- SciPy 0.7.0 Release Notes
- Python 2.6 and 3.0
- Major documentation improvements
- Running Tests
- Building SciPy
- Sandbox Removed
- Sparse Matrices
- Statistics package
- Reworking of IO package
- New Hierarchical Clustering module
- New Spatial package
- Reworked fftpack package
- New Constants package
- New Radial Basis Function module
- New complex ODE integrator
- New generalized symmetric and hermitian eigenvalue problem solver
- Bug fixes in the interpolation package
- Weave clean up
- Known problems
SciPy 0.7.0 is the culmination of 16 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 0.7.x branch, and on adding new features on the development trunk. This release requires Python 2.4 or 2.5 and NumPy 1.2 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. For example, in addition to fixing numerous bugs in this release, we have also doubled the number of unit tests since the last release.
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.
Over the last year, we have seen a rapid increase in community involvement, and numerous infrastructure improvements to lower the barrier to contributions (e.g., more explicit coding standards, improved testing infrastructure, better documentation tools). Over the next year, we hope to see this trend continue and invite everyone to become more involved.
A significant amount of work has gone into making SciPy compatible with Python 2.6; however, there are still some issues in this regard. The main issue with 2.6 support is NumPy. On UNIX (including Mac OS X), NumPy 1.2.1 mostly works, with a few caveats. On Windows, there are problems related to the compilation process. The upcoming NumPy 1.3 release will fix these problems. Any remaining issues with 2.6 support for SciPy 0.7 will be addressed in a bug-fix release.
Python 3.0 is not supported at all; it requires NumPy to be ported to Python 3.0. This requires immense effort, since a lot of C code has to be ported. The transition to 3.0 is still under consideration; currently, we don’t have any timeline or roadmap for this transition.
This release also includes an updated tutorial, which hadn’t been available since SciPy was ported to NumPy in 2005. Though not comprehensive, the tutorial shows how to use several essential parts of Scipy. It also includes the ndimage documentation from the numarray manual.
Nevertheless, more effort is needed on the documentation front. Luckily, contributing to Scipy documentation is now easier than before: if you find that a part of it requires improvements, and want to help us out, please register a user name in our web-based documentation editor at https://docs.scipy.org/ and correct the issues.
NumPy 1.2 introduced a new testing framework based on nose. Starting with this release, SciPy now uses the new NumPy test framework as well. Taking advantage of the new testing framework requires nose version 0.10, or later. One major advantage of the new framework is that it greatly simplifies writing unit tests - which has all ready paid off, given the rapid increase in tests. To run the full test suite:
>>> import scipy >>> scipy.test('full')
For more information, please see The NumPy/SciPy Testing Guide.
We have also greatly improved our test coverage. There were just over 2,000 unit tests in the 0.6.0 release; this release nearly doubles that number, with just over 4,000 unit tests.
Support for NumScons has been added. NumScons is a tentative new build system for NumPy/SciPy, using SCons at its core.
SCons is a next-generation build system, intended to replace the venerable Make with the integrated functionality of autoconf/automake and ccache. Scons is written in Python and its configuration files are Python scripts. NumScons is meant to replace NumPy’s custom version of distutils providing more advanced functionality, such as autoconf, improved fortran support, more tools, and support for numpy.distutils/scons cooperation.
While porting SciPy to NumPy in 2005, several packages and modules were moved into scipy.sandbox. The sandbox was a staging ground for packages that were undergoing rapid development and whose APIs were in flux. It was also a place where broken code could live. The sandbox has served its purpose well, but was starting to create confusion. Thus scipy.sandbox was removed. Most of the code was moved into scipy, some code was made into a scikit, and the remaining code was just deleted, as the functionality had been replaced by other code.
Sparse matrices have seen extensive improvements. There is now support for integer dtypes such int8, uint32, etc. Two new sparse formats were added:
- new class dia_matrix : the sparse DIAgonal format
- new class bsr_matrix : the Block CSR format
Several new sparse matrix construction functions were added:
- sparse.kron : sparse Kronecker product
- sparse.bmat : sparse version of numpy.bmat
- sparse.vstack : sparse version of numpy.vstack
- sparse.hstack : sparse version of numpy.hstack
Extraction of submatrices and nonzero values have been added:
- sparse.tril : extract lower triangle
- sparse.triu : extract upper triangle
- sparse.find : nonzero values and their indices
csr_matrix and csc_matrix now support slicing and fancy indexing (e.g., A[1:3, 4:7] and A[[3,2,6,8],:]). Conversions among all sparse formats are now possible:
- using member functions such as .tocsr() and .tolil()
- using the .asformat() member function, e.g. A.asformat('csr')
- using constructors A = lil_matrix([[1,2]]); B = csr_matrix(A)
All sparse constructors now accept dense matrices and lists of lists. For example:
- A = csr_matrix( rand(3,3) ) and B = lil_matrix( [[1,2],[3,4]] )
The handling of diagonals in the spdiags function has been changed. It now agrees with the MATLAB(TM) function of the same name.
Numerous efficiency improvements to format conversions and sparse matrix arithmetic have been made. Finally, this release contains numerous bugfixes.
Statistical functions for masked arrays have been added, and are accessible through scipy.stats.mstats. The functions are similar to their counterparts in scipy.stats but they have not yet been verified for identical interfaces and algorithms.
Several bugs were fixed for statistical functions, of those, kstest and percentileofscore gained new keyword arguments.
Added deprecation warning for mean, median, var, std, cov, and corrcoef. These functions should be replaced by their numpy counterparts. Note, however, that some of the default options differ between the scipy.stats and numpy versions of these functions.
Numerous bug fixes to stats.distributions: all generic methods now work correctly, several methods in individual distributions were corrected. However, a few issues remain with higher moments (skew, kurtosis) and entropy. The maximum likelihood estimator, fit, does not work out-of-the-box for some distributions - in some cases, starting values have to be carefully chosen, in other cases, the generic implementation of the maximum likelihood method might not be the numerically appropriate estimation method.
We expect more bugfixes, increases in numerical precision and enhancements in the next release of scipy.
The IO code in both NumPy and SciPy is being extensively reworked. NumPy will be where basic code for reading and writing NumPy arrays is located, while SciPy will house file readers and writers for various data formats (data, audio, video, images, matlab, etc.).
Several functions in scipy.io have been deprecated and will be removed in the 0.8.0 release including npfile, save, load, create_module, create_shelf, objload, objsave, fopen, read_array, write_array, fread, fwrite, bswap, packbits, unpackbits, and convert_objectarray. Some of these functions have been replaced by NumPy’s raw reading and writing capabilities, memory-mapping capabilities, or array methods. Others have been moved from SciPy to NumPy, since basic array reading and writing capability is now handled by NumPy.
The Matlab (TM) file readers/writers have a number of improvements:
- default version 5
- v5 writers for structures, cell arrays, and objects
- v5 readers/writers for function handles and 64-bit integers
- new struct_as_record keyword argument to loadmat, which loads struct arrays in matlab as record arrays in numpy
- string arrays have dtype='U...' instead of dtype=object
- loadmat no longer squeezes singleton dimensions, i.e. squeeze_me=False by default
This module adds new hierarchical clustering functionality to the scipy.cluster package. The function interfaces are similar to the functions provided MATLAB(TM)’s Statistics Toolbox to help facilitate easier migration to the NumPy/SciPy framework. Linkage methods implemented include single, complete, average, weighted, centroid, median, and ward.
In addition, several functions are provided for computing inconsistency statistics, cophenetic distance, and maximum distance between descendants. The fcluster and fclusterdata functions transform a hierarchical clustering into a set of flat clusters. Since these flat clusters are generated by cutting the tree into a forest of trees, the leaders function takes a linkage and a flat clustering, and finds the root of each tree in the forest. The ClusterNode class represents a hierarchical clusterings as a field-navigable tree object. to_tree converts a matrix-encoded hierarchical clustering to a ClusterNode object. Routines for converting between MATLAB and SciPy linkage encodings are provided. Finally, a dendrogram function plots hierarchical clusterings as a dendrogram, using matplotlib.
The new spatial package contains a collection of spatial algorithms and data structures, useful for spatial statistics and clustering applications. It includes rapidly compiled code for computing exact and approximate nearest neighbors, as well as a pure-python kd-tree with the same interface, but that supports annotation and a variety of other algorithms. The API for both modules may change somewhat, as user requirements become clearer.
It also includes a distance module, containing a collection of distance and dissimilarity functions for computing distances between vectors, which is useful for spatial statistics, clustering, and kd-trees. Distance and dissimilarity functions provided include Bray-Curtis, Canberra, Chebyshev, City Block, Cosine, Dice, Euclidean, Hamming, Jaccard, Kulsinski, Mahalanobis, Matching, Minkowski, Rogers-Tanimoto, Russell-Rao, Squared Euclidean, Standardized Euclidean, Sokal-Michener, Sokal-Sneath, and Yule.
The pdist function computes pairwise distance between all unordered pairs of vectors in a set of vectors. The cdist computes the distance on all pairs of vectors in the Cartesian product of two sets of vectors. Pairwise distance matrices are stored in condensed form; only the upper triangular is stored. squareform converts distance matrices between square and condensed forms.
FFTW2, FFTW3, MKL and DJBFFT wrappers have been removed. Only (NETLIB) fftpack remains. By focusing on one backend, we hope to add new features - like float32 support - more easily.
scipy.constants provides a collection of physical constants and conversion factors. These constants are taken from CODATA Recommended Values of the Fundamental Physical Constants: 2002. They may be found at physics.nist.gov/constants. The values are stored in the dictionary physical_constants as a tuple containing the value, the units, and the relative precision - in that order. All constants are in SI units, unless otherwise stated. Several helper functions are provided.
scipy.interpolate now contains a Radial Basis Function module. Radial basis functions can be used for smoothing/interpolating scattered data in n-dimensions, but should be used with caution for extrapolation outside of the observed data range.
scipy.integrate.ode now contains a wrapper for the ZVODE complex-valued ordinary differential equation solver (by Peter N. Brown, Alan C. Hindmarsh, and George D. Byrne).
scipy.linalg.eigh now contains wrappers for more LAPACK symmetric and hermitian eigenvalue problem solvers. Users can now solve generalized problems, select a range of eigenvalues only, and choose to use a faster algorithm at the expense of increased memory usage. The signature of the scipy.linalg.eigh changed accordingly.
The shape of return values from scipy.interpolate.interp1d used to be incorrect, if interpolated data had more than 2 dimensions and the axis keyword was set to a non-default value. This has been fixed. Moreover, interp1d returns now a scalar (0D-array) if the input is a scalar. Users of scipy.interpolate.interp1d may need to revise their code if it relies on the previous behavior.
There were numerous improvements to scipy.weave. blitz++ was relicensed by the author to be compatible with the SciPy license. wx_spec.py was removed.
Here are known problems with scipy 0.7.0:
- weave test failures on windows: those are known, and are being revised.
- weave test failure with gcc 4.3 (std::labs): this is a gcc 4.3 bug. A workaround is to add #include <cstdlib> in scipy/weave/blitz/blitz/funcs.h (line 27). You can make the change in the installed scipy (in site-packages).