[Numpy-discussion] ANN: SciPy 1.3.0

Tyler Reddy tyler.je.reddy at gmail.com
Fri May 17 18:36:14 EDT 2019


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Hi all,

On behalf of the SciPy development team I'm pleased to announce
the release of SciPy 1.3.0.

Sources and binary wheels can be found at:
https://pypi.org/project/scipy/
and at:
https://github.com/scipy/scipy/releases/tag/v1.3.0

One of a few ways to install this release with pip:

pip install scipy==1.3.0

==========================
SciPy 1.3.0 Release Notes
==========================

SciPy 1.3.0 is the culmination of 5 months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been some 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
1.3.x branch, and on adding new features on the master branch.

This release requires Python 3.5+ and NumPy 1.13.3 or greater.

For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required.

Highlights of this release
---------------------------------

- - Three new ``stats`` functions, a rewrite of ``pearsonr``, and an exact
  computation of the Kolmogorov-Smirnov two-sample test
- - A new Cython API for bounded scalar-function root-finders in
`scipy.optimize`
- - Substantial ``CSR`` and ``CSC`` sparse matrix indexing performance
  improvements
- - Added support for interpolation of rotations with continuous angular
  rate and acceleration in ``RotationSpline``


New features
============

`scipy.interpolate` improvements
-------------------------------------------

A new class ``CubicHermiteSpline`` is introduced. It is a piecewise-cubic
interpolator which matches observed values and first derivatives. Existing
cubic interpolators ``CubicSpline``, ``PchipInterpolator`` and
``Akima1DInterpolator`` were made subclasses of ``CubicHermiteSpline``.

`scipy.io` improvements
--------------------------------

For the Attribute-Relation File Format (ARFF) `scipy.io.arff.loadarff`
now supports relational attributes.

`scipy.io.mmread` can now parse Matrix Market format files with empty lines.

`scipy.linalg` improvements
------------------------------------

Added wrappers for ``?syconv`` routines, which convert a symmetric matrix
given by a triangular matrix factorization into two matrices and vice versa.

`scipy.linalg.clarkson_woodruff_transform` now uses an algorithm that
leverages
sparsity. This may provide a 60-90 percent speedup for dense input matrices.
Truly sparse input matrices should also benefit from the improved sketch
algorithm, which now correctly runs in ``O(nnz(A))`` time.

Added new functions to calculate symmetric Fiedler matrices and
Fiedler companion matrices, named `scipy.linalg.fiedler` and
`scipy.linalg.fiedler_companion`, respectively. These may be used
for root finding.

`scipy.ndimage` improvements
----------------------------------------

Gaussian filter performances may improve by an order of magnitude in
some cases, thanks to removal of a dependence on ``np.polynomial``. This
may impact `scipy.ndimage.gaussian_filter` for example.

`scipy.optimize` improvements
----------------------------------------

The `scipy.optimize.brute` minimizer obtained a new keyword ``workers``,
which
can be used to parallelize computation.

A Cython API for bounded scalar-function root-finders in `scipy.optimize`
is available in a new module `scipy.optimize.cython_optimize` via
``cimport``.
This API may be used with ``nogil`` and ``prange`` to loop
over an array of function arguments to solve for an array of roots more
quickly than with pure Python.

``'interior-point'`` is now the default method for ``linprog``, and
``'interior-point'`` now uses SuiteSparse for sparse problems when the
required scikits  (scikit-umfpack and scikit-sparse) are available.
On benchmark problems (gh-10026), execution time reductions by factors of
2-3
were typical. Also, a new ``method='revised simplex'`` has been added.
It is not as fast or robust as ``method='interior-point'``, but it is a
faster,
more robust, and equally accurate substitute for the legacy
``method='simplex'``.

``differential_evolution`` can now use a ``Bounds`` class to specify the
bounds for the optimizing argument of a function.

`scipy.optimize.dual_annealing` performance improvements related to
vectorisation of some internal code.

`scipy.signal` improvements
-------------------------------------

Two additional methods of discretization are now supported by
`scipy.signal.cont2discrete`: ``impulse`` and ``foh``.

`scipy.signal.firls` now uses faster solvers

`scipy.signal.detrend` now has a lower physical memory footprint in some
cases, which may be leveraged using the new ``overwrite_data`` keyword
argument

`scipy.signal.firwin` ``pass_zero`` argument now accepts new string
arguments
that allow specification of the desired filter type: ``'bandpass'``,
``'lowpass'``, ``'highpass'``, and ``'bandstop'``

`scipy.signal.sosfilt` may have improved performance due to lower retention
of the global interpreter lock (GIL) in algorithm

`scipy.sparse` improvements
--------------------------------------

A new keyword was added to ``csgraph.dijsktra`` that
allows users to query the shortest path to ANY of the passed in indices,
as opposed to the shortest path to EVERY passed index.

`scipy.sparse.linalg.lsmr` performance has been improved by roughly 10
percent
on large problems

Improved performance and reduced physical memory footprint of the algorithm
used by `scipy.sparse.linalg.lobpcg`

``CSR`` and ``CSC`` sparse matrix fancy indexing performance has been
improved substantially

`scipy.spatial` improvements
--------------------------------------

`scipy.spatial.ConvexHull` now has a ``good`` attribute that can be used
alongsize the ``QGn`` Qhull options to determine which external facets of a
convex hull are visible from an external query point.

`scipy.spatial.cKDTree.query_ball_point` has been modernized to use some
newer
Cython features, including GIL handling and exception translation. An issue
with ``return_sorted=True`` and scalar queries was fixed, and a new mode
named
``return_length`` was added. ``return_length`` only computes the length of
the
returned indices list instead of allocating the array every time.

`scipy.spatial.transform.RotationSpline` has been added to enable
interpolation
of rotations with continuous angular rates and acceleration

`scipy.stats` improvements
------------------------------------

Added a new function to compute the Epps-Singleton test statistic,
`scipy.stats.epps_singleton_2samp`, which can be applied to continuous and
discrete distributions.

New functions `scipy.stats.median_absolute_deviation` and `scipy.stats.gstd`
(geometric standard deviation) were added. The
`scipy.stats.combine_pvalues`
method now supports ``pearson``,  ``tippett`` and ``mudholkar_george``
pvalue
combination methods.

The `scipy.stats.ortho_group` and `scipy.stats.special_ortho_group`
``rvs(dim)`` functions' algorithms were updated from a ``O(dim^4)``
implementation to a ``O(dim^3)`` which gives large speed improvements
for ``dim>100``.

A rewrite of `scipy.stats.pearsonr` to use a more robust algorithm,
provide meaningful exceptions and warnings on potentially pathological
input,
and fix at least five separate reported issues in the original
implementation.

Improved the precision of ``hypergeom.logcdf`` and ``hypergeom.logsf``.

Added exact computation for Kolmogorov-Smirnov (KS) two-sample test,
replacing
the previously approximate computation for the two-sided test
`stats.ks_2samp`.
Also added a one-sided, two-sample KS test, and a keyword ``alternative``
to
`stats.ks_2samp`.

Backwards incompatible changes
==========================

`scipy.interpolate` changes
------------------------------------

Functions from ``scipy.interpolate`` (``spleval``, ``spline``, ``splmake``,
and ``spltopp``) and functions from ``scipy.misc`` (``bytescale``,
``fromimage``, ``imfilter``, ``imread``, ``imresize``, ``imrotate``,
``imsave``, ``imshow``, ``toimage``) have been removed. The former set has
been deprecated since v0.19.0 and the latter has been deprecated since
v1.0.0.
Similarly, aliases from ``scipy.misc`` (``comb``, ``factorial``,
``factorial2``, ``factorialk``, ``logsumexp``, ``pade``, ``info``,
``source``,
``who``) which have been deprecated since v1.0.0 are removed.
`SciPy documentation for
v1.1.0 <https://docs.scipy.org/doc/scipy-1.1.0/reference/misc.html>`__
can be used to track the new import locations for the relocated functions.

`scipy.linalg` changes
-----------------------------

For ``pinv``, ``pinv2``, and ``pinvh``, the default cutoff values are
changed
for consistency (see the docs for the actual values).

`scipy.optimize` changes
---------------------------------

The default method for ``linprog`` is now ``'interior-point'``. The method's
robustness and speed come at a cost: solutions may not be accurate to
machine precision or correspond with a vertex of the polytope defined
by the constraints. To revert to the original simplex method,
include the argument ``method='simplex'``.

`scipy.stats` changes
----------------------------

Previously, ``ks_2samp(data1, data2)`` would run a two-sided test and
return
the approximated p-value. The new signature, ``ks_2samp(data1, data2,
alternative="two-sided", method="auto")``, still runs the two-sided test by
default but returns the exact p-value for small samples and the approximated
value for large samples. ``method="asymp"`` would be equivalent to the
old version but ``auto`` is the better choice.

Other changes
=============

Our tutorial has been expanded with a new section on global optimizers

There has been a rework of the ``stats.distributions`` tutorials.

`scipy.optimize` now correctly sets the convergence flag of the result to
``CONVERR``, a convergence error, for bounded scalar-function root-finders
if the maximum iterations has been exceeded, ``disp`` is false, and
``full_output`` is true.

`scipy.optimize.curve_fit` no longer fails if ``xdata`` and ``ydata``
dtypes
differ; they are both now automatically cast to ``float64``.

`scipy.ndimage` functions including ``binary_erosion``, ``binary_closing``,
and
``binary_dilation`` now require an integer value for the number of
iterations,
which alleviates a number of reported issues.

Fixed normal approximation in case ``zero_method == "pratt"`` in
`scipy.stats.wilcoxon`.

Fixes for incorrect probabilities, broadcasting issues and thread-safety
related to stats distributions setting member variables inside
``_argcheck()``.

`scipy.optimize.newton` now correctly raises a ``RuntimeError``, when
default
arguments are used, in the case that a derivative of value zero is obtained,
which is a special case of failing to converge.

A draft toolchain roadmap is now available, laying out a compatibility plan
including Python versions, C standards, and NumPy versions.


Authors
=======

* ananyashreyjain +
* ApamNapat +
* Scott Calabrese Barton +
* Christoph Baumgarten
* Peter Bell +
* Jacob Blomgren +
* Doctor Bob +
* Mana Borwornpadungkitti +
* Matthew Brett
* Evgeni Burovski
* CJ Carey
* Vega Theil Carstensen +
* Robert Cimrman
* Forrest Collman +
* Pietro Cottone +
* David +
* Idan David +
* Christoph Deil
* Dieter Werthmüller
* Conner DiPaolo +
* Dowon
* Michael Dunphy +
* Peter Andreas Entschev +
* Gökçen Eraslan +
* Johann Faouzi +
* Yu Feng
* Piotr Figiel +
* Matthew H Flamm
* Franz Forstmayr +
* Christoph Gohlke
* Richard Janis Goldschmidt +
* Ralf Gommers
* Lars Grueter
* Sylvain Gubian
* Matt Haberland
* Yaroslav Halchenko
* Charles Harris
* Lindsey Hiltner
* JakobStruye +
* He Jia +
* Jwink3101 +
* Greg Kiar +
* Julius Bier Kirkegaard
* John Kirkham +
* Thomas Kluyver
* Vladimir Korolev +
* Joseph Kuo +
* Michael Lamparski +
* Eric Larson
* Denis Laxalde
* Katrin Leinweber
* Jesse Livezey
* ludcila +
* Dhruv Madeka +
* Magnus +
* Nikolay Mayorov
* Mark Mikofski
* Jarrod Millman
* Markus Mohrhard +
* Eric Moore
* Andrew Nelson
* Aki Nishimura +
* OGordon100 +
* Petar Mlinarić +
* Stefan Peterson
* Matti Picus +
* Ilhan Polat
* Aaron Pries +
* Matteo Ravasi +
* Tyler Reddy
* Ashton Reimer +
* Joscha Reimer
* rfezzani +
* Riadh +
* Lucas Roberts
* Heshy Roskes +
* Mirko Scholz +
* Taylor D. Scott +
* Srikrishna Sekhar +
* Kevin Sheppard +
* Sourav Singh
* skjerns +
* Kai Striega
* SyedSaifAliAlvi +
* Gopi Manohar T +
* Albert Thomas +
* Timon +
* Paul van Mulbregt
* Jacob Vanderplas
* Daniel Vargas +
* Pauli Virtanen
* VNMabus +
* Stefan van der Walt
* Warren Weckesser
* Josh Wilson
* Nate Yoder +
* Roman Yurchak

A total of 97 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 1.3.0
-------------------------------

* `#1320 <https://github.com/scipy/scipy/issues/1320>`__:
scipy.stats.distribution: problem with self.a, self.b if they...
* `#2002 <https://github.com/scipy/scipy/issues/2002>`__: members set in
scipy.stats.distributions.##._argcheck (Trac #1477)
* `#2823 <https://github.com/scipy/scipy/issues/2823>`__: distribution
methods add tmp
* `#3220 <https://github.com/scipy/scipy/issues/3220>`__:
Scipy.opimize.fmin_powell direc argument syntax unclear
* `#3728 <https://github.com/scipy/scipy/issues/3728>`__:
scipy.stats.pearsonr: possible bug with zero variance input
* `#6805 <https://github.com/scipy/scipy/issues/6805>`__:
error-in-scipy-wilcoxon-signed-rank-test-for-equal-series
* `#6873 <https://github.com/scipy/scipy/issues/6873>`__: 'stats.boxcox'
return all same values
* `#7117 <https://github.com/scipy/scipy/issues/7117>`__: Warn users when
using float32 input data to curve_fit and friends
* `#7632 <https://github.com/scipy/scipy/issues/7632>`__: it's not possible
to tell the \`optimize.least_squares\` solver...
* `#7730 <https://github.com/scipy/scipy/issues/7730>`__: stats.pearsonr:
Potential division by zero for dataset of length...
* `#7933 <https://github.com/scipy/scipy/issues/7933>`__: stats.truncnorm
fails when providing values outside truncation...
* `#8033 <https://github.com/scipy/scipy/issues/8033>`__: Add standard
filter types to firwin to set pass_zero intuitively...
* `#8600 <https://github.com/scipy/scipy/issues/8600>`__: lfilter.c.src
zfill has erroneous header
* `#8692 <https://github.com/scipy/scipy/issues/8692>`__: Non-negative
values of \`stats.hypergeom.logcdf\`
* `#8734 <https://github.com/scipy/scipy/issues/8734>`__: Enable pip build
isolation
* `#8861 <https://github.com/scipy/scipy/issues/8861>`__: scipy.linalg.pinv
gives wrong result while scipy.linalg.pinv2...
* `#8915 <https://github.com/scipy/scipy/issues/8915>`__: need to fix macOS
build against older numpy versions
* `#8980 <https://github.com/scipy/scipy/issues/8980>`__:
scipy.stats.pearsonr overflows with high values of x and y
* `#9226 <https://github.com/scipy/scipy/issues/9226>`__: BUG: signal:
SystemError: <built-in function _linear_filter>...
* `#9254 <https://github.com/scipy/scipy/issues/9254>`__: BUG: root finders
brentq, etc, flag says "converged" even if...
* `#9308 <https://github.com/scipy/scipy/issues/9308>`__: Test failure -
test_initial_constraints_as_canonical
* `#9353 <https://github.com/scipy/scipy/issues/9353>`__:
scipy.stats.pearsonr returns r=1 if r_num/r_den = inf
* `#9359 <https://github.com/scipy/scipy/issues/9359>`__: Planck
distribution is a geometric distribution
* `#9381 <https://github.com/scipy/scipy/issues/9381>`__: linregress should
warn user in 2x2 array case
* `#9406 <https://github.com/scipy/scipy/issues/9406>`__: BUG: stats: In
pearsonr, when r is nan, the p-value must also...
* `#9437 <https://github.com/scipy/scipy/issues/9437>`__: Cannot create
sparse matrix from size_t indexes
* `#9518 <https://github.com/scipy/scipy/issues/9518>`__: Relational
attributes in loadarff
* `#9551 <https://github.com/scipy/scipy/issues/9551>`__: BUG:
scipy.optimize.newton says the root of x^2+1 is zero.
* `#9564 <https://github.com/scipy/scipy/issues/9564>`__: rv_sample accepts
invalid input in scipy.stats
* `#9565 <https://github.com/scipy/scipy/issues/9565>`__: improper handling
of multidimensional input in stats.rv_sample
* `#9581 <https://github.com/scipy/scipy/issues/9581>`__: Least-squares
minimization fails silently when x and y data are...
* `#9587 <https://github.com/scipy/scipy/issues/9587>`__: Outdated value
for scipy.constants.au
* `#9611 <https://github.com/scipy/scipy/issues/9611>`__: Overflow error
with new way of p-value calculation in kendall...
* `#9645 <https://github.com/scipy/scipy/issues/9645>`__:
\`scipy.stats.mode\` crashes with variable length arrays (\`dtype=object\`)
* `#9734 <https://github.com/scipy/scipy/issues/9734>`__:
PendingDeprecationWarning for np.matrix with pytest
* `#9786 <https://github.com/scipy/scipy/issues/9786>`__: stats.ks_2samp()
misleading for small data sets.
* `#9790 <https://github.com/scipy/scipy/issues/9790>`__: Excessive memory
usage on detrend
* `#9801 <https://github.com/scipy/scipy/issues/9801>`__: dual_annealing
does not set the success attribute in OptimizeResult
* `#9833 <https://github.com/scipy/scipy/issues/9833>`__:
IntegrationWarning from mielke.stats() during build of html doc.
* `#9835 <https://github.com/scipy/scipy/issues/9835>`__:
scipy.signal.firls seems to be inefficient versus MATLAB firls
* `#9864 <https://github.com/scipy/scipy/issues/9864>`__: Curve_fit does
not check for empty input data if called with...
* `#9869 <https://github.com/scipy/scipy/issues/9869>`__:
scipy.ndimage.label: Minor documentation issue
* `#9882 <https://github.com/scipy/scipy/issues/9882>`__: format at the
wrong paranthesis in scipy.spatial.transform
* `#9889 <https://github.com/scipy/scipy/issues/9889>`__:
scipy.signal.find_peaks minor documentation issue
* `#9890 <https://github.com/scipy/scipy/issues/9890>`__: Minkowski p-norm
Issues in cKDTree For Values Other Than 2 Or...
* `#9896 <https://github.com/scipy/scipy/issues/9896>`__:
scipy.stats._argcheck sets (not just checks) values
* `#9905 <https://github.com/scipy/scipy/issues/9905>`__: Memory error in
ndimage.binary_erosion
* `#9909 <https://github.com/scipy/scipy/issues/9909>`__:
binary_dilation/erosion/closing crashes when iterations is float
* `#9919 <https://github.com/scipy/scipy/issues/9919>`__: BUG:
\`coo_matrix\` does not validate the \`shape\` argument.
* `#9982 <https://github.com/scipy/scipy/issues/9982>`__: lsq_linear
hangs/infinite loop with 'trf' method
* `#10003 <https://github.com/scipy/scipy/issues/10003>`__: exponnorm.pdf
returns NAN for small K
* `#10011 <https://github.com/scipy/scipy/issues/10011>`__: Incorrect check
for invalid rotation plane in scipy.ndimage.rotate
* `#10024 <https://github.com/scipy/scipy/issues/10024>`__: Fails to build
from git
* `#10048 <https://github.com/scipy/scipy/issues/10048>`__: DOC:
scipy.optimize.root_scalar
* `#10068 <https://github.com/scipy/scipy/issues/10068>`__: DOC:
scipy.interpolate.splev
* `#10074 <https://github.com/scipy/scipy/issues/10074>`__: BUG: \`expm\`
calculates the wrong coefficients in the backward...


Pull requests for 1.3.0
------------------------------

* `#7827 <https://github.com/scipy/scipy/pull/7827>`__: ENH: sparse:
overhaul of sparse matrix indexing
* `#8431 <https://github.com/scipy/scipy/pull/8431>`__: ENH: Cython
optimize zeros api
* `#8743 <https://github.com/scipy/scipy/pull/8743>`__: DOC: Updated
linalg.pinv, .pinv2, .pinvh docstrings
* `#8744 <https://github.com/scipy/scipy/pull/8744>`__: DOC: added examples
to remez docstring
* `#9227 <https://github.com/scipy/scipy/pull/9227>`__: DOC: update
description of "direc" parameter of "fmin_powell"
* `#9263 <https://github.com/scipy/scipy/pull/9263>`__: ENH: optimize:
added "revised simplex" for scipy.optimize.linprog
* `#9325 <https://github.com/scipy/scipy/pull/9325>`__: DEP: Remove
deprecated functions for 1.3.0
* `#9330 <https://github.com/scipy/scipy/pull/9330>`__: Add note on push
and pull affine transformations
* `#9423 <https://github.com/scipy/scipy/pull/9423>`__: DOC: Clearly state
how 2x2 input arrays are handled in stats.linregress
* `#9428 <https://github.com/scipy/scipy/pull/9428>`__: ENH: parallelised
brute
* `#9438 <https://github.com/scipy/scipy/pull/9438>`__: BUG: Initialize coo
matrix with size_t indexes
* `#9455 <https://github.com/scipy/scipy/pull/9455>`__: MAINT: Speed up
get_(lapack,blas)_func
* `#9465 <https://github.com/scipy/scipy/pull/9465>`__: MAINT: Clean up
optimize.zeros C solvers interfaces/code.
* `#9477 <https://github.com/scipy/scipy/pull/9477>`__: DOC: linalg: fix
lstsq docstring on residues shape
* `#9478 <https://github.com/scipy/scipy/pull/9478>`__: DOC: Add docstring
examples for rosen functions
* `#9479 <https://github.com/scipy/scipy/pull/9479>`__: DOC: Add docstring
example for ai_zeros and bi_zeros
* `#9480 <https://github.com/scipy/scipy/pull/9480>`__: MAINT: linalg:
lstsq clean up
* `#9489 <https://github.com/scipy/scipy/pull/9489>`__: DOC: roadmap update
for changes over the last year.
* `#9492 <https://github.com/scipy/scipy/pull/9492>`__: MAINT: stats:
Improve implementation of chi2 ppf method.
* `#9497 <https://github.com/scipy/scipy/pull/9497>`__: DOC: Improve
docstrings sparse.linalg.isolve
* `#9499 <https://github.com/scipy/scipy/pull/9499>`__: DOC: Replace
"Scipy" with "SciPy" in the .rst doc files for consistency.
* `#9500 <https://github.com/scipy/scipy/pull/9500>`__: DOC: Document the
toolchain and its roadmap.
* `#9505 <https://github.com/scipy/scipy/pull/9505>`__: DOC: specify which
definition of skewness is used
* `#9511 <https://github.com/scipy/scipy/pull/9511>`__: DEP: interpolate:
remove deprecated interpolate_wrapper
* `#9517 <https://github.com/scipy/scipy/pull/9517>`__: BUG: improve error
handling in stats.iqr
* `#9522 <https://github.com/scipy/scipy/pull/9522>`__: ENH: Add Fiedler
and fiedler companion to special matrices
* `#9526 <https://github.com/scipy/scipy/pull/9526>`__: TST: relax
precision requirements in signal.correlate tests
* `#9529 <https://github.com/scipy/scipy/pull/9529>`__: DOC: fix missing
random seed in optimize.newton example
* `#9533 <https://github.com/scipy/scipy/pull/9533>`__: MAINT: Use list
comprehension when possible
* `#9537 <https://github.com/scipy/scipy/pull/9537>`__: DOC: add a "big
picture" roadmap
* `#9538 <https://github.com/scipy/scipy/pull/9538>`__: DOC: Replace
"Numpy" with "NumPy" in .py, .rst and .txt doc files...
* `#9539 <https://github.com/scipy/scipy/pull/9539>`__: ENH: add two-sample
test (Epps-Singleton) to scipy.stats
* `#9559 <https://github.com/scipy/scipy/pull/9559>`__: DOC: add section on
global optimizers to tutorial
* `#9561 <https://github.com/scipy/scipy/pull/9561>`__: ENH: remove
noprefix.h, change code appropriately
* `#9562 <https://github.com/scipy/scipy/pull/9562>`__: MAINT: stats:
Rewrite pearsonr.
* `#9563 <https://github.com/scipy/scipy/pull/9563>`__: BUG: Minor bug fix
Callback in linprog(method='simplex')
* `#9568 <https://github.com/scipy/scipy/pull/9568>`__: MAINT: raise
runtime error for newton with zeroder if disp true,...
* `#9570 <https://github.com/scipy/scipy/pull/9570>`__: Correct docstring
in show_options in optimize. Fixes #9407
* `#9573 <https://github.com/scipy/scipy/pull/9573>`__: BUG fixes range of
pk variable pre-check
* `#9577 <https://github.com/scipy/scipy/pull/9577>`__: TST: fix minor
issue in a signal.stft test.
* `#9580 <https://github.com/scipy/scipy/pull/9580>`__: Included blank line
before list - Fixes #8658
* `#9582 <https://github.com/scipy/scipy/pull/9582>`__: MAINT: drop Python
2.7 and 3.4
* `#9588 <https://github.com/scipy/scipy/pull/9588>`__: MAINT: update
\`constants.astronomical_unit\` to new 2012 value.
* `#9592 <https://github.com/scipy/scipy/pull/9592>`__: TST: Add 32-bit
testing to CI
* `#9593 <https://github.com/scipy/scipy/pull/9593>`__: DOC: Replace
cumulative density with cumulative distribution
* `#9596 <https://github.com/scipy/scipy/pull/9596>`__: TST: remove VC 9.0
from Azure CI
* `#9599 <https://github.com/scipy/scipy/pull/9599>`__: Hyperlink DOI to
preferred resolver
* `#9601 <https://github.com/scipy/scipy/pull/9601>`__: DEV: try to limit
GC memory use on PyPy
* `#9603 <https://github.com/scipy/scipy/pull/9603>`__: MAINT: improve
logcdf and logsf of hypergeometric distribution
* `#9605 <https://github.com/scipy/scipy/pull/9605>`__: Reference to pylops
in LinearOperator notes and ARPACK example
* `#9617 <https://github.com/scipy/scipy/pull/9617>`__: TST: reduce max
memory usage for sparse.linalg.lgmres test
* `#9619 <https://github.com/scipy/scipy/pull/9619>`__: FIX: Sparse matrix
addition/subtraction eliminates explicit zeros
* `#9621 <https://github.com/scipy/scipy/pull/9621>`__: bugfix in rv_sample
in scipy.stats
* `#9622 <https://github.com/scipy/scipy/pull/9622>`__: MAINT: Raise error
in directed_hausdorff distance
* `#9623 <https://github.com/scipy/scipy/pull/9623>`__: DOC: Build docs
with warnings as errors
* `#9625 <https://github.com/scipy/scipy/pull/9625>`__: Return the number
of calls to 'hessp' (not just 'hess') in trust...
* `#9627 <https://github.com/scipy/scipy/pull/9627>`__: BUG: ignore empty
lines in mmio
* `#9637 <https://github.com/scipy/scipy/pull/9637>`__: Function to
calculate the MAD of an array
* `#9646 <https://github.com/scipy/scipy/pull/9646>`__: BUG: stats: mode
for objects w/ndim > 1
* `#9648 <https://github.com/scipy/scipy/pull/9648>`__: Add
\`stats.contingency\` to refguide-check
* `#9650 <https://github.com/scipy/scipy/pull/9650>`__: ENH: many lobpcg()
algorithm improvements
* `#9652 <https://github.com/scipy/scipy/pull/9652>`__: Move misc.doccer to
_lib.doccer
* `#9660 <https://github.com/scipy/scipy/pull/9660>`__: ENH: add pearson,
tippett, and mudholkar-george to combine_pvalues
* `#9661 <https://github.com/scipy/scipy/pull/9661>`__: BUG: Fix ksone
right-hand endpoint, documentation and tests.
* `#9664 <https://github.com/scipy/scipy/pull/9664>`__: ENH: adding
multi-target dijsktra performance enhancement
* `#9670 <https://github.com/scipy/scipy/pull/9670>`__: MAINT: link planck
and geometric distribution in scipy.stats
* `#9676 <https://github.com/scipy/scipy/pull/9676>`__: ENH: optimize:
change default linprog method to interior-point
* `#9685 <https://github.com/scipy/scipy/pull/9685>`__: Added reference to
ndimage.filters.median_filter
* `#9705 <https://github.com/scipy/scipy/pull/9705>`__: Fix coefficients in
expm helper function
* `#9711 <https://github.com/scipy/scipy/pull/9711>`__: Release the GIL
during sosfilt processing for simple types
* `#9721 <https://github.com/scipy/scipy/pull/9721>`__: ENH: Convexhull
visiblefacets
* `#9723 <https://github.com/scipy/scipy/pull/9723>`__: BLD: Modify
rv_generic._construct_doc to print out failing distribution...
* `#9726 <https://github.com/scipy/scipy/pull/9726>`__: BUG: Fix small
issues with \`signal.lfilter'
* `#9729 <https://github.com/scipy/scipy/pull/9729>`__: BUG: Typecheck
iterations for binary image operations
* `#9730 <https://github.com/scipy/scipy/pull/9730>`__: ENH: reduce
sizeof(NI_WatershedElement) by 20%
* `#9731 <https://github.com/scipy/scipy/pull/9731>`__: ENH: remove
suspicious sequence of type castings
* `#9739 <https://github.com/scipy/scipy/pull/9739>`__: BUG: qr_updates
fails if u is exactly in span Q
* `#9749 <https://github.com/scipy/scipy/pull/9749>`__: BUG:
MapWrapper.__exit__ should terminate
* `#9753 <https://github.com/scipy/scipy/pull/9753>`__: ENH: Added exact
computation for Kolmogorov-Smirnov two-sample...
* `#9755 <https://github.com/scipy/scipy/pull/9755>`__: DOC: Added example
for signal.impulse, copied from impulse2
* `#9756 <https://github.com/scipy/scipy/pull/9756>`__: DOC: Added
docstring example for iirdesign
* `#9757 <https://github.com/scipy/scipy/pull/9757>`__: DOC: Added examples
for step functions
* `#9759 <https://github.com/scipy/scipy/pull/9759>`__: ENH: Allow
pass_zero to act like btype
* `#9760 <https://github.com/scipy/scipy/pull/9760>`__: DOC: Added
docstring for lp2bs
* `#9761 <https://github.com/scipy/scipy/pull/9761>`__: DOC: Added
docstring and example for lp2bp
* `#9764 <https://github.com/scipy/scipy/pull/9764>`__: BUG: Catch internal
warnings for matrix
* `#9766 <https://github.com/scipy/scipy/pull/9766>`__: ENH: Speed up
_gaussian_kernel1d by removing dependence on np.polynomial
* `#9769 <https://github.com/scipy/scipy/pull/9769>`__: BUG: Fix Cubic
Spline Read Only issues
* `#9773 <https://github.com/scipy/scipy/pull/9773>`__: DOC: Several
docstrings
* `#9774 <https://github.com/scipy/scipy/pull/9774>`__: TST: bump Azure CI
OpenBLAS version to match wheels
* `#9775 <https://github.com/scipy/scipy/pull/9775>`__: DOC: Improve
clarity of cov_x documentation for scipy.optimize.leastsq
* `#9779 <https://github.com/scipy/scipy/pull/9779>`__: ENH: dual_annealing
vectorise visit_fn
* `#9788 <https://github.com/scipy/scipy/pull/9788>`__: TST, BUG:
f2py-related issues with NumPy < 1.14.0
* `#9791 <https://github.com/scipy/scipy/pull/9791>`__: BUG: fix amax
constraint not enforced in scalar_search_wolfe2
* `#9792 <https://github.com/scipy/scipy/pull/9792>`__: ENH: Allow inplace
copying in place in "detrend" function
* `#9795 <https://github.com/scipy/scipy/pull/9795>`__: DOC: Fix/update
docstring for dstn and dst
* `#9796 <https://github.com/scipy/scipy/pull/9796>`__: MAINT: Allow None
tolerances in least_squares
* `#9798 <https://github.com/scipy/scipy/pull/9798>`__: BUG: fixes abort
trap 6 error in scipy issue 9785 in unit tests
* `#9807 <https://github.com/scipy/scipy/pull/9807>`__: MAINT: improve doc
and add alternative keyword to wilcoxon in...
* `#9808 <https://github.com/scipy/scipy/pull/9808>`__: Fix PPoly integrate
and test for CubicSpline
* `#9810 <https://github.com/scipy/scipy/pull/9810>`__: ENH: Add the
geometric standard deviation function
* `#9811 <https://github.com/scipy/scipy/pull/9811>`__: MAINT: remove
invalid derphi default None value in scalar_search_wolfe2
* `#9813 <https://github.com/scipy/scipy/pull/9813>`__: Adapt hamming
distance in C to support weights
* `#9817 <https://github.com/scipy/scipy/pull/9817>`__: DOC: Copy solver
description to solver modules
* `#9829 <https://github.com/scipy/scipy/pull/9829>`__: ENH: Add FOH and
equivalent impulse response discretizations...
* `#9831 <https://github.com/scipy/scipy/pull/9831>`__: ENH: Implement
RotationSpline
* `#9834 <https://github.com/scipy/scipy/pull/9834>`__: DOC: Change mielke
distribution default parameters to ensure...
* `#9838 <https://github.com/scipy/scipy/pull/9838>`__: ENH: Use faster
solvers for firls
* `#9854 <https://github.com/scipy/scipy/pull/9854>`__: ENH: loadarff now
supports relational attributes.
* `#9856 <https://github.com/scipy/scipy/pull/9856>`__: integrate.bvp -
improve handling of nonlinear boundary conditions
* `#9862 <https://github.com/scipy/scipy/pull/9862>`__: TST: reduce
Appveyor CI load
* `#9874 <https://github.com/scipy/scipy/pull/9874>`__: DOC: Update
requirements in release notes
* `#9883 <https://github.com/scipy/scipy/pull/9883>`__: BUG: fixed
parenthesis in spatial.rotation
* `#9884 <https://github.com/scipy/scipy/pull/9884>`__: ENH: Use Sparsity
in Clarkson-Woodruff Sketch
* `#9888 <https://github.com/scipy/scipy/pull/9888>`__: MAINT: Replace
NumPy aliased functions
* `#9892 <https://github.com/scipy/scipy/pull/9892>`__: BUG: Fix 9890
query_ball_point returns wrong result when p is...
* `#9893 <https://github.com/scipy/scipy/pull/9893>`__: BUG: curve_fit
doesn't check for empty input if called with bounds
* `#9894 <https://github.com/scipy/scipy/pull/9894>`__:
scipy.signal.find_peaks documentation error
* `#9898 <https://github.com/scipy/scipy/pull/9898>`__: BUG: Set success
attribute in OptimizeResult. See #9801
* `#9900 <https://github.com/scipy/scipy/pull/9900>`__: BUG: Restrict
rv_generic._argcheck() and its overrides from setting...
* `#9906 <https://github.com/scipy/scipy/pull/9906>`__: fixed a bug in kde
logpdf
* `#9911 <https://github.com/scipy/scipy/pull/9911>`__: DOC: replace
example for "np.select" with the one from numpy...
* `#9912 <https://github.com/scipy/scipy/pull/9912>`__: BF(DOC): point to
numpy.select instead of plain (python) .select
* `#9914 <https://github.com/scipy/scipy/pull/9914>`__: DOC: change
ValueError message in _validate_pad of signaltools.
* `#9915 <https://github.com/scipy/scipy/pull/9915>`__: cKDTree
query_ball_point improvements
* `#9918 <https://github.com/scipy/scipy/pull/9918>`__: Update ckdtree.pyx
with boxsize argument in docstring
* `#9920 <https://github.com/scipy/scipy/pull/9920>`__: BUG: sparse:
Validate explicit shape if given with dense argument...
* `#9924 <https://github.com/scipy/scipy/pull/9924>`__: BLD: add back
pyproject.toml
* `#9931 <https://github.com/scipy/scipy/pull/9931>`__: Fix empty constraint
* `#9935 <https://github.com/scipy/scipy/pull/9935>`__: DOC: fix references
for stats.f_oneway
* `#9936 <https://github.com/scipy/scipy/pull/9936>`__: Revert gh-9619:
"FIX: Sparse matrix addition/subtraction eliminates...
* `#9937 <https://github.com/scipy/scipy/pull/9937>`__: MAINT: fix PEP8
issues and update to pycodestyle 2.5.0
* `#9939 <https://github.com/scipy/scipy/pull/9939>`__: DOC: correct
\`structure\` description in \`ndimage.label\` docstring
* `#9940 <https://github.com/scipy/scipy/pull/9940>`__: MAINT: remove
extraneous distutils copies
* `#9945 <https://github.com/scipy/scipy/pull/9945>`__: ENH:
differential_evolution can use Bounds object
* `#9949 <https://github.com/scipy/scipy/pull/9949>`__: Added 'std' to add
doctstrings since it is a \`known_stats\`...
* `#9953 <https://github.com/scipy/scipy/pull/9953>`__: DOC: Documentation
cleanup for stats tutorials.
* `#9962 <https://github.com/scipy/scipy/pull/9962>`__: __repr__ for Bounds
* `#9971 <https://github.com/scipy/scipy/pull/9971>`__: ENH: Improve
performance of lsmr
* `#9987 <https://github.com/scipy/scipy/pull/9987>`__: CI: pin Sphinx
version to 1.8.5
* `#9990 <https://github.com/scipy/scipy/pull/9990>`__: ENH: constraint
violation
* `#9991 <https://github.com/scipy/scipy/pull/9991>`__: BUG: Avoid inplace
modification of input array in newton
* `#9995 <https://github.com/scipy/scipy/pull/9995>`__: MAINT:
sparse.csgraph: Add cdef to stop build warning.
* `#9996 <https://github.com/scipy/scipy/pull/9996>`__: BUG: Make
minimize_quadratic_1d work with infinite bounds correctly
* `#10004 <https://github.com/scipy/scipy/pull/10004>`__: BUG: Fix unbound
local error in linprog - simplex.
* `#10007 <https://github.com/scipy/scipy/pull/10007>`__: BLD: fix Python
3.7 build with build isolation
* `#10009 <https://github.com/scipy/scipy/pull/10009>`__: BUG: Make sure
that _binary_erosion only accepts an integer number...
* `#10016 <https://github.com/scipy/scipy/pull/10016>`__: Update link to
airspeed-velocity
* `#10017 <https://github.com/scipy/scipy/pull/10017>`__: DOC: Update
\`interpolate.LSQSphereBivariateSpline\` to include...
* `#10018 <https://github.com/scipy/scipy/pull/10018>`__: MAINT: special:
Fix a few warnings that occur when compiling...
* `#10019 <https://github.com/scipy/scipy/pull/10019>`__: TST: Azure
summarizes test failures
* `#10021 <https://github.com/scipy/scipy/pull/10021>`__: ENH: Introduce
CubicHermiteSpline
* `#10022 <https://github.com/scipy/scipy/pull/10022>`__: BENCH: Increase
cython version in asv to fix benchmark builds
* `#10023 <https://github.com/scipy/scipy/pull/10023>`__: BUG: Avoid
exponnorm producing nan for small K values.
* `#10025 <https://github.com/scipy/scipy/pull/10025>`__: BUG: optimize:
tweaked linprog status 4 error message
* `#10026 <https://github.com/scipy/scipy/pull/10026>`__: ENH: optimize:
use SuiteSparse in linprog interior-point when...
* `#10027 <https://github.com/scipy/scipy/pull/10027>`__: MAINT: cluster:
clean up the use of malloc() in the function...
* `#10028 <https://github.com/scipy/scipy/pull/10028>`__: Fix rotate
invalid plane check
* `#10040 <https://github.com/scipy/scipy/pull/10040>`__: MAINT: fix pratt
method of wilcox test in scipy.stats
* `#10041 <https://github.com/scipy/scipy/pull/10041>`__: MAINT: special:
Fix a warning generated when building the AMOS...
* `#10044 <https://github.com/scipy/scipy/pull/10044>`__: DOC: fix up
spatial.transform.Rotation docstrings
* `#10047 <https://github.com/scipy/scipy/pull/10047>`__: MAINT:
interpolate: Fix a few build warnings.
* `#10051 <https://github.com/scipy/scipy/pull/10051>`__: Add project_urls
to setup
* `#10052 <https://github.com/scipy/scipy/pull/10052>`__: don't set flag to
"converged" if max iter exceeded
* `#10054 <https://github.com/scipy/scipy/pull/10054>`__: MAINT: signal:
Fix a few build warnings and modernize some C...
* `#10056 <https://github.com/scipy/scipy/pull/10056>`__: BUG: Ensure
factorial is not too large in kendaltau
* `#10058 <https://github.com/scipy/scipy/pull/10058>`__: Small speedup in
samping from ortho and special_ortho groups
* `#10059 <https://github.com/scipy/scipy/pull/10059>`__: BUG: optimize:
fix #10038 by increasing tol
* `#10061 <https://github.com/scipy/scipy/pull/10061>`__: BLD: DOC: make
building docs easier by parsing python version.
* `#10064 <https://github.com/scipy/scipy/pull/10064>`__: ENH: Significant
speedup for ortho and special ortho group
* `#10065 <https://github.com/scipy/scipy/pull/10065>`__: DOC: Reword
parameter descriptions in \`optimize.root_scalar\`
* `#10066 <https://github.com/scipy/scipy/pull/10066>`__: BUG: signal: Fix
error raised by savgol_coeffs when deriv > polyorder.
* `#10067 <https://github.com/scipy/scipy/pull/10067>`__: MAINT: Fix the
cutoff value inconsistency for pinv2 and pinvh
* `#10072 <https://github.com/scipy/scipy/pull/10072>`__: BUG: stats: Fix
boxcox_llf to avoid loss of precision.
* `#10075 <https://github.com/scipy/scipy/pull/10075>`__: ENH: Add wrappers
for ?syconv routines
* `#10076 <https://github.com/scipy/scipy/pull/10076>`__: BUG: optimize:
fix curve_fit for mixed float32/float64 input
* `#10077 <https://github.com/scipy/scipy/pull/10077>`__: DOC: Replace
undefined \`k\` in \`interpolate.splev\` docstring
* `#10079 <https://github.com/scipy/scipy/pull/10079>`__: DOC: Fixed typo,
rearranged some doc of stats.morestats.wilcoxon.
* `#10080 <https://github.com/scipy/scipy/pull/10080>`__: TST: install
scikit-sparse for full TravisCI tests
* `#10083 <https://github.com/scipy/scipy/pull/10083>`__: Clean
\`\`_clean_inputs\`\` in optimize.linprog
* `#10088 <https://github.com/scipy/scipy/pull/10088>`__: ENH: optimize:
linprog test CHOLMOD/UMFPACK solvers when available
* `#10090 <https://github.com/scipy/scipy/pull/10090>`__: MAINT: Fix
CubicSplinerInterpolator for pandas
* `#10091 <https://github.com/scipy/scipy/pull/10091>`__: MAINT: improve
logcdf and logsf of hypergeometric distribution
* `#10095 <https://github.com/scipy/scipy/pull/10095>`__: MAINT: Clean
\`\`_clean_inputs\`\` in linprog
* `#10116 <https://github.com/scipy/scipy/pull/10116>`__: MAINT: update
scipy-sphinx-theme
* `#10135 <https://github.com/scipy/scipy/pull/10135>`__: BUG: fix linprog
revised simplex docstring problem failure

Checksums
=========

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