[SciPy-Dev] ANN: SciPy 1.3.0rc1 -- please test
Tyler Reddy
tyler.je.reddy at gmail.com
Fri Apr 26 21:25:19 EDT 2019
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Hi all,
On behalf of the SciPy development team I'm pleased to announce
the release candidate SciPy 1.3.0rc1. Please help us test this pre-release.
Sources and binary wheels can be found at:https://pypi.org/project/scipy/
and at:https://github.com/scipy/scipy/releases/tag/v1.3.0rc1
One of a few ways to install the release candidate with pip:
pip install scipy==1.3.0rc1
==========================
SciPy 1.3.0 Release Notes
==========================
Note: Scipy 1.3.0 is not released yet!
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.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
Checksums
=========
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