[Numpy-discussion] ANN: Scipy 0.15.0 beta 1 release

[Matthew Brett]

Hi,

On Sun, Nov 23, 2014 at 3:13 PM, Pauli Virtanen <pav at iki.fi> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Dear all,
>
> We have finally finished preparing the Scipy 0.15.0 beta 1 release.
> Please try it and report any issues on the scipy-dev mailing list,
> and/or on Github.
>
> If no surprises turn up, the final release is planned on Dec 20 in
> three weeks.
>
> Source tarballs and full release notes are available at
> https://sourceforge.net/projects/scipy/files/SciPy/0.15.0b1/
> Binary installers should also be up soon.
>
> Best regards,
> Pauli Virtanen
>
>
> - --------------------------------------------
>
> SciPy 0.15.0 is the culmination of 6 months of hard work. It contains
> several 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 0.16.x branch, and on adding
> new features on the master branch.
>
> This release requires Python 2.6, 2.7 or 3.2-3.3 and NumPy 1.5.1 or
> greater.
>
>
> New features
> ============
>
> Linear Programming Interface
> - - ----------------------------
>
> The new function ``scipy.optimize.linprog`` provides a generic
> linear programming similar to the way ``scipy.optimize.minimize``
> provides a generic interface to nonlinear programming optimizers.
> Currently the only method supported is *simplex* which provides
> a two-phase, dense-matrix-based simplex algorithm. Callbacks
> functions are supported,allowing the user to monitor the progress
> of the algorithm.
>
> Differential_evolution, a global optimizer
> - - ------------------------------------------
>
> A new ``differential_evolution`` function is available in the
> ``scipy.optimize``
> module.  Differential Evolution is an algorithm used for finding the
> global
> minimum of multivariate functions. It is stochastic in nature (does
> not use
> gradient methods), and can search large areas of candidate space, but
> often
> requires larger numbers of function evaluations than conventional gradient
> based techniques.
>
> ``scipy.signal`` improvements
> - - -----------------------------
>
> The function ``max_len_seq`` was added, which computes a Maximum
> Length Sequence (MLS) signal.
>
> ``scipy.integrate`` improvements
> - - --------------------------------
>
> It is now possible to use ``scipy.integrate`` routines to integrate
> multivariate ctypes functions, thus avoiding callbacks to Python and
> providing better performance.
>
> ``scipy.linalg`` improvements
> - - -----------------------------
>
> Add function ``orthogonal_procrustes`` for solving the procrustes
> linear algebra problem.
>
> ``scipy.sparse`` improvements
> - - -----------------------------
>
> ``scipy.sparse.linalg.svds`` can now take a ``LinearOperator`` as its
> main input.
>
> ``scipy.special`` improvements
> - - ------------------------------
>
> Values of ellipsoidal harmonic (i.e. Lame) functions and associated
> normalization constants can be now computed using ``ellip_harm``,
> ``ellip_harm_2``, and ``ellip_normal``.
>
> New convenience functions ``entr``, ``rel_entr`` ``kl_div``,
> ``huber``, and ``pseudo_huber`` were added.
>
> ``scipy.sparse.csgraph`` improvements
> - - -------------------------------------
>
> Routines ``reverse_cuthill_mckee`` and ``maximum_bipartite_matching``
> for computing reorderings of sparse graphs were added.
>
> ``scipy.stats`` improvements
> - - ----------------------------
>
> Added a Dirichlet distribution as multivariate distribution.
>
> The new function ``scipy.stats.median_test`` computes Mood's median test.
>
> The new function ``scipy.stats.combine_pvalues`` implements Fisher's
> and Stouffer's methods for combining p-values.
>
> ``scipy.stats.describe`` returns a namedtuple rather than a tuple,
> allowing
> users to access results by index or by name.
>
> Deprecated features
> ===================
>
> The ``scipy.weave`` module is deprecated.  It was the only module
> never ported
> to Python 3.x, and is not recommended to be used for new code - use Cython
> instead.  In order to support existing code, ``scipy.weave`` has been
> packaged
> separately: `https://github.com/scipy/weave`_.  It is a pure Python
> package, and
> can easily be installed with ``pip install weave``.
>
> ``scipy.special.bessel_diff_formula`` is deprecated.  It is a private
> function,
> and therefore will be removed from the public API in a following release.
>
>
> Backwards incompatible changes
> ==============================
>
> scipy.ndimage
> - - -------------
>
> The functions ``scipy.ndimage.minimum_positions``,
> ``scipy.ndimage.maximum_positions`` and ``scipy.ndimage.extrema`` return
> positions as ints instead of floats.
>
> scipy.integrate
> - - ---------------
>
> The format of banded Jacobians in ``scipy.integrate.ode`` solvers is
> changed. Note that the previous documentation of this feature was
> erroneous.

I ran against current scipy stack packages, and get these errors:

https://travis-ci.org/MacPython/scipy-stack-osx-testing/jobs/42022929#L324

======================================================================
ERROR: test_netcdf.test_byte_gatts
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/tests/test_netcdf.py",
line 268, in test_byte_gatts
    f = netcdf_file(filename, 'w')
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/netcdf.py",
line 226, in __init__
    self.fp = open(self.filename, '%sb' % omode)
IOError: [Errno 13] Permission denied:
'/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/tests/data/g_byte_atts.nc'
======================================================================
ERROR: test_netcdf.test_open_append
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/tests/test_netcdf.py",
line 284, in test_open_append
    f = netcdf_file(filename, 'w')
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/netcdf.py",
line 226, in __init__
    self.fp = open(self.filename, '%sb' % omode)
IOError: [Errno 13] Permission denied:
'/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/scipy/io/tests/data/append_dat.nc'

This turns out to be because the netcdf tests are trying to write into
the scipy/io/tests/data directory:

https://github.com/scipy/scipy/pull/4198

Otherwise, it looks clean.  I uploaded the OSX wheels to sourceforge.

Cheers,

Matthew