SciPy 1.0.0 Release Notes¶
Contents

scipy.cluster
improvementsscipy.fftpack
improvementsscipy.integrate
improvementsscipy.linalg
improvementsscipy.ndimage
improvementsscipy.optimize
improvementsscipy.signal
improvementsscipy.sparse
improvementsscipy.sparse.linalg
improvementsscipy.spatial
improvementsscipy.stats
improvements
We are extremely pleased to announce the release of SciPy 1.0, 16 years after version 0.1 saw the light of day. It has been a long, productive journey to get here, and we anticipate many more exciting new features and releases in the future.
Why 1.0 now?¶
A version number should reflect the maturity of a project  and SciPy was a mature and stable library that is heavily used in production settings for a long time already. From that perspective, the 1.0 version number is long overdue.
Some key project goals, both technical (e.g. Windows wheels and continuous integration) and organisational (a governance structure, code of conduct and a roadmap), have been achieved recently.
Many of us are a bit perfectionist, and therefore are reluctant to call something “1.0” because it may imply that it’s “finished” or “we are 100% happy with it”. This is normal for many open source projects, however that doesn’t make it right. We acknowledge to ourselves that it’s not perfect, and there are some dusty corners left (that will probably always be the case). Despite that, SciPy is extremely useful to its users, on average has high quality code and documentation, and gives the stability and backwards compatibility guarantees that a 1.0 label imply.
Some history and perspectives¶
2001: the first SciPy release
2005: transition to NumPy
2007: creation of scikits
2008: scipy.spatial module and first Cython code added
2010: moving to a 6monthly release cycle
2011: SciPy development moves to GitHub
2011: Python 3 support
2012: adding a sparse graph module and unified optimization interface
2012: removal of scipy.maxentropy
2013: continuous integration with TravisCI
2015: adding Cython interface for BLAS/LAPACK and a benchmark suite
2017: adding a unified C API with scipy.LowLevelCallable; removal of scipy.weave
2017: SciPy 1.0 release
Pauli Virtanen is SciPy’s Benevolent Dictator For Life (BDFL). He says:
Truthfully speaking, we could have released a SciPy 1.0 a long time ago, so I’m happy we do it now at long last. The project has a long history, and during the years it has matured also as a software project. I believe it has well proved its merit to warrant a version number starting with unity.
Since its conception 15+ years ago, SciPy has largely been written by and for scientists, to provide a box of basic tools that they need. Over time, the set of people active in its development has undergone some rotation, and we have evolved towards a somewhat more systematic approach to development. Regardless, this underlying drive has stayed the same, and I think it will also continue propelling the project forward in future. This is all good, since not long after 1.0 comes 1.1.
Travis Oliphant is one of SciPy’s creators. He says:
I’m honored to write a note of congratulations to the SciPy developers and the entire SciPy community for the release of SciPy 1.0. This release represents a dream of many that has been patiently pursued by a stalwart group of pioneers for nearly 2 decades. Efforts have been broad and consistent over that time from many hundreds of people. From initial discussions to efforts coding and packaging to documentation efforts to extensive conference and community building, the SciPy effort has been a global phenomenon that it has been a privilege to participate in.
The idea of SciPy was already in multiple people’s minds in 1997 when I first joined the Python community as a young graduate student who had just fallen in love with the expressibility and extensibility of Python. The internet was just starting to bringing together likeminded mathematicians and scientists in nascent electronicallyconnected communities. In 1998, there was a concerted discussion on the matrixSIG, python mailing list with people like Paul Barrett, Joe Harrington, Perry Greenfield, Paul Dubois, Konrad Hinsen, David Ascher, and others. This discussion encouraged me in 1998 and 1999 to procrastinate my PhD and spend a lot of time writing extension modules to Python that mostly wrapped battletested Fortran and Ccode making it available to the Python user. This work attracted the help of others like Robert Kern, Pearu Peterson and Eric Jones who joined their efforts with mine in 2000 so that by 2001, the first SciPy release was ready. This was long before Github simplified collaboration and input from others and the “patch” command and email was how you helped a project improve.
Since that time, hundreds of people have spent an enormous amount of time improving the SciPy library and the community surrounding this library has dramatically grown. I stopped being able to participate actively in developing the SciPy library around 2010. Fortunately, at that time, Pauli Virtanen and Ralf Gommers picked up the pace of development supported by dozens of other key contributors such as David Cournapeau, Evgeni Burovski, Josef Perktold, and Warren Weckesser. While I have only been able to admire the development of SciPy from a distance for the past 7 years, I have never lost my love of the project and the concept of communitydriven development. I remain driven even now by a desire to help sustain the development of not only the SciPy library but many other affiliated and related opensource projects. I am extremely pleased that SciPy is in the hands of a worldwide community of talented developers who will ensure that SciPy remains an example of how grassroots, communitydriven development can succeed.
Fernando Perez offers a wider community perspective:
The existence of a nascent Scipy library, and the incredible –if tiny by today’s standards– community surrounding it is what drew me into the scientific Python world while still a physics graduate student in 2001. Today, I am awed when I see these tools power everything from high school education to the research that led to the 2017 Nobel Prize in physics.
Don’t be fooled by the 1.0 number: this project is a mature cornerstone of the modern scientific computing ecosystem. I am grateful for the many who have made it possible, and hope to be able to contribute again to it in the future. My sincere congratulations to the whole team!
Highlights of this release¶
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.
Upgrading and compatibility¶
There have been a number of deprecations and API changes in this release, which
are documented below. 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).
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¶
Ndimensional 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 lowrank matrix approximation via the ClarksonWoodruff 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 trustregionexact
and trustkrylov
have been added to the
function scipy.optimize.minimize
. These new trustregion 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 largescale 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. stringbased 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.
scipy.spatial.distance.matching
is deprecated. It is an alias of
scipy.spatial.distance.hamming
, which should be used instead.
Implementation of scipy.spatial.distance.wminkowski
was based on a wrong
interpretation of the metric definition. In scipy 1.0 it has been just
deprecated in the documentation to keep retrocompatibility but is recommended
to use the new version of scipy.spatial.distance.minkowski
that implements
the correct behaviour.
Positional arguments of scipy.spatial.distance.pdist
and
scipy.spatial.distance.cdist
should be replaced with their keyword version.
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 crossclass 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
>1D raises a ValueError
. This
was a corner case for which it was unclear that the behavior was welldefined.
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
backwardscompatibility.
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 4channeled…#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 LBFGSB mention nonexistent parameter
#4893: misc.imsave does not work with file type defined
#5231: Discrepancies in scipy.optimize.minimize(method=’LBFGSB’)
#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: Sketchingbased 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 poly1dobject 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: 32bit Linux test errors on TestCephes
#7893: scipy.spatial.distance.wminkowski behaviour change in 1.0.0b1
#7898: DOC: Window functions
#7959: BUG maybe: fmin_bfgs possibly broken in 1.0
#7969: scipy 1.0.0rc1 windows wheels depend on missing msvcp140.dll
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 strictlyincreasing checks for x to 1D splines
#7031: BUG: Fix
linear_sum_assignment
hanging on an undefined matrix#7041: DOC: Clairfy that windows are DFTeven 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 “interiorpoint” method for
scipy.optimize.linprog
#7137: DOC: clarify stats.linregress docstring, closes gh7074
#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/kmeans 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 trusttrlib
#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 ifstatements 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 ndimensional 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 trustregionexact 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 32bit 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 crosssystem properties
#7484: MAINT: Cleanup 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 0shaped 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 Cramérvon 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 avoiding 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/ noncanonical 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 outofdate 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: Followup 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 gh7658.
#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 bsplines against…
#7674: Tests tuning
#7675: CI: move refguidecheck to faster build
#7676: DOC: bump scipysphinxtheme to fix copybutton.js
#7678: Note the zeropadding of the results of
splrep
andsplprep
#7681: MAINT:
_lib
: add useroverridable 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 intlike parameters in several routines
#7691: DOC: Drop nonworking 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 MannWhitney 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: Copyedit and add examples to the Kaiserrelated…
#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 AndersonDarling ksample 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 ‘interiorpoint’, not ‘interior…
#7751: BUG: optimize:
show_options('linprog', method='interiorpoint')
…#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 specifying 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 copyediting 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 gh5910
#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.
#7876: GEN: Add comments to the tests for clarification
#7891: ENH: backport #7879 to 1.0.x
#7902: MAINT: signal: Make freqz handling of multidim. arrays match…
#7905: REV: restore wminkowski
#7908: FIX: Avoid bad
__del__
(close) behavior#7918: TST: mark two optimize.linprog tests as xfail. See gh7877.
#7929: MAINT: changed defaults to lower in sytf2, sytrf and hetrf
#7939: Fix umfpack solver construction for winamd64
#7948: DOC: add note on checking for deprecations before upgrade to…
#7952: DOC: update SciPy Roadmap for 1.0 release and recent discussions.
#7960: BUG: optimize: revert changes to bfgs in gh7165
#7962: TST: special: mark a failing hyp2f1 test as xfail
#7973: BUG: fixed keyword in ‘info’ in
_get_mem_available
utility#8001: TST: fix test failures from Matplotlib 2.1 update
#8010: BUG: signal: fix crash in lfilter
#8019: MAINT: fix test failures with NumPy master