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ANN: SciPy 1.6.0
by Tyler Reddy Dec. 31, 2020

Dec. 31, 2020

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 estimation * `#12353 <https://github.com/scipy/scipy/pull/12353>`__: Fix exception causes in vq.py * `#12354 <https://github.com/scipy/scipy/pull/12354>`__: MAINT: Cleanup unneeded void\* cast in setlist.pxd * `#12355 <https://github.com/scipy/scipy/pull/12355>`__: TST: Remove hack for old win-amd64 bug * `#12356 <https://github.com/scipy/scipy/pull/12356>`__: ENH: Faster implementation of scipy.sparse.block_diag (#9411... * `#12357 <https://github.com/scipy/scipy/pull/12357>`__: MAINT,TST: update and run scipy/special/utils/convert.py * `#12358 <https://github.com/scipy/scipy/pull/12358>`__: TST: Check mstat.skewtest pvalue * `#12359 <https://github.com/scipy/scipy/pull/12359>`__: TST: Sparse matrix test with int64 indptr and indices * `#12363 <https://github.com/scipy/scipy/pull/12363>`__: DOC: ref. in CloughTocher2DInterpolator * `#12364 <https://github.com/scipy/scipy/pull/12364>`__: DOC: \`sparse_distance_matrix\` and \`count_neighbors\` examples * `#12371 <https://github.com/scipy/scipy/pull/12371>`__: MAINT, CI: bump to latest stable OpenBLAS * `#12372 <https://github.com/scipy/scipy/pull/12372>`__: MAINT: Minor cleanup of (c)KDTree tests * `#12374 <https://github.com/scipy/scipy/pull/12374>`__: DEP: Deprecate \`distance.wminkowski\` * `#12375 <https://github.com/scipy/scipy/pull/12375>`__: ENH: Add fast path for minkowski distance with p=1,2 and support... * `#12376 <https://github.com/scipy/scipy/pull/12376>`__: Fix exception causes in most of the codebase * `#12377 <https://github.com/scipy/scipy/pull/12377>`__: DOC: Quick fix - adds newline to correlation_lags docstring Examples... * `#12381 <https://github.com/scipy/scipy/pull/12381>`__: BENCH: remove obsolete goal_time param * `#12382 <https://github.com/scipy/scipy/pull/12382>`__: ENH: Replace KDTree with a thin wrapper over cKDTree * `#12385 <https://github.com/scipy/scipy/pull/12385>`__: DOC: improve docstrings of interpolate.NearestNDInterpolator.__call__... * `#12387 <https://github.com/scipy/scipy/pull/12387>`__: DOC/STY: add example to scipy.signal.correlate * `#12393 <https://github.com/scipy/scipy/pull/12393>`__: CI: Replace the existing check for non-ASCII characters with... * `#12394 <https://github.com/scipy/scipy/pull/12394>`__: CI: arm64 numpy now available * `#12395 <https://github.com/scipy/scipy/pull/12395>`__: ENH: improve stats.binned_statistic_dd performance * `#12396 <https://github.com/scipy/scipy/pull/12396>`__: DOC, MAINT: forward port 1.5.0 relnotes * `#12398 <https://github.com/scipy/scipy/pull/12398>`__: API: Disable len() and indexing of Rotation instances with single... * `#12399 <https://github.com/scipy/scipy/pull/12399>`__: MAINT: Replace some Unicode dash-like chars with an ASCII hyphen. * `#12402 <https://github.com/scipy/scipy/pull/12402>`__: update .mailmap * `#12404 <https://github.com/scipy/scipy/pull/12404>`__: MAINT: io: Change the encoding comment of test_mio.py to utf-8. * `#12416 <https://github.com/scipy/scipy/pull/12416>`__: CI: cache mingw, azure pipelines * `#12427 <https://github.com/scipy/scipy/pull/12427>`__: BUG: logic error in loop unrolling (cKDTree) * `#12432 <https://github.com/scipy/scipy/pull/12432>`__: DOC: Remove the "Basic functions" section from the SciPy tutorial. * `#12434 <https://github.com/scipy/scipy/pull/12434>`__: ENH:linalg: Add LAPACK wrappers pptrf/pptrs/ppsv/pptri/ppcon * `#12435 <https://github.com/scipy/scipy/pull/12435>`__: DOC: fix simplex math for scipy.stats.dirichlet documentation * `#12439 <https://github.com/scipy/scipy/pull/12439>`__: DOC: add API methods summary for NdPPoly * `#12443 <https://github.com/scipy/scipy/pull/12443>`__: BUG: stats: Improve calculation of exponnorm.pdf * `#12448 <https://github.com/scipy/scipy/pull/12448>`__: DOC: stats: Add "Examples" to the ansari docstring. * `#12450 <https://github.com/scipy/scipy/pull/12450>`__: ENH: add \`leaves_color_list\` for cluster.dendrogram dictionary. * `#12451 <https://github.com/scipy/scipy/pull/12451>`__: MAINT: remove "blacklist" terminology from code base * `#12452 <https://github.com/scipy/scipy/pull/12452>`__: DOC: clarify the meaning of whitening for cluster.vq.whiten() * `#12455 <https://github.com/scipy/scipy/pull/12455>`__: MAINT: clearer error message in setup.py * `#12457 <https://github.com/scipy/scipy/pull/12457>`__: ENH: stats: override stats.pareto.fit with analytical MLE * `#12460 <https://github.com/scipy/scipy/pull/12460>`__: check if column in spearman rho is entirely NaN or Inf * `#12463 <https://github.com/scipy/scipy/pull/12463>`__: DOC: improve and clean up \*Spline docstrings in fitpack2.py * `#12474 <https://github.com/scipy/scipy/pull/12474>`__: ENH: linalg: speedup _sqrtm_triu by moving tight loop to Cython * `#12476 <https://github.com/scipy/scipy/pull/12476>`__: ENH: add IIR comb filter to scipy.signal * `#12484 <https://github.com/scipy/scipy/pull/12484>`__: Fix documentation for minimize * `#12486 <https://github.com/scipy/scipy/pull/12486>`__: DOC: add a note in poisson distribution when mu=0 and k=0 in... * `#12491 <https://github.com/scipy/scipy/pull/12491>`__: MAINT: forward port 1.5.1 release notes * `#12508 <https://github.com/scipy/scipy/pull/12508>`__: Fix exception causes all over the codebase * `#12514 <https://github.com/scipy/scipy/pull/12514>`__: ENH: stats: override stats.invgauss.fit with analytical MLE * `#12519 <https://github.com/scipy/scipy/pull/12519>`__: PERF: Avoid np.zeros when custom initialization is needed anyway * `#12520 <https://github.com/scipy/scipy/pull/12520>`__: DOC: Minor RST section renaming. * `#12521 <https://github.com/scipy/scipy/pull/12521>`__: MAINT: Remove unused imports * `#12522 <https://github.com/scipy/scipy/pull/12522>`__: PERF: Get rid of unnececssary allocation in VarReader5.cread_fieldnames * `#12524 <https://github.com/scipy/scipy/pull/12524>`__: DOC: special: Set Axes3D rect to avoid clipping labels in plot. * `#12525 <https://github.com/scipy/scipy/pull/12525>`__: Fix large sparse nnz * `#12526 <https://github.com/scipy/scipy/pull/12526>`__: DOC: Remove double section and too long header underline. * `#12527 <https://github.com/scipy/scipy/pull/12527>`__: Improve error message for wrong interpolation type * `#12530 <https://github.com/scipy/scipy/pull/12530>`__: Move redundant logic outside loop for conditional speedup in... * `#12532 <https://github.com/scipy/scipy/pull/12532>`__: ENH: Add norm={"forward", "backward"} to \`scipy.fft\` * `#12535 <https://github.com/scipy/scipy/pull/12535>`__: MAINT: Avoid sphinx deprecated aliases for SeeAlso and Only * `#12540 <https://github.com/scipy/scipy/pull/12540>`__: BUG: fix odr.output.work_ind key bug and add its test. * `#12541 <https://github.com/scipy/scipy/pull/12541>`__: ENH: add solver for minimum weight full bipartite matching * `#12550 <https://github.com/scipy/scipy/pull/12550>`__: PERF: pickling speed of rv\* * `#12551 <https://github.com/scipy/scipy/pull/12551>`__: DOC: fix typo in cluster/_hierarchy.pyx * `#12552 <https://github.com/scipy/scipy/pull/12552>`__: CI: Cleanup travis pip installs * `#12556 <https://github.com/scipy/scipy/pull/12556>`__: BUG: Fix problem with Scipy.integrate.solve_bvp for big problems * `#12557 <https://github.com/scipy/scipy/pull/12557>`__: MAINT: Use extern templates to improve sparsetools compile time * `#12558 <https://github.com/scipy/scipy/pull/12558>`__: MAINT: Remove hack to allow scipy.fft to act like a function * `#12563 <https://github.com/scipy/scipy/pull/12563>`__: MAINT: Remove unused mu0 in special/orthogonal.py * `#12564 <https://github.com/scipy/scipy/pull/12564>`__: DOC: fix return type docstring for least_squares * `#12565 <https://github.com/scipy/scipy/pull/12565>`__: DOC: stats: respond to query about Kruskal-Wallis test being... * `#12566 <https://github.com/scipy/scipy/pull/12566>`__: BUG: Interpolate: use stable sort * `#12568 <https://github.com/scipy/scipy/pull/12568>`__: Updated documentation for as_quat * `#12571 <https://github.com/scipy/scipy/pull/12571>`__: DEP: remove deprecated slepian window * `#12573 <https://github.com/scipy/scipy/pull/12573>`__: DEP: remove \`frechet_l\` and \`frechet_r\` * `#12575 <https://github.com/scipy/scipy/pull/12575>`__: BUG: stats: fix multinomial.pmf NaNs when params sum > 1 * `#12576 <https://github.com/scipy/scipy/pull/12576>`__: MAINT: remove warning from LSQSphereBivariateSpline * `#12582 <https://github.com/scipy/scipy/pull/12582>`__: ENH: Multivariate t-distribution * `#12587 <https://github.com/scipy/scipy/pull/12587>`__: ENH: speed up rvs of gengamma in scipy.stats * `#12588 <https://github.com/scipy/scipy/pull/12588>`__: DOC: add Examples add see also sections for LinearNDInterpolator,... * `#12597 <https://github.com/scipy/scipy/pull/12597>`__: ENH: Add single-sided p-values to t-tests * `#12599 <https://github.com/scipy/scipy/pull/12599>`__: Small update to scipy FFT tutorial * `#12600 <https://github.com/scipy/scipy/pull/12600>`__: ENH: disjoint set data structure * `#12602 <https://github.com/scipy/scipy/pull/12602>`__: BUG: add const for Read-only views in interpnd.pyx * `#12605 <https://github.com/scipy/scipy/pull/12605>`__: BUG: correct \`np.asanyarray\` use in \`scipy.constants.lambda2nu\` * `#12610 <https://github.com/scipy/scipy/pull/12610>`__: MAINT: forward port 1.5.2 release notes * `#12612 <https://github.com/scipy/scipy/pull/12612>`__: MAINT: stats: Use explicit keyword parameters instead of \`\*\*kwds\`. * `#12616 <https://github.com/scipy/scipy/pull/12616>`__: DOC: make explicit docstring that interpolate.interp1d only accepts... * `#12618 <https://github.com/scipy/scipy/pull/12618>`__: DOC: Minor doc formatting. * `#12640 <https://github.com/scipy/scipy/pull/12640>`__: MAINT: stats: fix issues with scipy.stats.pearson3 docs, moment,... * `#12647 <https://github.com/scipy/scipy/pull/12647>`__: TST: Add Boost ellipr[cdfgj]_data test data * `#12648 <https://github.com/scipy/scipy/pull/12648>`__: DOC: Update special/utils/README with instructions * `#12649 <https://github.com/scipy/scipy/pull/12649>`__: DOC: simplified pip quickstart guide * `#12650 <https://github.com/scipy/scipy/pull/12650>`__: DOC: stats: Fix boxcox docstring: lambda can be negative. * `#12655 <https://github.com/scipy/scipy/pull/12655>`__: DOC: update Steering Council members listed in governance docs * `#12659 <https://github.com/scipy/scipy/pull/12659>`__: rv_sample expect bug * `#12663 <https://github.com/scipy/scipy/pull/12663>`__: DOC: optimize: try to fix linprog method-specific documentation * `#12664 <https://github.com/scipy/scipy/pull/12664>`__: BUG: stats: Fix logpdf with large negative values for logistic... * `#12666 <https://github.com/scipy/scipy/pull/12666>`__: MAINT: Fixes from static analysis * `#12667 <https://github.com/scipy/scipy/pull/12667>`__: ENH: Adding Modified Rodrigues Parameters to the Rotation class * `#12670 <https://github.com/scipy/scipy/pull/12670>`__: DOC: Update documentation for Gamma distribution * `#12673 <https://github.com/scipy/scipy/pull/12673>`__: API: Unconditionally return np.intp from cKDTree.query * `#12677 <https://github.com/scipy/scipy/pull/12677>`__: MAINT: Add Autogenerated notice to ufuncs.pyi * `#12682 <https://github.com/scipy/scipy/pull/12682>`__: MAINT: Remove _util._valarray * `#12688 <https://github.com/scipy/scipy/pull/12688>`__: MAINT: add f2py-generated scipy.integrate files to .gitignore * `#12689 <https://github.com/scipy/scipy/pull/12689>`__: BENCH: simplify benchmark setup, remove benchmarks/run.py * `#12694 <https://github.com/scipy/scipy/pull/12694>`__: scipy/stats: Add laplace_asymmetric continuous distribution * `#12695 <https://github.com/scipy/scipy/pull/12695>`__: DOC: update Ubuntu quickstart; conda compilers now work! * `#12698 <https://github.com/scipy/scipy/pull/12698>`__: MAINT: Replace np.max with np.maximum * `#12700 <https://github.com/scipy/scipy/pull/12700>`__: TST: bump test precision for constrained trustregion test * `#12702 <https://github.com/scipy/scipy/pull/12702>`__: TST: bump test tolerance for \`DifferentialEvolutionSolver.test_L4\` * `#12703 <https://github.com/scipy/scipy/pull/12703>`__: BUG: Improve input validation for sepfir2d * `#12708 <https://github.com/scipy/scipy/pull/12708>`__: MAINT: fix a typo in scipy.sparse * `#12709 <https://github.com/scipy/scipy/pull/12709>`__: BUG: bvls can fail catastrophically to converge * `#12711 <https://github.com/scipy/scipy/pull/12711>`__: MAINT: Use platform.python_implementation to determine IS_PYPY * `#12713 <https://github.com/scipy/scipy/pull/12713>`__: TST: Fix flaky test_lgmres * `#12716 <https://github.com/scipy/scipy/pull/12716>`__: DOC: add examples and tutorial links for interpolate functions... * `#12717 <https://github.com/scipy/scipy/pull/12717>`__: DOC: Fix Issue #5396 * `#12725 <https://github.com/scipy/scipy/pull/12725>`__: ENH: Support complex-valued images and kernels for many ndimage... * `#12729 <https://github.com/scipy/scipy/pull/12729>`__: DEP: remove setup_requires * `#12732 <https://github.com/scipy/scipy/pull/12732>`__: BENCH: skip benchmarks instead of hiding them when SCIPY_XSLOW=0 * `#12734 <https://github.com/scipy/scipy/pull/12734>`__: CI: Don't ignore line-length in the lint_diff check. * `#12736 <https://github.com/scipy/scipy/pull/12736>`__: DOC: Fix signal.windows.get_window() 'exponential' docstring * `#12737 <https://github.com/scipy/scipy/pull/12737>`__: ENH: stats: override stats.gumbel_r.fit and stats.gumbel_l.fit... * `#12738 <https://github.com/scipy/scipy/pull/12738>`__: ENH: stats: override stats.logistic.fit with system of equations... * `#12743 <https://github.com/scipy/scipy/pull/12743>`__: BUG: Avoid negative variances in circular statistics * `#12744 <https://github.com/scipy/scipy/pull/12744>`__: Prevent build error on GNU/Hurd * `#12746 <https://github.com/scipy/scipy/pull/12746>`__: TST: parameterize the test cases in test_ndimage.py * `#12752 <https://github.com/scipy/scipy/pull/12752>`__: DOC: Add examples for some root finding functions. * `#12754 <https://github.com/scipy/scipy/pull/12754>`__: MAINT, CI: Azure windows deps multiline * `#12756 <https://github.com/scipy/scipy/pull/12756>`__: ENH: stats: Add an sf method to levy for improved precision in... * `#12757 <https://github.com/scipy/scipy/pull/12757>`__: ENH: stats: Add an sf method to levy_l for improved precision. * `#12765 <https://github.com/scipy/scipy/pull/12765>`__: TST, MAINT: infeasible_2 context * `#12767 <https://github.com/scipy/scipy/pull/12767>`__: Fix spline interpolation boundary handling for modes reflect... * `#12769 <https://github.com/scipy/scipy/pull/12769>`__: DOC: syntax error in scipy.interpolate.bspl * `#12770 <https://github.com/scipy/scipy/pull/12770>`__: ENH: add nearest-up rounding to scipy.interpolate.interp1d * `#12771 <https://github.com/scipy/scipy/pull/12771>`__: TST: fix invalid input unit test for scipy.signal.gammatone * `#12775 <https://github.com/scipy/scipy/pull/12775>`__: ENH: Adds quadratic_assignment with two methods * `#12776 <https://github.com/scipy/scipy/pull/12776>`__: ENH: add grid-constant boundary handling in ndimage interpolation... * `#12777 <https://github.com/scipy/scipy/pull/12777>`__: Add Taylor Window function - Common in Radar DSP * `#12779 <https://github.com/scipy/scipy/pull/12779>`__: ENH: Improvements to pocketfft thread pool and ARM neon vectorization * `#12788 <https://github.com/scipy/scipy/pull/12788>`__: API: Rename cKDTree n_jobs argument to workers * `#12792 <https://github.com/scipy/scipy/pull/12792>`__: DOC: remove THANKS.txt file in favor of scipy.org * `#12793 <https://github.com/scipy/scipy/pull/12793>`__: Add new flag to authors tool * `#12802 <https://github.com/scipy/scipy/pull/12802>`__: BENCH: add scipy.ndimage.interpolation benchmarks * `#12803 <https://github.com/scipy/scipy/pull/12803>`__: Do not pin the version of numpy in unsupported python versions * `#12810 <https://github.com/scipy/scipy/pull/12810>`__: CI: fix 32-bit Linux build failure on Azure CI runs * `#12812 <https://github.com/scipy/scipy/pull/12812>`__: ENH: support interpolation of complex-valued images * `#12814 <https://github.com/scipy/scipy/pull/12814>`__: BUG: nonlin_solve shouldn't pass non-vector dx to tol_norm * `#12818 <https://github.com/scipy/scipy/pull/12818>`__: Update ckdtree.pyx * `#12822 <https://github.com/scipy/scipy/pull/12822>`__: MAINT: simplify directed_hausdorff * `#12827 <https://github.com/scipy/scipy/pull/12827>`__: DOC: Fix wrong name w being used instead of worN in docs. * `#12831 <https://github.com/scipy/scipy/pull/12831>`__: DOC: fix typo in sparse/base.py * `#12835 <https://github.com/scipy/scipy/pull/12835>`__: MAINT: stats: Improve vonmises PDF calculation. * `#12839 <https://github.com/scipy/scipy/pull/12839>`__: ENH: scipy.stats: add multivariate hypergeometric distribution * `#12843 <https://github.com/scipy/scipy/pull/12843>`__: changed M to N in windows.dpss * `#12846 <https://github.com/scipy/scipy/pull/12846>`__: MAINT: update minimum NumPy version to 1.16.5 * `#12847 <https://github.com/scipy/scipy/pull/12847>`__: DOC: Unify the formula in docs of scipy.stats.pearsonr() * `#12849 <https://github.com/scipy/scipy/pull/12849>`__: DOC: polish QAP docs for consistency and readability * `#12852 <https://github.com/scipy/scipy/pull/12852>`__: ENH, MAINT: Bring KDTree interface to feature-parity with cKDTree * `#12858 <https://github.com/scipy/scipy/pull/12858>`__: DOC: use :doi: and :arxiv: directives for references * `#12872 <https://github.com/scipy/scipy/pull/12872>`__: lazily import multiprocessing.Pool in MapWrapper * `#12878 <https://github.com/scipy/scipy/pull/12878>`__: DOC: document ScalarFunction * `#12882 <https://github.com/scipy/scipy/pull/12882>`__: MAINT: stats: Change a test to use <= instead of strictly less... * `#12885 <https://github.com/scipy/scipy/pull/12885>`__: numpy.linspace calls edited to ensure correct spacing. * `#12886 <https://github.com/scipy/scipy/pull/12886>`__: DOC: stats: Add 'versionadded' to cramervonmises docstring. * `#12899 <https://github.com/scipy/scipy/pull/12899>`__: TST: make a couple of tests expected to fail on 32-bit architectures * `#12903 <https://github.com/scipy/scipy/pull/12903>`__: DOC: update Windows build guide and move into contributor guide * `#12907 <https://github.com/scipy/scipy/pull/12907>`__: DOC: clarify which array the precenter option applies to * `#12908 <https://github.com/scipy/scipy/pull/12908>`__: MAINT: spatial: Remove two occurrences of unused variables in... * `#12909 <https://github.com/scipy/scipy/pull/12909>`__: ENH: stats: Add methods gumbel_r._sf and gumbel_r._isf * `#12910 <https://github.com/scipy/scipy/pull/12910>`__: CI: travis: Remove some unnecessary code from .travis.yml. * `#12911 <https://github.com/scipy/scipy/pull/12911>`__: Minor fixes to dendrogram plotting * `#12921 <https://github.com/scipy/scipy/pull/12921>`__: CI: don't run GitHub Actions on fork or in cron job * `#12927 <https://github.com/scipy/scipy/pull/12927>`__: MAINT: rename integrate.simps to simpson * `#12934 <https://github.com/scipy/scipy/pull/12934>`__: MAINT: rename trapz and cumtrapz to (cumulative\_)trapezoid * `#12936 <https://github.com/scipy/scipy/pull/12936>`__: MAINT: fix numerical precision in nct.stats * `#12938 <https://github.com/scipy/scipy/pull/12938>`__: MAINT: fix linter on master * `#12941 <https://github.com/scipy/scipy/pull/12941>`__: Update minimum AIX pinnings to match non AIX builds * `#12955 <https://github.com/scipy/scipy/pull/12955>`__: BUG: Fixed wrong NaNs check in scipy.stats.weightedtau * `#12958 <https://github.com/scipy/scipy/pull/12958>`__: ENH: stats: Implement _logpdf, _sf and _isf for nakagami. * `#12962 <https://github.com/scipy/scipy/pull/12962>`__: Correcting that p should be in [0,1] for a variety of discrete... * `#12964 <https://github.com/scipy/scipy/pull/12964>`__: BUG: added line.strip() to split_data_line() * `#12968 <https://github.com/scipy/scipy/pull/12968>`__: ENH: stats: Use only an analytical formula or scalar root-finding... * `#12971 <https://github.com/scipy/scipy/pull/12971>`__: MAINT: Declare support for Python 3.9 * `#12972 <https://github.com/scipy/scipy/pull/12972>`__: MAINT: Remove redundant Python < 3.6 code * `#12980 <https://github.com/scipy/scipy/pull/12980>`__: DOC: Update documentation on optimize.rosen * `#12983 <https://github.com/scipy/scipy/pull/12983>`__: ENH: improvements to stats.linregress * `#12990 <https://github.com/scipy/scipy/pull/12990>`__: DOC: Clarify that using sos as output type for iirdesign can... * `#12992 <https://github.com/scipy/scipy/pull/12992>`__: DOC: capitalization and formatting in lsmr * `#12995 <https://github.com/scipy/scipy/pull/12995>`__: DOC: stats: Several documentation fixes. * `#12996 <https://github.com/scipy/scipy/pull/12996>`__: BUG: Improve error messages for \`range\` arg of binned_statistic_dd * `#12998 <https://github.com/scipy/scipy/pull/12998>`__: MAINT: approx_derivative with FP32 closes #12991 * `#13004 <https://github.com/scipy/scipy/pull/13004>`__: TST: isinstance(OptimizeResult.message, str) closes #13001 * `#13006 <https://github.com/scipy/scipy/pull/13006>`__: Keep correct dtype when loading empty mat arrays. * `#13009 <https://github.com/scipy/scipy/pull/13009>`__: MAINT: clip SLSQP step within bounds * `#13012 <https://github.com/scipy/scipy/pull/13012>`__: DOC: fix bilinear_zpk example labels * `#13013 <https://github.com/scipy/scipy/pull/13013>`__: ENH: Add \`subset\` and \`subsets\` methods to \`DisjointSet\`... * `#13029 <https://github.com/scipy/scipy/pull/13029>`__: MAINT: basinhopping callback for initial mininmisation * `#13032 <https://github.com/scipy/scipy/pull/13032>`__: DOC: fix docstring errors in in stats.wilcoxon * `#13036 <https://github.com/scipy/scipy/pull/13036>`__: BUG: forward port lint_diff shims * `#13041 <https://github.com/scipy/scipy/pull/13041>`__: MAINT: dogbox ensure x is within bounds closes #11403 * `#13042 <https://github.com/scipy/scipy/pull/13042>`__: MAINT: forward port 1.5.4 release notes * `#13046 <https://github.com/scipy/scipy/pull/13046>`__: DOC: Update optimize.least_squares doc for all tolerance must... * `#13052 <https://github.com/scipy/scipy/pull/13052>`__: Typo fix for cluster documentation * `#13054 <https://github.com/scipy/scipy/pull/13054>`__: BUG: fix \`scipy.optimize.show_options\` for unknown methods.... * `#13056 <https://github.com/scipy/scipy/pull/13056>`__: MAINT: fft: Fix a C++ compiler warning. * `#13057 <https://github.com/scipy/scipy/pull/13057>`__: Minor fixes on doc of function csr_tocsc * `#13058 <https://github.com/scipy/scipy/pull/13058>`__: DOC: stats: Replace np.float with np.float64 in a tutorial file. * `#13059 <https://github.com/scipy/scipy/pull/13059>`__: DOC: stats: Update the "Returns" section of the linregress docstring. * `#13060 <https://github.com/scipy/scipy/pull/13060>`__: MAINT: clip_x_for_func should be private * `#13061 <https://github.com/scipy/scipy/pull/13061>`__: DOC: signal.win -> signal.windows.win in Examples * `#13063 <https://github.com/scipy/scipy/pull/13063>`__: MAINT: Add suite-sparse and sksparse installation check * `#13070 <https://github.com/scipy/scipy/pull/13070>`__: MAINT: stats: Remove a couple obsolete comments. * `#13073 <https://github.com/scipy/scipy/pull/13073>`__: BUG: Fix scalar_search_wolfe2 to resolve #12157 * `#13078 <https://github.com/scipy/scipy/pull/13078>`__: CI, MAINT: migrate Lint to Azure * `#13081 <https://github.com/scipy/scipy/pull/13081>`__: BLD: drop Python 3.6 support (NEP 29) * `#13082 <https://github.com/scipy/scipy/pull/13082>`__: MAINT: update minimum NumPy version to 1.16.5 in a couple more... * `#13083 <https://github.com/scipy/scipy/pull/13083>`__: DOC: update toolchain.rst * `#13086 <https://github.com/scipy/scipy/pull/13086>`__: DOC: Update the Parameters section of the correlation docstring * `#13087 <https://github.com/scipy/scipy/pull/13087>`__: ENH:signal: Speed-up Cython implementation of _sosfilt * `#13089 <https://github.com/scipy/scipy/pull/13089>`__: BLD, BUG: add c99 compiler flag to HiGHS basiclu library * `#13091 <https://github.com/scipy/scipy/pull/13091>`__: BUG: Fix GIL handling in _sosfilt * `#13094 <https://github.com/scipy/scipy/pull/13094>`__: DOC: clarify "location" in docstring of cKDTree.query * `#13095 <https://github.com/scipy/scipy/pull/13095>`__: Zoom resize update * `#13097 <https://github.com/scipy/scipy/pull/13097>`__: BUG: fix CubicSpline(..., bc_type="periodic") #11758 * `#13100 <https://github.com/scipy/scipy/pull/13100>`__: BUG: sparse: Correct output format of kron * `#13107 <https://github.com/scipy/scipy/pull/13107>`__: ENH: faster linear_sum_assignment for small cost matrices * `#13110 <https://github.com/scipy/scipy/pull/13110>`__: CI, MAINT: refguide/asv checks to azure * `#13112 <https://github.com/scipy/scipy/pull/13112>`__: CI: fix MacOS CI * `#13113 <https://github.com/scipy/scipy/pull/13113>`__: CI: Install word list package for refguide-check * `#13115 <https://github.com/scipy/scipy/pull/13115>`__: BUG: add value range check for signal.iirdesign() * `#13116 <https://github.com/scipy/scipy/pull/13116>`__: CI: Don't report name errors after an exception in refguide-check * `#13117 <https://github.com/scipy/scipy/pull/13117>`__: CI: move sdist/pre-release test Azure * `#13119 <https://github.com/scipy/scipy/pull/13119>`__: Improve error message on friedmanchisquare function * `#13121 <https://github.com/scipy/scipy/pull/13121>`__: Fix factorial() for NaN on Python 3.10 * `#13123 <https://github.com/scipy/scipy/pull/13123>`__: BLD: Specify file extension for language standard version tests * `#13128 <https://github.com/scipy/scipy/pull/13128>`__: TST: skip Fortran I/O test for ODR * `#13130 <https://github.com/scipy/scipy/pull/13130>`__: TST: skip factorial() float tests on Python 3.10 * `#13136 <https://github.com/scipy/scipy/pull/13136>`__: CI:Add python dbg run to GH Actions * `#13138 <https://github.com/scipy/scipy/pull/13138>`__: CI: Port coverage, 64-bit BLAS, GCC 4.8 build to azure * `#13139 <https://github.com/scipy/scipy/pull/13139>`__: Fix edge case for mode='nearest' in ndimage.interpolation functions * `#13141 <https://github.com/scipy/scipy/pull/13141>`__: BUG: signal: Fix data type of the numerator returned by ss2tf. * `#13144 <https://github.com/scipy/scipy/pull/13144>`__: MAINT: stats: restrict gausshyper z > -1 * `#13146 <https://github.com/scipy/scipy/pull/13146>`__: typo in csr.py * `#13148 <https://github.com/scipy/scipy/pull/13148>`__: BUG: stats: fix typo in stable rvs per gh-12870 * `#13149 <https://github.com/scipy/scipy/pull/13149>`__: DOC: spatial/stats: cross-ref random rotation matrix functions * `#13151 <https://github.com/scipy/scipy/pull/13151>`__: MAINT: stats: Fix a test and a couple PEP-8 issues. * `#13152 <https://github.com/scipy/scipy/pull/13152>`__: MAINT: stats: Use np.take_along_axis in the private function... * `#13154 <https://github.com/scipy/scipy/pull/13154>`__: ENH: stats: Implement defined handling of constant inputs in... * `#13156 <https://github.com/scipy/scipy/pull/13156>`__: DOC: maintain equal display range for ndimage.zoom example * `#13159 <https://github.com/scipy/scipy/pull/13159>`__: CI: Azure: Don't run tests on merge commits, except for coverage * `#13160 <https://github.com/scipy/scipy/pull/13160>`__: DOC: stats: disambiguate location-shifted/noncentral * `#13161 <https://github.com/scipy/scipy/pull/13161>`__: BUG: DifferentialEvolutionSolver.__del__ can fail in garbage... * `#13163 <https://github.com/scipy/scipy/pull/13163>`__: BUG: stats: fix bug in spearmanr nan propagation * `#13167 <https://github.com/scipy/scipy/pull/13167>`__: MAINT: stats: Fix a test. * `#13169 <https://github.com/scipy/scipy/pull/13169>`__: BUG: stats: Fix handling of misaligned masks in mstats.pearsonr. * `#13178 <https://github.com/scipy/scipy/pull/13178>`__: CI: testing.yml --> macos.yml * `#13181 <https://github.com/scipy/scipy/pull/13181>`__: CI: fix lint * `#13190 <https://github.com/scipy/scipy/pull/13190>`__: BUG: optimize: fix a duplicate key bug for \`test_show_options\` * `#13192 <https://github.com/scipy/scipy/pull/13192>`__: BUG:linalg: Add overwrite option to gejsv wrapper * `#13194 <https://github.com/scipy/scipy/pull/13194>`__: BUG: slsqp should be able to use rel_step * `#13199 <https://github.com/scipy/scipy/pull/13199>`__: [skip travis] DOC: 1.6.0 release notes * `#13203 <https://github.com/scipy/scipy/pull/13203>`__: fix typos * `#13209 <https://github.com/scipy/scipy/pull/13209>`__: TST:linalg: set the seed for cossin test * `#13212 <https://github.com/scipy/scipy/pull/13212>`__: [DOC] Backtick and directive consistency. * `#13217 <https://github.com/scipy/scipy/pull/13217>`__: REL: add necessary setuptools and numpy version 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Re: [Numpy-discussion] NumPy-Discussion Digest, Vol 171, Issue 39
by Brian Soto Dec. 29, 2020

Dec. 29, 2020

I'm still learning proper mailing list etiquette so I'm not sure if this is where I should respond. But users just getting into debugging might also benefit from knowing this: You can turn off optimizations when compiling numpy by passing CFLAGS to setup.py like so: *CFLAGS="-O0 -g3" python setup.py build_ext -i * **Assuming you have the source code and setup.py available * This will remove optimizations while compiling and will make it easier to see more variables. That took me a long time to figure out so I wanted to share the knowledge Thanks! On Mon, Dec 28, 2020 at 10:38 PM <numpy-discussion-request(a)python.org> wrote: > Send NumPy-Discussion mailing list submissions to > numpy-discussion(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mailman/listinfo/numpy-discussion > or, via email, send a message with subject or body 'help' to > numpy-discussion-request(a)python.org > > You can reach the person managing the list at > numpy-discussion-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of NumPy-Discussion digest..." > > > Today's Topics: > > 1. Re: Addition of new distributions: Polya-gamma (Robert Kern) > 2. Help needed GDB (Amardeep Singh) > 3. ANN: NumExpr 2.7.2 (Robert McLeod) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 28 Dec 2020 13:06:33 -0500 > From: Robert Kern <robert.kern(a)gmail.com> > To: Discussion of Numerical Python <numpy-discussion(a)python.org> > Subject: Re: [Numpy-discussion] Addition of new distributions: > Polya-gamma > Message-ID: > < > CAF6FJivqpLsXqvyUQcAUL67VHQw0viQWTry1+L1pq4GipfDdhw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > My view is that we will not add more non-uniform distribution (i.e. "named" > statistical probability distributions like Polya-Gamma) methods to > `Generator`. I think that we might add a couple more methods to handle some > more fundamental issues (like sampling from the unit interval with control > over whether each boundary is open or closed, maybe one more variation on > shuffling) that helps write randomized algorithms. Now that we have the C > and Cython APIs which allow one to implement non-uniform distributions in > other packages, we strongly encourage that. > > As I commented on the linked PR, `scipy.stats` would be a reasonable place > for a Polya-Gamma sampling function, even if it's not feasible to implement > an `rv_continuous` class for it. You have convinced me that the nature of > the Polya-Gamma distribution warrants this. The only issue is that scipy > still depends on a pre-`Generator` version of numpy. So I recommend > implementing this function in your own package with an eye towards > contributing it to scipy later. > > On Sun, Dec 27, 2020 at 6:05 AM Zolisa Bleki <BLKZOL001(a)myuct.ac.za> > wrote: > > > Hi All, > > > > I would like to know if Numpy accepts addition of new distributions since > > the implementation of the Generator interface. If so, what is the > criteria > > for a particular distribution to be accepted? The reason why i'm asking > is > > because I would like to propose adding the Polya-gamma distribution to > > numpy, for the following reasons: > > > > 1) Polya-gamma random variables are commonly used as auxiliary variables > > during data augmentation in Bayesian sampling algorithms, which have > > wide-spread usage in Statistics and recently, Machine learning. > > 2) Since this distribution is mostly useful for random sampling, it since > > appropriate to have it in numpy and not projects like scipy [1]. > > 3) The only python/C++ implementation of the sampler available is > licensed > > under GPLv3 which I believe limits copying into packages that choose to > use > > a different license [2]. > > 4) Numpy's random API makes adding the distribution painless. > > > > I have done preliminary work on this by implementing the distribution > > sampler as decribed in [3]; see: > > https://github.com/numpy/numpy/compare/master...zoj613:polyagamma . > > There is a more efficient sampling algorithm described in a later paper > > [4], but I chose not to start with that one unless I know it is worth > > investing time in. > > > > I would appreciate your thoughts on this proposal. > > > > Regards, > > Zolisa > > > > > > Refs: > > [1] https://github.com/scipy/scipy/issues/11009 > > [2] https://github.com/slinderman/pypolyagamma > > [3] https://arxiv.org/pdf/1205.0310v1.pdf > > [4] https://arxiv.org/pdf/1405.0506.pdf > > > > > > > > Disclaimer - University of Cape Town This email is subject to UCT > policies > > and email disclaimer published on our website at > > http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 > > 9111. If this email is not related to the business of UCT, it is sent by > > the sender in an individual capacity. Please report security incidents or > > abuse via https://csirt.uct.ac.za/page/report-an-incident.php. > > _______________________________________________ > > NumPy-Discussion mailing list > > NumPy-Discussion(a)python.org > > https://mail.python.org/mailman/listinfo/numpy-discussion > > > > > -- > Robert Kern >

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Help needed GDB
by Amardeep Singh Dec. 29, 2020

Dec. 29, 2020

Hi All, I am trying to debug c code of numpy via gdb.Can someone help me with this? i am getting " Python scripting is not supported in this copy of GDB". How to install python supported gdb on win10? https://numpy.org/doc/stable/dev/development_environment.html I am following the steps in the docs. machine is windows 10. Debugging <https://numpy.org/doc/stable/dev/development_environment.html#debugging> Another frequently asked question is “How do I debug C code inside NumPy?”. First, ensure that you have gdb installed on your system with the Python extensions (often the default on Linux). You can see which version of Python is running inside gdb to verify your setup: (gdb) python>import sys>print(sys.version_info)>endsys.version_info(major=3, minor=7, micro=0, releaselevel='final', serial=0) $ gdb -v GNU gdb (GDB) 7.6.1 This GDB was configured as "mingw32". $ gdb (gdb) python >import sys >print(sys.version_info) >end (gdb) Python scripting is not supported in this copy of GDB.

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ANN: NumExpr 2.7.2
by Robert McLeod Dec. 28, 2020

Dec. 28, 2020

======================== Announcing NumExpr 2.7.2 ======================== Hi everyone, It's been awhile since the last update to NumExpr, mostly as the existing scientific Python tool chain for building wheels on PyPi became defunct and we have had to redevelop a new one based on `cibuildwheel` and GitHub Actions. This release also brings us support (and wheels for) Python 3.9. There have been a number of changes to enhance how NumExpr works when NumPy uses MKL as a backend. Project documentation is available at: http://numexpr.readthedocs.io/ Changes from 2.7.1 to 2.7.2 --------------------------- - Support for Python 2.7 and 3.5 is deprecated and will be discontinued when `cibuildwheels` and/or GitHub Actions no longer support these versions. - Wheels are now provided for Python 3.7, 3.5, 3.6, 3.7, 3.8, and 3.9 via GitHub Actions. - The block size is now exported into the namespace as `numexpr.__BLOCK_SIZE1__` as a read-only value. - If using MKL, the number of threads for VML is no longer forced to 1 on loading the module. Testing has shown that VML never runs in multi-threaded mode for the default BLOCKSIZE1 of 1024 elements, and forcing to 1 can have deleterious effects on NumPy functions when built with MKL. See issue #355 for details. - Use of `ndarray.tostring()` in tests has been switch to `ndarray.tobytes()` for future-proofing deprecation of `.tostring()`, if the version of NumPy is greater than 1.9. - Added a utility method `get_num_threads` that returns the (maximum) number of threads currently in use by the virtual machine. The functionality of `set_num_threads` whereby it returns the previous value has been deprecated and will be removed in 2.8.X. What's Numexpr? --------------- Numexpr is a fast numerical expression evaluator for NumPy. With it, expressions that operate on arrays (like "3*a+4*b") are accelerated and use less memory than doing the same calculation in Python. It has multi-threaded capabilities, as well as support for Intel's MKL (Math Kernel Library), which allows an extremely fast evaluation of transcendental functions (sin, cos, tan, exp, log...) while squeezing the last drop of performance out of your multi-core processors. Look here for a some benchmarks of numexpr using MKL: https://github.com/pydata/numexpr/wiki/NumexprMKL Its only dependency is NumPy (MKL is optional), so it works well as an easy-to-deploy, easy-to-use, computational engine for projects that don't want to adopt other solutions requiring more heavy dependencies. Where I can find Numexpr? ------------------------- The project is hosted at GitHub in: https://github.com/pydata/numexpr You can get the packages from PyPI as well (but not for RC releases): http://pypi.python.org/pypi/numexpr Documentation is hosted at: http://numexpr.readthedocs.io/en/latest/ Share your experience --------------------- Let us know of any bugs, suggestions, gripes, kudos, etc. you may have. Enjoy data! -- Robert McLeod robbmcleod(a)gmail.com robert.mcleod(a)hitachi-hhtc.ca

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ANN: SfePy 2020.4
by Robert Cimrman Dec. 26, 2020

Dec. 26, 2020

I am pleased to announce the release of SfePy 2020.4. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by finite element methods. It is distributed under the new BSD license. Home page: https://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - Ogden hyperelastic term - serendipity finite element basis of orders 1-3 For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Jan Heczko Vladimir Lukes

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NumPy 1.20.0rc2 released
by Charles R Harris Dec. 24, 2020

Dec. 24, 2020

Hi All, On behalf of the NumPy team I am pleased to announce the release of NumPy 1.20.0rc2. This NumPy release is the largest to date, containing some 670 merged pull requests contributed by 184 people. See the list of highlights below. The Python versions supported for this release are 3.7-3.9, support for Python 3.6 has been dropped. Wheels can be downloaded from PyPI <https://pypi.org/project/numpy/1.20.0rc2/>; source archives, release notes, and wheel hashes are available on Github <https://github.com/numpy/numpy/releases/tag/v1.20.0rc2>. Linux users will need pip >= 0.19.3 in order to install manylinux2010 and manylinux2014 wheels. *Highlights* - Annotations for NumPy functions. This work is ongoing and improvements can be expected pending feedback from users. - Wider use of SIMD to increase execution speed of ufuncs. Much work has been done in introducing universal functions that will ease use of modern features across different hardware platforms. This work is ongoing. - Preliminary work in changing the dtype and casting implementations in order to provide an easier path to extending dtypes. This work is ongoing but enough has been done to allow experimentation and feedback. - Extensive documentation improvements comprising some 185 PR merges. This work is ongoing and part of the larger project to improve NumPy's online presence and usefulness to new users. - Further cleanups related to removing Python 2.7. This improves code readability and removes technical debt. - Preliminary support for the upcoming Cython 3.0. *Contributors* A total of 184 people contributed to this release. People with a "+" by their names contributed a patch for the first time. * Aaron Meurer + * Abhilash Barigidad + * Abhinav Reddy + * Abhishek Singh + * Al-Baraa El-Hag + * Albert Villanova del Moral + * Alex Leontiev + * Alex Rockhill + * Alex Rogozhnikov * Alexander Belopolsky * Alexander Kuhn-Regnier + * Allen Downey + * Andras Deak * Andrea Olivo + * Andrew Eckart + * Anirudh Subramanian * Anthony Byuraev + * Antonio Larrosa + * Ashutosh Singh + * Bangcheng Yang + * Bas van Beek + * Ben Derrett + * Ben Elliston + * Ben Nathanson + * Bernie Gray + * Bharat Medasani + * Bharat Raghunathan * Bijesh Mohan + * Bradley Dice + * Brandon David + * Brandt Bucher * Brian Soto + * Brigitta Sipocz * Cameron Blocker + * Carl Leake + * Charles Harris * Chris Brown + * Chris Vavaliaris + * Christoph Gohlke * Chunlin Fang * CloseChoice + * Daniel G. A. Smith + * Daniel Hrisca * Daniel Vanzo + * David Pitchford + * Davide Dal Bosco + * Derek Homeier * Dima Kogan + * Dmitry Kutlenkov + * Douglas Fenstermacher + * Dustin Spicuzza + * E. Madison Bray + * Elia Franzella + * Enrique Matías Sánchez + * Erfan Nariman | Veneficus + * Eric Larson * Eric Moore * Eric Wieser * Erik M. Bray * EthanCJ-git + * Etienne Guesnet + * FX Coudert + * Felix Divo * Frankie Robertson + * Ganesh Kathiresan * Gengxin Xie * Gerry Manoim + * Guilherme Leobas * Hassan Kibirige * Hugo Mendes + * Hugo van Kemenade * Ian Thomas + * InessaPawson + * Isabela Presedo-Floyd + * Isuru Fernando * Jakob Jakobson + * Jakub Wilk * James Myatt + * Jesse Li + * John Hagen + * John Zwinck * Joseph Fox-Rabinovitz * Josh Wilson * Jovial Joe Jayarson + * Julia Signell + * Jun Kudo + * Karan Dhir + * Kaspar Thommen + * Kerem Hallaç * Kevin Moore + * Kevin Sheppard * Klaus Zimmermann + * LSchroefl + * Laurie + * Laurie Stephey + * Levi Stovall + * Lisa Schwetlick + * Lukas Geiger + * Madhulika Jain Chambers + * Matthias Bussonnier * Matti Picus * Melissa Weber Mendonça * Michael Hirsch * Nick R. Papior * Nikola Forró * Noman Arshad + * Paul YS Lee + * Pauli Virtanen * Paweł Redzyński + * Peter Andreas Entschev * Peter Bell * Philippe Ombredanne + * Phoenix Meadowlark + * Piotr Gaiński * Raghav Khanna + * Raghuveer Devulapalli * Rajas Rade + * Rakesh Vasudevan * Ralf Gommers * Raphael Kruse + * Rashmi K A + * Robert Kern * Rohit Sanjay + * Roman Yurchak * Ross Barnowski * Royston E Tauro + * Ryan C Cooper + * Ryan Soklaski * Safouane Chergui + * Sahil Siddiq + * Sarthak Vineet Kumar + * Sayed Adel * Sebastian Berg * Sergei Vorfolomeev + * Seth Troisi * Sidhant Bansal + * Simon Gasse * Simon Graham + * Stefan Appelhoff + * Stefan Behnel + * Stefan van der Walt * Steve Dower * Steve Joachim + * Steven Pitman + * Stuart Archibald * Sturla Molden * Susan Chang + * Takanori H + * Tapajyoti Bose + * Thomas A Caswell * Tina Oberoi * Tirth Patel * Tobias Pitters + * Tomoki, Karatsu + * Tyler Reddy * Veniamin Petrenko + * Wansoo Kim + * Warren Weckesser * Wei Yang + * Wojciech Rzadkowski * Yang Hau + * Yogesh Raisinghani + * Yu Feng * Yuya Unno + * Zac Hatfield-Dodds * Zuhair Ali-Khan + * @abhilash42 + * @danbeibei + * @dojafrat * @dpitch40 + * @forfun + * @iamsoto + * @jbrockmendel + * @leeyspaul + * @mitch + * @prateek arora + * @serge-sans-paille + * @skywalker + * @stphnlyd + * @xoviat * @谭九鼎 + * @JMFT + * @Jack + * @Neal C + Cheers, Charles Harris

1 0

Deprecate np.testing.dec
by rpolley Dec. 23, 2020

Dec. 23, 2020

Saw some discussion in this issue <https://github.com/numpy/numpy/issues/17566> that since the decorators in np.testing.dec are there to support the nose testing framework, and since we use pytest mainly for testing now, that the decorators there should be deprecated. I created a pull request <https://github.com/numpy/numpy/pull/18051> that does this, and wanted to get the mailing list's opinion before it went forward. Any thoughts, suggestions, or objections? -- Sent from: http://numpy-discussion.10968.n7.nabble.com/

3 2

Suggestion: add an pad parameter to np.memmap
by Tom Swirly Dec. 23, 2020

Dec. 23, 2020

Hello, and thanks for all your work on the amazing numpy. I'm using np.memmap() with great success for memory mapping WAV audio files, with one tiny blemish - the WAV spec wants me to sometimes put one byte after the list of samples that I'm memory mapping, which I can't do easily when writing a new file. This little patch is probably backward compatible and would accomplish what I need: https://github.com/rec/numpy/commit/4dd855b14bed5947f2f9120979c9ee936c17158f If there were interest, I could figure out numpy's test system and write tests for it. (For the foreseeable future, I'm intercepting the call to mmap.mmap() to add the padding, so I'm not blocked, though the code has aspects of ugliness.) -- /t PGP Key: https://flowcrypt.com/pub/tom.ritchford@gmail.com *https://tom.ritchford.com <https://tom.ritchford.com>* *https://tom.swirly.com <https://tom.swirly.com>*

1 0

ANN: SciPy 1.6.0rc2 -- please test
by Tyler Reddy Dec. 22, 2020

Dec. 22, 2020

Hi all, On behalf of the SciPy development team I'm pleased to announce the release candidate SciPy 1.6.0rc2. 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/v1.6.0rc2 One of a few ways to install the release candidate with pip: pip install scipy==1.6.0rc2 ========================== SciPy 1.6.0 Release Notes ========================== Note: Scipy 1.6.0 is not released yet! 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.interpolate` changes ------------------------------------ `scipy.linalg` changes ----------------------------- `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 * `#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 estimation * `#12353 <https://github.com/scipy/scipy/pull/12353>`__: Fix exception causes in vq.py * `#12354 <https://github.com/scipy/scipy/pull/12354>`__: MAINT: Cleanup unneeded void\* cast in setlist.pxd * `#12355 <https://github.com/scipy/scipy/pull/12355>`__: TST: Remove hack for old win-amd64 bug * `#12356 <https://github.com/scipy/scipy/pull/12356>`__: ENH: Faster implementation of scipy.sparse.block_diag (#9411... * `#12357 <https://github.com/scipy/scipy/pull/12357>`__: MAINT,TST: update and run scipy/special/utils/convert.py * `#12358 <https://github.com/scipy/scipy/pull/12358>`__: TST: Check mstat.skewtest pvalue * `#12359 <https://github.com/scipy/scipy/pull/12359>`__: TST: Sparse matrix test with int64 indptr and indices * `#12363 <https://github.com/scipy/scipy/pull/12363>`__: DOC: ref. in CloughTocher2DInterpolator * `#12364 <https://github.com/scipy/scipy/pull/12364>`__: DOC: \`sparse_distance_matrix\` and \`count_neighbors\` examples * `#12371 <https://github.com/scipy/scipy/pull/12371>`__: MAINT, CI: bump to latest stable OpenBLAS * `#12372 <https://github.com/scipy/scipy/pull/12372>`__: MAINT: Minor cleanup of (c)KDTree tests * `#12374 <https://github.com/scipy/scipy/pull/12374>`__: DEP: Deprecate \`distance.wminkowski\` * `#12375 <https://github.com/scipy/scipy/pull/12375>`__: ENH: Add fast path for minkowski distance with p=1,2 and support... * `#12376 <https://github.com/scipy/scipy/pull/12376>`__: Fix exception causes in most of the codebase * `#12377 <https://github.com/scipy/scipy/pull/12377>`__: DOC: Quick fix - adds newline to correlation_lags docstring Examples... * `#12381 <https://github.com/scipy/scipy/pull/12381>`__: BENCH: remove obsolete goal_time param * `#12382 <https://github.com/scipy/scipy/pull/12382>`__: ENH: Replace KDTree with a thin wrapper over cKDTree * `#12385 <https://github.com/scipy/scipy/pull/12385>`__: DOC: improve docstrings of interpolate.NearestNDInterpolator.__call__... * `#12387 <https://github.com/scipy/scipy/pull/12387>`__: DOC/STY: add example to scipy.signal.correlate * `#12393 <https://github.com/scipy/scipy/pull/12393>`__: CI: Replace the existing check for non-ASCII characters with... * `#12394 <https://github.com/scipy/scipy/pull/12394>`__: CI: arm64 numpy now available * `#12395 <https://github.com/scipy/scipy/pull/12395>`__: ENH: improve stats.binned_statistic_dd performance * `#12396 <https://github.com/scipy/scipy/pull/12396>`__: DOC, MAINT: forward port 1.5.0 relnotes * `#12398 <https://github.com/scipy/scipy/pull/12398>`__: API: Disable len() and indexing of Rotation instances with single... * `#12399 <https://github.com/scipy/scipy/pull/12399>`__: MAINT: Replace some Unicode dash-like chars with an ASCII hyphen. * `#12402 <https://github.com/scipy/scipy/pull/12402>`__: update .mailmap * `#12404 <https://github.com/scipy/scipy/pull/12404>`__: MAINT: io: Change the encoding comment of test_mio.py to utf-8. * `#12416 <https://github.com/scipy/scipy/pull/12416>`__: CI: cache mingw, azure pipelines * `#12427 <https://github.com/scipy/scipy/pull/12427>`__: BUG: logic error in loop unrolling (cKDTree) * `#12432 <https://github.com/scipy/scipy/pull/12432>`__: DOC: Remove the "Basic functions" section from the SciPy tutorial. * `#12434 <https://github.com/scipy/scipy/pull/12434>`__: ENH:linalg: Add LAPACK wrappers pptrf/pptrs/ppsv/pptri/ppcon * `#12435 <https://github.com/scipy/scipy/pull/12435>`__: DOC: fix simplex math for scipy.stats.dirichlet documentation * `#12439 <https://github.com/scipy/scipy/pull/12439>`__: DOC: add API methods summary for NdPPoly * `#12443 <https://github.com/scipy/scipy/pull/12443>`__: BUG: stats: Improve calculation of exponnorm.pdf * `#12448 <https://github.com/scipy/scipy/pull/12448>`__: DOC: stats: Add "Examples" to the ansari docstring. * `#12450 <https://github.com/scipy/scipy/pull/12450>`__: ENH: add \`leaves_color_list\` for cluster.dendrogram dictionary. * `#12451 <https://github.com/scipy/scipy/pull/12451>`__: MAINT: remove "blacklist" terminology from code base * `#12452 <https://github.com/scipy/scipy/pull/12452>`__: DOC: clarify the meaning of whitening for cluster.vq.whiten() * `#12455 <https://github.com/scipy/scipy/pull/12455>`__: MAINT: clearer error message in setup.py * `#12457 <https://github.com/scipy/scipy/pull/12457>`__: ENH: stats: override stats.pareto.fit with analytical MLE * `#12460 <https://github.com/scipy/scipy/pull/12460>`__: check if column in spearman rho is entirely NaN or Inf * `#12463 <https://github.com/scipy/scipy/pull/12463>`__: DOC: improve and clean up \*Spline docstrings in fitpack2.py * `#12474 <https://github.com/scipy/scipy/pull/12474>`__: ENH: linalg: speedup _sqrtm_triu by moving tight loop to Cython * `#12476 <https://github.com/scipy/scipy/pull/12476>`__: ENH: add IIR comb filter to scipy.signal * `#12484 <https://github.com/scipy/scipy/pull/12484>`__: Fix documentation for minimize * `#12486 <https://github.com/scipy/scipy/pull/12486>`__: DOC: add a note in poisson distribution when mu=0 and k=0 in... * `#12491 <https://github.com/scipy/scipy/pull/12491>`__: MAINT: forward port 1.5.1 release notes * `#12508 <https://github.com/scipy/scipy/pull/12508>`__: Fix exception causes all over the codebase * `#12514 <https://github.com/scipy/scipy/pull/12514>`__: ENH: stats: override stats.invgauss.fit with analytical MLE * `#12519 <https://github.com/scipy/scipy/pull/12519>`__: PERF: Avoid np.zeros when custom initialization is needed anyway * `#12520 <https://github.com/scipy/scipy/pull/12520>`__: DOC: Minor RST section renaming. * `#12521 <https://github.com/scipy/scipy/pull/12521>`__: MAINT: Remove unused imports * `#12522 <https://github.com/scipy/scipy/pull/12522>`__: PERF: Get rid of unnececssary allocation in VarReader5.cread_fieldnames * `#12524 <https://github.com/scipy/scipy/pull/12524>`__: DOC: special: Set Axes3D rect to avoid clipping labels in plot. * `#12525 <https://github.com/scipy/scipy/pull/12525>`__: Fix large sparse nnz * `#12526 <https://github.com/scipy/scipy/pull/12526>`__: DOC: Remove double section and too long header underline. * `#12527 <https://github.com/scipy/scipy/pull/12527>`__: Improve error message for wrong interpolation type * `#12530 <https://github.com/scipy/scipy/pull/12530>`__: Move redundant logic outside loop for conditional speedup in... * `#12532 <https://github.com/scipy/scipy/pull/12532>`__: ENH: Add norm={"forward", "backward"} to \`scipy.fft\` * `#12535 <https://github.com/scipy/scipy/pull/12535>`__: MAINT: Avoid sphinx deprecated aliases for SeeAlso and Only * `#12540 <https://github.com/scipy/scipy/pull/12540>`__: BUG: fix odr.output.work_ind key bug and add its test. * `#12541 <https://github.com/scipy/scipy/pull/12541>`__: ENH: add solver for minimum weight full bipartite matching * `#12550 <https://github.com/scipy/scipy/pull/12550>`__: PERF: pickling speed of rv\* * `#12551 <https://github.com/scipy/scipy/pull/12551>`__: DOC: fix typo in cluster/_hierarchy.pyx * `#12552 <https://github.com/scipy/scipy/pull/12552>`__: CI: Cleanup travis pip installs * `#12556 <https://github.com/scipy/scipy/pull/12556>`__: BUG: Fix problem with Scipy.integrate.solve_bvp for big problems * `#12557 <https://github.com/scipy/scipy/pull/12557>`__: MAINT: Use extern templates to improve sparsetools compile time * `#12558 <https://github.com/scipy/scipy/pull/12558>`__: MAINT: Remove hack to allow scipy.fft to act like a function * `#12563 <https://github.com/scipy/scipy/pull/12563>`__: MAINT: Remove unused mu0 in special/orthogonal.py * `#12564 <https://github.com/scipy/scipy/pull/12564>`__: DOC: fix return type docstring for least_squares * `#12565 <https://github.com/scipy/scipy/pull/12565>`__: DOC: stats: respond to query about Kruskal-Wallis test being... * `#12566 <https://github.com/scipy/scipy/pull/12566>`__: BUG: Interpolate: use stable sort * `#12568 <https://github.com/scipy/scipy/pull/12568>`__: Updated documentation for as_quat * `#12571 <https://github.com/scipy/scipy/pull/12571>`__: DEP: remove deprecated slepian window * `#12573 <https://github.com/scipy/scipy/pull/12573>`__: DEP: remove \`frechet_l\` and \`frechet_r\` * `#12575 <https://github.com/scipy/scipy/pull/12575>`__: BUG: stats: fix multinomial.pmf NaNs when params sum > 1 * `#12576 <https://github.com/scipy/scipy/pull/12576>`__: MAINT: remove warning from LSQSphereBivariateSpline * `#12582 <https://github.com/scipy/scipy/pull/12582>`__: ENH: Multivariate t-distribution * `#12587 <https://github.com/scipy/scipy/pull/12587>`__: ENH: speed up rvs of gengamma in scipy.stats * `#12588 <https://github.com/scipy/scipy/pull/12588>`__: DOC: add Examples add see also sections for LinearNDInterpolator,... * `#12597 <https://github.com/scipy/scipy/pull/12597>`__: ENH: Add single-sided p-values to t-tests * `#12599 <https://github.com/scipy/scipy/pull/12599>`__: Small update to scipy FFT tutorial * `#12600 <https://github.com/scipy/scipy/pull/12600>`__: ENH: disjoint set data structure * `#12602 <https://github.com/scipy/scipy/pull/12602>`__: BUG: add const for Read-only views in interpnd.pyx * `#12605 <https://github.com/scipy/scipy/pull/12605>`__: BUG: correct \`np.asanyarray\` use in \`scipy.constants.lambda2nu\` * `#12610 <https://github.com/scipy/scipy/pull/12610>`__: MAINT: forward port 1.5.2 release notes * `#12612 <https://github.com/scipy/scipy/pull/12612>`__: MAINT: stats: Use explicit keyword parameters instead of \`\*\*kwds\`. * `#12616 <https://github.com/scipy/scipy/pull/12616>`__: DOC: make explicit docstring that interpolate.interp1d only accepts... * `#12618 <https://github.com/scipy/scipy/pull/12618>`__: DOC: Minor doc formatting. * `#12640 <https://github.com/scipy/scipy/pull/12640>`__: MAINT: stats: fix issues with scipy.stats.pearson3 docs, moment,... * `#12647 <https://github.com/scipy/scipy/pull/12647>`__: TST: Add Boost ellipr[cdfgj]_data test data * `#12648 <https://github.com/scipy/scipy/pull/12648>`__: DOC: Update special/utils/README with instructions * `#12649 <https://github.com/scipy/scipy/pull/12649>`__: DOC: simplified pip quickstart guide * `#12650 <https://github.com/scipy/scipy/pull/12650>`__: DOC: stats: Fix boxcox docstring: lambda can be negative. * `#12655 <https://github.com/scipy/scipy/pull/12655>`__: DOC: update Steering Council members listed in governance docs * `#12659 <https://github.com/scipy/scipy/pull/12659>`__: rv_sample expect bug * `#12663 <https://github.com/scipy/scipy/pull/12663>`__: DOC: optimize: try to fix linprog method-specific documentation * `#12664 <https://github.com/scipy/scipy/pull/12664>`__: BUG: stats: Fix logpdf with large negative values for logistic... * `#12666 <https://github.com/scipy/scipy/pull/12666>`__: MAINT: Fixes from static analysis * `#12667 <https://github.com/scipy/scipy/pull/12667>`__: ENH: Adding Modified Rodrigues Parameters to the Rotation class * `#12670 <https://github.com/scipy/scipy/pull/12670>`__: DOC: Update documentation for Gamma distribution * `#12673 <https://github.com/scipy/scipy/pull/12673>`__: API: Unconditionally return np.intp from cKDTree.query * `#12677 <https://github.com/scipy/scipy/pull/12677>`__: MAINT: Add Autogenerated notice to ufuncs.pyi * `#12682 <https://github.com/scipy/scipy/pull/12682>`__: MAINT: Remove _util._valarray * `#12688 <https://github.com/scipy/scipy/pull/12688>`__: MAINT: add f2py-generated scipy.integrate files to .gitignore * `#12689 <https://github.com/scipy/scipy/pull/12689>`__: BENCH: simplify benchmark setup, remove benchmarks/run.py * `#12694 <https://github.com/scipy/scipy/pull/12694>`__: scipy/stats: Add laplace_asymmetric continuous distribution * `#12695 <https://github.com/scipy/scipy/pull/12695>`__: DOC: update Ubuntu quickstart; conda compilers now work! * `#12698 <https://github.com/scipy/scipy/pull/12698>`__: MAINT: Replace np.max with np.maximum * `#12700 <https://github.com/scipy/scipy/pull/12700>`__: TST: bump test precision for constrained trustregion test * `#12702 <https://github.com/scipy/scipy/pull/12702>`__: TST: bump test tolerance for \`DifferentialEvolutionSolver.test_L4\` * `#12703 <https://github.com/scipy/scipy/pull/12703>`__: BUG: Improve input validation for sepfir2d * `#12708 <https://github.com/scipy/scipy/pull/12708>`__: MAINT: fix a typo in scipy.sparse * `#12709 <https://github.com/scipy/scipy/pull/12709>`__: BUG: bvls can fail catastrophically to converge * `#12711 <https://github.com/scipy/scipy/pull/12711>`__: MAINT: Use platform.python_implementation to determine IS_PYPY * `#12713 <https://github.com/scipy/scipy/pull/12713>`__: TST: Fix flaky test_lgmres * `#12716 <https://github.com/scipy/scipy/pull/12716>`__: DOC: add examples and tutorial links for interpolate functions... * `#12717 <https://github.com/scipy/scipy/pull/12717>`__: DOC: Fix Issue #5396 * `#12725 <https://github.com/scipy/scipy/pull/12725>`__: ENH: Support complex-valued images and kernels for many ndimage... * `#12729 <https://github.com/scipy/scipy/pull/12729>`__: DEP: remove setup_requires * `#12732 <https://github.com/scipy/scipy/pull/12732>`__: BENCH: skip benchmarks instead of hiding them when SCIPY_XSLOW=0 * `#12734 <https://github.com/scipy/scipy/pull/12734>`__: CI: Don't ignore line-length in the lint_diff check. * `#12736 <https://github.com/scipy/scipy/pull/12736>`__: DOC: Fix signal.windows.get_window() 'exponential' docstring * `#12737 <https://github.com/scipy/scipy/pull/12737>`__: ENH: stats: override stats.gumbel_r.fit and stats.gumbel_l.fit... * `#12738 <https://github.com/scipy/scipy/pull/12738>`__: ENH: stats: override stats.logistic.fit with system of equations... * `#12743 <https://github.com/scipy/scipy/pull/12743>`__: BUG: Avoid negative variances in circular statistics * `#12744 <https://github.com/scipy/scipy/pull/12744>`__: Prevent build error on GNU/Hurd * `#12746 <https://github.com/scipy/scipy/pull/12746>`__: TST: parameterize the test cases in test_ndimage.py * `#12752 <https://github.com/scipy/scipy/pull/12752>`__: DOC: Add examples for some root finding functions. * `#12754 <https://github.com/scipy/scipy/pull/12754>`__: MAINT, CI: Azure windows deps multiline * `#12756 <https://github.com/scipy/scipy/pull/12756>`__: ENH: stats: Add an sf method to levy for improved precision in... * `#12757 <https://github.com/scipy/scipy/pull/12757>`__: ENH: stats: Add an sf method to levy_l for improved precision. * `#12765 <https://github.com/scipy/scipy/pull/12765>`__: TST, MAINT: infeasible_2 context * `#12767 <https://github.com/scipy/scipy/pull/12767>`__: Fix spline interpolation boundary handling for modes reflect... * `#12769 <https://github.com/scipy/scipy/pull/12769>`__: DOC: syntax error in scipy.interpolate.bspl * `#12770 <https://github.com/scipy/scipy/pull/12770>`__: ENH: add nearest-up rounding to scipy.interpolate.interp1d * `#12771 <https://github.com/scipy/scipy/pull/12771>`__: TST: fix invalid input unit test for scipy.signal.gammatone * `#12775 <https://github.com/scipy/scipy/pull/12775>`__: ENH: Adds quadratic_assignment with two methods * `#12776 <https://github.com/scipy/scipy/pull/12776>`__: ENH: add grid-constant boundary handling in ndimage interpolation... * `#12777 <https://github.com/scipy/scipy/pull/12777>`__: Add Taylor Window function - Common in Radar DSP * `#12779 <https://github.com/scipy/scipy/pull/12779>`__: ENH: Improvements to pocketfft thread pool and ARM neon vectorization * `#12788 <https://github.com/scipy/scipy/pull/12788>`__: API: Rename cKDTree n_jobs argument to workers * `#12792 <https://github.com/scipy/scipy/pull/12792>`__: DOC: remove THANKS.txt file in favor of scipy.org * `#12793 <https://github.com/scipy/scipy/pull/12793>`__: Add new flag to authors tool * `#12802 <https://github.com/scipy/scipy/pull/12802>`__: BENCH: add scipy.ndimage.interpolation benchmarks * `#12803 <https://github.com/scipy/scipy/pull/12803>`__: Do not pin the version of numpy in unsupported python versions * `#12810 <https://github.com/scipy/scipy/pull/12810>`__: CI: fix 32-bit Linux build failure on Azure CI runs * `#12812 <https://github.com/scipy/scipy/pull/12812>`__: ENH: support interpolation of complex-valued images * `#12814 <https://github.com/scipy/scipy/pull/12814>`__: BUG: nonlin_solve shouldn't pass non-vector dx to tol_norm * `#12818 <https://github.com/scipy/scipy/pull/12818>`__: Update ckdtree.pyx * `#12822 <https://github.com/scipy/scipy/pull/12822>`__: MAINT: simplify directed_hausdorff * `#12827 <https://github.com/scipy/scipy/pull/12827>`__: DOC: Fix wrong name w being used instead of worN in docs. * `#12831 <https://github.com/scipy/scipy/pull/12831>`__: DOC: fix typo in sparse/base.py * `#12835 <https://github.com/scipy/scipy/pull/12835>`__: MAINT: stats: Improve vonmises PDF calculation. * `#12839 <https://github.com/scipy/scipy/pull/12839>`__: ENH: scipy.stats: add multivariate hypergeometric distribution * `#12843 <https://github.com/scipy/scipy/pull/12843>`__: changed M to N in windows.dpss * `#12846 <https://github.com/scipy/scipy/pull/12846>`__: MAINT: update minimum NumPy version to 1.16.5 * `#12847 <https://github.com/scipy/scipy/pull/12847>`__: DOC: Unify the formula in docs of scipy.stats.pearsonr() * `#12849 <https://github.com/scipy/scipy/pull/12849>`__: DOC: polish QAP docs for consistency and readability * `#12852 <https://github.com/scipy/scipy/pull/12852>`__: ENH, MAINT: Bring KDTree interface to feature-parity with cKDTree * `#12858 <https://github.com/scipy/scipy/pull/12858>`__: DOC: use :doi: and :arxiv: directives for references * `#12872 <https://github.com/scipy/scipy/pull/12872>`__: lazily import multiprocessing.Pool in MapWrapper * `#12878 <https://github.com/scipy/scipy/pull/12878>`__: DOC: document ScalarFunction * `#12882 <https://github.com/scipy/scipy/pull/12882>`__: MAINT: stats: Change a test to use <= instead of strictly less... * `#12885 <https://github.com/scipy/scipy/pull/12885>`__: numpy.linspace calls edited to ensure correct spacing. * `#12886 <https://github.com/scipy/scipy/pull/12886>`__: DOC: stats: Add 'versionadded' to cramervonmises docstring. * `#12899 <https://github.com/scipy/scipy/pull/12899>`__: TST: make a couple of tests expected to fail on 32-bit architectures * `#12903 <https://github.com/scipy/scipy/pull/12903>`__: DOC: update Windows build guide and move into contributor guide * `#12907 <https://github.com/scipy/scipy/pull/12907>`__: DOC: clarify which array the precenter option applies to * `#12908 <https://github.com/scipy/scipy/pull/12908>`__: MAINT: spatial: Remove two occurrences of unused variables in... * `#12909 <https://github.com/scipy/scipy/pull/12909>`__: ENH: stats: Add methods gumbel_r._sf and gumbel_r._isf * `#12910 <https://github.com/scipy/scipy/pull/12910>`__: CI: travis: Remove some unnecessary code from .travis.yml. * `#12911 <https://github.com/scipy/scipy/pull/12911>`__: Minor fixes to dendrogram plotting * `#12921 <https://github.com/scipy/scipy/pull/12921>`__: CI: don't run GitHub Actions on fork or in cron job * `#12927 <https://github.com/scipy/scipy/pull/12927>`__: MAINT: rename integrate.simps to simpson * `#12934 <https://github.com/scipy/scipy/pull/12934>`__: MAINT: rename trapz and cumtrapz to (cumulative\_)trapezoid * `#12936 <https://github.com/scipy/scipy/pull/12936>`__: MAINT: fix numerical precision in nct.stats * `#12938 <https://github.com/scipy/scipy/pull/12938>`__: MAINT: fix linter on master * `#12941 <https://github.com/scipy/scipy/pull/12941>`__: Update minimum AIX pinnings to match non AIX builds * `#12955 <https://github.com/scipy/scipy/pull/12955>`__: BUG: Fixed wrong NaNs check in scipy.stats.weightedtau * `#12958 <https://github.com/scipy/scipy/pull/12958>`__: ENH: stats: Implement _logpdf, _sf and _isf for nakagami. * `#12962 <https://github.com/scipy/scipy/pull/12962>`__: Correcting that p should be in [0,1] for a variety of discrete... * `#12964 <https://github.com/scipy/scipy/pull/12964>`__: BUG: added line.strip() to split_data_line() * `#12968 <https://github.com/scipy/scipy/pull/12968>`__: ENH: stats: Use only an analytical formula or scalar root-finding... * `#12971 <https://github.com/scipy/scipy/pull/12971>`__: MAINT: Declare support for Python 3.9 * `#12972 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<https://github.com/scipy/scipy/pull/13006>`__: Keep correct dtype when loading empty mat arrays. * `#13009 <https://github.com/scipy/scipy/pull/13009>`__: MAINT: clip SLSQP step within bounds * `#13012 <https://github.com/scipy/scipy/pull/13012>`__: DOC: fix bilinear_zpk example labels * `#13013 <https://github.com/scipy/scipy/pull/13013>`__: ENH: Add \`subset\` and \`subsets\` methods to \`DisjointSet\`... * `#13029 <https://github.com/scipy/scipy/pull/13029>`__: MAINT: basinhopping callback for initial mininmisation * `#13032 <https://github.com/scipy/scipy/pull/13032>`__: DOC: fix docstring errors in in stats.wilcoxon * `#13036 <https://github.com/scipy/scipy/pull/13036>`__: BUG: forward port lint_diff shims * `#13041 <https://github.com/scipy/scipy/pull/13041>`__: MAINT: dogbox ensure x is within bounds closes #11403 * `#13042 <https://github.com/scipy/scipy/pull/13042>`__: MAINT: forward port 1.5.4 release notes * `#13046 <https://github.com/scipy/scipy/pull/13046>`__: DOC: 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suite-sparse and sksparse installation check * `#13070 <https://github.com/scipy/scipy/pull/13070>`__: MAINT: stats: Remove a couple obsolete comments. * `#13073 <https://github.com/scipy/scipy/pull/13073>`__: BUG: Fix scalar_search_wolfe2 to resolve #12157 * `#13078 <https://github.com/scipy/scipy/pull/13078>`__: CI, MAINT: migrate Lint to Azure * `#13081 <https://github.com/scipy/scipy/pull/13081>`__: BLD: drop Python 3.6 support (NEP 29) * `#13082 <https://github.com/scipy/scipy/pull/13082>`__: MAINT: update minimum NumPy version to 1.16.5 in a couple more... * `#13083 <https://github.com/scipy/scipy/pull/13083>`__: DOC: update toolchain.rst * `#13086 <https://github.com/scipy/scipy/pull/13086>`__: DOC: Update the Parameters section of the correlation docstring * `#13087 <https://github.com/scipy/scipy/pull/13087>`__: ENH:signal: Speed-up Cython implementation of _sosfilt * `#13089 <https://github.com/scipy/scipy/pull/13089>`__: BLD, BUG: add c99 compiler flag to HiGHS basiclu 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signal.iirdesign() * `#13116 <https://github.com/scipy/scipy/pull/13116>`__: CI: Don't report name errors after an exception in refguide-check * `#13117 <https://github.com/scipy/scipy/pull/13117>`__: CI: move sdist/pre-release test Azure * `#13119 <https://github.com/scipy/scipy/pull/13119>`__: Improve error message on friedmanchisquare function * `#13121 <https://github.com/scipy/scipy/pull/13121>`__: Fix factorial() for NaN on Python 3.10 * `#13123 <https://github.com/scipy/scipy/pull/13123>`__: BLD: Specify file extension for language standard version tests * `#13128 <https://github.com/scipy/scipy/pull/13128>`__: TST: skip Fortran I/O test for ODR * `#13130 <https://github.com/scipy/scipy/pull/13130>`__: TST: skip factorial() float tests on Python 3.10 * `#13136 <https://github.com/scipy/scipy/pull/13136>`__: CI:Add python dbg run to GH Actions * `#13138 <https://github.com/scipy/scipy/pull/13138>`__: CI: Port coverage, 64-bit BLAS, GCC 4.8 build to azure * `#13139 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Optimized np.digitize for equidistant bins
by Martín Chalela Dec. 18, 2020

Dec. 18, 2020

Hi all! I was wondering if there is a way around to using np.digitize when dealing with equidistant bins. For example: bins = np.linspace(0, 1, 20) The main problem I encountered is that digitize calls np.searchsorted. This is the correct way, I think, for generic bins, i.e. bins that have different widths. However, in the special, but not uncommon, case of equidistant bins, the searchsorted call can be very expensive and unnecessary. One can perform a simple calculation like the following: def digitize_eqbins(x, bins): """ Return the indices of the bins to which each value in input array belongs. Assumes equidistant bins. """ nbins = len(bins) - 1 digit = (nbins * (x - bins[0]) / (bins[-1] - bins[0])).astype(np.int) return digit + 1 Is there a better way of computing this for equidistant bins? Thank you! Martin.

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