FortranFile` facilitates reading unformatted
sequential files written by Fortran code.

``scipy.io.wavfile`` enhancements
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

`scipy.io.wavfile.write` now accepts a file buffer. Previously it only
accepted a filename.

`scipy.io.wavfile.read` and `scipy.io.wavfile.write` can now handle floating
point WAV files.


``scipy.interpolate`` improvements
----------------------------------

B-spline derivatives and antiderivatives
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

`scipy.interpolate.splder` and `scipy.interpolate.splantider` functions 
for computing B-splines that represent derivatives and antiderivatives
of B-splines were added.  These functions are also available in the 
class-based FITPACK interface as ``UnivariateSpline.derivative`` and
``UnivariateSpline.antiderivative``.


``scipy.stats`` improvements
----------------------------

Distributions now allow using keyword parameters in addition to
positional parameters in all methods.

The function `scipy.stats.power_divergence` has been added for the
Cressie-Read power divergence statistic and goodness of fit test.
Included in this family of statistics is the "G-test"
(http://en.wikipedia.org/wiki/G-test).

`scipy.stats.mood` now accepts multidimensional input.

An option was added to `scipy.stats.wilcoxon` for continuity correction.

`scipy.stats.chisquare` now has an `axis` argument.

`scipy.stats.mstats.chisquare` now has `axis` and `ddof` arguments.


Deprecated features
===================

``expm2`` and ``expm3``
-----------------------

The matrix exponential functions `scipy.linalg.expm2` and `scipy.linalg.expm3`
are deprecated. All users should use the numerically more robust
`scipy.linalg.expm` function instead.

``scipy.stats`` functions
-------------------------

`scipy.stats.oneway` is deprecated; `scipy.stats.f_oneway` should be used
instead.

`scipy.stats.glm` is deprecated.  `scipy.stats.ttest_ind` is an equivalent
function; more full-featured general (and generalized) linear model
implementations can be found in statsmodels.

`scipy.stats.cmedian` is deprecated; ``numpy.median`` should be used instead.


Backwards incompatible changes
==============================

LIL matrix assignment
---------------------
Assigning values to LIL matrices with two index arrays now works similarly as
assigning into ndarrays::

    >>> x = lil_matrix((3, 3))
    >>> x[[0,1,2],[0,1,2]]=[0,1,2]
    >>> x.todense()
    matrix([[ 0.,  0.,  0.],
            [ 0.,  1.,  0.],
            [ 0.,  0.,  2.]])

rather than giving the result::

    >>> x.todense()
    matrix([[ 0.,  1.,  2.],
            [ 0.,  1.,  2.],
            [ 0.,  1.,  2.]])

Users relying on the previous behavior will need to revisit their code.
The previous behavior is obtained by ``x[numpy.ix_([0,1,2],[0,1,2])] = ...``.


Deprecated ``radon`` function removed
-------------------------------------

The ``misc.radon`` function, which was deprecated in scipy 0.11.0, has been
removed.  Users can find a more full-featured ``radon`` function in
scikit-image.


Removed deprecated keywords ``xa`` and ``xb`` from ``stats.distributions``
--------------------------------------------------------------------------

The keywords ``xa`` and ``xb``, which were deprecated since 0.11.0, have
been removed from the distributions in ``scipy.stats``.

Changes to MATLAB file readers / writers
----------------------------------------

The major change is that 1D arrays in numpy now become row vectors (shape 1, N)
when saved to a MATLAB 5 format file.  Previously 1D arrays saved as column
vectors (N, 1).  This is to harmonize the behavior of writing MATLAB 4 and 5
formats, and adapt to the defaults of numpy and MATLAB - for example
``np.atleast_2d`` returns 1D arrays as row vectors.

Trying to save arrays of greater than 2 dimensions in MATLAB 4 format now raises
an error instead of silently reshaping the array as 2D.

``scipy.io.loadmat('afile')`` used to look for `afile` on the Python system path
(``sys.path``); now ``loadmat`` only looks in the current directory for a
relative path filename.


Other changes
=============

Security fix: ``scipy.weave`` previously used temporary directories in an
insecure manner under certain circumstances.

Cython is now required to build *unreleased* versions of scipy.
The C files generated from Cython sources are not included in the git repo
anymore.  They are however still shipped in source releases.

The code base received a fairly large PEP8 cleanup.  A ``tox pep8`` 
command has been added; new code should pass this test command.

Scipy cannot be compiled with gfortran 4.1 anymore (at least on RH5), likely
due to that compiler version not supporting entry constructs well.


Authors
=======

This release contains work by the following people (contributed at least
one patch to this release, names in alphabetical order):

* Jorge Cañardo Alastuey +
* Tom Aldcroft +
* Max Bolingbroke +
* Joseph Jon Booker +
* François Boulogne
* Matthew Brett
* Christian Brodbeck +
* Per Brodtkorb +
* Christian Brueffer +
* Lars Buitinck
* Evgeni Burovski +
* Tim Cera
* Lawrence Chan +
* David Cournapeau
* Dražen Lučanin +
* Alexander J. Dunlap +
* endolith
* André Gaul +
* Christoph Gohlke
* Ralf Gommers
* Alex Griffing +
* Blake Griffith +
* Charles Harris
* Bob Helmbold +
* Andreas Hilboll
* Kat Huang +
* Oleksandr (Sasha) Huziy +
* Gert-Ludwig Ingold +
* Thouis (Ray) Jones
* Juan Luis Cano Rodríguez +
* Robert Kern
* Andreas Kloeckner +
* Sytse Knypstra +
* Gustav Larsson +
* Denis Laxalde
* Christopher Lee
* Tim Leslie
* Wendy Liu +
* Clemens Novak +
* Takuya Oshima +
* Josef Perktold
* Illia Polosukhin +
* Przemek Porebski +
* Steve Richardson +
* Branden Rolston +
* Skipper Seabold
* Fazlul Shahriar
* Leo Singer +
* Rohit Sivaprasad +
* Daniel B. Smith +
* Julian Taylor
* Louis Thibault +
* Tomas Tomecek +
* John Travers
* Richard Tsai +
* Jacob Vanderplas
* Patrick Varilly
* Pauli Virtanen
* Stefan van der Walt
* Warren Weckesser
* Pedro Werneck +
* Nils Werner +
* Michael Wimmer +
* Nathan Woods +
* Tony S. Yu +

A total of 65 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.