ANN: SciPy 0.9.0

[Ralf Gommers]

I'm pleased to announce the release of SciPy 0.9.0.

SciPy is a package of tools for science and engineering for Python. It
includes modules for statistics, optimization, integration, linear
algebra, Fourier transforms, signal and image processing, ODE solvers,
and more. This release comes seven months after the 0.8.0 release and
contains several new features, numerous bug-fixes, improved test
coverage, and better documentation. This is the first release that
supports Python 3 (with the exception of the scipy.weave module).

Sources, binaries, documentation and release notes can be found at
http://sourceforge.net/projects/scipy/files/scipy/0.9.0/

Thank you to everybody who contributed to this release.

Enjoy,
The SciPy developers



=========================
SciPy 0.9.0 Release Notes
=========================

.. contents::

SciPy 0.9.0 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 0.9.x branch, and on adding
new features on the development trunk.

This release requires Python 2.4 - 2.7 or 3.1 - and NumPy 1.5 or greater.

Please note that SciPy is still considered to have "Beta" status, as
we work toward a SciPy 1.0.0 release.  The 1.0.0 release will mark a
major milestone in the development of SciPy, after which changing the
package structure or API will be much more difficult.  Whilst these
pre-1.0 releases are considered to have "Beta" status, we are
committed to making them as bug-free as possible.

However, until the 1.0 release, we are aggressively reviewing and
refining the functionality, organization, and interface. This is being
done in an effort to make the package as coherent, intuitive, and
useful as possible.  To achieve this, we need help from the community
of users.  Specifically, we need feedback regarding all aspects of the
project - everything - from which algorithms we implement, to details
about our function's call signatures.


Python 3
========

Scipy 0.9.0 is the first SciPy release to support Python 3. The only module
that is not yet ported is ``scipy.weave``.


Scipy source code location to be changed
========================================

Soon after this release, Scipy will stop using SVN as the version control
system, and move to Git. The development source code for Scipy can from then on
be found at

    http://github.com/scipy/scipy


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

Delaunay tesselations (``scipy.spatial``)
-----------------------------------------

Scipy now includes routines for computing Delaunay tesselations in N
dimensions, powered by the Qhull_ computational geometry library. Such
calculations can now make use of the new ``scipy.spatial.Delaunay``
interface.

.. _Qhull: http://www.qhull.org/

N-dimensional interpolation (``scipy.interpolate``)
---------------------------------------------------

Support for scattered data interpolation is now significantly
improved.  This version includes a ``scipy.interpolate.griddata``
function that can perform linear and nearest-neighbour interpolation
for N-dimensional scattered data, in addition to cubic spline
(C1-smooth) interpolation in 2D and 1D.  An object-oriented interface
to each interpolator type is also available.

Nonlinear equation solvers (``scipy.optimize``)
-----------------------------------------------

Scipy includes new routines for large-scale nonlinear equation solving
in ``scipy.optimize``.  The following methods are implemented:

* Newton-Krylov (``scipy.optimize.newton_krylov``)

* (Generalized) secant methods:

  - Limited-memory Broyden methods (``scipy.optimize.broyden1``,
    ``scipy.optimize.broyden2``)

  - Anderson method (``scipy.optimize.anderson``)

* Simple iterations (``scipy.optimize.diagbroyden``,
  ``scipy.optimize.excitingmixing``, ``scipy.optimize.linearmixing``)

The ``scipy.optimize.nonlin`` module was completely rewritten, and
some of the functions were deprecated (see above).


New linear algebra routines (``scipy.linalg``)
----------------------------------------------

Scipy now contains routines for effectively solving triangular
equation systems (``scipy.linalg.solve_triangular``).


Improved FIR filter design functions (``scipy.signal``)
-------------------------------------------------------

The function ``scipy.signal.firwin`` was enhanced to allow the
design of highpass, bandpass, bandstop and multi-band FIR filters.

The function ``scipy.signal.firwin2`` was added.  This function
uses the window method to create a linear phase FIR filter with
an arbitrary frequency response.

The functions ``scipy.signal.kaiser_atten`` and ``scipy.signal.kaiser_beta``
were added.


Improved statistical tests (``scipy.stats``)
--------------------------------------------

A new function ``scipy.stats.fisher_exact`` was added, that provides Fisher's
exact test for 2x2 contingency tables.

The function ``scipy.stats.kendalltau`` was rewritten to make it much faster
(O(n log(n)) vs O(n^2)).


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

Obsolete nonlinear solvers (in ``scipy.optimize``)
--------------------------------------------------

The following nonlinear solvers from ``scipy.optimize`` are
deprecated:

- ``broyden_modified`` (bad performance)
- ``broyden1_modified`` (bad performance)
- ``broyden_generalized`` (equivalent to ``anderson``)
- ``anderson2`` (equivalent to ``anderson``)
- ``broyden3`` (obsoleted by new limited-memory broyden methods)
- ``vackar`` (renamed to ``diagbroyden``)


Removed features
================

The deprecated modules ``helpmod``, ``pexec`` and ``ppimport`` were removed
from ``scipy.misc``.

The ``output_type`` keyword in many ``scipy.ndimage`` interpolation functions
has been removed.

The ``econ`` keyword in ``scipy.linalg.qr`` has been removed. The same
functionality is still available by specifying ``mode='economic'``.


Old correlate/convolve behavior (in ``scipy.signal``)
-----------------------------------------------------

The old behavior for ``scipy.signal.convolve``, ``scipy.signal.convolve2d``,
``scipy.signal.correlate`` and ``scipy.signal.correlate2d`` was deprecated in
0.8.0 and has now been removed.  Convolve and correlate used to swap their
arguments if the second argument has dimensions larger than the first one, and
the mode was relative to the input with the largest dimension. The current
behavior is to never swap the inputs, which is what most people expect, and is
how correlation is usually defined.


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

Many functions in ``scipy.stats`` that are either available from numpy or have
been superseded, and have been deprecated since version 0.7, have been removed:
`std`, `var`, `mean`, `median`, `cov`, `corrcoef`, `z`, `zs`, `stderr`,
`samplestd`, `samplevar`, `pdfapprox`, `pdf_moments` and `erfc`.  These changes
are mirrored in ``scipy.stats.mstats``.


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

Several methods of the sparse matrix classes in ``scipy.sparse`` which had
been deprecated since version 0.7 were removed: `save`, `rowcol`, `getdata`,
`listprint`, `ensure_sorted_indices`, `matvec`, `matmat` and `rmatvec`.

The functions ``spkron``, ``speye``, ``spidentity``, ``lil_eye`` and
``lil_diags`` were removed from ``scipy.sparse``.  The first three functions
are still available as ``scipy.sparse.kron``, ``scipy.sparse.eye`` and
``scipy.sparse.identity``.

The `dims` and `nzmax` keywords were removed from the sparse matrix
constructor. The `colind` and `rowind` attributes were removed from CSR and CSC
matrices respectively.

``scipy.sparse.linalg.arpack.speigs``
-------------------------------------

A duplicated interface to the ARPACK library was removed.


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

ARPACK interface changes
------------------------

The interface to the ARPACK eigenvalue routines in
``scipy.sparse.linalg`` was changed for more robustness.

The eigenvalue and SVD routines now raise ``ArpackNoConvergence`` if
the eigenvalue iteration fails to converge. If partially converged results
are desired, they can be accessed as follows::

    import numpy as np
    from scipy.sparse.linalg import eigs, ArpackNoConvergence

    m = np.random.randn(30, 30)
    try:
        w, v = eigs(m, 6)
    except ArpackNoConvergence, err:
        partially_converged_w = err.eigenvalues
        partially_converged_v = err.eigenvectors

Several bugs were also fixed.

The routines were moreover renamed as follows:

    - eigen --> eigs
    - eigen_symmetric --> eigsh
    - svd --> svds