SciPy 0.11.0 Release Notes ¶

Contents

SciPy 0.11.0 is the culmination of 8 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. Highlights of this release are:

A new module has been added which provides a number of common sparse graph algorithms.

New unified interfaces to the existing optimization and root finding functions have been added.

All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Our development attention will now shift to bug-fix releases on the 0.11.x branch, and on adding new features on the master branch.

This release requires Python 2.4-2.7 or 3.1-3.2 and NumPy 1.5.1 or greater.

New features ¶

Sparse Graph Submodule ¶

The new submodule scipy.sparse.csgraph implements a number of efficient graph algorithms for graphs stored as sparse adjacency matrices. Available routines are:

connected_components - determine connected components of a graph

laplacian - compute the laplacian of a graph

shortest_path - compute the shortest path between points on a positive graph

dijkstra - use Dijkstra’s algorithm for shortest path

floyd_warshall - use the Floyd-Warshall algorithm for shortest path

breadth_first_order - compute a breadth-first order of nodes

depth_first_order - compute a depth-first order of nodes

breadth_first_tree - construct the breadth-first tree from a given node

depth_first_tree - construct a depth-first tree from a given node

minimum_spanning_tree - construct the minimum spanning tree of a graph

`scipy.optimize` improvements ¶

The optimize module has received a lot of attention this release. In addition to added tests, documentation improvements, bug fixes and code clean-up, the following improvements were made:

A unified interface to minimizers of univariate and multivariate functions has been added.
A unified interface to root finding algorithms for multivariate functions has been added.
The L-BFGS-B algorithm has been updated to version 3.0.

Unified interfaces to minimizers ¶

Two new functions scipy.optimize.minimize and scipy.optimize.minimize_scalar were added to provide a common interface to minimizers of multivariate and univariate functions respectively. For multivariate functions, scipy.optimize.minimize provides an interface to methods for unconstrained optimization (fmin, fmin_powell, fmin_cg, fmin_ncg, fmin_bfgs and anneal) or constrained optimization (fmin_l_bfgs_b, fmin_tnc, fmin_cobyla and fmin_slsqp). For univariate functions, scipy.optimize.minimize_scalar provides an interface to methods for unconstrained and bounded optimization (brent, golden, fminbound). This allows for easier comparing and switching between solvers.

Unified interface to root finding algorithms ¶

The new function scipy.optimize.root provides a common interface to root finding algorithms for multivariate functions, embeding fsolve, leastsq and nonlin solvers.

`scipy.linalg` improvements ¶

New matrix equation solvers ¶

Solvers for the Sylvester equation (scipy.linalg.solve_sylvester, discrete and continuous Lyapunov equations (scipy.linalg.solve_lyapunov, scipy.linalg.solve_discrete_lyapunov) and discrete and continuous algebraic Riccati equations (scipy.linalg.solve_continuous_are, scipy.linalg.solve_discrete_are) have been added to scipy.linalg. These solvers are often used in the field of linear control theory.

QZ and QR Decomposition ¶

It is now possible to calculate the QZ, or Generalized Schur, decomposition using scipy.linalg.qz. This function wraps the LAPACK routines sgges, dgges, cgges, and zgges.

The function scipy.linalg.qr_multiply, which allows efficient computation of the matrix product of Q (from a QR decompostion) and a vector, has been added.

Pascal matrices ¶

A function for creating Pascal matrices, scipy.linalg.pascal, was added.

Sparse matrix construction and operations ¶

Two new functions, scipy.sparse.diags and scipy.sparse.block_diag, were added to easily construct diagonal and block-diagonal sparse matrices respectively.

scipy.sparse.csc_matrix and csr_matrix now support the operations sin, tan, arcsin, arctan, sinh, tanh, arcsinh, arctanh, rint, sign, expm1, log1p, deg2rad, rad2deg, floor, ceil and trunc. Previously, these operations had to be performed by operating on the matrices’ data attribute.

LSMR iterative solver ¶

LSMR, an iterative method for solving (sparse) linear and linear least-squares systems, was added as scipy.sparse.linalg.lsmr.

Discrete Sine Transform ¶

Bindings for the discrete sine transform functions have been added to scipy.fftpack.

`scipy.interpolate` improvements ¶

For interpolation in spherical coordinates, the three classes scipy.interpolate.SmoothSphereBivariateSpline, scipy.interpolate.LSQSphereBivariateSpline, and scipy.interpolate.RectSphereBivariateSpline have been added.

Binned statistics (`scipy.stats`)¶

The stats module has gained functions to do binned statistics, which are a generalization of histograms, in 1-D, 2-D and multiple dimensions: scipy.stats.binned_statistic, scipy.stats.binned_statistic_2d and scipy.stats.binned_statistic_dd.

Deprecated features ¶

scipy.sparse.cs_graph_components has been made a part of the sparse graph submodule, and renamed to scipy.sparse.csgraph.connected_components. Calling the former routine will result in a deprecation warning.

scipy.misc.radon has been deprecated. A more full-featured radon transform can be found in scikits-image.

scipy.io.save_as_module has been deprecated. A better way to save multiple Numpy arrays is the numpy.savez function.

The xa and xb parameters for all distributions in scipy.stats.distributions already weren’t used; they have now been deprecated.

Backwards incompatible changes ¶

Removal of `scipy.maxentropy`¶

The scipy.maxentropy module, which was deprecated in the 0.10.0 release, has been removed. Logistic regression in scikits.learn is a good and modern alternative for this functionality.

Minor change in behavior of `splev`¶

The spline evaluation function now behaves similarly to interp1d for size-1 arrays. Previous behavior:

>>> from scipy.interpolate import splev, splrep, interp1d
>>> x = [1,2,3,4,5]
>>> y = [4,5,6,7,8]
>>> tck = splrep(x, y)
>>> splev([1], tck)
4.
>>> splev(1, tck)
4.

Corrected behavior:

>>> splev([1], tck)
array([ 4.])
>>> splev(1, tck)
array(4.)

This affects also the UnivariateSpline classes.

Behavior of `scipy.integrate.complex_ode`¶

The behavior of the y attribute of complex_ode is changed. Previously, it expressed the complex-valued solution in the form:

z = ode.y[::2] + 1j * ode.y[1::2]

Now, it is directly the complex-valued solution:

z = ode.y

Minor change in behavior of T-tests ¶

The T-tests scipy.stats.ttest_ind, scipy.stats.ttest_rel and scipy.stats.ttest_1samp have been changed so that 0 / 0 now returns NaN instead of 1.

Other changes ¶

The SuperLU sources in scipy.sparse.linalg have been updated to version 4.3 from upstream.

The function scipy.signal.bode, which calculates magnitude and phase data for a continuous-time system, has been added.

The two-sample T-test scipy.stats.ttest_ind gained an option to compare samples with unequal variances, i.e. Welch’s T-test.

scipy.misc.logsumexp now takes an optional axis keyword argument.

Authors ¶

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

Jeff Armstrong
Chad Baker
Brandon Beacher +
behrisch +
borishim +
Matthew Brett
Lars Buitinck
Luis Pedro Coelho +
Johann Cohen-Tanugi
David Cournapeau
dougal +
Ali Ebrahim +
endolith +
Bjørn Forsman +
Robert Gantner +
Sebastian Gassner +
Christoph Gohlke
Ralf Gommers
Yaroslav Halchenko
Charles Harris
Jonathan Helmus +
Andreas Hilboll +
Marc Honnorat +
Jonathan Hunt +
Maxim Ivanov +
Thouis (Ray) Jones
Christopher Kuster +
Josh Lawrence +
Denis Laxalde +
Travis Oliphant
Joonas Paalasmaa +
Fabian Pedregosa
Josef Perktold
Gavin Price +
Jim Radford +
Andrew Schein +
Skipper Seabold
Jacob Silterra +
Scott Sinclair
Alexis Tabary +
Martin Teichmann
Matt Terry +
Nicky van Foreest +
Jacob Vanderplas
Patrick Varilly +
Pauli Virtanen
Nils Wagner +
Darryl Wally +
Stefan van der Walt
Liming Wang +
David Warde-Farley +
Warren Weckesser
Sebastian Werk +
Mike Wimmer +
Tony S Yu +

A total of 55 people contributed to this release. People with a “+” by their names contributed a patch for the first time.