SciPy 1.9.0 Release Notes#

SciPy 1.9.0 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 1.9.x branch, and on adding new features on the main branch.

This release requires Python 3.8-3.11 and NumPy 1.18.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release#

  • We have modernized our build system to use meson, substantially improving our build performance, and providing better build-time configuration and cross-compilation support,

  • Added scipy.optimize.milp, new function for mixed-integer linear programming,

  • Added scipy.stats.fit for fitting discrete and continuous distributions to data,

  • Tensor-product spline interpolation modes were added to scipy.interpolate.RegularGridInterpolator,

  • A new global optimizer (DIviding RECTangles algorithm) scipy.optimize.direct.

New features#

scipy.interpolate improvements#

  • Speed up the RBFInterpolator evaluation with high dimensional interpolants.

  • Added new spline based interpolation methods for scipy.interpolate.RegularGridInterpolator and its tutorial.

  • scipy.interpolate.RegularGridInterpolator and scipy.interpolate.interpn now accept descending ordered points.

  • RegularGridInterpolator now handles length-1 grid axes.

  • The BivariateSpline subclasses have a new method partial_derivative which constructs a new spline object representing a derivative of an original spline. This mirrors the corresponding functionality for univariate splines, splder and BSpline.derivative, and can substantially speed up repeated evaluation of derivatives.

scipy.linalg improvements#

  • scipy.linalg.expm now accepts nD arrays. Its speed is also improved.

  • Minimum required LAPACK version is bumped to 3.7.1.

scipy.fft improvements#

  • Added uarray multimethods for scipy.fft.fht and scipy.fft.ifht to allow provision of third party backend implementations such as those recently added to CuPy.

scipy.optimize improvements#

  • A new global optimizer, scipy.optimize.direct (DIviding RECTangles algorithm) was added. For problems with inexpensive function evaluations, like the ones in the SciPy benchmark suite, direct is competitive with the best other solvers in SciPy (dual_annealing and differential_evolution) in terms of execution time. See gh-14300 for more details.

  • Add a full_output parameter to scipy.optimize.curve_fit to output additional solution information.

  • Add a integrality parameter to scipy.optimize.differential_evolution, enabling integer constraints on parameters.

  • Add a vectorized parameter to call a vectorized objective function only once per iteration. This can improve minimization speed by reducing interpreter overhead from the multiple objective function calls.

  • The default method of scipy.optimize.linprog is now 'highs'.

  • Added scipy.optimize.milp, new function for mixed-integer linear programming.

  • Added Newton-TFQMR method to newton_krylov.

  • Added support for the Bounds class in shgo and dual_annealing for a more uniform API across scipy.optimize.

  • Added the vectorized keyword to differential_evolution.

  • approx_fprime now works with vector-valued functions.

scipy.signal improvements#

  • The new window function scipy.signal.windows.kaiser_bessel_derived was added to compute the Kaiser-Bessel derived window.

  • Single-precision hilbert operations are now faster as a result of more consistent dtype handling.

scipy.sparse improvements#

  • Add a copy parameter to scipy.sparce.csgraph.laplacian. Using inplace computation with copy=False reduces the memory footprint.

  • Add a dtype parameter to scipy.sparce.csgraph.laplacian for type casting.

  • Add a symmetrized parameter to scipy.sparce.csgraph.laplacian to produce symmetric Laplacian for directed graphs.

  • Add a form parameter to scipy.sparce.csgraph.laplacian taking one of the three values: array, or function, or lo determining the format of the output Laplacian: * array is a numpy array (backward compatible default); * function is a pointer to a lambda-function evaluating the Laplacian-vector or Laplacian-matrix product; * lo results in the format of the LinearOperator.

scipy.sparse.linalg improvements#

  • lobpcg performance improvements for small input cases.

scipy.spatial improvements#

scipy.stats improvements#

  • scipy.stats.monte_carlo_test performs one-sample Monte Carlo hypothesis tests to assess whether a sample was drawn from a given distribution. Besides reproducing the results of hypothesis tests like scipy.stats.ks_1samp, scipy.stats.normaltest, and scipy.stats.cramervonmises without small sample size limitations, it makes it possible to perform similar tests using arbitrary statistics and distributions.

  • Several scipy.stats functions support new axis (integer or tuple of integers) and nan_policy (‘raise’, ‘omit’, or ‘propagate’), and keepdims arguments. These functions also support masked arrays as inputs, even if they do not have a scipy.stats.mstats counterpart. Edge cases for multidimensional arrays, such as when axis-slices have no unmasked elements or entire inputs are of size zero, are handled consistently.

  • Add a weights parameter to scipy.stats.hmean.

  • Several improvements have been made to scipy.stats.levy_stable. Substantial improvement has been made for numerical evaluation of the pdf and cdf, resolving [#12658](scipy/scipy#12658) and [#14944](scipy/scipy#14994). The improvement is particularly dramatic for stability parameter alpha close to or equal to 1 and for alpha below but approaching its maximum value of 2. The alternative fast Fourier transform based method for pdf calculation has also been updated to use the approach of Wang and Zhang from their 2008 conference paper Simpson’s rule based FFT method to compute densities of stable distribution, making this method more competitive with the default method. In addition, users now have the option to change the parametrization of the Levy Stable distribution to Nolan’s “S0” parametrization which is used internally by SciPy’s pdf and cdf implementations. The “S0” parametrization is described in Nolan’s paper [Numerical calculation of stable densities and distribution functions](https://doi.org/10.1080/15326349708807450) upon which SciPy’s implementation is based. “S0” has the advantage that delta and gamma are proper location and scale parameters. With delta and gamma fixed, the location and scale of the resulting distribution remain unchanged as alpha and beta change. This is not the case for the default “S1” parametrization. Finally, more options have been exposed to allow users to trade off between runtime and accuracy for both the default and FFT methods of pdf and cdf calculation. More information can be found in the documentation here (to be linked).

  • Added scipy.stats.fit for fitting discrete and continuous distributions to data.

  • The methods "pearson" and "tippet" from scipy.stats.combine_pvalues have been fixed to return the correct p-values, resolving [#15373](scipy/scipy#15373). In addition, the documentation for scipy.stats.combine_pvalues has been expanded and improved.

  • Unlike other reduction functions, stats.mode didn’t consume the axis being operated on and failed for negative axis inputs. Both the bugs have been fixed. Note that stats.mode will now consume the input axis and return an ndarray with the axis dimension removed.

  • Replaced implementation of scipy.stats.ncf with the implementation from Boost for improved reliability.

  • Add a bits parameter to scipy.stats.qmc.Sobol. It allows to use from 0 to 64 bits to compute the sequence. Default is None which corresponds to 30 for backward compatibility. Using a higher value allow to sample more points. Note: bits does not affect the output dtype.

  • Add a integers method to scipy.stats.qmc.QMCEngine. It allows sampling integers using any QMC sampler.

  • Improved the fit speed and accuracy of stats.pareto.

  • Added qrvs method to NumericalInversePolynomial to match the situation for NumericalInverseHermite.

  • Faster random variate generation for gennorm and nakagami.

  • lloyd_centroidal_voronoi_tessellation has been added to allow improved sample distributions via iterative application of Voronoi diagrams and centering operations

  • Add scipy.stats.qmc.PoissonDisk to sample using the Poisson disk sampling method. It guarantees that samples are separated from each other by a given radius.

  • Add scipy.stats.pmean to calculate the weighted power mean also called generalized mean.

Deprecated features#

  • Due to collision with the shape parameter n of several distributions, use of the distribution moment method with keyword argument n is deprecated. Keyword n is replaced with keyword order.

  • Similarly, use of the distribution interval method with keyword arguments alpha is deprecated. Keyword alpha is replaced with keyword confidence.

  • The 'simplex', 'revised simplex', and 'interior-point' methods of scipy.optimize.linprog are deprecated. Methods highs, highs-ds, or highs-ipm should be used in new code.

  • Support for non-numeric arrays has been deprecated from stats.mode. pandas.DataFrame.mode can be used instead.

  • The function spatial.distance.kulsinski has been deprecated in favor of spatial.distance.kulczynski1.

  • The maxiter keyword of the truncated Newton (TNC) algorithm has been deprecated in favour of maxfun.

  • The vertices keyword of Delauney.qhull now raises a DeprecationWarning, after having been deprecated in documentation only for a long time.

  • The extradoc keyword of rv_continuous, rv_discrete and rv_sample now raises a DeprecationWarning, after having been deprecated in documentation only for a long time.

Expired Deprecations#

There is an ongoing effort to follow through on long-standing deprecations. The following previously deprecated features are affected:

  • Object arrays in sparse matrices now raise an error.

  • Inexact indices into sparse matrices now raise an error.

  • Passing radius=None to scipy.spatial.SphericalVoronoi now raises an error (not adding radius defaults to 1, as before).

  • Several BSpline methods now raise an error if inputs have ndim > 1.

  • The _rvs method of statistical distributions now requires a size parameter.

  • Passing a fillvalue that cannot be cast to the output type in scipy.signal.convolve2d now raises an error.

  • scipy.spatial.distance now enforces that the input vectors are one-dimensional.

  • Removed stats.itemfreq.

  • Removed stats.median_absolute_deviation.

  • Removed n_jobs keyword argument and use of k=None from kdtree.query.

  • Removed right keyword from interpolate.PPoly.extend.

  • Removed debug keyword from scipy.linalg.solve_*.

  • Removed class _ppform scipy.interpolate.

  • Removed BSR methods matvec and matmat.

  • Removed mlab truncation mode from cluster.dendrogram.

  • Removed cluster.vq.py_vq2.

  • Removed keyword arguments ftol and xtol from optimize.minimize(method='Nelder-Mead').

  • Removed signal.windows.hanning.

  • Removed LAPACK gegv functions from linalg; this raises the minimally required LAPACK version to 3.7.1.

  • Removed spatial.distance.matching.

  • Removed the alias scipy.random for numpy.random.

  • Removed docstring related functions from scipy.misc (docformat, inherit_docstring_from, extend_notes_in_docstring, replace_notes_in_docstring, indentcount_lines, filldoc, unindent_dict, unindent_string).

  • Removed linalg.pinv2.

Backwards incompatible changes#

  • Several scipy.stats functions now convert np.matrix to np.ndarray``s before the calculation is performed. In this case, the output will be a scalar or ``np.ndarray of appropriate shape rather than a 2D np.matrix. Similarly, while masked elements of masked arrays are still ignored, the output will be a scalar or np.ndarray rather than a masked array with mask=False.

  • The default method of scipy.optimize.linprog is now 'highs', not 'interior-point' (which is now deprecated), so callback functions and some options are no longer supported with the default method. With the default method, the x attribute of the returned OptimizeResult is now None (instead of a non-optimal array) when an optimal solution cannot be found (e.g. infeasible problem).

  • For scipy.stats.combine_pvalues, the sign of the test statistic returned for the method "pearson" has been flipped so that higher values of the statistic now correspond to lower p-values, making the statistic more consistent with those of the other methods and with the majority of the literature.

  • scipy.linalg.expm due to historical reasons was using the sparse implementation and thus was accepting sparse arrays. Now it only works with nDarrays. For sparse usage, scipy.sparse.linalg.expm needs to be used explicitly.

  • The definition of scipy.stats.circvar has reverted to the one that is standard in the literature; note that this is not the same as the square of scipy.stats.circstd.

  • Remove inheritance to QMCEngine in MultinomialQMC and MultivariateNormalQMC. It removes the methods fast_forward and reset.

  • Init of MultinomialQMC now require the number of trials with n_trials. Hence, MultinomialQMC.random output has now the correct shape (n, pvals).

  • Several function-specific warnings (F_onewayConstantInputWarning, F_onewayBadInputSizesWarning, PearsonRConstantInputWarning, PearsonRNearConstantInputWarning, SpearmanRConstantInputWarning, and BootstrapDegenerateDistributionWarning) have been replaced with more general warnings.

Other changes#

  • A draft developer CLI is available for SciPy, leveraging the doit, click and rich-click tools. For more details, see [gh-15959](scipy/scipy#15959).

  • The SciPy contributor guide has been reorganized and updated (see [#15947](scipy/scipy#15947) for details).

  • QUADPACK Fortran routines in scipy.integrate, which power scipy.integrate.quad, have been marked as recursive. This should fix rare issues in multivariate integration (nquad and friends) and obviate the need for compiler-specific compile flags (/recursive for ifort etc). Please file an issue if this change turns out problematic for you. This is also true for FITPACK routines in scipy.interpolate, which power splrep, splev etc., and *UnivariateSpline and *BivariateSpline classes.

  • the USE_PROPACK environment variable has been renamed to SCIPY_USE_PROPACK; setting to a non-zero value will enable the usage of the PROPACK library as before

  • Building SciPy on windows with MSVC now requires at least the vc142 toolset (available in Visual Studio 2019 and higher).

Lazy access to subpackages#

Before this release, all subpackages of SciPy (cluster, fft, ndimage, etc.) had to be explicitly imported. Now, these subpackages are lazily loaded as soon as they are accessed, so that the following is possible (if desired for interactive use, it’s not actually recommended for code, see SciPy API): import scipy as sp; sp.fft.dct([1, 2, 3]). Advantages include: making it easier to navigate SciPy in interactive terminals, reducing subpackage import conflicts (which before required import networkx.linalg as nla; import scipy.linalg as sla), and avoiding repeatedly having to update imports during teaching & experimentation. Also see [the related community specification document](https://scientific-python.org/specs/spec-0001/).

SciPy switched to Meson as its build system#

This is the first release that ships with [Meson](https://mesonbuild.com) as the build system. When installing with pip or pypa/build, Meson will be used (invoked via the meson-python build hook). This change brings significant benefits - most importantly much faster build times, but also better support for cross-compilation and cleaner build logs.

Note

This release still ships with support for numpy.distutils-based builds as well. Those can be invoked through the setup.py command-line interface (e.g., python setup.py install). It is planned to remove numpy.distutils support before the 1.10.0 release.

When building from source, a number of things have changed compared to building with numpy.distutils:

  • New build dependencies: meson, ninja, and pkg-config. setuptools and wheel are no longer needed.

  • BLAS and LAPACK libraries that are supported haven’t changed, however the discovery mechanism has: that is now using pkg-config instead of hardcoded paths or a site.cfg file.

  • The build defaults to using OpenBLAS. See Selecting BLAS and LAPACK libraries for details.

The two CLIs that can be used to build wheels are pip and build. In addition, the SciPy repo contains a python dev.py CLI for any kind of development task (see its --help for details). For a comparison between old (distutils) and new (meson) build commands, see Meson and distutils ways of doing things.

For more information on the introduction of Meson support in SciPy, see gh-13615 and this blog post.

Authors#

  • endolith (12)

  • h-vetinari (11)

  • Caio Agiani (2) +

  • Emmy Albert (1) +

  • Joseph Albert (1)

  • Tania Allard (3)

  • Carsten Allefeld (1) +

  • Kartik Anand (1) +

  • Virgile Andreani (2) +

  • Weh Andreas (1) +

  • Francesco Andreuzzi (5) +

  • Kian-Meng Ang (2) +

  • Gerrit Ansmann (1)

  • Ar-Kareem (1) +

  • Shehan Atukorala (1) +

  • avishai231 (1) +

  • Blair Azzopardi (1)

  • Sayantika Banik (2) +

  • Ross Barnowski (9)

  • Christoph Baumgarten (3)

  • Nickolai Belakovski (1)

  • Peter Bell (9)

  • Sebastian Berg (3)

  • Bharath (1) +

  • bobcatCA (2) +

  • boussoffara (2) +

  • Islem BOUZENIA (1) +

  • Jake Bowhay (41) +

  • Matthew Brett (11)

  • Dietrich Brunn (2) +

  • Michael Burkhart (2) +

  • Evgeni Burovski (96)

  • Matthias Bussonnier (20)

  • Dominic C (1)

  • Cameron (1) +

  • CJ Carey (3)

  • Thomas A Caswell (2)

  • Ali Cetin (2) +

  • Hood Chatham (5) +

  • Klesk Chonkin (1)

  • Craig Citro (1) +

  • Dan Cogswell (1) +

  • Luigi Cruz (1) +

  • Anirudh Dagar (5)

  • Brandon David (1)

  • deepakdinesh1123 (1) +

  • Denton DeLoss (1) +

  • derbuihan (2) +

  • Sameer Deshmukh (13) +

  • Niels Doucet (1) +

  • DWesl (8)

  • eytanadler (30) +

  • Thomas J. Fan (5)

  • Isuru Fernando (3)

  • Joseph Fox-Rabinovitz (1)

  • Ryan Gibson (4) +

  • Ralf Gommers (327)

  • Srinivas Gorur-Shandilya (1) +

  • Alex Griffing (2)

  • Matt Haberland (461)

  • Tristan Hearn (1) +

  • Jonathan Helgert (1) +

  • Samuel Hinton (1) +

  • Jake (1) +

  • Stewart Jamieson (1) +

  • Jan-Hendrik Müller (1)

  • Yikun Jiang (1) +

  • JuliaMelle01 (1) +

  • jyuv (12) +

  • Toshiki Kataoka (1)

  • Chris Keefe (1) +

  • Robert Kern (4)

  • Andrew Knyazev (11)

  • Matthias Koeppe (4) +

  • Sergey Koposov (1)

  • Volodymyr Kozachynskyi (1) +

  • Yotaro Kubo (2) +

  • Jacob Lapenna (1) +

  • Peter Mahler Larsen (8)

  • Eric Larson (4)

  • Laurynas Mikšys (1) +

  • Antony Lee (1)

  • Gregory R. Lee (2)

  • lerichi (1) +

  • Tim Leslie (2)

      1. Lim (1)

  • Smit Lunagariya (43)

  • lutefiskhotdish (1) +

  • Cong Ma (12)

  • Syrtis Major (1)

  • Nicholas McKibben (18)

  • Melissa Weber Mendonça (10)

  • Mark Mikofski (1)

  • Jarrod Millman (13)

  • Harsh Mishra (6)

  • ML-Nielsen (3) +

  • Matthew Murray (1) +

  • Andrew Nelson (50)

  • Dimitri Papadopoulos Orfanos (1) +

  • Evgueni Ovtchinnikov (2) +

  • Sambit Panda (1)

  • Nick Papior (2)

  • Tirth Patel (43)

  • Petar Mlinarić (1)

  • petroselo (1) +

  • Ilhan Polat (64)

  • Anthony Polloreno (1)

  • Amit Portnoy (1) +

  • Quentin Barthélemy (9)

  • Patrick N. Raanes (1) +

  • Tyler Reddy (185)

  • Pamphile Roy (199)

  • Vivek Roy (2) +

  • sabonerune (1) +

  • Niyas Sait (2) +

  • Atsushi Sakai (25)

  • Mazen Sayed (1) +

  • Eduardo Schettino (5) +

  • Daniel Schmitz (6) +

  • Eli Schwartz (4) +

  • SELEE (2) +

  • Namami Shanker (4)

  • siddhantwahal (1) +

  • Gagandeep Singh (8)

  • Soph (1) +

  • Shivnaren Srinivasan (1) +

  • Scott Staniewicz (1) +

  • Leo C. Stein (4)

  • Albert Steppi (7)

  • Christopher Strickland (1) +

  • Kai Striega (4)

  • Søren Fuglede Jørgensen (1)

  • Aleksandr Tagilov (1) +

  • Masayuki Takagi (1) +

  • Sai Teja (1) +

  • Ewout ter Hoeven (2) +

  • Will Tirone (2)

  • Bas van Beek (7)

  • Dhruv Vats (1)

  • Arthur Volant (1)

  • Samuel Wallan (5)

  • Stefan van der Walt (8)

  • Warren Weckesser (84)

  • Anreas Weh (1)

  • Nils Werner (1)

  • Aviv Yaish (1) +

  • Dowon Yi (1)

  • Rory Yorke (1)

  • Yosshi999 (1) +

  • yuanx749 (2) +

  • Gang Zhao (23)

  • ZhihuiChen0903 (1)

  • Pavel Zun (1) +

  • David Zwicker (1) +

A total of 154 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 1.9.0#

  • #1884: stats distributions fit problems (Trac #1359)

  • #2047: derivatives() method is missing in BivariateSpline (Trac #1522)

  • #2071: TST: stats: `check_sample_var` should be two-sided (Trac #1546)

  • #2414: stats binom at non-integer n (Trac #1895)

  • #2623: stats.distributions statistical power of test suite

  • #2625: wilcoxon() function does not return z-statistic

  • #2650: (2D) Interpolation functions should work with complex numbers

  • #2834: ksone fitting

  • #2868: nan and stats.percentileofscore

  • #2877: distributions.ncf numerical issues

  • #2993: optimize.approx_fprime & jacobians

  • #3214: stats distributions ppf-cdf roundtrip

  • #3758: discrete distribution defined by `values` with non-integer…

  • #4130: BUG: stats: fisher_exact returns incorrect p-value

  • #4897: expm is 10x as slow as matlab according to http://stackoverflow.com/questions/30048315

  • #5103: Docs suggest scipy.sparse.linalg.expm_multiply supports LinearOperator…

  • #5266: Deprecated routines in Netlib LAPACK >3.5.0

  • #5890: Undefined behavior when using scipy.interpolate.RegularGridInterpolator…

  • #5982: Keyword collision in scipy.stats.levy_stable.interval

  • #6472: scipy.stats.invwishart does not check if scale matrix is symmetric

  • #6551: BUG: stats: inconsistency in docs and behavior of gmean and hmean

  • #6624: incorrect handling of nan by RegularGridInterpolator

  • #6882: Certain recursive scipy.integrate.quad (e.g. dblquad and nquad)…

  • #7469: Misleading interp2d documentation

  • #7560: Should RegularGridInterpolator support length 1 dimensions?

  • #8850: Scipy.interpolate.griddata Error : Exception ignored in: ‘scipy.spatial.qhull._Qhull.__dealloc__’

  • #8928: BUG: scipy.stats.norm wrong expected value of function when loc…

  • #9213: __STDC_VERSION__ check in C++ code

  • #9231: infinite loop in stats.fisher_exact

  • #9313: geometric distribution stats.geom returns negative values if…

  • #9524: interpn returns nan with perfectly valid data

  • #9591: scipy.interpolate.interp1d with kind=“previous” doesn’t extrapolate…

  • #9815: stats.mode’s nan_policy ‘propagate’ not working?

  • #9944: documentation for `scipy.interpolate.RectBivariateSpline` is…

  • #9999: BUG: malloc() calls in Cython and C that are not checked for…

  • #10096: Add literature reference for circstd (and circvar?)

  • #10446: RuntimeWarning: invalid value encountered in stats.genextreme

  • #10577: Additional discussion for scipy.stats roadmap

  • #10821: Errors with the Yeo-Johnson Transform that also Appear in Scikit-Learn

  • #10983: LOBPCG inefficinet when computing > 20% of eigenvalues

  • #11145: unexpected SparseEfficiencyWarning at scipy.sparse.linalg.splu

  • #11406: scipy.sparse.linalg.svds (v1.4.1) on singular matrix does not…

  • #11447: scipy.interpolate.interpn: Handle ValueError(‘The points in dimension…

  • #11673: intlinprog: integer linear program solver

  • #11742: MAINT: stats: getting skewness alone takes 34000x longer than…

  • #11806: Unexpectedly poor results when distribution fitting with `weibull_min`…

  • #11828: UnivariateSpline gives varying results when multithreaded on…

  • #11948: fitting discrete distributions

  • #12073: Add note in documentation

  • #12370: truncnorm.rvs is painfully slow on version 1.5.0rc2

  • #12456: Add generalized mean calculation

  • #12480: RectBivariateSpline derivative evaluator is slow

  • #12485: linprog returns an incorrect message

  • #12506: ENH: stats: one-sided p-values for statistical tests

  • #12545: stats.pareto.fit raises RuntimeWarning

  • #12548: scipy.stats.skew returning MaskedArray

  • #12633: Offer simpler development workflow?

  • #12658: scipy.stats.levy_stable.pdf can be inaccurate and return nan

  • #12733: scipy.stats.truncnorm.cdf slow

  • #12838: Accept multiple matrices in `scipy.linalg.expm`

  • #12848: DOC: stats: multivariate distribution documentation issues

  • #12870: Levy Stable Random Variates Code has a typo

  • #12871: Levy Stable distribution uses parameterisation that is not location…

  • #13200: Errors made by scipy.optimize.linprog

  • #13462: Too many warnings and results objects in public API for scipy.stats

  • #13582: ENH: stats: `rv_continuous.stats` with array shapes: use `_stats`…

  • #13615: RFC: switch to Meson as a build system

  • #13632: stats.rv_discrete is not checking that xk values are integers

  • #13655: MAINT: stats.rv_generic: `moment` method falls back to `_munp`…

  • #13689: Wilcoxon does not appropriately detect ties when mode=exact.

  • #13835: Change name of `alpha` parameter in `interval()` method

  • #13872: Add method details or reference to `scipy.integrate.dblquad`

  • #13912: Adding Poisson Disc sampling to QMC

  • #13996: Fisk distribution documentation typo

  • #14035: `roots_jacobi` support for large parameter values

  • #14081: `scipy.optimize._linprog_simplex._apply_pivot` relies on asymmetric…

  • #14095: scipy.stats.norm.pdf takes too much time and memory

  • #14162: Thread safety RectBivariateSpline

  • #14267: BUG: online doc returns 404 - wrong `reference` in url

  • #14313: ks_2samp: example description does not match example output

  • #14418: `ttest_ind` for two sampled distributions with the same single…

  • #14455: Adds Mixed Integer Linear Programming from highs

  • #14462: Shapiro test returning negative p-value

  • #14471: methods ‘revised simplex’ and ‘interior-point’ are extremely…

  • #14505: `Optimization converged to parameters that are outside the range`…

  • #14527: Segmentation fault with KDTree

  • #14548: Add convention flag to quanternion in `Scipy.spatial.transform.rotation.Rotation`

  • #14565: optimize.minimize: Presence of callback causes method TNC to…

  • #14622: BUG: (sort of) mannwhitneyu hits max recursion limit with imbalanced…

  • #14645: ENH: MemoryError when trying to bootstrap with large amounts…

  • #14716: BUG: stats: The `loguniform` distribution is overparametrized.

  • #14731: BUG: Incorrect residual graph in scipy.sparse.csgraph.maximum_flow

  • #14745: BUG: scipy.ndimage.convolve documentation is incorrect

  • #14750: ENH: Add one more derivative-free optimization method

  • #14753: Offer to collaborate on truncated normal estimation by minimax…

  • #14777: BUG: Wrong limit and no warning in stats.t for df=np.inf

  • #14793: BUG: Missing pairs in cKDTree.query_pairs when coordinates contain…

  • #14861: BUG: unclear error message when all bounds are all equal for…

  • #14889: BUG: NumPy’s `random` module should not be in the `scipy`…

  • #14914: CI job with code coverage is failing (yet again)

  • #14926: RegularGridInterpolator should be called RectilinearGridInterpolator

  • #14986: Prevent new Python versions from trying to install older releases…

  • #14994: BUG: Levy stable

  • #15009: BUG: scipy.stats.multiscale_graphcorr p-values are computed differently…

  • #15059: BUG: documentation inconsistent with code for find_peaks_cwt

  • #15082: DOC: Sampling from the truncated normal

  • #15110: BUG: truncnorm.cdf returns incorrect values at tail

  • #15125: Deprecate `scipy.spatial.distance.kulsinski`

  • #15133: BUG: Log_norm description is incorrect and produces incorrect…

  • #15150: BUG: RBFInterpolator is much slower than Rbf for vector data

  • #15172: BUG: special: High relative error in `log_ndtr`

  • #15195: BUGS: stats: Tracking issue for distributions that warn and/or…

  • #15199: BUG: Error occured `spsolve_triangular`

  • #15210: BUG: A sparse matrix raises a ValueError when `__rmul__` with…

  • #15245: MAINT: scipy.stats._levy_stable should be treated as subpackage…

  • #15252: DOC: Multivariate normal CDF docstring typo

  • #15296: BUG: SciPy 1.7.x build failure on Cygwin

  • #15308: BUG: OpenBLAS 0.3.18 support

  • #15338: DOC: Rename `*args` param in `f_oneway` to `*samples`

  • #15345: BUG: boschloo_exact gives pvalue > 1 (and sometimes nan)

  • #15368: build warnings for `unuran_wrapper.pyx`

  • #15373: BUG: Tippett’s and Pearson’s method for combine_pvalues are not…

  • #15415: `integrate.quad_vec` missing documentation for `limit` parameter

  • #15456: Segfault in HiGHS code when building with Mingw-w64 on Windows

  • #15458: DOC: Documentation inaccuracy of scipy.interpolate.bisplev

  • #15488: ENH: missing examples for scipy.optimize in docs

  • #15507: BUG: scipy.optimize.linprog: the algorithm determines the problem…

  • #15508: BUG: Incorrect error message in multivariate_normal

  • #15541: BUG: scipy.stats.powerlaw, why should x ∈ (0,1)? x can exceed…

  • #15551: MAINT: stats: deprecating non-numeric array support in `stats.mode`

  • #15568: BENCH/CI: Benchmark timeout

  • #15572: BUG: `scipy.spatial.transform.rotation`, wrong deprecation…

  • #15575: BUG: Tests failing for initial build [arm64 machine]

  • #15589: BUG: scipy.special.factorialk docstring inconsistent with behaviour

  • #15601: BUG: Scalefactors for `signal.csd` with `average==’median’`…

  • #15617: ENH: stats: all multivariate distributions should be freezable

  • #15631: BUG: stats.fit: intermittent failure in doctest

  • #15635: CI:ASK: Remove LaTeX doc builds?

  • #15638: DEV: `dev.py` missing PYTHONPATH when building doc

  • #15644: DOC: stats.ks_1samp: incorrect commentary in examples

  • #15666: CI: CircleCI build_docs failure on main

  • #15670: BUG: AssertionError in test__dual_annealing.py in test_bounds_class

  • #15689: BUG: default value of shape parameter in fit method of rv_continuous…

  • #15692: CI: scipy.scipy (Main refguide_asv_check) failure in main

  • #15696: DOC: False information in docs - scipy.stats.ttest_1samp

  • #15700: BUG: AssertionError in test_propack.py

  • #15730: BUG: “terminate called after throwing an instance of ‘std::out_of_range’”…

  • #15732: DEP: execute deprecation of inexact indices into sparse matrices

  • #15734: DEP: deal with deprecation of ndim >1 in bspline

  • #15735: DEP: add actual DeprecationWarning for sym_pos-keyword of scipy.linalg.solve

  • #15736: DEP: Remove `debug` keyword from `scipy.linalg.solve_*`

  • #15737: DEP: Execute deprecation of pinv2

  • #15739: DEP: sharpen deprecation for >1-dim inputs in optimize.minimize

  • #15740: DEP: Execute deprecation for squeezing input vectors in spatial.distance

  • #15741: DEP: remove spatial.distance.matching

  • #15742: DEP: raise if fillvalue cannot be cast to output type in `signal.convolve2d`

  • #15743: DEP: enforce radius for `spatial.SphericalVoronoi`

  • #15744: DEP: sharpen deprecation of dual_annealing argument ‘local_search_options’

  • #15745: DEP: remove signal.windows.hanning

  • #15746: DEP: remove k=None from KDTree.query

  • #15747: DEP: stats: remove support for `_rvs` without `size` parameter

  • #15750: DEP: remove `n_jobs` from kdtree

  • #15751: DEP: remove ftol/xtol from neldermead

  • #15752: DEP: remove right keyword from interpolate.PPoly.extend

  • #15753: DEP: remove `_ppform`

  • #15754: DEP: Remove mlab mode from dendrogram

  • #15757: DEP: docstring-related deprecations

  • #15758: DEP: remove LAPACK *gegv functions

  • #15759: DEP: remove old BSR methods

  • #15760: DEP: remove py_vq2

  • #15761: DEP: remove stats.itemfreq

  • #15762: DEP: remove stats.median_absolute_deviation

  • #15773: BUG: iirfilter allows Wn[1] < Wn[0] for band-pass and band-stop…

  • #15780: BUG: CI on Azure broken with PyTest 7.1

  • #15843: BUG: scipy.stats.brunnermunzel incorrectly returns nan for undocumented…

  • #15854: CI: Windows Meson job failing sometimes on OpenBLAS binary download

  • #15866: BUG/CI: Wrong python version used for tests labeled “Linux Tests…

  • #15871: BUG: stats: Test failure of `TestTruncnorm.test_moments` on…

  • #15899: BUG: _calc_uniform_order_statistic_medians documentation example…

  • #15927: BUG: Inconsistent handling of INF and NAN in signal.convolve

  • #15931: BUG: scipy/io/arff/tests/test_arffread.py::TestNoData::test_nodata…

  • #15960: BUG: Documentation Error in scipy.signal.lfilter

  • #15961: BUG: scipy.stats.beta and bernoulli fails with float32 inputs

  • #15962: Race condition in macOS Meson build between `_matfuncs_expm`…

  • #15987: CI: `np.matrix` deprecation warning

  • #16007: BUG: Confusing documentation in `ttest_ind_from_stats`

  • #16011: BUG: typo in documentation for scipy.optimize.basinhopping

  • #16020: BUG: dev.py FileNotFoundError

  • #16027: jc should be (n-1)/2

  • #16031: BUG: scipy.sparse.linalg.norm does not work on sparse arrays

  • #16036: Missing `f` prefix on f-strings

  • #16054: Bug: Meson build with dev.py fails to detect SciPy with debian…

  • #16065: BUG: Gitpod build with `python runtests.py` fails; move to…

  • #16074: BUG: refguide check fails with `numpydoc==1.3`

  • #16081: CI, MAINT: minor refguide failure with stats.describe

  • #16121: DOC: scipy.interpolate.RegularGridInterpolator and interpn works…

  • #16162: BUG: curve_fit gives wrong results with Pandas float32

  • #16171: BUG: scipy.stats.multivariate_hypergeom.rvs raises ValueError…

  • #16219: `TestSobol.test_0dim` failure on 32-bit Linux job

  • #16233: BUG: Memory leak in function `sf_error` due to new reference…

  • #16254: DEP: add deprecation warning to `maxiter` kwarg in `_minimize_tnc`

  • #16292: BUG: compilation error: no matching constructor for initialization…

  • #16300: BLD: pip install build issue with meson in Ubuntu virtualenv

  • #16337: TST: stats/tests/test_axis_nan_policy.py::test_axis_nan_policy_full…

  • #16347: TST, MAINT: 32-bit Linux test failures in wheels repo

  • #16358: TST, MAINT: test_theilslopes_warnings fails on 32-bit Windows

  • #16378: DOC: pydata-sphinx-theme v0.9 defaults to darkmode depending…

  • #16381: BUG: bootstrap get ValueError for paired statistic

  • #16382: BUG: truncnorm.fit does not fit correctly

  • #16403: MAINT: NumPy main will require a few updates due to new floating…

  • #16409: BUG: SIGSEGV in qhull when array type is wrong

  • #16418: BUG: breaking change: scipy.stats.mode returned value has changed…

  • #16419: BUG: scipy.stats.nbinom.logcdf returns wrong results when some…

  • #16426: BUG: stats.shapiro inplace modification of user array

  • #16446: BUG: Issue with stripping on macOS Monterey + xcode 13.2

  • #16465: BLD: new sdist has some metadata issues

  • #16466: BUG: linprog failure - OptimizeResult.x returns NoneType

  • #16495: HiGHS does not compile on windows (on conda-forge infra)

  • #16523: BUG: test failure in pre-release job: `TestFactorized.test_singular_with_umfpack`

  • #16540: BLD: meson 0.63.0 and new CI testing failures on Linux

  • #16555: Building 1.9.x branch from source requires fix in meson-python…

  • #16609: BUG: `scipy.optimize.linprog` reports optimal for trivially…

  • #16681: BUG: linprog integrality only accepts list, not array

  • #16718: BUG: memoryview error with Cython 0.29.31

Pull requests for 1.9.0#

  • #9523: ENH: improvements to the Stable distribution

  • #11829: Fixes safe handling of small singular values in svds.

  • #13490: DEV: stats: check for distribution/method keyword name collisions

  • #13572: ENH: n-D and nan_policy support for scipy.stats.percentileofscore

  • #13918: ENH: Poisson Disk sampling for QMC

  • #13955: DOC: SciPy extensions for code style and docstring guidelines.

  • #14003: DOC: clarify the definition of the pdf of `stats.fisk`

  • #14036: ENH: fix numerical issues in roots_jacobi and related special…

  • #14087: DOC: explain null hypotheses in ttest functions

  • #14142: DOC: Add better error message for unpacking issue

  • #14143: Support LinearOperator in expm_multiply

  • #14300: ENH: Adding DIRECT algorithm to ``scipy.optimize``

  • #14576: ENH: stats: add one-sample Monte Carlo hypothesis test

  • #14642: ENH: add Lloyd’s algorithm to `scipy.spatial` to improve a…

  • #14718: DOC: stats: adjust bootstrap doc to emphasize that batch controls…

  • #14781: BUG: stats: handle infinite `df` in `t` distribution

  • #14847: ENH: BLD: enable building SciPy with Meson

  • #14877: DOC: ndimage convolve origin documentation (#14745)

  • #15001: ENH: sparse.linalg: More comprehensive tests (Not only for 1-D…

  • #15026: ENH: allow approx_fprime to work with vector-valued func

  • #15079: ENH:linalg: expm overhaul and ndarray processing

  • #15140: ENH: Make `stats.kappa3` work with array inputs

  • #15154: DOC: a small bug in docstring example of `lobpcg`

  • #15165: MAINT: Avoid using del to remove numpy symbols in scipy.__init__.py

  • #15168: REL: set version to 1.9.0.dev0

  • #15169: DOC: fix formatting of Methods in multivariate distributions

  • #15171: `AttrDict` raises `AttributeError` on missing attributes,…

  • #15176: BUG: special: Clean up some private namespaces and fix `special.__all__`

  • #15182: MAINT: fix typos principle -> principal

  • #15184: MAINT: CI: Rename ‘Nightly CPython’ job to ‘NumPy main’

  • #15187: BUG: special: Fix numerical precision issue of log_ndtr

  • #15188: MAINT: sparse.linalg: Using more concise and user-friendly f-string…

  • #15190: MAINT: interpolate: speed up the RBFInterpolator evaluation with…

  • #15196: BUG: stats: Fix handling of support endpoints in two distributions.

  • #15197: MAINT: build dependency updates

  • #15202: MAINT: special: Don’t use macro for ‘extern “C”’ in strictly…

  • #15205: BUG: stats: Fix spurious warnings generated by several distributions.

  • #15207: MAINT: sparse.linalg: Using the interface with the trace of sparse…

  • #15219: DOC: Corrected docstring of ndimage.sum_labels

  • #15223: DOC: x0->x for finite_diff_rel_step docstring closes #15208

  • #15230: ENH: expose submodules via `__getattr__` to allow lazy access

  • #15234: TST: stats: mark very slow tests as `xslow`

  • #15235: BUG: Fix rmul dispatch of spmatrix

  • #15243: DOC: stats: add reference for gstd

  • #15244: Added example for morphology: binary_dilation and erosion

  • #15250: ENH: Make `stats.kappa4` work with array

  • #15251: [MRG] ENH: Update `laplacian` function introducing the new…

  • #15255: MAINT: Remove `distutils` usage in `runtests.py` to fix deprecation…

  • #15259: MAINT: optimize, special, signal: Use custom warnings instead…

  • #15261: DOC: Add inline comment in Hausdorff distance calculation

  • #15265: DOC: update .mailmap

  • #15266: CI: remove coverage usage from Windows jobs

  • #15269: BLD: add setup.py for `stats/_levy_stable`

  • #15272: BUG: Fix owens_t function when a tends to infinity

  • #15274: DOC: fix docstring in _cdf() function of _multivariate.py

  • #15284: TST: silence RuntimeWarning from `np.det` in `signal.place_poles`…

  • #15285: CI: simplify 32-bit Linux testing

  • #15286: MAINT: Highs submodule CI issue - use shallow cloning

  • #15289: DOC: Misc numpydoc formatting.

  • #15291: DOC: some more docstring/numpydoc formatting.

  • #15294: ENH: add integrality constraints for linprog

  • #15300: DOC: Misc manual docs updates.

  • #15302: DOC: More docstring reformatting.

  • #15304: CI: fix Gitpod build by adding HiGHS submodule checkout

  • #15305: BLD: update NumPy to >=1.18.5, setuptools to <60.0

  • #15309: CI: update OpenBLAS to 0.3.18 in Azure jobs

  • #15310: ENH: signal: Add Kaiser-Bessel derived window function

  • #15312: BUG: special: Fix loss of precision in pseudo_huber when r/delta…

  • #15314: MAINT: changed needed after renaming `master` branch to `main`

  • #15315: MAINT: account for NumPy master -> main renaming

  • #15325: CI: reshuffle two Windows Azure CI jobs, and don’t run ‘full’…

  • #15330: ENH: optimize: support undocumented option `full_output` for…

  • #15336: DOC: update detailed roadmap

  • #15344: MAINT:stats: Renamed `*args` param to `*samples`

  • #15347: ENH: stats: add weights in harmonic mean

  • #15352: BLD: put upper bound `setuptools<60.0` in conda environment…

  • #15357: ENH: interpolate: add new methods for RegularGridInterpolator.

  • #15360: MAINT: speed up rvs of nakagami in scipy.stats

  • #15361: MAINT: sparse.linalg: Remove unnecessary operations

  • #15366: Make signal functions respect input dtype.

  • #15370: DOC: governance members moved to scipy.org

  • #15371: MAINT: stats: fix unuran compile-time warnings

  • #15378: MAINT: remove version pinning on gmpy2

  • #15380: ENH/MAINT: Version switcher from the sphinx theme

  • #15385: DOC: fix typo

  • #15387: MAINT: Fix a couple build warnings.

  • #15388: DOC: interpolate: improve `RectBivariateSpline` doc

  • #15391: ENH: graph Laplacian as LinearOperator, add dtype and symmetrized…

  • #15392: ENH: integrality constraints for differential_evolution

  • #15394: ENH: optimize: improvements to `LinearConstraint` class

  • #15396: DOC: Git:// protocol on github pending removal.

  • #15399: ENH: stats: add `axis` tuple and `nan_policy` to `hmean`

  • #15400: MAINT: sparse.linalg: Move the test function of GMRES to the…

  • #15401: MAINT: DOC: analytics from analytics.scientific-python

  • #15402: DOC: update pip_quickstart (submodules)

  • #15406: MAINT: use `Rotation.Random` instead of manual generation

  • #15407: BLD: meson: split pyx->c and Python extension build

  • #15408: MAINT: check for negative weights in `Rotation.align_vectors`

  • #15410: ENH: add `order` parameter to specify quaternion format

  • #15413: ENH: stats: add `rvs` method for `gennorm`

  • #15424: ENH: bypass LinearOperator in lobpcg for small-size cases

  • #15427: MAINT: Manage imports in `sparse.linalg`

  • #15431: Revert “ENH: add `order` parameter to specify quaternion format”

  • #15436: ENH: stats: fit: function for fitting discrete and continuous…

  • #15439: ENH: differential_evolution vectorized kwd

  • #15440: MAINT: Try to detect scipy path in `runtests.py` while not…

  • #15442: MAINT: Fix meson build warnings on windows

  • #15443: DOC, BUG: Fix error in heading remapping for custom `scipy.optimize:function` domain directive

  • #15445: ENH: stats: add `nnlf` method for discrete distributions

  • #15451: BLD: further refinement of Cython dependencies

  • #15452: BUG/DOC/TST: combine_pvalues: fix Tippett and Pearson

  • #15453: ENH: Make dual_annealing work with Bounds class

  • #15454: BLD: remove dependency on libnpymath from `spatial._distance_wrap`

  • #15455: ENH: Support Bounds class in shgo

  • #15459: DOC: documents parameter `limit` for function `integrate.quad_vec`.

  • #15460: ENH: optimize: milp: mixed integer linear programming

  • #15462: CI: switch one macOS CI job from distutils to meson

  • #15464: ENH: Performance improvements for `linear_sum_assignment`

  • #15465: DOC: stats: add weights in formulas and examples for gmean and…

  • #15466: MAINT: fix compile errors with CPython 3.11

  • #15469: MAINT: Remove `distutils` usage

  • #15470: ENH: `stats.qmc`: faster hypercube point comparison and scrambling…

  • #15472: ENH: stats: add `axis` tuple and `nan_policy` to `skew`

  • #15485: BLD: updates to Meson build files for more correct linking and…

  • #15487: MAINT: typo in bsplines.py

  • #15496: DOC: signal: fixed parameter ‘order’ for butter bandpass

  • #15497: MAINT: update vendored uarray

  • #15499: CI: remove matplotlib from 32-bit linux job, it fails to build

  • #15501: MAINT: Remove unused variable warnings

  • #15502: DEV: meson: allow specifying build directory and install prefix

  • #15512: MAINT: optimize.linprog: make HiGHS default and deprecate old…

  • #15523: DOC: fixed the link for fluiddyn’s transonic vision in dev/roadmap.html.

  • #15526: MAINT: add qrvs method to NumericalInversePolynomial in scipy.stats

  • #15529: DOC: forward port 1.8.0 relnotes

  • #15532: TST: parametrize test_ldl_type_size_combinations

  • #15546: DOC: missing section for metrics

  • #15555: MAINT: make unuran clone shallow

  • #15557: DOC: fixes inaccuracy in bisplev documentation

  • #15559: BENCH: selection of linalg solvers to facilitate expansion

  • #15560: DOC: types and return values for Bessel Functions

  • #15561: MAINT: update HiGHS submodule to include fix for Windows segfault

  • #15563: CI: add a Windows CI job on GitHub Actions using Meson

  • #15564: DOC: stray backticks

  • #15565: DOC: incorrect underline lenght in section.

  • #15567: ENH: stats.pareto fit improvement for parameter combinations

  • #15569: DOC: pip quickstart: setup.py -> meson

  • #15570: MAINT: bump test tolerance in test_linprog

  • #15571: DOC: Wrong underline length

  • #15578: Make Windows Python setup more standard

  • #15581: MAINT: clarify deprecation warning spatial.transform.rotation

  • #15583: DOC: clarify O(N) SO(N) in random rotations

  • #15586: ENH: stats: Add ‘alternative’ and confidence interval to pearsonr

  • #15590: DOC: factorialk docstring inconsistent with code

  • #15597: DOC: update `hyp2f1` docstring example based on doctest

  • #15598: BUG/ENH: `lsq_linear`: fixed incorrect `lsmr_tol` in first…

  • #15603: BENCH: optimize: milp: add MILP benchmarks

  • #15606: MAINT: allow multiplication sign `×`

  • #15611: BUG:signal: Fix median bias in csd(…, average=”median”)

  • #15616: CI: pin asv to avoid slowdowns in 0.5/0.5.1

  • #15619: DOC: stats: update interval and moment method signatures

  • #15625: MAINT: Clean up `type: ignore` comments related to third-party…

  • #15626: TST, MAINT: ignore np distutils dep

  • #15629: MAINT: stats: fix `trim1` `axis` behavior

  • #15632: ENH: stats.wilcoxon: return z-statistic (as requested)

  • #15634: CI: Improve concurrency to cancel running jobs on PR update

  • #15645: DOC: Add code example to the documentation of `sparse.linalg.cg`.

  • #15646: DOC: stats.ks_1samp: correct examples

  • #15647: ENH: add variable bits to `stats.qmc.Sobol`

  • #15648: DOC: Add examples to documentation for `scipy.special.ellipr{c,d,f,g,j}`

  • #15649: DEV/DOC: remove latex/pdf documentation

  • #15651: DOC: stats.ks_2samp/stats.kstest: correct examples

  • #15652: DOC: stats.circstd: add reference, notes, comments

  • #15655: REL: fix small issue in pavement.py for release note writing

  • #15656: DOC: Fix example for subset_by_index in eigh doc

  • #15661: DOC: Additional examples for optimize user guide

  • #15662: DOC: stats.fit: fix intermittent failure in doctest

  • #15663: DOC: stats.burr12: fix typo

  • #15664: BENCH: Add benchmarks for special.factorial/factorial2/factorialk

  • #15673: DOC: fix intersphinx links

  • #15682: MAINT: sparse.linalg: Clear up unnecessary modules imported in…

  • #15684: DOC: add formula and documentation improvements for scipy.special.chndtr…

  • #15690: ENH: add uarray multimethods for fast Hankel transforms

  • #15694: MAINT,CI: signal: fix failing refguide check

  • #15699: DOC: stats.ttest_1samp: update example

  • #15701: BUG: Fix dual_annealing bounds test

  • #15703: BUG: fix test fail in test_propack.py (loosen atol)

  • #15710: MAINT: sparse.linalg: `bnorm` only calculate once

  • #15712: ENH: `scipy.stats.qmc.Sobol`: allow 32 or 64 bit computation

  • #15715: ENH: stats: add _axis_nan_policy_factory to moment

  • #15718: ENH: Migration of `write_release_and_log` into standalone script

  • #15723: TST: stats: make `check_sample_var` two-sided

  • #15724: TST: stats: simplify `check_sample_mean`

  • #15725: DEV: Try to detect scipy from dev installed path

  • #15728: ENH: changed vague exception messages to a more descriptive ones…

  • #15729: ENH: stats: add weighted power mean

  • #15763: ENH: stats: replace ncf with Boost non_central_f distribution

  • #15766: BUG: improve exceptions for private attributes in refactored…

  • #15768: [DOC] fix typo in cython optimize help example

  • #15769: MAINT: stats: check integrality in `_argcheck` as needed

  • #15771: MAINT: stats: resolve discrete rvs dtype platform dependency

  • #15774: MAINT: stats: remove deprecated `median_absolute_deviation`

  • #15775: DOC: stats.lognorm: rephrase note about parameterization

  • #15776: DOC: stats.powerlaw: more explicit explanation of support

  • #15777: MAINT: stats.shapiro: subtract median from shapiro input

  • #15778: MAINT: stats: more specific error type from `rv_continuous.fit`

  • #15779: CI: don’t run meson tests on forks and remove skip flags

  • #15782: DEPR: remove k=None in KDTree.query

  • #15783: CI:Pin pytest version to 7.0.1 on Azure

  • #15785: MAINT: stats: remove deprecated itemfreq

  • #15786: DOC: Add examples of integrals to integrate.quadpack

  • #15788: DOC: update macOS and Linux contributor docs to use Python 3.9

  • #15789: DOC, MAINT: Remove numpydoc submodule

  • #15791: MAINT: add ShapeInfo to continuous distributions in scipy.stats

  • #15795: DEP: remove n_jobs from cKDTree

  • #15797: scipy/_lib/boost: Update to d8626c9d2d937abf6a38a844522714ad72e63281

  • #15799: DEP: add warning for documented-as-deprecated extradoc

  • #15802: DOC: Import Error in examples

  • #15803: DOC: error in TransferFunctionDiscrete example

  • #15804: DEP: sharpen warning message on >1-dim for optimize.minimize

  • #15805: DEP: specify version to remove dual_annealing argument ‘local_search_options’

  • #15809: DOC,MAINT: remove `quad_explain` that has become irrelevant.

  • #15810: DOC: stats.mood: validity only when observations are unique

  • #15811: DOC: fix evaluate_all_bspl example.

  • #15812: DOC: Couple of single to double backticks

  • #15813: DOC: information about skip on CircleCI

  • #15817: MAINT: stats.fisher_exact: improve docs and fix bugs

  • #15819: DEP: docstring-related deprecations (#15757)

  • #15821: DEP: add actual DeprecationWarning for sym_pos-keyword of scipy.linalg.solve

  • #15822: DEP: remove `right` from interpolate.PPoly.extend

  • #15823: DOC: Interpolative tutorial - wrong matrix fill var

  • #15824: BUG: Handle base case for scipy.integrate.simpson when span along…

  • #15825: TST: stats: xfail_on_32bit studentized_range moment test

  • #15827: DOC: change docs that specify the SNR ratio definition for find_peaks_cwt().

  • #15828: DEP: raise value error for object arrays

  • #15830: MAINT: stats: collocate bootstrap/permutation_test/monte_carlo_test

  • #15831: MAINT: stats.rv_generic: fix unnecessary call to `_munp` in…

  • #15835: FIX: Incorect boschloo pvalue

  • #15837: DOC: Simplify conda command

  • #15840: DOC: special: Add ‘Examples’ for wrightomega.

  • #15842: DOC: Add examples for `CGS`, `GCROTMK` and `BiCGSTAB` iterative…

  • #15846: DOC: Add efficiency condition for CSC sparse matrix and remove…

  • #15847: BUG: adds warning to scipy.stats.brunnermunzel

  • #15848: DOC: fix interp2d docs showing wrong Z array ordering.

  • #15850: MAINT: sparse.linalg: Missing tfqmr in the re-entrancy test

  • #15853: DEP: remove the keyword debug from linalg.solve

  • #15855: ENH: stats.rv_continuous.expect: split interval to improve reliability

  • #15867: CI: fix python version matrix in linux workflow

  • #15868: CI: fix Azure workflows

  • #15872: DEP: remove mlab from dendrogram

  • #15874: DEP: remove py_vq2

  • #15875: DEP: remove old BSR methods

  • #15876: DEP: remove _ppform

  • #15881: DEP: remove signal.windows.hanning

  • #15882: DEP: enforced radius in spherical voronoi

  • #15885: DOC: stats: clarify truncnorm shape parameter definition

  • #15886: BUG: check that iirfilter argument Wn satisfies Wn[0] < Wn[1]

  • #15887: DEP: remove ftol/xtol from neldermead

  • #15894: [BUG] make p-values consistent with the literature

  • #15895: CI: remove pin on Jinja2

  • #15898: DOC: stats: correct documentation of `wilcoxon`’s behavior…

  • #15900: DOC: fix import in example in _morestats

  • #15905: MAINT: stats._moment: warn when catastrophic cancellation occurs

  • #15909: DEP: deal with deprecation of ndim >1 in bspline

  • #15911: MAINT: stats: fix `gibrat` name

  • #15914: MAINT: special: Clean up C style in ndtr.c

  • #15916: MAINT: stats: adjust tolerance of failing TestTruncnorm

  • #15917: MAINT: stats: remove support for `_rvs` without `size` parameter

  • #15920: ENH: stats.mannwhitneyu: add iterative implementation

  • #15923: MAINT: stats: attempt to consolidate warnings and errors

  • #15932: MAINT: stats: fix and thoroughly test `rv_sample` at non-integer…

  • #15933: TST: test_nodata respect endianness

  • #15938: DOC: sparse.linalg: add citations for COLAMD

  • #15939: Update _dual_annealing.py

  • #15945: BUG/ENH: `MultinomialQMC.random` shape to (n, pvals)

  • #15946: DEP: remove inheritance to `QMCEngine` in `MultinomialQMC`…

  • #15947: DOC: Revamp contributor setup guides

  • #15953: DOC: Add meson docs to use gcc, clang build in parallel and optimization…

  • #15955: BUG Fix signature of D_IIR_forback(1,2)

  • #15959: ENH: Developer CLI for SciPy

  • #15965: MAINT: stats: ensure that `rv_continuous._fitstart` shapes…

  • #15968: BUG: Fix debug and coverage arguments with dev.py

  • #15970: BLD: specify `cython_lapack` dependency for `matfuncs_expm`

  • #15973: DOC: Add formula renderings to integrate.nquad.

  • #15981: ENH: optimize: Add Newton-TFQMR method and some tests for Newton-Krylov

  • #15982: BENCH: stats: Distribution memory and CDF/PPF round trip benchmarks

  • #15983: TST: sparse.linalg: Add tests for the parameter `show`

  • #15991: TST: fix for np.kron matrix issue.

  • #15992: DOC: Fixed `degrees` parameter in return section

  • #15997: MAINT: integrate: add `recursive` to QUADPACK Fortran sources

  • #15998: BUG: Fix yeojohnson when transformed data has zero variance

  • #15999: MAINT: Adds doit.db.db to gitignore

  • #16004: MAINT: rename MaximumFlowResult.residual to flow

  • #16005: DOC: sparse.linalg: Fixed the description of input matrix of…

  • #16010: MAINT: Add a check to verify all `.pyi` files are installed…

  • #16012: DOC: Fix broken link and add python headers to contributing guide

  • #16015: DEP: bump version for deprecating residual to flow.

  • #16018: Doc: fix arch linux building from source local dependencies instructions

  • #16019: DOC: fix conda env name in quickstart guide [skip ci]

  • #16021: DOC: typos in basinhopping documentation

  • #16024: CI: unpin pytest and pytest-xdist

  • #16026: BUG: Allow `spsolve_triangular` to work with matrices with…

  • #16029: BUG: Fix meson-info file errors and add more informative exception

  • #16030: MAINT: stats: more accurate error message for `multivariate_normal`

  • #16032: FIX: show warning when passing NAN into input of convolve method

  • #16037: MAINT: fix missing `f` prefix on f-strings

  • #16042: MAINT: stats.dirichlet: fix interface inconsistency

  • #16044: DEV: do.py, adoption of pkg pydevtool (removed non SciPy specific…

  • #16045: ENH: Use circleci-artifacts-redirector-action

  • #16051: MAINT: Miscellaneous small changes to filter_design

  • #16053: Mark fitpack sources as `recursive`

  • #16055: MAINT: stats: replace `np.var` with `_moment(…, 2)` to…

  • #16058: DEV: Fix meson debian python build

  • #16060: MAINT: Allow all Latin-1 Unicode letters in the source code.

  • #16062: DOC: Document QUADPACK routines used in `*quad`

  • #16067: DEP: remove spatial.distance.matching

  • #16070: ENH: interpolate: handle length-1 grid axes in RegularGridInterpolator

  • #16073: DOC: expand RegularGridInterpolator docstring

  • #16075: CI: Fix refguidecheck failures; unpin Sphinx

  • #16077: BUG: interpolate: RGI(nan) is nan

  • #16078: DEV,BLD: Use Meson in Gitpod builds

  • #16082: BUG: refguide-check: allow multiline namedtuples

  • #16083: DOC: fixing a sign issue in FFTlog function documentation

  • #16092: ENH: interpolate: Add functionality to accept descending points…

  • #16095: MAINT: Remove old filtered warnings

  • #16100: MAINT: Fix a couple compiler warnings.

  • #16104: DOC: stats: symmetry not checked for (inv)wishart distributions

  • #16111: BUG: Fix norm for sparse arrays

  • #16115: MAINT: merge `environment.yml` and `environment_meson.yml`

  • #16117: MAINT: stats.wilcoxon: return `zstatistic` only when `method=’approx’`

  • #16118: Download openblas binary from GH repo

  • #16122: CI: Speed up ci build that keeps timing out

  • #16125: DOC: interpolate: fix typos “the the” -> “the”

  • #16126: DOC: interpolate: details rectilinear grids in docstrings

  • #16128: BUG: interpolate: fix extrapolation behaviors of `previous`…

  • #16130: Increase time to timeout on azure

  • #16134: BUG: signal: Fix calculation of extended image indices in convolve2d.

  • #16135: MAINT: sparse.linalg: A minor improvement with zero initial guess

  • #16137: Clean up fitpack smoke tests

  • #16138: TST: interpolate: mark rbf chunking tests as slow

  • #16141: DOC: Plot poles as x and zeros as o in signal

  • #16144: DEP: Execute deprecation for squeezing input vectors in spatial.distance

  • #16145: ENH: Fix signal.iircomb w0 bugs, add support for both frequency…

  • #16150: Add typing info for Rotation.concatenate

  • #16165: BUG: fix extension module initialization, needs use of `PyMODINIT_FUNC`

  • #16166: MAINT:linalg: Expose Cython functions for generic use

  • #16167: ENH: Tweak theilslopes and siegelslopes to return a tuple_bunch

  • #16168: BUG: special: Fix the test ‘test_d’ that is run when SCIPY_XSLOW…

  • #16173: Adds note to the curve_fit() docstring to use float64.

  • #16176: MAINT: remove questionable uses of `Py_FatalError` in module…

  • #16177: MAINT: Cleanup unused code in meson-files

  • #16180: DEV: do.py build. On setup checks if intro-buildoptions.json…

  • #16181: BUG: stats: fix multivariate_hypergeom.rvs method

  • #16183: ENH: Simplify return names in stats.theil/siegelslopes (and fix…

  • #16184: DEP: raise if fillvalue cannot be cast to output type in signal.convolve2d

  • #16185: BUG: stats: Fix handling of float32 inputs for the boost-based…

  • #16187: BLD: default to Meson in pyproject.toml

  • #16194: BLD: add a build option to force use of the g77 ABI with Meson

  • #16198: DEP: sharpen deprecation in NumericalInverseHermite

  • #16206: CI: Test NumPy main branch also with Python 3.11

  • #16220: Create a new spline from a partial derivative of a bivariate…

  • #16223: MAINT: interpolate: move RGI to a separate file

  • #16228: TST: interpolate: move test_spalde_scalar to other fitpack tests

  • #16229: REL: DOC: fix documentation URLs

  • #16230: BUG: fix extension module initialization, needs use of PyMODINIT_FUNC,…

  • #16239: MAINT: tools: Add more output to a refguide-check error message.

  • #16241: DOC: stats: update roadmap

  • #16242: BUG: Make KDTree more robust against nans.

  • #16245: DEP: Execute deprecation of pinv2

  • #16247: DOC:linalg: Remove references to removed pinv2 function

  • #16248: DOC: prep 1.9.0 release notes

  • #16249: Refguide check verbosity abs names

  • #16257: DEP: Deprecation follow-ups

  • #16259: Revert “CI: pin Pip to 22.0.4 to avoid issues with `–no-build-isolation`”

  • #16261: DEP: add deprecation warning to maxiter kwarg in _minimize_tnc

  • #16264: DOC: update the RegularGridInterpolator docstring

  • #16265: DEP: deprecate spatial.distance.kulsinski

  • #16267: DOC: broken donation link on GitHub

  • #16273: DOC: remove deprecated functions from refguide

  • #16276: MAINT: sparse.linalg: Update some docstrings.

  • #16279: MAINT: stats: override `loguniform.fit` to resolve overparameterization

  • #16282: BUG: special: DECREF scipy_special object before exiting sf_error().

  • #16283: Corrections To Docs

  • #16287: BLD: sync pyproject.toml changes from oldest-supported-numpy

  • #16289: MAINT: stats: remove function-specific warning messages

  • #16290: BLD: fix issue with `python setup.py install` and `_directmodule`

  • #16295: MAINT: move `import_array` before module creation in module…

  • #16296: DOC: REL: fix `make dist` issue with missing dependencies

  • #16303: MAINT: revert addition of multivariate_beta

  • #16304: MAINT: add a more informative error message for broken installs

  • #16309: BLD: CI: fix issue in wheel metadata, and add basic “build in…

  • #16316: REL: update version switcher for 1.8.1

  • #16321: DOC: fix incorrect formatting of deprecation tags

  • #16326: REL: update version switcher for 1.9

  • #16329: MAINT: git security shim for 1.9.x

  • #16339: MAINT, TST: bump tol for _axis_nan_policy_test

  • #16341: BLD: update Pythran requirement to 0.11.0, to support Clang >=13

  • #16353: MAINT: version bounds 1.9.0rc1

  • #16360: MAINT, TST: sup warning for theilslopes

  • #16361: MAINT: SCIPY_USE_PROPACK

  • #16370: MAINT: update Boost submodule to include Cygwin fix

  • #16374: MAINT: update pydata-sphinx-theme

  • #16379: DOC: dark theme css adjustments

  • #16390: TST, MAINT: adjust 32-bit xfails for HiGHS

  • #16393: MAINT: use correct type for element wise comparison

  • #16414: BUG: spatial: Handle integer arrays in HalfspaceIntersection.

  • #16420: MAINT: next round of 1.9.0 backports

  • #16422: TST: fix test issues with casting-related warnings with numpy…

  • #16427: MAINT: stats.shapiro: don’t modify input in place

  • #16429: MAINT: stats.mode: revert gh-15423

  • #16436: DOC: optimize: Mark deprecated linprog methods explicitly

  • #16444: BUG: fix fail to open tempfile in messagestream.pyx (#8850)

  • #16451: MAINT: few more 1.9.0 backports

  • #16453: DOC: Copy-edit 1.9.0-notes.rst

  • #16457: TST: skip 32-bit test_pdist_correlation_iris_nonC

  • #16458: MAINT: 1.9.0 backports

  • #16473: REL: update 1.9.0 release notes

  • #16482: DOC: Update Returns section of optimize.linprog.

  • #16484: MAINT: remove raw html from README.rst

  • #16485: BLD: fix warnings from f2py templating parsing

  • #16493: BLD: clean up unwanted files in sdist, via `.gitattributes`

  • #16507: REL: more tweaks to sdist contents

  • #16512: [1.9] MAINT: skip complex128 propack tests on windows

  • #16514: DOC: reflect correctly where windows wheels are built

  • #16526: MAINT: 1.9.0rc2 backports

  • #16530: MAINT: fix umfpack test failure with numpy 1.23

  • #16539: MAINT: more 1.9.0rc2 backports

  • #16541: BLD: fix regression in building _lsap with symbol visibility

  • #16549: BLD: fix an outdated requirement for macOS arm64 in pyproject.toml

  • #16551: BLD: fix `__STDC_VERSION__` check in `special/_round.h`

  • #16553: BLD: raise an error with clear message for too-new Python version

  • #16556: DOC: small tweaks to 1.9.0 release notes

  • #16563: DOC: Reflect MSVC minimum toolchain requirement

  • #16570: MAINT: backports before 1.9.0rc3

  • #16572: MAINT: update bundled licenses for removal of scipy-sphinx-theme

  • #16581: MAINT: stats: fix skew/kurtosis empty 1d input

  • #16586: MAINT: stats.truncnorm: improve CDF accuracy/speed

  • #16593: TST: stats: replace TestTruncnorm::test_moments

  • #16599: MAINT: stats.truncnorm.rvs: improve performance

  • #16605: MAINT: stats.truncnorm: simplify remaining methods

  • #16622: ENH: FIX: update HiGHS submodule to resolve MIP infeasibility…

  • #16638: DOC: update docs on building with Meson

  • #16664: MAINT: stats._axis_nan_policy: preserve dtype of masked arrays…

  • #16671: BLD: update `meson` and `meson-python` versions for 1.9.0…

  • #16684: MAINT: optimize.linprog: ensure integrality can be an array

  • #16688: DOC: a few mailmap updates

  • #16719: MAINT: stats: Work around Cython bug.

  • #16721: MAINT: stats.monte_carlo_test: used biased estimate of p-value

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