[SciPy-User] ANN: SciPy 0.12.0 release

Sebastian Bassi sbassi@gmail....
Sun Apr 7 17:09:16 CDT 2013


Hello,

I tried to install it on Ubuntu 10.04.1 64bits and I got:

(...)
Wrote C/API module "_flapack" to file
"build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/_flapackmodule.c"
Fortran 77 wrappers are saved to
"build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/_flapack-f2pywrappers.f"
  adding 'build/src.linux-x86_64-2.7/fortranobject.c' to sources.
  adding 'build/src.linux-x86_64-2.7' to include_dirs.
  adding 'build/src.linux-x86_64-2.7/build/src.linux-x86_64-2.7/scipy/linalg/_flapack-f2pywrappers.f'
to sources.
building extension "scipy.linalg._cblas" sources
from_template:> build/src.linux-x86_64-2.7/cblas.pyf
error: cblas.pyf.src: No such file or directory

I have Numpy:

ubuntu@ip-10-174-23-251:~/bioinfo/scipy-0.12.0$ python
Python 2.7.3 (default, Aug  1 2012, 05:14:39)
[GCC 4.6.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> numpy.version.version
'1.7.1'
>>>



On Sun, Apr 7, 2013 at 5:09 PM, Ralf Gommers <ralf.gommers@gmail.com> wrote:
> We are pleased to announce the availability of SciPy 0.12.0. This release
> has some cool new features (see highlights below) and a large amount of bug
> fixes and maintenance work under the hood. The number of contributors also
> keeps rising steadily - 75 people contributed patches to this release. We
> hope to see this trend continue.
>
> Some of the highlights of this release are:
>
>   - Completed QHull wrappers in scipy.spatial.
>   - cKDTree now a drop-in replacement for KDTree.
>   - A new global optimizer, basinhopping.
>   - Support for Python 2 and Python 3 from the same code base (no more
> 2to3).
>
> This release requires Python 2.6, 2.7 or 3.1-3.3 and NumPy 1.5.1 or greater.
> Support for Python 2.4 and 2.5 has been dropped as of this release.
>
> Sources and binaries can be found at
> http://sourceforge.net/projects/scipy/files/scipy/0.12.0/, release notes are
> copied below.
>
> Enjoy,
> The SciPy developers
>
>
>
> ==========================
> SciPy 0.12.0 Release Notes
> ==========================
>
> SciPy 0.12.0 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 0.12.x branch, and on adding
> new features on the master branch.
>
> Some of the highlights of this release are:
>
>   - Completed QHull wrappers in scipy.spatial.
>   - cKDTree now a drop-in replacement for KDTree.
>   - A new global optimizer, basinhopping.
>   - Support for Python 2 and Python 3 from the same code base (no more
> 2to3).
>
> This release requires Python 2.6, 2.7 or 3.1-3.3 and NumPy 1.5.1 or greater.
> Support for Python 2.4 and 2.5 has been dropped as of this release.
>
>
> New features
> ============
>
> ``scipy.spatial`` improvements
> ------------------------------
>
> cKDTree feature-complete
> ^^^^^^^^^^^^^^^^^^^^^^^^
> Cython version of KDTree, cKDTree, is now feature-complete.  Most operations
> (construction, query, query_ball_point, query_pairs, count_neighbors and
> sparse_distance_matrix) are between 200 and 1000 times faster in cKDTree
> than
> in KDTree.  With very minor caveats, cKDTree has exactly the same interface
> as
> KDTree, and can be used as a drop-in replacement.
>
> Voronoi diagrams and convex hulls
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> `scipy.spatial` now contains functionality for computing Voronoi
> diagrams and convex hulls using the Qhull library. (Delaunay
> triangulation was available since Scipy 0.9.0.)
>
> Delaunay improvements
> ^^^^^^^^^^^^^^^^^^^^^
> It's now possible to pass in custom Qhull options in Delaunay
> triangulation. Coplanar points are now also recorded, if present.
> Incremental construction of Delaunay triangulations is now also
> possible.
>
> Spectral estimators (``scipy.signal``)
> --------------------------------------
> The functions ``scipy.signal.periodogram`` and ``scipy.signal.welch`` were
> added, providing DFT-based spectral estimators.
>
>
> ``scipy.optimize`` improvements
> -------------------------------
>
> Callback functions in L-BFGS-B and TNC
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> A callback mechanism was added to L-BFGS-B and TNC minimization solvers.
>
> Basin hopping global optimization (``scipy.optimize.basinhopping``)
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> A new global optimization algorithm.  Basinhopping is designed to
> efficiently
> find the global minimum of a smooth function.
>
>
> ``scipy.special`` improvements
> ------------------------------
>
> Revised complex error functions
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> The computation of special functions related to the error function now uses
> a
> new `Faddeeva library from MIT <http://ab-initio.mit.edu/Faddeeva>`__ which
> increases their numerical precision. The scaled and imaginary error
> functions
> ``erfcx`` and ``erfi`` were also added, and the Dawson integral ``dawsn``
> can
> now be evaluated for a complex argument.
>
> Faster orthogonal polynomials
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Evaluation of orthogonal polynomials (the ``eval_*`` routines) in now
> faster in ``scipy.special``, and their ``out=`` argument functions
> properly.
>
>
> ``scipy.sparse.linalg`` features
> --------------------------------
> - In ``scipy.sparse.linalg.spsolve``, the ``b`` argument can now be either
>   a vector or a matrix.
> - ``scipy.sparse.linalg.inv`` was added.  This uses ``spsolve`` to compute
>   a sparse matrix inverse.
> - ``scipy.sparse.linalg.expm`` was added.  This computes the exponential of
>   a sparse matrix using a similar algorithm to the existing dense array
>   implementation in ``scipy.linalg.expm``.
>
>
> Listing Matlab(R) file contents in ``scipy.io``
> -----------------------------------------------
> A new function ``whosmat`` is available in ``scipy.io`` for inspecting
> contents
> of MAT files without reading them to memory.
>
>
> Documented BLAS and LAPACK low-level interfaces (``scipy.linalg``)
> ------------------------------------------------------------------
> The modules `scipy.linalg.blas` and `scipy.linalg.lapack` can be used
> to access low-level BLAS and LAPACK functions.
>
>
> Polynomial interpolation improvements (``scipy.interpolate``)
> -------------------------------------------------------------
> The barycentric, Krogh, piecewise and pchip polynomial interpolators in
> ``scipy.interpolate`` accept now an ``axis`` argument.
>
>
> Deprecated features
> ===================
>
> `scipy.lib.lapack`
> ------------------
> The module `scipy.lib.lapack` is deprecated. You can use
> `scipy.linalg.lapack`
> instead. The module `scipy.lib.blas` was deprecated earlier in Scipy 0.10.0.
>
>
> `fblas` and `cblas`
> -------------------
> Accessing the modules `scipy.linalg.fblas`, `cblas`, `flapack`, `clapack` is
> deprecated. Instead, use the modules `scipy.linalg.lapack` and
> `scipy.linalg.blas`.
>
>
> Backwards incompatible changes
> ==============================
>
> Removal of ``scipy.io.save_as_module``
> --------------------------------------
> The function ``scipy.io.save_as_module`` was deprecated in Scipy 0.11.0, and
> is
> now removed.
>
> Its private support modules ``scipy.io.dumbdbm_patched`` and
> ``scipy.io.dumb_shelve`` are also removed.
>
>
> Other changes
> =============
>
>
> Authors
> =======
> * Anton Akhmerov +
> * Alexander Eberspächer +
> * Anne Archibald
> * Jisk Attema +
> * K.-Michael Aye +
> * bemasc +
> * Sebastian Berg +
> * François Boulogne +
> * Matthew Brett
> * Lars Buitinck
> * Steven Byrnes +
> * Tim Cera +
> * Christian +
> * Keith Clawson +
> * David Cournapeau
> * Nathan Crock +
> * endolith
> * Bradley M. Froehle +
> * Matthew R Goodman
> * Christoph Gohlke
> * Ralf Gommers
> * Robert David Grant +
> * Yaroslav Halchenko
> * Charles Harris
> * Jonathan Helmus
> * Andreas Hilboll
> * Hugo +
> * Oleksandr Huziy
> * Jeroen Demeyer +
> * Johannes Schönberger +
> * Steven G. Johnson +
> * Chris Jordan-Squire
> * Jonathan Taylor +
> * Niklas Kroeger +
> * Jerome Kieffer +
> * kingson +
> * Josh Lawrence
> * Denis Laxalde
> * Alex Leach +
> * Tim Leslie
> * Richard Lindsley +
> * Lorenzo Luengo +
> * Stephen McQuay +
> * MinRK
> * Sturla Molden +
> * Eric Moore +
> * mszep +
> * Matt Newville +
> * Vlad Niculae
> * Travis Oliphant
> * David Parker +
> * Fabian Pedregosa
> * Josef Perktold
> * Zach Ploskey +
> * Alex Reinhart +
> * Gilles Rochefort +
> * Ciro Duran Santillli +
> * Jan Schlueter +
> * Jonathan Scholz +
> * Anthony Scopatz
> * Skipper Seabold
> * Fabrice Silva +
> * Scott Sinclair
> * Jacob Stevenson +
> * Sturla Molden +
> * Julian Taylor +
> * thorstenkranz +
> * John Travers +
> * True Price +
> * Nicky van Foreest
> * Jacob Vanderplas
> * Patrick Varilly
> * Daniel Velkov +
> * Pauli Virtanen
> * Stefan van der Walt
> * Warren Weckesser
>
> A total of 75 people contributed to this release.
> People with a "+" by their names contributed a patch for the first time.
>
>
> _______________________________________________
> SciPy-User mailing list
> SciPy-User@scipy.org
> http://mail.scipy.org/mailman/listinfo/scipy-user
>



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