SciPy 1.4.0
SciPy 1.4.0 Release Notes
SciPy 1.4.0
is the culmination of 6 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. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with python -Wd
and check for DeprecationWarning
s).
Our development attention will now shift to bug-fix releases on the
1.4.x branch, and on adding new features on the master branch.
This release requires Python 3.5+
and NumPy >=1.13.3
(for Python 3.5
, 3.6
),
>=1.14.5
(for Python 3.7
), >= 1.17.3
(for Python 3.8
)
For running on PyPy, PyPy3 6.0+
and NumPy 1.15.0
are required.
Highlights of this release
- a new submodule,
scipy.fft
, now supersedesscipy.fftpack
; this
means support forlong double
transforms, faster multi-dimensional
transforms, improved algorithm time complexity, release of the global
intepreter lock, and control over threading behavior - support for
pydata/sparse
arrays inscipy.sparse.linalg
- substantial improvement to the documentation and functionality of
severalscipy.special
functions, and some new additions - the generalized inverse Gaussian distribution has been added to
scipy.stats
- an implementation of the Edmonds-Karp algorithm in
scipy.sparse.csgraph.maximum_flow
scipy.spatial.SphericalVoronoi
now supports n-dimensional input,
has linear memory complexity, improved performance, and
supports single-hemisphere generators
New features
Infrastructure
Documentation can now be built with runtests.py --doc
A Dockerfile
is now available in the scipy/scipy-dev
repository to
facilitate getting started with SciPy development.
scipy.constants
improvements
scipy.constants
has been updated with the CODATA 2018 constants.
scipy.fft
added
scipy.fft
is a new submodule that supersedes the scipy.fftpack
submodule.
For the most part, this is a drop-in replacement for numpy.fft
and
scipy.fftpack
alike. With some important differences, scipy.fft
:
- uses NumPy's conventions for real transforms (
rfft
). This means the
return value is a complex array, half the size of the fullfft
output.
This is different from the output offftpack
which returned a real array
representing complex components packed together. - the inverse real to real transforms (
idct
andidst
) are normalized
fornorm=None
in thesame way asifft
. This means the identity
idct(dct(x)) == x
is nowTrue
for all norm modes. - does not include the convolutions or pseudo-differential operators
fromfftpack
.
This submodule is based on the pypocketfft
library, developed by the
author of pocketfft
which was recently adopted by NumPy as well.
pypocketfft
offers a number of advantages over fortran FFTPACK
:
- support for long double (
np.longfloat
) precision transforms. - faster multi-dimensional transforms using vectorisation
- Bluestein’s algorithm removes the worst-case
O(n^2)
complexity of
FFTPACK
- the global interpreter lock (
GIL
) is released during transforms - optional multithreading of multi-dimensional transforms via the
workers
argument
Note that scipy.fftpack
has not been deprecated and will continue to be
maintained but is now considered legacy. New code is recommended to use
scipy.fft
instead, where possible.
scipy.fftpack
improvements
scipy.fftpack
now uses pypocketfft to perform its FFTs, offering the same
speed and accuracy benefits listed for scipy.fft above but without the
improved API.
scipy.integrate
improvements
The function scipy.integrate.solve_ivp
now has an args
argument.
This allows the user-defined functions passed to the function to have
additional parameters without having to create wrapper functions or
lambda expressions for them.
scipy.integrate.solve_ivp
can now return a y_events
attribute
representing the solution of the ODE at event times
New OdeSolver
is implemented --- DOP853
. This is a high-order explicit
Runge-Kutta method originally implemented in Fortran. Now we provide a pure
Python implementation usable through solve_ivp
with all its features.
scipy.integrate.quad
provides better user feedback when break points are
specified with a weighted integrand.
scipy.integrate.quad_vec
is now available for general purpose integration
of vector-valued functions
scipy.interpolate
improvements
scipy.interpolate.pade
now handles complex input data gracefully
scipy.interpolate.Rbf
can now interpolate multi-dimensional functions
scipy.io
improvements
scipy.io.wavfile.read
can now read data from a WAV
file that has a
malformed header, similar to other modern WAV
file parsers
scipy.io.FortranFile
now has an expanded set of available Exception
classes for handling poorly-formatted files
scipy.linalg
improvements
The function scipy.linalg.subspace_angles(A, B)
now gives correct
results for complex-valued matrices. Before this, the function only returned
correct values for real-valued matrices.
New boolean keyword argument check_finite
for scipy.linalg.norm
; whether
to check that the input matrix contains only finite numbers. Disabling may
give a performance gain, but may result in problems (crashes, non-termination)
if the inputs do contain infinities or NaNs.
scipy.linalg.solve_triangular
has improved performance for a C-ordered
triangular matrix
LAPACK
wrappers have been added for ?geequ
, ?geequb
, ?syequb
,
and ?heequb
Some performance improvements may be observed due to an internal optimization
in operations involving LAPACK routines via _compute_lwork
. This is
particularly true for operations on small arrays.
Block QR
wrappers are now available in scipy.linalg.lapack
scipy.ndimage
improvements
scipy.optimize
improvements
It is now possible to use linear and non-linear constraints with
scipy.optimize.differential_evolution
.
scipy.optimize.linear_sum_assignment
has been re-written in C++ to improve
performance, and now allows input costs to be infinite.
A ScalarFunction.fun_and_grad
method was added for convenient simultaneous
retrieval of a function and gradient evaluation
scipy.optimize.minimize
BFGS
method has improved performance by avoiding
duplicate evaluations in some cases
Better user feedback is provided when an objective function returns an array
instead of a scalar.
scipy.signal
improvements
Added a new function to calculate convolution using the overlap-add method,
named scipy.signal.oaconvolve
. Like scipy.signal.fftconvolve
, this
function supports specifying dimensions along which to do the convolution.
scipy.signal.cwt
now supports complex wavelets.
The implementation of choose_conv_method
has been updated to reflect the
new FFT implementation. In addition, the performance has been significantly
improved (with rather drastic improvements in edge cases).
The function upfirdn
now has a mode
keyword argument that can be used
to select the signal extension mode used at the signal boundaries. These modes
are also available for use in resample_poly
via a newly added padtype
argument.
scipy.signal.sosfilt
now benefits from Cython code for improved performance
scipy.signal.resample
should be more efficient by leveraging rfft
when
possible
scipy.sparse
improvements
It is now possible to use the LOBPCG method in scipy.sparse.linalg.svds
.
scipy.sparse.linalg.LinearOperator
now supports the operation rmatmat
for adjoint matrix-matrix multiplication, in addition to rmatvec
.
Multiple stability updates enable float32 support in the LOBPCG eigenvalue
solver for symmetric and Hermitian eigenvalues problems in
scipy.sparse.linalg.lobpcg
.
A solver for the maximum flow problem has been added as
scipy.sparse.csgraph.maximum_flow
.
scipy.sparse.csgraph.maximum_bipartite_matching
now allows non-square inputs,
no longer requires a perfect matching to exist, and has improved performance.
scipy.sparse.lil_matrix
conversions now perform better in some scenarios
Basic support is available for pydata/sparse
arrays in
scipy.sparse.linalg
scipy.sparse.linalg.spsolve_triangular
now supports the unit_diagonal
argument to improve call signature similarity with its dense counterpart,
scipy.linalg.solve_triangular
assertAlmostEqual
may now be used with sparse matrices, which have added
support for __round__
scipy.spatial
improvements
The bundled Qhull library was upgraded to version 2019.1, fixing several
issues. Scipy-specific patches are no longer applied to it.
scipy.spatial.SphericalVoronoi
now has linear memory complexity, improved
performance, and supports single-hemisphere generators. Support has also been
added for handling generators that lie on a great circle arc (geodesic input)
and for generators in n-dimensions.
scipy.spatial.transform.Rotation
now includes functions for calculation of a
mean rotation, generation of the 3D rotation groups, and reduction of rotations
with rotational symmetries.
scipy.spatial.transform.Slerp
is now callable with a scalar argument
scipy.spatial.voronoi_plot_2d
now supports furthest site Voronoi diagrams
scipy.spatial.Delaunay
and scipy.spatial.Voronoi
now have attributes
for tracking whether they are furthest site diagrams
scipy.special
improvements
The Voigt profile has been added as scipy.special.voigt_profile
.
A real dispatch has been added for the Wright Omega function
(scipy.special.wrightomega
).
The analytic continuation of the Riemann zeta function has been added. (The
Riemann zeta function is the one-argument variant of scipy.special.zeta
.)
The complete elliptic integral of the first kind (scipy.special.ellipk
) is
now available in scipy.special.cython_special
.
The accuracy of scipy.special.hyp1f1
for real arguments has been improved.
The documentation of many functions has been improved.
scipy.stats
improvements
scipy.stats.multiscale_graphcorr
added as an independence test that
operates on high dimensional and nonlinear data sets. It has higher statistical
power than other scipy.stats
tests while being the only one that operates on
multivariate data.
The generalized inverse Gaussian distribution (scipy.stats.geninvgauss
) has
been added.
It is now possible to efficiently reuse scipy.stats.binned_statistic_dd
with new values by providing the result of a previous call to the function.
scipy.stats.hmean
now handles input with zeros more gracefully.
The beta-binomial distribution is now available in scipy.stats.betabinom
.
scipy.stats.zscore
, scipy.stats.circmean
, scipy.stats.circstd
, and
scipy.stats.circvar
now support the nan_policy
argument for enhanced
handling of NaN
values
scipy.stats.entropy
now accepts an axis
argument
scipy.stats.gaussian_kde.resample
now accepts a seed
argument to empower
reproducibility
scipy.stats.kendalltau
performance has improved, especially for large inputs,
due to improved cache usage
scipy.stats.truncnorm
distribution has been rewritten to support much wider
tails
Deprecated features
scipy
deprecations
Support for NumPy functions exposed via the root SciPy namespace is deprecated
and will be removed in 2.0.0. For example, if you use scipy.rand
or
scipy.diag
, you should change your code to directly use
numpy.random.default_rng
or numpy.diag
, respectively.
They remain available in the currently continuing Scipy 1.x release series.
The exception to this rule is using scipy.fft
as a function --
:mod:scipy.fft
is now meant to be used only as a module, so the ability to
call scipy.fft(...)
will be removed in SciPy 1.5.0.
In scipy.spatial.Rotation
methods from_dcm
, as_dcm
were renamed to
from_matrix
, as_matrix
respectively. The old names will be removed in
SciPy 1.6.0.
Method Rotation.match_vectors
was deprecated in favor of
Rotation.align_vectors
, which provides a more logical and
general API to the same functionality. The old method
will be removed in SciPy 1.6.0.
Backwards incompatible changes
scipy.special
changes
The deprecated functions hyp2f0
, hyp1f2
, and hyp3f0
have been
removed.
The deprecated function bessel_diff_formula
has been removed.
The function i0
is no longer registered with numpy.dual
, so that
numpy.dual.i0
will unconditionally refer to the NumPy version regardless
of whether scipy.special
is imported.
The function expn
has been changed to return nan
outside of its
domain of definition (x, n < 0
) instead of inf
.
scipy.sparse
changes
Sparse matrix reshape now raises an error if shape is not two-dimensional,
rather than guessing what was meant. The behavior is now the same as before
SciPy 1.1.0.
CSR
and CSC
sparse matrix classes should now return empty matrices
of the same type when indexed out of bounds. Previously, for some versions
of SciPy, this would raise an IndexError
. The change is largely motivated
by greater consistency with ndarray
and numpy.matrix
semantics.
scipy.signal
changes
scipy.signal.resample
behavior for length-1 signal inputs has been
fixed to output a constant (DC) value rather than an impulse, consistent with
the assumption of signal periodicity in the FFT method.
scipy.signal.cwt
now performs complex conjugation and time-reversal of
wavelet data, which is a backwards-incompatible bugfix for
time-asymmetric wavelets.
scipy.stats
changes
scipy.stats.loguniform
added with better documentation as (an alias for
scipy.stats.reciprocal
). loguniform
generates random variables
that are equally likely in the log space; e.g., 1
, 10
and 100
are all equally likely if loguniform(10 ** 0, 10 ** 2).rvs()
is used.
Other changes
The LSODA
method of scipy.integrate.solve_ivp
now correctly detects stiff
problems.
scipy.spatial.cKDTree
now accepts and correctly handles empty input data
scipy.stats.binned_statistic_dd
now calculates the standard deviation
statistic in a numerically stable way.
scipy.stats.binned_statistic_dd
now throws an error if the input data
contains either np.nan
or np.inf
. Similarly, in scipy.stats
now all
continuous distributions' .fit()
methods throw an error if the input data
contain any instance of either np.nan
or np.inf
.
Authors
- @endolith
- @wenhui-prudencemed +
- Abhinav +
- Anne Archibald
- ashwinpathak20nov1996 +
- Danilo Augusto +
- Nelson Auner +
- aypiggott +
- Christoph Baumgarten
- Peter Bell
- Sebastian Berg
- Arman Bilge +
- Benedikt Boecking +
- Christoph Boeddeker +
- Daniel Bunting
- Evgeni Burovski
- Angeline Burrell +
- Angeline G. Burrell +
- CJ Carey
- Carlos Ramos Carreño +
- Mak Sze Chun +
- Malayaja Chutani +
- Christian Clauss +
- Jonathan Conroy +
- Stephen P Cook +
- Dylan Cutler +
- Anirudh Dagar +
- Aidan Dang +
- dankleeman +
- Brandon David +
- Tyler Dawson +
- Dieter Werthmüller
- Joe Driscoll +
- Jakub Dyczek +
- Dávid Bodnár
- Fletcher Easton +
- Stefan Endres
- etienne +
- Johann Faouzi
- Yu Feng
- Isuru Fernando +
- Matthew H Flamm
- Martin Gauch +
- Gabriel Gerlero +
- Ralf Gommers
- Chris Gorgolewski +
- Domen Gorjup +
- Edouard Goudenhoofdt +
- Jan Gwinner +
- Maja Gwozdz +
- Matt Haberland
- hadshirt +
- Pierre Haessig +
- David Hagen
- Charles Harris
- Gina Helfrich +
- Alex Henrie +
- Francisco J. Hernandez Heras +
- Andreas Hilboll
- Lindsey Hiltner
- Thomas Hisch
- Min ho Kim +
- Gert-Ludwig Ingold
- jakobjakobson13 +
- Todd Jennings
- He Jia
- Muhammad Firmansyah Kasim +
- Andrew Knyazev +
- Holger Kohr +
- Mateusz Konieczny +
- Krzysztof Pióro +
- Philipp Lang +
- Peter Mahler Larsen +
- Eric Larson
- Antony Lee
- Gregory R. Lee
- Chelsea Liu +
- Jesse Livezey
- Peter Lysakovski +
- Jason Manley +
- Michael Marien +
- Nikolay Mayorov
- G. D. McBain +
- Sam McCormack +
- Melissa Weber Mendonça +
- Kevin Michel +
- mikeWShef +
- Sturla Molden
- Eric Moore
- Peyton Murray +
- Andrew Nelson
- Clement Ng +
- Juan Nunez-Iglesias
- Renee Otten +
- Kellie Ottoboni +
- Ayappan P
- Sambit Panda +
- Tapasweni Pathak +
- Oleksandr Pavlyk
- Fabian Pedregosa
- Petar Mlinarić
- Matti Picus
- Marcel Plch +
- Christoph Pohl +
- Ilhan Polat
- Siddhesh Poyarekar +
- Ioannis Prapas +
- James Alan Preiss +
- Yisheng Qiu +
- Eric Quintero
- Bharat Raghunathan +
- Tyler Reddy
- Joscha Reimer
- Antonio Horta Ribeiro
- Lucas Roberts
- rtshort +
- Josua Sassen
- Kevin Sheppard
- Scott Sievert
- Leo Singer
- Kai Striega
- Søren Fuglede Jørgensen
- tborisow +
- Étienne Tremblay +
- tuxcell +
- Miguel de Val-Borro
- Andrew Valentine +
- Hugo van Kemenade
- Paul van Mulbregt
- Sebastiano Vigna
- Pauli Virtanen
- Dany Vohl +
- Ben Walsh +
- Huize Wang +
- Warren Weckesser
- Anreas Weh +
- Joseph Weston +
- Adrian Wijaya +
- Timothy Willard +
- Josh Wilson
- Kentaro Yamamoto +
- Dave Zbarsky +
A total of 142 people contributed to this release.
People with a "+" by their names contributed a patch for the first time.
This list of names is automatically generated, and may not be fully complete.