[SciPy-Dev] ANN: SciPy 0.10 beta 1

Bruce Southey bsouthey@gmail....
Tue Sep 13 10:40:50 CDT 2011


On 09/12/2011 04:36 PM, Ralf Gommers wrote:
> Hi,
>
> I am pleased to announce the availability of the first beta release of 
> SciPy 0.10.0. For this release over a 100 tickets and pull requests 
> have been closed, and many new features have been added. Some of the 
> highlights are:
>
>   - support for Bento as a build system for scipy
>   - generalized and shift-invert eigenvalue problems in sparse.linalg
>   - addition of discrete-time linear systems in the signal module
>
> Sources and binaries can be found at 
> https://sourceforge.net/projects/scipy/files/scipy/0.10.0b1/, release 
> notes are copied below.
> Binaries for Python 2.x are available, on Python 3 there are a few 
> known problems that should be solved first. When they are, a second 
> beta will follow.
>
> Please try this release and report problems on the mailing list.
>
> Cheers,
> Ralf
>
>
>
>
> ==========================
> SciPy 0.10.0 Release Notes
> ==========================
>
> .. note:: Scipy 0.10.0 is not released yet!
>
> .. contents::
>
> SciPy 0.10.0 is the culmination of XXX 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 0.10.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.
>
>
> New features
> ============
>
> Bento: new optional build system
> --------------------------------
>
> Scipy can now be built with `Bento <http://cournape.github.com/Bento/>`_.
> Bento has some nice features like parallel builds and partial 
> rebuilds, that
> are not possible with the default build system (distutils).  For usage
> instructions see BENTO_BUILD.txt in the scipy top-level directory.
>
> Currently Scipy has three build systems, distutils, numscons and bento.
> Numscons is deprecated and is planned and will likely be removed in 
> the next
> release.
>
>
> Generalized and shift-invert eigenvalue problems in 
> ``scipy.sparse.linalg``
> ---------------------------------------------------------------------------
>
> The sparse eigenvalue problem solver functions
> ``scipy.sparse.eigs/eigh`` now support generalized eigenvalue
> problems, and all shift-invert modes available in ARPACK.
>
>
> Discrete-Time Linear Systems (``scipy.signal``)
> -----------------------------------------------
>
> Support for simulating discrete-time linear systems, including
> ``scipy.signal.dlsim``, ``scipy.signal.dimpulse``, and 
> ``scipy.signal.dstep``,
> has been added to SciPy.  Conversion of linear systems from 
> continuous-time to
> discrete-time representations is also present via the
> ``scipy.signal.cont2discrete`` function.
>
>
> Enhancements to ``scipy.signal``
> --------------------------------
>
> A Lomb-Scargle periodogram can now be computed with the new function
> ``scipy.signal.lombscargle``.
>
> The forward-backward filter function ``scipy.signal.filtfilt`` can now
> filter the data in a given axis of an n-dimensional numpy array.
> (Previously it only handled a 1-dimensional array.)  Options have been
> added to allow more control over how the data is extended before 
> filtering.
>
> FIR filter design with ``scipy.signal.firwin2`` now has options to create
> filters of type III (zero at zero and Nyquist frequencies) and IV 
> (zero at zero
> frequency).
>
>
> Additional decomposition options (``scipy.linalg``)
> ---------------------------------------------------
>
> A sort keyword has been added to the Schur decomposition routine
> (``scipy.linalg.schur``) to allow the sorting of eigenvalues in
> the resultant Schur form.
>
> Additional special matrices (``scipy.linalg``)
> ----------------------------------------------
>
> The functions ``hilbert`` and ``invhilbert`` were added to 
> ``scipy.linalg``.
>
>
> Enhancements to ``scipy.stats``
> -------------------------------
>
> * The *one-sided form* of Fisher's exact test is now also implemented in
>   ``stats.fisher_exact``.
> * The function ``stats.chi2_contingency`` for computing the chi-square 
> test of
>   independence of factors in a contingency table has been added, along 
> with
>   the related utility functions ``stats.contingency.margins`` and
>   ``stats.contingency.expected_freq``.
>
>
> Basic support for Harwell-Boeing file format for sparse matrices
> ----------------------------------------------------------------
>
> Both read and write are support through a simple function-based API, 
> as well as
> a more complete API to control number format. The functions may be 
> found in
> scipy.sparse.io <http://scipy.sparse.io>.
>
> The following features are supported:
>
>     * Read and write sparse matrices in the CSC format
>     * Only real, symmetric, assembled matrix are supported (RUA format)
>
>
> Deprecated features
> ===================
>
> ``scipy.maxentropy``
> --------------------
>
> The maxentropy module is unmaintained, rarely used and has not been 
> functioning
> well for several releases.  Therefore it has been deprecated for this 
> release,
> and will be removed for scipy 0.11.  Logistic regression in 
> scikits.learn is a
> good alternative for this functionality.  The 
> ``scipy.maxentropy.logsumexp``
> function has been moved to ``scipy.misc``.
>
>
> ``scipy.lib.blas``
> ------------------
>
> There are similar BLAS wrappers in ``scipy.linalg`` and 
> ``scipy.lib``.  These
> have now been consolidated as ``scipy.linalg.blas``, and 
> ``scipy.lib.blas`` is
> deprecated.
>
>
> Numscons build system
> ---------------------
>
> The numscons build system is being replaced by Bento, and will be 
> removed in
> one of the next scipy releases.
>
>
> Removed features
> ================
>
> The deprecated name `invnorm` was removed from 
> ``scipy.stats.distributions``,
> this distribution is available as `invgauss`.
>
> The following deprecated nonlinear solvers from ``scipy.optimize`` 
> have been
> removed::
>
>   - ``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``)
>
>
> Other changes
> =============
>
> ``scipy.constants`` has been updated with the CODATA 2010 constants.
>
> ``__all__`` dicts have been added to all modules, which has cleaned up the
> namespaces (particularly useful for interactive work).
>
> An API section has been added to the documentation, giving recommended 
> import
> guidelines and specifying which submodules are public and which aren't.
>
>
> Checksums
> =========
>
> f30a85149ebc3d023fce5e012cc7a28a  
> release/installers/scipy-0.10.0b1-py2.7-python.org-macosx10.6.dmg
> 5c4a74cca13e9225efd1840d99af9ee8  
> release/installers/scipy-0.10.0b1-win32-superpack-python2.5.exe
> b24dd33bfeb07058038ba85d2b1ddfd3  
> release/installers/scipy-0.10.0b1-win32-superpack-python2.6.exe
> c5222bb7b7fcc28cec4730e3caebf43f  
> release/installers/scipy-0.10.0b1-win32-superpack-python2.7.exe
> c8c6f3870f9d0ef571861da63b4b374b  release/installers/scipy-0.10.0b1.tar.gz
> 1ce4f01acfccb68dcd6c387eb08a8a88  release/installers/scipy-0.10.0b1.zip
>
>
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The INSTALL.TXT and weave documentation still refers to svn and not git.
Also, I do not know if the usage of 'svn' in the tools directory of the 
developmental version are valid.

I noticed these two usages of svn in the release version:
1) 'scipy/setup.py': 'config.make_svn_version_py()  # installs 
__svn_version__.py'?
2) scipy/special/special_version.py

The  __svn_version__.py was removed so  scipy/special/special_version.py 
fails:
$ git log -p scipy/version.py
commit 28a5f5f0e03b7746a43ae31925806cbf8df958a8
Author: David Cournapeau <cournape@gmail.com>
Date:   Sun May 10 06:57:17 2009 +0000
[snip]

With over a year and no complaints, perhaps we could just remove these 
rather than fix scipy/special/special_version.py?
It is easy to fix but it has not changed since 2007 when it was 
apparently created!

Can file a ticket if needed.

Bruce

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