[SciPy-Dev] ANN: SciPy 1.6.0

Thu Dec 31 11:05:23 EST 2020

Thanks Tyler!

чт, 31 дек. 2020 г., 18:58 Tyler Reddy <tyler.je.reddy at gmail.com>:

> Hi all,
>
> On behalf of the SciPy development team I'm pleased to announce
> the release of SciPy 1.6.0.
>
> Sources and binary wheels can be found at:
> https://pypi.org/project/scipy/
> and at:
> https://github.com/scipy/scipy/releases/tag/v1.6.0
>
> One of a few ways to install this release with pip:
>
> pip install scipy==1.6.0
>
> =====================
> SciPy 1.6.0 Release Notes
> =====================
>
> SciPy 1.6.0 is the culmination of 6 months of hard work. It contains
> many new features, numerous bug-fixes, improved test coverage and better
> documentation. There have been a number of deprecations and API changes
> in this release, which are documented below. All users are encouraged to
> upgrade to this release, as there are a large number of bug-fixes and
> optimizations. Before upgrading, we recommend that users check that
> their own code does not use deprecated SciPy functionality (to do so,
> run your code with ``python -Wd`` and check for ``DeprecationWarning`` s).
> Our development attention will now shift to bug-fix releases on the
> 1.6.x branch, and on adding new features on the master branch.
>
> This release requires Python 3.7+ and NumPy 1.16.5 or greater.
>
> For running on PyPy, PyPy3 6.0+ is required.
>
> Highlights of this release
> ---------------------------------
>
> -  `scipy.ndimage` improvements: Fixes and ehancements to boundary
> extension
>   modes for interpolation functions. Support for complex-valued inputs in
> many
>   filtering and interpolation functions. New ``grid_mode`` option for
>   `scipy.ndimage.zoom` to enable results consistent with scikit-image's
>   ``rescale``.
> -  `scipy.optimize.linprog` has fast, new methods for large, sparse
> problems
>   from the ``HiGHS`` library.
> -  `scipy.stats` improvements including new distributions, a new test, and
>   enhancements to existing distributions and tests
>
>
> New features
> ==========
>
> `scipy.special` improvements
> ---------------------------------------
> `scipy.special` now has improved support for 64-bit ``LAPACK`` backend
>
> `scipy.odr` improvements
> ----------------------------------
> `scipy.odr` now has support for 64-bit integer ``BLAS``
>
> `scipy.odr.ODR` has gained an optional ``overwrite`` argument so that
> existing
> files may be overwritten.
>
> `scipy.integrate` improvements
> ------------------------------------------
> Some renames of functions with poor names were done, with the old names
> retained without being in the reference guide for backwards compatibility
> reasons:
> -  ``integrate.simps`` was renamed to ``integrate.simpson``
> -  ``integrate.trapz`` was renamed to ``integrate.trapezoid``
> -  ``integrate.cumtrapz`` was renamed to ``integrate.cumulative_trapezoid``
>
> `scipy.cluster` improvements
> ---------------------------------------
> `scipy.cluster.hierarchy.DisjointSet` has been added for incremental
> connectivity queries.
>
> `scipy.cluster.hierarchy.dendrogram` return value now also includes leaf
> color
> information in `leaves_color_list`.
>
> `scipy.interpolate` improvements
> --------------------------------------------
> `scipy.interpolate.interp1d` has a new method ``nearest-up``, similar to
> the
> existing method ``nearest`` but rounds half-integers up instead of down.
>
> `scipy.io` improvements
> --------------------------------
> Support has been added for reading arbitrary bit depth integer PCM WAV
> files
> from 1- to 32-bit, including the commonly-requested 24-bit depth.
>
> `scipy.linalg` improvements
> -------------------------------------
> The new function `scipy.linalg.matmul_toeplitz` uses the FFT to compute
> the
> product of a Toeplitz matrix with another matrix.
>
> `scipy.linalg.sqrtm` and `scipy.linalg.logm` have performance improvements
> thanks to additional Cython code.
>
> Python ``LAPACK`` wrappers have been added for ``pptrf``, ``pptrs``,
> ``ppsv``,
> ``pptri``, and ``ppcon``.
>
> `scipy.linalg.norm` and the ``svd`` family of functions will now use 64-bit
> integer backends when available.
>
> `scipy.ndimage` improvements
> ------------------------------------------
> `scipy.ndimage.convolve`, `scipy.ndimage.correlate` and their 1d
> counterparts
> now accept both complex-valued images and/or complex-valued filter
> kernels. All
> convolution-based filters also now accept complex-valued inputs
> (e.g. ``gaussian_filter``, ``uniform_filter``, etc.).
>
> Multiple fixes and enhancements to boundary handling were introduced to
> `scipy.ndimage` interpolation functions (i.e. ``affine_transform``,
> ``geometric_transform``, ``map_coordinates``, ``rotate``, ``shift``,
> ``zoom``).
>
> A new boundary mode, ``grid-wrap`` was added which wraps images
> periodically,
> using a period equal to the shape of the input image grid. This is in
> contrast
> to the existing ``wrap`` mode which uses a period that is one sample
> smaller
> than the original signal extent along each dimension.
>
> A long-standing bug in the ``reflect`` boundary condition has been fixed
> and
> the mode ``grid-mirror`` was introduced as a synonym for ``reflect``.
>
> A new boundary mode, ``grid-constant`` is now available. This is similar
> to
> the existing ndimage ``constant`` mode, but interpolation will still
> performed
> at coordinate values outside of the original image extent. This
> ``grid-constant`` mode is consistent with OpenCV's ``BORDER_CONSTANT``
> mode
> and scikit-image's ``constant`` mode.
>
> Spline pre-filtering (used internally by ``ndimage`` interpolation
> functions
> when ``order >= 2``), now supports all boundary modes rather than always
> defaulting to mirror boundary conditions. The standalone functions
> ``spline_filter`` and ``spline_filter1d`` have analytical boundary
> conditions
> that match modes ``mirror``, ``grid-wrap`` and ``reflect``.
>
> `scipy.ndimage` interpolation functions now accept complex-valued inputs.
> In
> this case, the interpolation is applied independently to the real and
> imaginary components.
>
> The ``ndimage`` tutorials
> (https://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html) have
> been
> updated with new figures to better clarify the exact behavior of all of
> the
> interpolation boundary modes.
>
> `scipy.ndimage.zoom` now has a ``grid_mode`` option that changes the
> coordinate
> of the center of the first pixel along an axis from 0 to 0.5. This allows
> resizing in a manner that is consistent with the behavior of
> scikit-image's
> ``resize`` and ``rescale`` functions (and OpenCV's ``cv2.resize``).
>
> `scipy.optimize` improvements
> -----------------------------------------
> `scipy.optimize.linprog` has fast, new methods for large, sparse problems
> from
> the ``HiGHS`` C++ library. ``method='highs-ds'`` uses a high performance
> dual
> revised simplex implementation (HSOL), ``method='highs-ipm'`` uses an
> interior-point method with crossover, and ``method='highs'`` chooses
> between
> the two automatically. These methods are typically much faster and often
> exceed
> the accuracy of other ``linprog`` methods, so we recommend explicitly
> specifying one of these three method values when using ``linprog``.
>
> `scipy.optimize.quadratic_assignment` has been added for approximate
> solution
> of the quadratic assignment problem.
>
> `scipy.optimize.linear_sum_assignment` now has a substantially reduced
> overhead
> for small cost matrix sizes
>
> `scipy.optimize.least_squares` has improved performance when the user
> provides
> the jacobian as a sparse jacobian already in ``csr_matrix`` format
>
> `scipy.optimize.linprog` now has an ``rr_method`` argument for
> specification
> of the method used for redundancy handling, and a new method for this
> purpose
> is available based on the interpolative decomposition approach.
>
> `scipy.signal` improvements
> --------------------------------------
> `scipy.signal.gammatone` has been added to design FIR or IIR filters that
> model the human auditory system.
>
> `scipy.signal.iircomb` has been added to design IIR peaking/notching comb
> filters that can boost/attenuate a frequency from a signal.
>
> `scipy.signal.sosfilt` performance has been improved to avoid some
> previously-
> observed slowdowns
>
> `scipy.signal.windows.taylor` has been added--the Taylor window function is
> commonly used in radar digital signal processing
>
> `scipy.signal.gauss_spline` now supports ``list`` type input for
> consistency
> with other related SciPy functions
>
> `scipy.signal.correlation_lags` has been added to allow calculation of the
> lag/
> displacement indices array for 1D cross-correlation.
>
> `scipy.sparse` improvements
> ---------------------------------------
> A solver for the minimum weight full matching problem for bipartite graphs,
> also known as the linear assignment problem, has been added in
> `scipy.sparse.csgraph.min_weight_full_bipartite_matching`. In particular,
> this
> provides functionality analogous to that of
> `scipy.optimize.linear_sum_assignment`, but with improved performance for
> sparse
> inputs, and the ability to handle inputs whose dense representations would
> not
> fit in memory.
>
> The time complexity of `scipy.sparse.block_diag` has been improved
> dramatically
> from quadratic to linear.
>
> `scipy.sparse.linalg` improvements
> -----------------------------------------------
> The vendored version of ``SuperLU`` has been updated
>
> `scipy.fft` improvements
> --------------------------------
>
> The vendored ``pocketfft`` library now supports compiling with ARM neon
> vector
> extensions and has improved thread pool behavior.
>
> `scipy.spatial` improvements
> ---------------------------------------
> The python implementation of ``KDTree`` has been dropped and ``KDTree`` is
> now
> implemented in terms of ``cKDTree``. You can now expect ``cKDTree``-like
> performance by default. This also means ``sys.setrecursionlimit`` no
> longer
> needs to be increased for querying large trees.
>
> ``transform.Rotation`` has been updated with support for Modified
> Rodrigues
> Parameters alongside the existing rotation representations (PR gh-12667).
>
> `scipy.spatial.transform.Rotation` has been partially cythonized, with some
> performance improvements observed
>
> `scipy.spatial.distance.cdist` has improved performance with the
> ``minkowski``
> metric, especially for p-norm values of 1 or 2.
>
> `scipy.stats` improvements
> ------------------------------------
> New distributions have been added to `scipy.stats`:
>
> -  The asymmetric Laplace continuous distribution has been added as
>   `scipy.stats.laplace_asymmetric`.
> -  The negative hypergeometric distribution has been added as
> `scipy.stats.nhypergeom`.
> -  The multivariate t distribution has been added as
> `scipy.stats.multivariate_t`.
> -  The multivariate hypergeometric distribution has been added as
> `scipy.stats.multivariate_hypergeom`.
>
> The ``fit`` method has been overridden for several distributions
> (``laplace``,
> ``pareto``, ``rayleigh``, ``invgauss``, ``logistic``, ``gumbel_l``,
> ``gumbel_r``); they now use analytical, distribution-specific maximum
> likelihood estimation results for greater speed and accuracy than the
> generic
> (numerical optimization) implementation.
>
> The one-sample Cramér-von Mises test has been added as
> `scipy.stats.cramervonmises`.
>
> An option to compute one-sided p-values was added to
> `scipy.stats.ttest_1samp`,
> `scipy.stats.ttest_ind_from_stats`, `scipy.stats.ttest_ind` and
> `scipy.stats.ttest_rel`.
>
> The function `scipy.stats.kendalltau` now has an option to compute
> Kendall's
> tau-c (also known as Stuart's tau-c), and support has been added for exact
> p-value calculations for sample sizes ``> 171``.
>
> `stats.trapz` was renamed to `stats.trapezoid`, with the former name
> retained
> as an alias for backwards compatibility reasons.
>
> The function `scipy.stats.linregress` now includes the standard error of
> the
> intercept in its return value.
>
> The ``_logpdf``, ``_sf``, and ``_isf`` methods have been added to
> `scipy.stats.nakagami`; ``_sf`` and ``_isf`` methods also added to
> `scipy.stats.gumbel_r`
>
> The ``sf`` method has been added to `scipy.stats.levy` and
> `scipy.stats.levy_l`
> for improved precision.
>
> `scipy.stats.binned_statistic_dd` performance improvements for the
> following
> computed statistics: ``max``, ``min``, ``median``, and ``std``.
>
> We gratefully acknowledge the Chan-Zuckerberg Initiative Essential Open
> Source
> Software for Science program for supporting many of these improvements to
> `scipy.stats`.
>
> Deprecated features
> ================
>
> `scipy.spatial` changes
> -------------------------------
> Calling ``KDTree.query`` with ``k=None`` to find all neighbours is
> deprecated.
> Use ``KDTree.query_ball_point`` instead.
>
> ``distance.wminkowski`` was deprecated; use ``distance.minkowski`` and
> supply
> weights with the ``w`` keyword instead.
>
> Backwards incompatible changes
> ==========================
>
> `scipy` changes
> ---------------------
> Using `scipy.fft` as a function aliasing ``numpy.fft.fft`` was removed
> after
> being deprecated in SciPy ``1.4.0``. As a result, the `scipy.fft`
> submodule
> must be explicitly imported now, in line with other SciPy subpackages.
>
> `scipy.signal` changes
> -------------------------------
> The output of ``decimate``, ``lfilter_zi``, ``lfiltic``, ``sos2tf``, and
> ``sosfilt_zi`` have been changed to match ``numpy.result_type`` of their
> inputs.
>
> The window function ``slepian`` was removed. It had been deprecated since
> SciPy
> ``1.1``.
>
> `scipy.spatial` changes
> -------------------------------
> ``cKDTree.query`` now returns 64-bit rather than 32-bit integers on
> Windows,
> making behaviour consistent between platforms (PR gh-12673).
>
>
> `scipy.stats` changes
> -----------------------------
> The ``frechet_l`` and ``frechet_r`` distributions were removed. They were
> deprecated since SciPy ``1.0``.
>
> Other changes
> =============
> ``setup_requires`` was removed from ``setup.py``. This means that users
> invoking ``python setup.py install`` without having numpy already
> installed
> will now get an error, rather than having numpy installed for them via
> ``easy_install``. This install method was always fragile and problematic,
> users
> are encouraged to use ``pip`` when installing from source.
>
> -  Fixed a bug in `scipy.optimize.dual_annealing` ``accept_reject``
> calculation
>   that caused uphill jumps to be accepted less frequently.
> -  The time required for (un)pickling of `scipy.stats.rv_continuous`,
>   `scipy.stats.rv_discrete`, and `scipy.stats.rv_frozen` has been
> significantly
>   reduced (gh12550). Inheriting subclasses should note that
> ``__setstate__`` no
>   longer calls ``__init__`` upon unpickling.
>
> Authors
> =======
>
> * @endolith
> * @vkk800
> * aditya +
> * George Bateman +
> * Christoph Baumgarten
> * Peter Bell
> * Tobias Biester +
> * Keaton J. Burns +
> * Evgeni Burovski
> * Rüdiger Busche +
> * Matthias Bussonnier
> * Dominic C +
> * Corallus Caninus +
> * CJ Carey
> * Thomas A Caswell
> * chapochn +
> * Lucía Cheung
> * Zach Colbert +
> * Coloquinte +
> * Yannick Copin +
> * Devin Crowley +
> * Terry Davis +
> * Michaël Defferrard +
> * devonwp +
> * Didier +
> * divenex +
> * Thomas Duvernay +
> * Eoghan O'Connell +
> * Gökçen Eraslan
> * Kristian Eschenburg +
> * Ralf Gommers
> * Thomas Grainger +
> * GreatV +
> * Gregory Gundersen +
> * h-vetinari +
> * Matt Haberland
> * Mark Harfouche +
> * He He +
> * Alex Henrie
> * Chun-Ming Huang +
> * Martin James McHugh III +
> * Alex Izvorski +
> * Joey +
> * ST John +
> * Jonas Jonker +
> * Julius Bier Kirkegaard
> * Marcin Konowalczyk +
> * Konrad0
> * Sam Van Kooten +
> * Sergey Koposov +
> * Peter Mahler Larsen
> * Eric Larson
> * Antony Lee
> * Gregory R. Lee
> * Loïc Estève
> * Jean-Luc Margot +
> * MarkusKoebis +
> * Nikolay Mayorov
> * G. D. McBain
> * Andrew McCluskey +
> * Nicholas McKibben
> * Sturla Molden
> * Denali Molitor +
> * Eric Moore
> * Shashaank N +
> * Prashanth Nadukandi +
> * nbelakovski +
> * Andrew Nelson
> * Nick +
> * Nikola Forró +
> * odidev
> * ofirr +
> * Sambit Panda
> * Dima Pasechnik
> * Tirth Patel +
> * Matti Picus
> * Paweł Redzyński +
> * Vladimir Philipenko +
> * Philipp Thölke +
> * Ilhan Polat
> * Eugene Prilepin +
> * Vladyslav Rachek
> * Ram Rachum +
> * Tyler Reddy
> * Martin Reinecke +
> * Simon Segerblom Rex +
> * Lucas Roberts
> * Benjamin Rowell +
> * Eli Rykoff +
> * Atsushi Sakai
> * Moritz Schulte +
> * Daniel B. Smith
> * Steve Smith +
> * Jan Soedingrekso +
> * Victor Stinner +
> * Jose Storopoli +
> * Diana Sukhoverkhova +
> * Søren Fuglede Jørgensen
> * taoky +
> * Mike Taves +
> * Ian Thomas +
> * Will Tirone +
> * Frank Torres +
> * Seth Troisi
> * Ronald van Elburg +
> * Hugo van Kemenade
> * Paul van Mulbregt
> * Saul Ivan Rivas Vega +
> * Pauli Virtanen
> * Jan Vleeshouwers
> * Samuel Wallan
> * Warren Weckesser
> * Ben West +
> * Eric Wieser
> * WillTirone +
> * Levi John Wolf +
> * Zhiqing Xiao
> * Rory Yorke +
> * Yun Wang (Maigo) +
> * Egor Zemlyanoy +
> * ZhihuiChen0903 +
> * Jacob Zhong +
>
> A total of 122 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 1.6.0
> -------------------------------
>
> * `#1323 <https://github.com/scipy/scipy/issues/1323>`__: ndimage.shift
> destroys data from edges (Trac #796)
> * `#1892 <https://github.com/scipy/scipy/issues/1892>`__: using rptfile=
> with an existing file causes a Fortran runtime...
> * `#1903 <https://github.com/scipy/scipy/issues/1903>`__: ndimage.rotate
> misses some values (Trac #1378)
> * `#1930 <https://github.com/scipy/scipy/issues/1930>`__:
> scipy.io.wavfile should be able to read 24 bit signed wave (Trac...
> * `#3158 <https://github.com/scipy/scipy/issues/3158>`__: Odd casting
> behaviour of signal.filtfilt
> * `#3203 <https://github.com/scipy/scipy/issues/3203>`__:
> interpolation.zoom incorrect output for certain cases
> * `#3645 <https://github.com/scipy/scipy/issues/3645>`__: BUG: stats:
> mstats.pearsonr calculation is wrong if the masks...
> * `#3665 <https://github.com/scipy/scipy/issues/3665>`__: Return Bunch
> objects from stats functions
> * `#4922 <https://github.com/scipy/scipy/issues/4922>`__: unexpected zero
> output values from zoom
> * `#5202 <https://github.com/scipy/scipy/issues/5202>`__: BUG: stats:
> Spurious warnings from the pdf method of several...
> * `#5223 <https://github.com/scipy/scipy/issues/5223>`__: Zoom does not
> return the same values when resizing a sub-array...
> * `#5396 <https://github.com/scipy/scipy/issues/5396>`__:
> scipy.spatial.distance.pdist documention bug
> * `#5489 <https://github.com/scipy/scipy/issues/5489>`__: ValueError:
> failed to create intent(cache|hide)|optional array--...
> * `#6096 <https://github.com/scipy/scipy/issues/6096>`__: loadmat drops
> dtype of empty arrays when squeeze_me=True
> * `#6713 <https://github.com/scipy/scipy/issues/6713>`__:
> sicpy.ndimage.zoom returns artefacts and boundaries in some cases
> * `#7125 <https://github.com/scipy/scipy/issues/7125>`__: Impossible to
> know number of dimensions in c function used by...
> * `#7324 <https://github.com/scipy/scipy/issues/7324>`__:
> scipy.ndimage.zoom bad interpolation when downsampling (zoom...
> * `#8131 <https://github.com/scipy/scipy/issues/8131>`__: BUG:
> geometric_transform wrap mode possible bug
> * `#8163 <https://github.com/scipy/scipy/issues/8163>`__: LSMR fails on
> some random values when providing an x0
> * `#8210 <https://github.com/scipy/scipy/issues/8210>`__: Why should I
> choose order > 1 for scipy.ndimage.zoom?
> * `#8465 <https://github.com/scipy/scipy/issues/8465>`__: Unexpected
> behavior with reflect mode of ndimage.rotate
> * `#8776 <https://github.com/scipy/scipy/issues/8776>`__: cdist behavior
> with Minkowsky and np.inf
> * `#9168 <https://github.com/scipy/scipy/issues/9168>`__: documentation
> of pearson3 in scipy.stats unclear
> * `#9223 <https://github.com/scipy/scipy/issues/9223>`__: Faster
> implementation of scipy.sparse.block_diag
> * `#9476 <https://github.com/scipy/scipy/issues/9476>`__: Invalid index
> in signal.medfilt2d's QUICK_SELECT
> * `#9857 <https://github.com/scipy/scipy/issues/9857>`__:
> scipy.odr.Output.sd_beta is not standard error
> * `#9865 <https://github.com/scipy/scipy/issues/9865>`__: Strange
> behavior of \`ndimage.shift\` and \`ndimage.affine_transform\`
> * `#10042 <https://github.com/scipy/scipy/issues/10042>`__: Consider
> support for multivariate student-t distribution?
> * `#10134 <https://github.com/scipy/scipy/issues/10134>`__: gausshyper
> distribution accepts invalid parameters
> * `#10179 <https://github.com/scipy/scipy/issues/10179>`__: str+bytes
> concatenation error in test_lapack.py
> * `#10216 <https://github.com/scipy/scipy/issues/10216>`__:
> cKDTree.query_ball_point speed regression
> * `#10463 <https://github.com/scipy/scipy/issues/10463>`__: ENH:
> vectorize scipy.fft for more CPU architectures
> * `#10593 <https://github.com/scipy/scipy/issues/10593>`__: Rename
> \`sum\` ndimage function
> * `#10595 <https://github.com/scipy/scipy/issues/10595>`__:
> scipy.stats.ttest_1samp should support alternative hypothesis
> * `#10610 <https://github.com/scipy/scipy/issues/10610>`__:
> ndimage.interpolation.spline_filter1d default value of mode
> * `#10620 <https://github.com/scipy/scipy/issues/10620>`__:
> ndimage.interpolation.zoom() option to work like skimage.transform.resize()
> * `#10711 <https://github.com/scipy/scipy/issues/10711>`__: Array Shapes
> Not Aligned Bug in scipy.optimize._lsq.lsq_linear.py
> * `#10782 <https://github.com/scipy/scipy/issues/10782>`__: BUG:
> optimize: methods unknown to \`scipy.optimize.show_options\`
> * `#10892 <https://github.com/scipy/scipy/issues/10892>`__: Possible typo
> in an equation of optimize/dual_annealing
> * `#11020 <https://github.com/scipy/scipy/issues/11020>`__:
> signal.fftconvolve return a tuple including lag information
> * `#11093 <https://github.com/scipy/scipy/issues/11093>`__:
> scipy.interpolate.interp1d can not handle datetime64
> * `#11170 <https://github.com/scipy/scipy/issues/11170>`__: Use
> manylinux2014 to get aarch64/ppc64le support
> * `#11186 <https://github.com/scipy/scipy/issues/11186>`__: BUG: stats:
> pearson3 CDF and SF functions incorrect when skew...
> * `#11366 <https://github.com/scipy/scipy/issues/11366>`__:
> DeprecationWarning due to invalid escape sequences
> * `#11403 <https://github.com/scipy/scipy/issues/11403>`__: Optimize
> raises "ValueError: \`x0\` violates bound constraints"...
> * `#11558 <https://github.com/scipy/scipy/issues/11558>`__: ENH: IIR comb
> filter
> * `#11559 <https://github.com/scipy/scipy/issues/11559>`__: BUG:
> iirdesign doesn't fail for frequencies above Nyquist
> * `#11567 <https://github.com/scipy/scipy/issues/11567>`__:
> scipy.signal.iirdesign doesn't check consistency of wp and ws...
> * `#11654 <https://github.com/scipy/scipy/issues/11654>`__: ENH: Add
> Negative Hypergeometric Distribution
> * `#11720 <https://github.com/scipy/scipy/issues/11720>`__: BUG: stats:
> wrong shape from median_absolute_deviation for arrays...
> * `#11746 <https://github.com/scipy/scipy/issues/11746>`__: BUG: stats:
> pearson3 returns size 1 arrays where other distributions...
> * `#11756 <https://github.com/scipy/scipy/issues/11756>`__: Improve and
> fix \*Spline docstrings and code
> * `#11758 <https://github.com/scipy/scipy/issues/11758>`__: BUG: of
> scipy.interpolate.CubicSpline when \`bc_type' is set...
> * `#11925 <https://github.com/scipy/scipy/issues/11925>`__: MAINT: remove
> character encoding check in CI?
> * `#11963 <https://github.com/scipy/scipy/issues/11963>`__: Test failures
> - TestLinprogIPSparseCholmod
> * `#12102 <https://github.com/scipy/scipy/issues/12102>`__: incorrect
> first moment of non central t-distribution
> * `#12113 <https://github.com/scipy/scipy/issues/12113>`__:
> scipy.stats.poisson docs for rate = 0
> * `#12152 <https://github.com/scipy/scipy/issues/12152>`__: ENH:
> signal.gauss_spline should accept a list
> * `#12157 <https://github.com/scipy/scipy/issues/12157>`__: BUG:
> Iteration index initialisation is wrong in
> scipy.optimize.linesearch.scalar_search_wolfe2
> * `#12162 <https://github.com/scipy/scipy/issues/12162>`__: Storing
> Rotation object in NumPy array returns an array with...
> * `#12176 <https://github.com/scipy/scipy/issues/12176>`__: cannot modify
> the slice of an array returned by \`wavfile.read\`
> * `#12190 <https://github.com/scipy/scipy/issues/12190>`__: retrieve
> leave colors from dendrogram
> * `#12196 <https://github.com/scipy/scipy/issues/12196>`__: PERF:
> scipy.linalg.pinv is very slow compared to numpy.linalg.pinv
> * `#12222 <https://github.com/scipy/scipy/issues/12222>`__: Interpolating
> categorical data (interp1d)
> * `#12231 <https://github.com/scipy/scipy/issues/12231>`__: Is the
> p-value of the Kruskal-Wallis test two-sided?
> * `#12249 <https://github.com/scipy/scipy/issues/12249>`__: ENH:
> least_squares: should not re-instanciate csr_matrix if already...
> * `#12264 <https://github.com/scipy/scipy/issues/12264>`__: DOC:
> optimize: linprog method-specific function signature
> * `#12290 <https://github.com/scipy/scipy/issues/12290>`__: DOC: Convex
> Hull areas are actually perimeters for 2-dimensional...
> * `#12308 <https://github.com/scipy/scipy/issues/12308>`__:
> integrate.solve_ivp with DOP853 method fails when yDot = 0
> * `#12326 <https://github.com/scipy/scipy/issues/12326>`__: BUG:
> stats.exponnorm.pdf returns 0 for small K
> * `#12337 <https://github.com/scipy/scipy/issues/12337>`__:
> scipy.sparse.linalg.eigsh documentation is misleading
> * `#12339 <https://github.com/scipy/scipy/issues/12339>`__:
> scipy.io.wavfile.write documentation has wrong example
> * `#12340 <https://github.com/scipy/scipy/issues/12340>`__:
> sparse.lil_matrix.tocsr() fails silently on matrices with nzn...
> * `#12350 <https://github.com/scipy/scipy/issues/12350>`__: Create a
> 2-parameter version of the gamma distribution
> * `#12369 <https://github.com/scipy/scipy/issues/12369>`__:
> scipy.signal.correlate has an error in the documentation, examples...
> * `#12373 <https://github.com/scipy/scipy/issues/12373>`__: interp1d
> returns incorrect values for step functions
> * `#12378 <https://github.com/scipy/scipy/issues/12378>`__:
> interpolate.NearestNDInterpolator.__call__ &
> LinearNDInterpolator.__call__...
> * `#12411 <https://github.com/scipy/scipy/issues/12411>`__:
> scipy.stats.spearmanr mishandles nan variables with "propogate"
> * `#12413 <https://github.com/scipy/scipy/issues/12413>`__: DOC: Remove
> the "Basic functions" section from the SciPy tutorial.
> * `#12415 <https://github.com/scipy/scipy/issues/12415>`__:
> scipy.stats.dirichlet documentation issue
> * `#12419 <https://github.com/scipy/scipy/issues/12419>`__: least_squares
> ValueError with 'lm' method - regression from 1.4.1...
> * `#12431 <https://github.com/scipy/scipy/issues/12431>`__: Request for
> Python wrapper for LAPACK's ?pptrf (Cholesky factorization...
> * `#12458 <https://github.com/scipy/scipy/issues/12458>`__: spearmanr
> with entire NaN columns produces errors
> * `#12477 <https://github.com/scipy/scipy/issues/12477>`__: WIP: Addition
> of MLE for stats.invgauss/wald
> * `#12483 <https://github.com/scipy/scipy/issues/12483>`__: reading .wav
> fails when the file is too big on python 3.6.0
> * `#12490 <https://github.com/scipy/scipy/issues/12490>`__: BUG: stats:
> logistic and genlogistic logpdf overflow for large...
> * `#12499 <https://github.com/scipy/scipy/issues/12499>`__:
> LinearNDInterpolator raises ValueError when value array has
> writeable=False...
> * `#12523 <https://github.com/scipy/scipy/issues/12523>`__: Wrong key in
> __odrpack.c
> * `#12547 <https://github.com/scipy/scipy/issues/12547>`__: typo in
> scipy/cluster/_hierarchy.pyx
> * `#12549 <https://github.com/scipy/scipy/issues/12549>`__: DOC:
> least_squares return type is poorly formatted.
> * `#12578 <https://github.com/scipy/scipy/issues/12578>`__: TST:
> test_bounds_infeasible_2 failing on wheels repo cron jobs
> * `#12585 <https://github.com/scipy/scipy/issues/12585>`__: ENH: Add
> Multivariate Hypergeometric Distribution
> * `#12604 <https://github.com/scipy/scipy/issues/12604>`__: unintuitive
> conversion in \`scipy.constants.lambda2nu\`
> * `#12606 <https://github.com/scipy/scipy/issues/12606>`__: DOC: Invalid
> syntax in example.
> * `#12665 <https://github.com/scipy/scipy/issues/12665>`__: List of
> possible bugs found by automated code analysis
> * `#12696 <https://github.com/scipy/scipy/issues/12696>`__:
> scipy.optimize.fminbound, numpy depreciation warning Creating...
> * `#12699 <https://github.com/scipy/scipy/issues/12699>`__:
> TestProjections.test_iterative_refinements_dense failure
> * `#12701 <https://github.com/scipy/scipy/issues/12701>`__:
> TestDifferentialEvolutionSolver::test_L4 failing
> * `#12719 <https://github.com/scipy/scipy/issues/12719>`__: Misleading
> scipy.signal.get_window() docstring with 'exponential'...
> * `#12740 <https://github.com/scipy/scipy/issues/12740>`__: circstd
> doesn't handle R = hypot(S, C) > 1
> * `#12749 <https://github.com/scipy/scipy/issues/12749>`__: ENH: interp1d
> Matlab compatibility
> * `#12773 <https://github.com/scipy/scipy/issues/12773>`__: Meta-issue:
> ndimage spline boundary handling (NumFOCUS proposal)
> * `#12813 <https://github.com/scipy/scipy/issues/12813>`__:
> optimize.root(method="krylov") fails if options["tol_norm"] expects...
> * `#12815 <https://github.com/scipy/scipy/issues/12815>`__: stats.zscore
> inconsistent behavior when all values are the same
> * `#12840 <https://github.com/scipy/scipy/issues/12840>`__:
> scipy.signal.windows.dpss docstring typo
> * `#12874 <https://github.com/scipy/scipy/issues/12874>`__:
> Rotation.random vs stats.special_ortho_group
> * `#12881 <https://github.com/scipy/scipy/issues/12881>`__: FFT -
> documentation - examples - linspace construction
> * `#12904 <https://github.com/scipy/scipy/issues/12904>`__: BUG: parsing
> in loadarff()
> * `#12917 <https://github.com/scipy/scipy/issues/12917>`__: GitHub
> Actions nightly build triggered on forks
> * `#12919 <https://github.com/scipy/scipy/issues/12919>`__: BUG:
> numerical precision, use gammaln in nct.mean
> * `#12924 <https://github.com/scipy/scipy/issues/12924>`__: Rename Sample
> Based Integration Methods to Comply with Code of...
> * `#12940 <https://github.com/scipy/scipy/issues/12940>`__: Should the
> minimum numpy for AIX be bumped to 1.16.5
> * `#12951 <https://github.com/scipy/scipy/issues/12951>`__: A possible
> typo in scipy.stats.weightedtau
> * `#12952 <https://github.com/scipy/scipy/issues/12952>`__:
> [Documentation question] Would it be more precise to specify...
> * `#12970 <https://github.com/scipy/scipy/issues/12970>`__: Documentation
> presents second order sections as the correct choice...
> * `#12982 <https://github.com/scipy/scipy/issues/12982>`__: Calculate
> standard error of the intercept in linregress
> * `#12985 <https://github.com/scipy/scipy/issues/12985>`__: Possible
> wrong link in scipy.stats.wilcoxon doc
> * `#12991 <https://github.com/scipy/scipy/issues/12991>`__: least_squares
> broken with float32
> * `#13001 <https://github.com/scipy/scipy/issues/13001>`__:
> \`OptimizeResult.message\` from \`L-BFGS-B\` is a bytes, not...
> * `#13030 <https://github.com/scipy/scipy/issues/13030>`__: BUG:
> lint_diff.py still fails for backport PRs
> * `#13077 <https://github.com/scipy/scipy/issues/13077>`__: CI: codecov
> proper patch diffs
> * `#13085 <https://github.com/scipy/scipy/issues/13085>`__: Build failing
> on main branch after HiGHS solver merge
> * `#13088 <https://github.com/scipy/scipy/issues/13088>`__: BLD, BUG:
> wheel builds failure with HiGHS/optimize
> * `#13099 <https://github.com/scipy/scipy/issues/13099>`__: Wrong output
> format for empty sparse results of kron
> * `#13108 <https://github.com/scipy/scipy/issues/13108>`__: TST, CI:
> GitHub Actions MacOS Failures
> * `#13111 <https://github.com/scipy/scipy/issues/13111>`__: BUG, DOC:
> refguide check is failing
> * `#13127 <https://github.com/scipy/scipy/issues/13127>`__: ODR output
> file writing broken in conda env with system compilers
> * `#13134 <https://github.com/scipy/scipy/issues/13134>`__: FromTravis
> migration tracker
> * `#13140 <https://github.com/scipy/scipy/issues/13140>`__: BUG: signal:
> \`ss2tf\` incorrectly truncates output to integers.
> * `#13179 <https://github.com/scipy/scipy/issues/13179>`__: CI: lint is
> failing because of output to stderr
> * `#13182 <https://github.com/scipy/scipy/issues/13182>`__: Key appears
> twice in \`test_optimize.test_show_options\`
> * `#13191 <https://github.com/scipy/scipy/issues/13191>`__:
> \`scipy.linalg.lapack.dgesjv\` overwrites original arrays if...
> * `#13207 <https://github.com/scipy/scipy/issues/13207>`__: TST: Erratic
> test failure in test_cossin_separate
> * `#13221 <https://github.com/scipy/scipy/issues/13221>`__: BUG:
> pavement.py glitch
> * `#13239 <https://github.com/scipy/scipy/issues/13239>`__: Segmentation
> fault with \`eigh(..., driver="evx")\` for 10x10...
> * `#13248 <https://github.com/scipy/scipy/issues/13248>`__: ndimage:
> improper cval handling for complex-valued inputs
>
> Pull requests for 1.6.0
> ------------------------------
>
> * `#8032 <https://github.com/scipy/scipy/pull/8032>`__: ENH: Add in
> taylor window common in Radar processing
> * `#8779 <https://github.com/scipy/scipy/pull/8779>`__: CI: Run benchmarks
> * `#9361 <https://github.com/scipy/scipy/pull/9361>`__: ENH: Add
> Kendall's tau-a and tau-c variants to scipy.stats.kendalltau()
> * `#11068 <https://github.com/scipy/scipy/pull/11068>`__: ENH: Adds
> correlation_lags function to scipy.signal
> * `#11119 <https://github.com/scipy/scipy/pull/11119>`__: ENH: add
> Cramer-von-Mises (one-sample) test to scipy.stats
> * `#11249 <https://github.com/scipy/scipy/pull/11249>`__: ENH: optimize:
> interpolative decomposition redundancy removal...
> * `#11346 <https://github.com/scipy/scipy/pull/11346>`__: ENH: add fast
> toeplitz matrix multiplication using FFT
> * `#11413 <https://github.com/scipy/scipy/pull/11413>`__: ENH:
> Multivariate t-distribution (stale)
> * `#11563 <https://github.com/scipy/scipy/pull/11563>`__: ENH: exact
> p-value in stats.kendalltau() for sample sizes > 171
> * `#11691 <https://github.com/scipy/scipy/pull/11691>`__: ENH: add a
> stack of reversal functions to linprog
> * `#12043 <https://github.com/scipy/scipy/pull/12043>`__: ENH: optimize:
> add HiGHS methods to linprog - continued
> * `#12061 <https://github.com/scipy/scipy/pull/12061>`__: Check parameter
> consistensy in signal.iirdesign
> * `#12067 <https://github.com/scipy/scipy/pull/12067>`__: MAINT: Cleanup
> OLDAPI in ndimage/src/_ctest.c
> * `#12069 <https://github.com/scipy/scipy/pull/12069>`__: DOC: Add
> developer guidelines for implementing the nan_policy...
> * `#12077 <https://github.com/scipy/scipy/pull/12077>`__: MAINT: malloc
> return value checks for cython
> * `#12080 <https://github.com/scipy/scipy/pull/12080>`__: MAINT: Remove
> suppress_warnings
> * `#12085 <https://github.com/scipy/scipy/pull/12085>`__: ENH: special:
> support ILP64 Lapack
> * `#12086 <https://github.com/scipy/scipy/pull/12086>`__: MAINT: Cleanup
> PyMODINIT_FUNC used during 2to3
> * `#12097 <https://github.com/scipy/scipy/pull/12097>`__: ENH: stats:
> override stats.rayleigh.fit with analytical MLE
> * `#12112 <https://github.com/scipy/scipy/pull/12112>`__: DOC: Improve
> integrate.nquad docstring
> * `#12125 <https://github.com/scipy/scipy/pull/12125>`__: TST: Add a test
> for stats.gmean with negative input
> * `#12139 <https://github.com/scipy/scipy/pull/12139>`__: TST: Reduce
> flakiness in lsmr test
> * `#12142 <https://github.com/scipy/scipy/pull/12142>`__: DOC: add a note
> in poisson distribution when mu=0 and k=0 in...
> * `#12144 <https://github.com/scipy/scipy/pull/12144>`__: DOC: Update
> ndimage.morphology.distance_transform\*
> * `#12154 <https://github.com/scipy/scipy/pull/12154>`__: ENH:
> scipy.signal: allow lists in gauss_spline
> * `#12170 <https://github.com/scipy/scipy/pull/12170>`__: ENH:
> scipy.stats: add negative hypergeometric distribution
> * `#12177 <https://github.com/scipy/scipy/pull/12177>`__: MAINT:
> Correctly add input line to ValueError
> * `#12183 <https://github.com/scipy/scipy/pull/12183>`__: ENH: Use
> fromfile where possible
> * `#12186 <https://github.com/scipy/scipy/pull/12186>`__: MAINT:
> generalize tests in SphericalVoronoi
> * `#12198 <https://github.com/scipy/scipy/pull/12198>`__: TST: Fix str +
> bytes error
> * `#12199 <https://github.com/scipy/scipy/pull/12199>`__: ENH: match
> np.result_type behaviour in some scipy.signal functions
> * `#12200 <https://github.com/scipy/scipy/pull/12200>`__: ENH: add FIR
> and IIR gammatone filters to scipy.signal
> * `#12204 <https://github.com/scipy/scipy/pull/12204>`__: ENH: Add
> overwrite argument for odr.ODR() and its test.
> * `#12206 <https://github.com/scipy/scipy/pull/12206>`__: MAINT:lstsq:
> Switch to tranposed problem if the array is tall
> * `#12208 <https://github.com/scipy/scipy/pull/12208>`__: wavfile
> bugfixes and maintenance
> * `#12214 <https://github.com/scipy/scipy/pull/12214>`__: DOC: fix
> docstring of "sd_beta" of odr.Output.
> * `#12234 <https://github.com/scipy/scipy/pull/12234>`__: MAINT: prevent
> divide by zero warnings in scipy.optimize BFGS...
> * `#12235 <https://github.com/scipy/scipy/pull/12235>`__: REL: set
> version to 1.6.0.dev0
> * `#12237 <https://github.com/scipy/scipy/pull/12237>`__: BUG: Fix exit
> condition for QUICK_SELECT pivot
> * `#12242 <https://github.com/scipy/scipy/pull/12242>`__: ENH: Rename
> ndimage.sum to ndimage.sum_labels (keep sum as alias)
> * `#12243 <https://github.com/scipy/scipy/pull/12243>`__: EHN: Update
> SuperLU
> * `#12244 <https://github.com/scipy/scipy/pull/12244>`__: MAINT: stats:
> avoid spurious warnings in ncx2.pdf
> * `#12245 <https://github.com/scipy/scipy/pull/12245>`__: DOC: Fixed
> incorrect default for mode in scipy.ndimage.spline_filter1d
> * `#12248 <https://github.com/scipy/scipy/pull/12248>`__: MAINT: clean up
> pavement.py
> * `#12250 <https://github.com/scipy/scipy/pull/12250>`__: ENH: Replaced
> csr_matrix() by tocsr() and complemented docstring
> * `#12253 <https://github.com/scipy/scipy/pull/12253>`__: TST, CI: turn
> on codecov patch diffs
> * `#12259 <https://github.com/scipy/scipy/pull/12259>`__: MAINT: Remove
> duplicated test for import cycles
> * `#12263 <https://github.com/scipy/scipy/pull/12263>`__: ENH: Rename
> LocalSearchWrapper bounds
> * `#12265 <https://github.com/scipy/scipy/pull/12265>`__: BUG optimize:
> Accept np.matrix in lsq_linear
> * `#12266 <https://github.com/scipy/scipy/pull/12266>`__: BUG: Fix paren
> error in dual annealing accept_reject calculation
> * `#12269 <https://github.com/scipy/scipy/pull/12269>`__: MAINT: Included
> mismatched shapes in error messages.
> * `#12279 <https://github.com/scipy/scipy/pull/12279>`__: MAINT:
> \`__array__\` and array protocols cannot be used in sparse.
> * `#12281 <https://github.com/scipy/scipy/pull/12281>`__: DOC: update
> wheel DL docs
> * `#12283 <https://github.com/scipy/scipy/pull/12283>`__: ENH: odr: ILP64
> Blas support in ODR
> * `#12284 <https://github.com/scipy/scipy/pull/12284>`__: ENH: linalg:
> support for ILP64 BLAS/LAPACK in f2py wrappers
> * `#12286 <https://github.com/scipy/scipy/pull/12286>`__: ENH: Cythonize
> scipy.spatial.transform.Rotation
> * `#12287 <https://github.com/scipy/scipy/pull/12287>`__: ENH: Read
> arbitrary bit depth (including 24-bit) WAVs
> * `#12292 <https://github.com/scipy/scipy/pull/12292>`__: BLD: fix musl
> compilation
> * `#12293 <https://github.com/scipy/scipy/pull/12293>`__: MAINT: Fix a
> DeprecationWarning in validate_runtests_log.py.
> * `#12296 <https://github.com/scipy/scipy/pull/12296>`__: DOC: Clarify
> area/volume in scipy.spatial.ConvexHull docstrings
> * `#12302 <https://github.com/scipy/scipy/pull/12302>`__: CI: Run travis
> builds on master to keep cache up to date
> * `#12305 <https://github.com/scipy/scipy/pull/12305>`__: TST: Cleanup
> print statements in tests
> * `#12323 <https://github.com/scipy/scipy/pull/12323>`__: ENH: Add a
> Bunch-like class to use as a backwards compatible...
> * `#12324 <https://github.com/scipy/scipy/pull/12324>`__: BUG: io: Fix an
> error that occurs when attempting to raise a...
> * `#12327 <https://github.com/scipy/scipy/pull/12327>`__: DOC: clarify
> docstrings of \`query_ball_tree\` and \`query_pairs\`
> * `#12334 <https://github.com/scipy/scipy/pull/12334>`__: PERF: Improve
> cKDTree.query_ball_point constant time cython overhead
> * `#12338 <https://github.com/scipy/scipy/pull/12338>`__: DOC: improve
> consistency and clarity of docs in linalg and sparse/linalg
> * `#12341 <https://github.com/scipy/scipy/pull/12341>`__: DOC: add
> Examples for KDTree query_ball_tree and query_pairs
> * `#12343 <https://github.com/scipy/scipy/pull/12343>`__: DOC: add
> examples for special.eval_legendre()
> * `#12349 <https://github.com/scipy/scipy/pull/12349>`__: BUG: avoid
> overflow in sum() for 32-bit systems
> * `#12351 <https://github.com/scipy/scipy/pull/12351>`__: DOC: Fix
> example wavfile to be 16bit
> * `#12352 <https://github.com/scipy/scipy/pull/12352>`__: [BUG] Consider
> 0/0 division in DOP853 error estima
>
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