SciPy 1.0.0 Release Notes¶
Note
Scipy 1.0.0 is not released yet!
Contents
- SciPy 1.0.0 Release Notes
- New features
scipy.cluster
improvementsscipy.fftpack
improvementsscipy.integrate
improvementsscipy.linalg
improvementsscipy.ndimage
improvementsscipy.optimize
improvementsscipy.signal
improvementsscipy.sparse
improvementsscipy.sparse.linalg
improvementsscipy.spatial
improvementsscipy.stats
improvements
- Deprecated features
- Backwards incompatible changes
- Other changes
- Authors
- New features
SciPy 1.0.0 is the culmination of 8 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 1.0.x branch, and on adding new features on the master branch.
Some of the highlights of this release are:
- Major build improvements. Windows wheels are available on PyPI for the first time, and continuous integration has been set up on Windows and OS X in addition to Linux.
- A set of new ODE solvers and a unified interface to them
(
scipy.integrate.solve_ivp
). - Two new trust region optimizers and a new linear programming method, with
improved performance compared to what
scipy.optimize
offered previously. - Many new BLAS and LAPACK functions were wrapped. The BLAS wrappers are now complete.
This release requires Python 2.7 or 3.4+ and NumPy 1.8.2 or greater.
This is also the last release to support LAPACK 3.1.x - 3.3.x. Moving the lowest supported LAPACK version to >3.2.x was long blocked by Apple Accelerate providing the LAPACK 3.2.1 API. We have decided that it’s time to either drop Accelerate or, if there is enough interest, provide shims for functions added in more recent LAPACK versions so it can still be used.
New features¶
scipy.cluster
improvements¶
scipy.cluster.hierarchy.optimal_leaf_ordering
, a function to reorder a
linkage matrix to minimize distances between adjacent leaves, was added.
scipy.fftpack
improvements¶
N-dimensional versions of the discrete sine and cosine transforms and their
inverses were added as dctn
, idctn
, dstn
and idstn
.
scipy.integrate
improvements¶
A set of new ODE solvers have been added to scipy.integrate
. The convenience
function scipy.integrate.solve_ivp
allows uniform access to all solvers.
The individual solvers (RK23
, RK45
, Radau
, BDF
and LSODA
)
can also be used directly.
scipy.linalg
improvements¶
The BLAS wrappers in scipy.linalg.blas
have been completed. Added functions
are *gbmv
, *hbmv
, *hpmv
, *hpr
, *hpr2
, *spmv
, *spr
,
*tbmv
, *tbsv
, *tpmv
, *tpsv
, *trsm
, *trsv
, *sbmv
,
*spr2
,
Wrappers for the LAPACK functions *gels
, *stev
, *sytrd
, *hetrd
,
*sytf2
, *hetrf
, *sytrf
, *sycon
, *hecon
, *gglse
,
*stebz
, *stemr
, *sterf
, and *stein
have been added.
The function scipy.linalg.subspace_angles
has been added to compute the
subspace angles between two matrices.
The function scipy.linalg.clarkson_woodruff_transform
has been added.
It finds low-rank matrix approximation via the Clarkson-Woodruff Transform.
The functions scipy.linalg.eigh_tridiagonal
and
scipy.linalg.eigvalsh_tridiagonal
, which find the eigenvalues and
eigenvectors of tridiagonal hermitian/symmetric matrices, were added.
scipy.ndimage
improvements¶
Support for homogeneous coordinate transforms has been added to
scipy.ndimage.affine_transform
.
The ndimage
C code underwent a significant refactoring, and is now
a lot easier to understand and maintain.
scipy.optimize
improvements¶
The methods trust-region-exact
and trust-krylov
have been added to the
function scipy.optimize.minimize
. These new trust-region methods solve the
subproblem with higher accuracy at the cost of more Hessian factorizations
(compared to dogleg) or more matrix vector products (compared to ncg) but
usually require less nonlinear iterations and are able to deal with indefinite
Hessians. They seem very competitive against the other Newton methods
implemented in scipy.
scipy.optimize.linprog
gained an interior point method. Its performance is
superior (both in accuracy and speed) to the older simplex method.
scipy.signal
improvements¶
An argument fs
(sampling frequency) was added to the following functions:
firwin
, firwin2
, firls
, and remez
. This makes these functions
consistent with many other functions in scipy.signal
in which the sampling
frequency can be specified.
scipy.signal.freqz
has been sped up significantly for FIR filters.
scipy.sparse
improvements¶
Iterating over and slicing of CSC and CSR matrices is now faster by up to ~35%.
The tocsr
method of COO matrices is now several times faster.
The diagonal
method of sparse matrices now takes a parameter, indicating
which diagonal to return.
scipy.sparse.linalg
improvements¶
A new iterative solver for large-scale nonsymmetric sparse linear systems,
scipy.sparse.linalg.gcrotmk
, was added. It implements GCROT(m,k)
, a
flexible variant of GCROT
.
scipy.sparse.linalg.lsmr
now accepts an initial guess, yielding potentially
faster convergence.
SuperLU was updated to version 5.2.1.
scipy.spatial
improvements¶
Many distance metrics in scipy.spatial.distance
gained support for weights.
The signatures of scipy.spatial.distance.pdist
and
scipy.spatial.distance.cdist
were changed to *args, **kwargs
in order to
support a wider range of metrics (e.g. string-based metrics that need extra
keywords). Also, an optional out
parameter was added to pdist
and
cdist
allowing the user to specify where the resulting distance matrix is
to be stored
scipy.stats
improvements¶
The methods cdf
and logcdf
were added to
scipy.stats.multivariate_normal
, providing the cumulative distribution
function of the multivariate normal distribution.
New statistical distance functions were added, namely
scipy.stats.wasserstein_distance
for the first Wasserstein distance and
scipy.stats.energy_distance
for the energy distance.
Deprecated features¶
The following functions in scipy.misc
are deprecated: bytescale
,
fromimage
, imfilter
, imread
, imresize
, imrotate
,
imsave
, imshow
and toimage
. Most of those functions have unexpected
behavior (like rescaling and type casting image data without the user asking
for that). Other functions simply have better alternatives.
scipy.interpolate.interpolate_wrapper
and all functions in that submodule
are deprecated. This was a never finished set of wrapper functions which is
not relevant anymore.
The fillvalue
of scipy.signal.convolve2d
will be cast directly to the
dtypes of the input arrays in the future and checked that it is a scalar or
an array with a single element.
Backwards incompatible changes¶
The following deprecated functions have been removed from scipy.stats
:
betai
, chisqprob
, f_value
, histogram
, histogram2
,
pdf_fromgamma
, signaltonoise
, square_of_sums
, ss
and
threshold
.
The following deprecated functions have been removed from scipy.stats.mstats
:
betai
, f_value_wilks_lambda
, signaltonoise
and threshold
.
The deprecated a
and reta
keywords have been removed from
scipy.stats.shapiro
.
The deprecated functions sparse.csgraph.cs_graph_components
and
sparse.linalg.symeig
have been removed from scipy.sparse
.
The following deprecated keywords have been removed in scipy.sparse.linalg
:
drop_tol
from splu
, and xtype
from bicg
, bicgstab
, cg
,
cgs
, gmres
, qmr
and minres
.
The deprecated functions expm2
and expm3
have been removed from
scipy.linalg
. The deprecated keyword q
was removed from
scipy.linalg.expm
. And the deprecated submodule linalg.calc_lwork
was
removed.
The deprecated functions C2K
, K2C
, F2C
, C2F
, F2K
and
K2F
have been removed from scipy.constants
.
The deprecated ppform
class was removed from scipy.interpolate
.
The deprecated keyword iprint
was removed from scipy.optimize.fmin_cobyla
.
The default value for the zero_phase
keyword of scipy.signal.decimate
has been changed to True.
The kmeans
and kmeans2
functions in scipy.cluster.vq
changed the
method used for random initialization, so using a fixed random seed will
not necessarily produce the same results as in previous versions.
scipy.special.gammaln
does not accept complex arguments anymore.
The deprecated functions sph_jn
, sph_yn
, sph_jnyn
, sph_in
,
sph_kn
, and sph_inkn
have been removed. Users should instead use
the functions spherical_jn
, spherical_yn
, spherical_in
, and
spherical_kn
. Be aware that the new functions have different
signatures.
The cross-class properties of scipy.signal.lti
systems have been removed.
The following properties/setters have been removed:
Name - (accessing/setting has been removed) - (setting has been removed)
- StateSpace - (
num
,den
,gain
) - (zeros
,poles
) - TransferFunction (
A
,B
,C
,D
,gain
) - (zeros
,poles
) - ZerosPolesGain (
A
,B
,C
,D
,num
,den
) - ()
signal.freqz(b, a)
with b
or a
>1-D raises a ValueError
. This
was a corner case for which it was unclear that the behavior was well-defined.
The method var
of scipy.stats.dirichlet
now returns a scalar rather than
an ndarray when the length of alpha is 1.
Other changes¶
SciPy now has a formal governance structure. It consists of a BDFL (Pauli Virtanen) and a Steering Committee. See the governance document for details.
It is now possible to build SciPy on Windows with MSVC + gfortran! Continuous integration has been set up for this build configuration on Appveyor, building against OpenBLAS.
Continuous integration for OS X has been set up on TravisCI.
The SciPy test suite has been migrated from nose
to pytest
.
scipy/_distributor_init.py
was added to allow redistributors of SciPy to
add custom code that needs to run when importing SciPy (e.g. checks for
hardware, DLL search paths, etc.).
Support for PEP 518 (specifying build system requirements) was added - see
pyproject.toml
in the root of the SciPy repository.
In order to have consistent function names, the function
scipy.linalg.solve_lyapunov
is renamed to
scipy.linalg.solve_continuous_lyapunov
. The old name is kept for
backwards-compatibility.
Authors¶
- @arcady +
- @xoviat +
- Anton Akhmerov
- Dominic Antonacci +
- Alessandro Pietro Bardelli
- Ved Basu +
- Michael James Bedford +
- Ray Bell +
- Juan M. Bello-Rivas +
- Sebastian Berg
- Felix Berkenkamp
- Jyotirmoy Bhattacharya +
- Matthew Brett
- Jonathan Bright
- Bruno Jiménez +
- Evgeni Burovski
- Patrick Callier
- Mark Campanelli +
- CJ Carey
- Adam Cox +
- Michael Danilov +
- David Haberthür +
- Andras Deak +
- Philip DeBoer
- Anne-Sylvie Deutsch
- Cathy Douglass +
- Dominic Else +
- Guo Fei +
- Roman Feldbauer +
- Yu Feng
- Jaime Fernandez del Rio
- Orestis Floros +
- David Freese +
- Adam Geitgey +
- James Gerity +
- Dezmond Goff +
- Christoph Gohlke
- Ralf Gommers
- Dirk Gorissen +
- Matt Haberland +
- David Hagen +
- Charles Harris
- Lam Yuen Hei +
- Jean Helie +
- Gaute Hope +
- Guillaume Horel +
- Franziska Horn +
- Yevhenii Hyzyla +
- Vladislav Iakovlev +
- Marvin Kastner +
- Mher Kazandjian
- Thomas Keck
- Adam Kurkiewicz +
- Ronan Lamy +
- J.L. Lanfranchi +
- Eric Larson
- Denis Laxalde
- Gregory R. Lee
- Felix Lenders +
- Evan Limanto
- Julian Lukwata +
- François Magimel
- Syrtis Major +
- Charles Masson +
- Nikolay Mayorov
- Tobias Megies
- Markus Meister +
- Roman Mirochnik +
- Jordi Montes +
- Nathan Musoke +
- Andrew Nelson
- M.J. Nichol
- Nico Schlömer +
- Juan Nunez-Iglesias
- Arno Onken +
- Dima Pasechnik +
- Ashwin Pathak +
- Stefan Peterson
- Ilhan Polat
- Andrey Portnoy +
- Ravi Kumar Prasad +
- Aman Pratik
- Eric Quintero
- Vedant Rathore +
- Tyler Reddy
- Joscha Reimer
- Philipp Rentzsch +
- Antonio Horta Ribeiro
- Ned Richards +
- Kevin Rose +
- Benoit Rostykus +
- Matt Ruffalo +
- Eli Sadoff +
- Pim Schellart
- Klaus Sembritzki +
- Nikolay Shebanov +
- Jonathan Tammo Siebert
- Scott Sievert
- Max Silbiger +
- Mandeep Singh +
- Michael Stewart +
- Jonathan Sutton +
- Deep Tavker +
- Martin Thoma
- James Tocknell +
- Aleksandar Trifunovic +
- Paul van Mulbregt +
- Jacob Vanderplas
- Aditya Vijaykumar
- Pauli Virtanen
- James Webber
- Warren Weckesser
- Eric Wieser +
- Josh Wilson
- Zhiqing Xiao +
- Evgeny Zhurko
- Nikolay Zinov +
- Zé Vinícius +
A total of 118 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.
Issues closed for 1.0.0¶
- #2300: scipy.misc.toimage (and therefore imresize) converts to uint32…
- #2347: Several
misc.im*
functions incorrectly handle 3 or 4-channeled… - #2442: scipy.misc.pilutil -> scipy.ndimage?
- #2829: Mingw Gfortran on Windows?
- #3154: scipy.misc.imsave creates wrong bitmap header
- #3505: scipy.linalg.lstsq() residual’s help text is a lil strange
- #3808: Is Brent’s method for minimizing the value of a function implemented…
- #4121: Add cdf() method to stats.multivariate_normal
- #4458: scipy.misc.imresize changes image range
- #4575: Docs for L-BFGS-B mention non-existent parameter
- #4893: misc.imsave does not work with file type defined
- #5231: Discrepancies in scipy.optimize.minimize(method=’L-BFGS-B’)
- #5238: Optimal leaf ordering in scipy.cluster.hierarchy.dendrogram
- #5305: Wrong image scaling in scipy/misc/pilutil.py with misc.imsave?
- #5823: test failure in
filter_design
- #6061: scipy.stats.spearmanr return values outside range -1 to 1
- #6242: Inconsistency / duplication for imread and imshow, imsave
- #6265: BUG: signal.iirfilter of bandpass type is unstable when high…
- #6370:
scipy.optimize.linear_sum_assignment
hangs on undefined matrix - #6417: scipy.misc.imresize converts images to uint8
- #6618: splrep and splprep inconsistent
- #6854: Support PEP 519 in I/O functions
- #6921: [Feature request] Random unitary matrix
- #6930:
uniform_filter1d
appears to truncate rather than round when output… - #6949: interp2d function crashes python
- #6959: scipy.interpolate.LSQUnivariateSpline - check for increasing…
- #7005: linear_sum_assignment in scipy.optimize never return if one of…
- #7010:
scipy.statsbinned_statistic_2d
: incorrect binnumbers returned - #7049:
expm_multiply
is excessively slow when called for intervals - #7050: Documenting
_argcheck
forrv_discrete
- #7077:
coo_matrix.tocsr()
still slow - #7093: Wheels licensing
- #7122: Sketching-based Matrix Computations
- #7133: Discontinuity of a scipy special function
- #7141: Improve documentation for Elliptic Integrals
- #7181: A change in
numpy.poly1d
is causing the scipy tests to fail. - #7220: String Formatting Issue in
LinearOperator.__init__
- #7239: Source tarball distribution
- #7247: genlaguerre poly1d-object doesn’t respect ‘monic’ option at evaluation
- #7248: BUG: regression in Legendre polynomials on master
- #7316: dgels is missing
- #7381: Krogh interpolation fails to produce derivatives for complex…
- #7416: scipy.stats.kappa4(h,k) raise a ValueError for positive integer…
- #7421: scipy.stats.arcsine().pdf and scipy.stats.beta(0.5, 0.5).pdf…
- #7429:
test_matrix_norms()
in scipy/linalg/tests/test_basic.py calls… - #7444: Doc: stats.dirichlet.var output description is wrong
- #7475: Parameter amax in
scalar_search_wolfe2
is not used - #7510: Operations between numpy.array and scipy.sparse matrix return…
- #7550: DOC: signal tutorial: Typo in explanation of convolution
- #7551: stdint.h included in SuperLU header files, but does not exist…
- #7553: Build for master broken on OS X
- #7557: Error in scipy.signal.periodogram example
- #7590: OSX test fail -
test_ltisys.TestPlacePoles.test_real
- #7658: optimize.BenchGlobal broken
- #7669: nan result from multivariate_normal.cdf
- #7733: Inconsistent usage of indices, indptr in
Delaunay.vertex_neighbor_vertices
- #7747: Numpy changes in np.random.dirichlet cause test failures
- #7772: Fix numpy lstsq rcond= parameter
- #7776: tests require nose
- #7798: contributor names for 1.0 release notes
- #7828: 32-bit Linux test errors on TestCephes
Pull requests for 1.0.0¶
- #4978: WIP: add pre_center and normalize options to lombscargle
- #5796: TST: Remove all permanent filter changes from tests
- #5910: ENH: sparse.linalg: add GCROT(m,k)
- #6326: ENH: New ODE solvers
- #6480: ENH: Make signal.decimate default to
zero_phase=True
- #6705: ENH: add initial guess to sparse.linalg.lsqr
- #6706: ENH: add initial guess to sparse.linalg.lsmr
- #6769: BUG: optimize: add sufficient descent condition check to CG line…
- #6855: Handle objects supporting PEP 519 in I/O functions
- #6945: MAINT: ckdtree codebase clean up
- #6953: DOC: add a SciPy Project Governance document
- #6998: fix documentation of spearman rank corrcoef
- #7017: ENH: add methods logcdf and cdf to
scipy.stats.multivariate_normal
- #7027: Add random unitary matrices
- #7030: ENH: Add strictly-increasing checks for x to 1D splines
- #7031: BUG: Fix
linear_sum_assignment
hanging on an undefined matrix - #7041: DOC: Clairfy that windows are DFT-even by default
- #7048: DOC: modified docs for
find_peak_cwt
. Fixes #6922 - #7056: Fix insufficient precision when calculating spearman/kendall…
- #7057: MAINT: change dtype comparison in
optimize.linear_sum_assignment
. - #7059: TST: make
Xdist_deprecated_args
cover all metrics - #7061: Fix msvc 9 and 10 compile errors
- #7070: ENH: sparse: optimizing CSR/CSC slicing fast paths
- #7078: ENH: sparse: defer
sum_duplicates
to csr/csc - #7079: ENH: sparse: allow subclasses to override specific math operations
- #7081: ENH: sparse: speed up CSR/CSC toarray()
- #7082: MAINT: Add missing
PyType_Ready(&SuperLUGlobalType)
for Py3 - #7083: Corrected typo in the doc of scipy.linalg.lstsq()
- #7086: Fix bug #7049 causing excessive slowness in
expm_multiply
- #7088: Documented
_argcheck
forrv_discrete
- #7094: MAINT: Fix mistake in PR #7082
- #7098: BF: return NULL from failed Py3 module check
- #7105: MAINT: Customize ?TRSYL call in lyapunov solver
- #7111: Fix error message typo in UnivariateSpline
- #7113: FIX: Add add float to return type in documentation
- #7119: ENH: sparse.linalg: remove
_count_nonzero
hack - #7123: ENH: added “interior-point” method for
scipy.optimize.linprog
- #7137: DOC: clarify stats.linregress docstring, closes gh-7074
- #7138: DOC: special: Add an example to the airy docstring.
- #7139: DOC: stats: Update stats tutorial
- #7142: BUG: special: prevent segfault in
pbwa
- #7143: DOC: special: warn about alternate elliptic integral parameterizations
- #7146: fix docstring of NearestNDInterpolator
- #7148: DOC: special: Add Parameters, Returns and Examples to gamma docstring
- #7152: MAINT: spatial: Remove two unused variables in ckdtree/src/distance.h
- #7153: MAINT: special: remove deprecated variant of
gammaln
- #7154: MAINT: Fix some code that generates C compiler warnings
- #7155: DOC: linalg: Add examples for
solve_banded
andsolve_triangular
- #7156: DOC: fix docstring of NearestNDInterpolator
- #7159: BUG: special: fix sign of derivative when
x < 0
inpbwa
- #7161: MAINT: interpolate: make Rbf.A array a property
- #7163: MAINT: special: return nan for inaccurate regions of
pbwa
- #7165: ENH: optimize: changes to make BFGS implementation more efficient.
- #7166: BUG: Prevent infinite loop in
optimize._lsq.trf_linear.py
- #7173: BUG: sparse: return a numpy matrix from
_add_dense
- #7179: DOC: Fix an error in sparse argmax docstring
- #7180: MAINT: interpolate: A bit of clean up in
interpolate/src/_interpolate.cpp
- #7182: Allow homogeneous coordinate transforms in
affine_transform
- #7184: MAINT: Remove hack modifying a readonly attr
- #7185: ENH: Add evaluation of periodic splines #6730
- #7186: MAINT: PPoly: improve error messages for wrong shape/axis
- #7187: DEP: interpolate: deprecate interpolate_wrapper
- #7198: DOC: linalg: Add examples for
solveh_banded
andsolve_toeplitz
. - #7200: DOC: stats: Added tutorial documentation for the generalized…
- #7208: DOC: Added docstrings to
issparse/isspmatrix(_...)
methods and… - #7213: DOC: Added examples to circmean, circvar, circstd
- #7215: DOC: Adding examples to scipy.sparse.linalg…. docstrings
- #7223: DOC: special: Add examples for expit and logit.
- #7224: BUG: interpolate: fix integer overflow in fitpack.bispev
- #7225: DOC: update 1.0 release notes for several recent PRs.
- #7226: MAINT: update docs and code for mailing list move to python.org
- #7233: Fix issue #7232: Do not mask exceptions in objective func evaluation
- #7234: MAINT: cluster: cleaning up VQ/k-means code
- #7236: DOC: Fixed typo
- #7238: BUG: fix syntaxerror due to unicode character in
trustregion_exact
. - #7243: DOC: Update docstring in misc/pilutil.py
- #7246: DEP: misc: deprecate imported names
- #7249: DOC: Add plotted example to scipy.cluster.vq.kmeans
- #7252: Fix 5231: docs of factr, ftol in sync w/ code
- #7254: ENH: SphericalVoronoi Input Handling
- #7256: fix for issue #7255 - Circular statistics functions give wrong…
- #7263: CI: use python’s faulthandler to ease tracing segfaults
- #7288: ENH: linalg: add
subspace_angles
function. - #7290: BUG: stats: Fix spurious warnings in genextreme.
- #7292: ENH: optimize: added trust region method trust-trlib
- #7296: DOC: stats: Add an example to the
ttest_ind_from_stats
docstring. - #7297: DOC: signal: Add examples for
chirp()
andsweep_poly()
. - #7299: DOC: Made difference between brent and fminbound clearer
- #7305: Simplify if-statements and constructor calls in
integrate._ode
- #7309: Comply with PEP 518.
- #7313: REL: add
python_requires
to setup.py, fix Python version check. - #7315: BUG: Fixed bug with Laguerre and Legendre polynomials
- #7320: DOC: clarify meaning of flags in ode.integrate
- #7333: DOC: Add examples to
scipy.ndimage.gaussian_filter1d
- #7337: ENH: add n-dimensional DCT and IDCT to fftpack
- #7353: Add
_gels
functions - #7357: DOC: linalg: Add examples to the svdvals docstring.
- #7359: Bump Sphinx version to 1.5.5
- #7361: DOC: linalg: Add some ‘See Also’ links among special matrices…
- #7362: TST: Fix some Fedora 25 test failures.
- #7363: DOC: linalg: tweak the docstring example of svd
- #7365: MAINT: fix
refguide_check.py
for Sphinx >= 1.5 - #7367: BUG: odrpack: fix invalid stride checks in
d_lpkbls.f
- #7368: DOC: constants: Add examples to the ‘find’ docstring.
- #7376: MAINT: bundle Mathjax with built docs
- #7377: MAINT: optimize: Better name for trust-region-exact method.
- #7378: Improve wording in tutorial
- #7383: fix KroghInterpolator.derivatives failure with complex input
- #7389: FIX: Copy mutable window in
resample_poly
- #7390: DOC: optimize: A few tweaks of the examples in the
curve_fit
- #7391: DOC: Add examples to scipy.stats
- #7394: “Weight” is actually mass. Add slugs and slinches/blobs to mass
- #7398: DOC: Correct minor typo in optimize.{brenth,brentq}
- #7401: DOC: zeta only accepts real input
- #7413: BUG: fix error messages in
_minimize_trustregion_exact
- #7414: DOC: fix
ndimage.distance_transform_bf
docstring [ci skip] - #7415: DOC: fix skew docstring [ci skip]
- #7423: Expand binnumbers with correct dimensions
- #7431: BUG: Extend scipy.stats.arcsine.pdf to endpoints 0 and 1 #7427
- #7432: DOC: Add examples to scipy.cluster.hierarchy
- #7448: ENH: stats: Implement the survival function for pareto.
- #7454: FIX Replaced
np.assert_allclose
with importedassert_allclose
- #7460: TST: fix integrate.ivp test that fails on 32-bit Python.
- #7461: Doc: Added tutorial documentation for stats distributions ksone
- #7463: DOC: Fix typos and remove trailing whitespace
- #7465: Fix some ndimage.interpolation endianness bugs
- #7468: del redundance in interpolate.py
- #7470: Initialize “info” in
minpack_lmdif
- #7478: Added more testing of smirnov/smirnovi functions
- #7479: MAINT: update for new FutureWarning’s in numpy 1.13.0
- #7480: DOC: correctly describe output shape of dirichlet.mean() and…
- #7482: signal.lti: Remove deprecated cross-system properties
- #7484: MAINT: Clean-up uses of np.asarray in ndimage
- #7485: ENH: support any order >=0 in
ndimage.gaussian_filter
- #7486: ENH: Support k!=0 for sparse.diagonal()
- #7498: BUG: sparse: pass assumeSortedIndices option to scikit.umfpack
- #7501: ENH: add optimal leaf ordering for linkage matrices
- #7506: MAINT: remove overflow in Metropolis fixes #7495
- #7507: TST: speed up full test suite by less eval points in mpmath tests.
- #7509: BUG: fix issue when using
python setup.py somecommand --force
. - #7511: fix some alerts found with lgtm
- #7514: Add explanation what the integer returned mean.
- #7516: BUG: Fix roundoff errors in
ndimage.uniform_filter1d
. - #7517: TST: fix signal.convolve test that was effectively being skipped.
- #7523: ENH: linalg: allow lstsq to work with 0-shaped arrays
- #7525: TST: Warning cleanup
- #7526: DOC: params in ndimage.interpolation functions not optional
- #7527: MAINT: Encapsulate error message handling in
NI_LineBuffer
. - #7528: MAINT: Remove ndimage aliases for
NPY_MAXDIMS
. - #7529: MAINT: Remove
NI_(UN)LIKELY
macros in favor of numpy ones. - #7537: MAINT: Use accessor function for numpy array internals
- #7541: MAINT: Remove some uses of Numarray types in ndimage.
- #7543: MAINT: Replace all NumarrayTypes uses in
ni_fourier.c
- #7544: MAINT: Replace all uses of NumarrayTypes in
ni_interpolation.c
- #7545: MAINT: Replace all uses of NumarrayTypes in
ni_measure.c
- #7546: MAINT: Replace all uses of NumarrayTypes in
ni_morphology.c
- #7548: DOC: make a note in benchmarks README on how to run without rebuilding.
- #7549: MAINT: Get rid of NumarrayTypes.
- #7552: TST: Fix new warnings -> error bugs found on OSX
- #7554: Update superlu to 5.2.1 + fix stdint.h issue on MSVC
- #7556: MAINT: Fix some types from #7549 + miscellaneous warnings.
- #7558: MAINT: Use correct #define
NO_IMPORT_ARRAY
, notNO_ARRAY_IMPORT
… - #7562: BUG: Copy
import_nose
from numpy. - #7563: ENH: Add the first Wasserstein and the Cramér-von Mises statistical…
- #7568: Test janitoring
- #7571: Test janitoring pt. 2
- #7572: Pytestifying
- #7574: TST: Remove ignore warnings filters from stats
- #7577: MAINT: Remove unused code in
ndimage/ni_measure.c
and .h - #7578: TST: Remove ignore warnings filters from sparse, clean up warning…
- #7581: BUG: properly deallocate memory from
PyArray_IntpConverter
. - #7582: DOC: signal tutorial: Typo in explanation of convolution
- #7583: Remove remaining ignore warnings filters
- #7586: DOC: add note to HACKING.rst on where to find build docs.
- #7587: DOC: Add examples to scipy.optimize
- #7594: TST: Add tests for ndimage converter functions.
- #7596: Added a sanity check to
signal.savgol_filter
- #7599: _upfirdn_apply stopping condition bugfix
- #7601: MAINT: special: remove
sph_jn
et al. - #7602: TST: fix test failures in trimmed statistics tests with numpy…
- #7605: Be clear about required dimension order
- #7606: MAINT: Remove unused function
NI_NormalizeType
. - #7607: TST: add osx to travis matrix
- #7608: DOC: improve HACKING guide - mention reviewing PRs as contribution.
- #7609: MAINT: Remove unnecessary warning filter by avoding unnecessary…
- #7610: #7557 : fix example code in periodogram
- #7611: #7220 : fix TypeError while raising ValueError for invalid shape
- #7612: Convert yield tests to pytest parametrized tests
- #7613: Add distributor init file
- #7614: fixup header
- #7615: BUG: sparse: Fix assignment w/ non-canonical sparse argument
- #7617: DOC: Clarify digital filter functions
- #7619: ENH: scipy.sparse.spmatrix.astype: casting and copy parameter…
- #7621: Expose VODE/ZVODE/LSODE IDID return code to user
- #7622: MAINT: special: remove out-of-date comment for
ellpk
- #7625: TST: Add a test for “ignore” warning filters
- #7628: MAINT: refactoring and cleaning distance.py/.c/.h
- #7629: DEP: deprecate args usage in xdist
- #7630: ENH: weighted metrics
- #7634: Follow-up to #6855
- #7635: interpolate.splprep: Test some error cases, give slightly better…
- #7642: Add an example to
interpolate.lagrange
- #7643: ENH: Added wrappers for LAPACK <s,d>stev
- #7649: Fix #7636, add PEP 519 test coverage to remaining I/O functions
- #7650: DOC: signal: Add ‘Examples’ to the docstring for sosfiltfilt.
- #7651: Fix up ccache usage on Travis + try enabling on OSX
- #7653: DOC: transition of examples from 2 to 3. Closes #7366
- #7659: BENCH: fix optimize.BenchGlobal. Closes gh-7658.
- #7662: CI: speed up continuous integration builds
- #7664: Update odr documentation
- #7665: BUG: wolfe2 line/scalar search now uses amax parameter
- #7671: MAINT:
_lib/ccallback.h
: PyCapsule_GetName returns constchar*
- #7672: TST: interpolate: test integrating periodic b-splines against…
- #7674: Tests tuning
- #7675: CI: move refguide-check to faster build
- #7676: DOC: bump scipy-sphinx-theme to fix copybutton.js
- #7678: Note the zero-padding of the results of
splrep
andsplprep
- #7681: MAINT:
_lib
: add user-overridable available memory determination - #7684: TST: linalg: explicitly close opened npz files
- #7686: MAINT: remove unnecessary shebang lines and executable bits
- #7687: BUG: stats: don’t emit invalid warnings if moments are infinite
- #7690: ENH: allow int-like parameters in several routines
- #7691: DOC: Drop non-working source links from docs
- #7694: fix
ma.rray
toma.array
in funcmedian_cihs
- #7698: BUG: stats: fix nan result from
multivariate_normal.cdf
(#7669) - #7703: DOC: special: Update the docstrings for noncentral F functions.
- #7709: BLD: integrate: avoid symbol clash between lsoda and vode
- #7711: TST:
_lib
: maketest_parallel_threads
to not fail falsely - #7712: TST: stats: bump test tolerance in
TestMultivariateNormal.test_broadcasting
- #7715: MAINT: fix deprecated use of numpy.issubdtype
- #7716: TST: integrate: drop timing tests
- #7717: MAINT: mstats.winsorize inclusion bug fix
- #7719: DOC: stats: Add a note about the special cases of the rdist distribution.
- #7720: DOC: Add example and math to stats.pearsonr
- #7723: DOC: Added Mann-Whitney U statistic reference
- #7727: BUG: special/cdflib: deal with nan and nonfinite inputs
- #7728: BLD: spatial: fix ckdtree depends header list
- #7732: BLD: update Bento build for optimal_leaf_ordering addition
- #7734: DOC: signal: Copy-edit and add examples to the Kaiser-related…
- #7736: BUG: Fixes #7735: Prevent integer overflow in concatenated index…
- #7737: DOC: rename indices/indptr for
spatial.Delaunay vertex_neighbor_vertices
- #7738: ENH: Speed up freqz computation
- #7739: TST: ignore ncfdtridfn failure in win32 and warn on FPU mode changes
- #7740: Fix overflow in Anderson-Darling k-sample test
- #7742: TST: special: limit expm1 mpmath comparison range
- #7748: TST: stats: don’t pass invalid alpha to np.random.dirichlet
- #7749: BUG/DOC: optimize: method is ‘interior-point’, not ‘interior…
- #7751: BUG: optimize:
show_options('linprog', method='interior-point')
… - #7753: ENH: io: easier syntax for FortranFile read/write of mixed records
- #7754: BLD: add
_lib._fpumode
extension to Bento build. - #7756: DOC: Show probability density functions as math
- #7757: MAINT: remove outdated OS X build scripts. Fixes pytest failure.
- #7758: MAINT: stats: pep8, wrap lines
- #7760: DOC: special: add instructions on how to add special functions
- #7761: DOC: allow specifing Python version for Sphinx makefile
- #7765: TST: fix test coverage of
mstats_extras.py
- #7767: DOC: update 1.0 release notes.
- #7768: DOC: update notes on how to release. Also change paver file to…
- #7769: Add the
_sf
and_logsf
function for planck dist - #7770: DOC: Replace rotten links in the docstring of minres
- #7771: MAINT: f2py build output cleanup
- #7773: DOC: optimize: Some copy-editing of linprog docs.
- #7774: MAINT: set rcond explicitly for np.linalg.lstsq calls
- #7777: remove leftover
nose
imports - #7780: ENH: Wrap LAPACK’s dsytrd
- #7781: DOC: Link rfft
- #7782: MAINT: run pyx autogeneration in cythonize & remove autogen files
- #7783: FIX: Disallow Wn==1 in digital filters
- #7790: Fix test errors introduced by gh-5910
- #7792: MAINT: fix syntax in pyproject.toml
- #7809: ENH: sketches - Clarkson Woodruff Transform
- #7810: ENH: Add
eig(vals)_tridiagonal
- #7811: BUG: stats: Fix warnings in
binned_statistics_dd
- #7814: ENH: signal: Replace ‘nyq’ and ‘Hz’ arguments with ‘fs’.
- #7820: DOC: update 1.0 release notes and mailmap
- #7823: BUG: memory leak in messagestream / qhull.pyx
- #7830: DOC: linalg: Add an example to the lstsq docstring.
- #7835: ENH: Automatic FIR order for
decimate
- #7838: MAINT: stats: Deprecate
frechet_l
andfrechet_r
. - #7841: slsqp PEP8 formatting fixes, typos, etc.
- #7843: ENH: Wrap all BLAS routines
- #7844: DOC: update LICENSE.txt with licenses of bundled libs as needed.
- #7851: ENH: Add wrappers for ?GGLSE, ?(HE/SY)CON, ?SYTF2, ?(HE/SY)TRF
- #7856: ENH: added out argument to Xdist
- #7858: BUG: special/cdflib: fix fatal loss of precision issues in cumfnc
- #7859: FIX: Squash
place_poles
warning corner case - #7861: dummy statement for undefined
WITH_THREAD
- #7863: MAINT: add license texts to binary distributions
- #7866: DOC, MAINT: fix links in the doc
- #7867: DOC: fix up descriptions of pdf’s in distribution docstrings.
- #7869: DEP: deprecate misc.pilutil functions
- #7870: DEP: remove deprecated functions
- #7872: TST: silence RuntimeWarning for stats.truncnorm test marked as…
- #7874: TST: fix an optimize.linprog test that fails intermittently.
- #7875: TST: filter two integration warnings in stats tests.