SciPy 1.12.0 Release Notes

Note: SciPy 1.12.0 is not released yet!

SciPy 1.12.0 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
1.12.x branch, and on adding new features on the main branch.

This release requires Python 3.9+ and NumPy 1.22.4 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

• Experimental support for the array API standard has been added to part of
  scipy.special, and to all of scipy.fft and scipy.cluster. There are
  likely to be bugs and early feedback for usage with CuPy arrays, PyTorch
  tensors, and other array API compatible libraries is appreciated. Use the
  SCIPY_ARRAY_API environment variable for testing.
• A new class, ShortTimeFFT, provides a more versatile implementation of the
  short-time Fourier transform (STFT), its inverse (ISTFT) as well as the (cross-)
  spectrogram. It utilizes an improved algorithm for calculating the ISTFT.
• Several new constructors have been added for sparse arrays, and many operations
  now additionally support sparse arrays, further facilitating the migration
  from sparse matrices.
• A large portion of the scipy.stats API now has improved support for handling
  NaN values, masked arrays, and more fine-grained shape-handling. The
  accuracy and performance of a number of stats methods have been improved,
  and a number of new statistical tests and distributions have been added.

New features

scipy.cluster improvements

• Experimental support added for the array API standard; PyTorch tensors,
  CuPy arrays and array API compatible array libraries are now accepted
  (GPU support is limited to functions with pure Python implementations).
  CPU arrays which can be converted to and from NumPy are supported
  module-wide and returned arrays will match the input type.
  This behaviour is enabled by setting the SCIPY_ARRAY_API environment
  variable before importing scipy. This experimental support is still
  under development and likely to contain bugs - testing is very welcome.

scipy.fft improvements

• Experimental support added for the array API standard; functions which are
  part of the fft array API standard extension module, as well as the
  Fast Hankel Transforms and the basic FFTs which are not in the extension
  module, now accept PyTorch tensors, CuPy arrays and array API compatible
  array libraries. CPU arrays which can be converted to and from NumPy arrays
  are supported module-wide and returned arrays will match the input type.
  This behaviour is enabled by setting the SCIPY_ARRAY_API environment
  variable before importing scipy. This experimental support is still under
  development and likely to contain bugs - testing is very welcome.

scipy.integrate improvements

• Added scipy.integrate.cumulative_simpson for cumulative quadrature
  from sampled data using Simpson's 1/3 rule.

scipy.interpolate improvements

• New class NdBSpline represents tensor-product splines in N dimensions.
  This class only knows how to evaluate a tensor product given coefficients
  and knot vectors. This way it generalizes BSpline for 1D data to N-D, and
  parallels NdPPoly (which represents N-D tensor product polynomials).
  Evaluations exploit the localized nature of b-splines.
• NearestNDInterpolator.__call__ accepts **query_options, which are
  passed through to the KDTree.query call to find nearest neighbors. This
  allows, for instance, to limit the neighbor search distance and parallelize
  the query using the workers keyword.
• BarycentricInterpolator now allows computing the derivatives.
• It is now possible to change interpolation values in an existing
  CloughTocher2DInterpolator instance, while also saving the barycentric
  coordinates of interpolation points.

scipy.linalg improvements

• Access to new low-level LAPACK functions is provided via dtgsyl and
  stgsyl.

scipy.ndimage improvements

scipy.optimize improvements

• scipy.optimize.nnls is rewritten in Python and now implements the so-called
  fnnls or fast nnls.
• The result object of scipy.optimize.root and scipy.optimize.root_scalar
  now reports the method used.
• The callback method of scipy.optimize.differential_evolution can now be
  passed more detailed information via the intermediate_results keyword
  parameter. Also, the evolution strategy now accepts a callable for
  additional customization. The performance of differential_evolution has
  also been improved.
• minimize method Newton-CG has been made slightly more efficient.
• minimize method BFGS now accepts an initial estimate for the inverse
  of the Hessian, which allows for more efficient workflows in some
  circumstances. The new parameter is hess_inv0.
• minimize methods CG, Newton-CG, and BFGS now accept parameters
  c1 and c2, allowing specification of the Armijo and curvature rule
  parameters, respectively.
• curve_fit performance has improved due to more efficient memoization
  of the callable function.
• isotonic_regression has been added to allow nonparametric isotonic
  regression.

scipy.signal improvements

• freqz, freqz_zpk, and group_delay are now more accurate
  when fs has a default value.
• The new class ShortTimeFFT provides a more versatile implementation of the
  short-time Fourier transform (STFT), its inverse (ISTFT) as well as the (cross-)
  spectrogram. It utilizes an improved algorithm for calculating the ISTFT based on
  dual windows and provides more fine-grained control of the parametrization especially
  in regard to scaling and phase-shift. Functionality was implemented to ease
  working with signal and STFT chunks. A section has been added to the "SciPy User Guide"
  providing algorithmic details. The functions stft, istft and spectrogram
  have been marked as legacy.

scipy.sparse improvements

• sparse.linalg iterative solvers sparse.linalg.cg,
  sparse.linalg.cgs, sparse.linalg.bicg, sparse.linalg.bicgstab,
  sparse.linalg.gmres, and sparse.linalg.qmr are rewritten in Python.
• Updated vendored SuperLU version to 6.0.1, along with a few additional
  fixes.
• Sparse arrays have gained additional constructors: eye_array,
  random_array, block_array, and identity. kron and kronsum
  have been adjusted to additionally support operation on sparse arrays.
• Sparse matrices now support a transpose with axes=(1, 0), to mirror
  the .T method.
• LaplacianNd now allows selection of the largest subset of eigenvalues,
  and additionally now supports retrieval of the corresponding eigenvectors.
  The performance of LaplacianNd has also been improved.
• The performance of dok_matrix and dok_array has been improved,
  and their inheritance behavior should be more robust.
• hstack, vstack, and block_diag now work with sparse arrays, and
  preserve the input sparse type.
• A new function, scipy.sparse.linalg.matrix_power, has been added, allowing
  for exponentiation of sparse arrays.

scipy.spatial improvements

• Two new methods were implemented for spatial.transform.Rotation:
  __pow__ to raise a rotation to integer or fractional power and
  approx_equal to check if two rotations are approximately equal.
• The method Rotation.align_vectors was extended to solve a constrained
  alignment problem where two vectors are required to be aligned precisely.
  Also when given a single pair of vectors, the algorithm now returns the
  rotation with minimal magnitude, which can be considered as a minor
  backward incompatible change.
• A new representation for spatial.transform.Rotation called Davenport
  angles is available through from_davenport and as_davenport methods.
• Performance improvements have been added to distance.hamming and
  distance.correlation.
• Improved performance of SphericalVoronoi sort_vertices_of_regions
  and two dimensional area calculations.

scipy.special improvements

• Added scipy.special.stirling2 for computation of Stirling numbers of the
  second kind. Both exact calculation and an asymptotic approximation
  (the default) are supported via exact=True and exact=False (the
  default) respectively.
• Added scipy.special.betaincc for computation of the complementary incomplete Beta function and scipy.special.betainccinv for computation of its inverse.
• Improved precision of scipy.special.betainc and scipy.special.betaincinv
• Experimental support added for alternative backends: functions
  scipy.special.log_ndtr, scipy.special.ndtr, scipy.special.ndtri,
  scipy.special.erf, scipy.special.erfc, scipy.special.i0,
  scipy.special.i0e, scipy.special.i1, scipy.special.i1e,
  scipy.special.gammaln, scipy.special.gammainc, scipy.special.gammaincc,
  scipy.special.logit, and scipy.special.expit now accept PyTorch tensors
  and CuPy arrays. These features are still under development and likely to
  contain bugs, so they are disabled by default; enable them by setting a
  SCIPY_ARRAY_API environment variable to 1 before importing scipy.
  Testing is appreciated!

scipy.stats improvements

• Added scipy.stats.quantile_test, a nonparametric test of whether a
  hypothesized value is the quantile associated with a specified probability.
  The confidence_interval method of the result object gives a confidence
  interval of the quantile.
• scipy.stats.wasserstein_distance now computes the Wasserstein distance
  in the multidimensional case.
• scipy.stats.sampling.FastGeneratorInversion provides a convenient
  interface to fast random sampling via numerical inversion of distribution
  CDFs.
• scipy.stats.geometric_discrepancy adds geometric/topological discrepancy
  metrics for random samples.
• scipy.stats.multivariate_normal now has a fit method for fitting
  distribution parameters to data via maximum likelihood estimation.
• scipy.stats.bws_test performs the Baumgartner-Weiss-Schindler test of
  whether two-samples were drawn from the same distribution.
• scipy.stats.jf_skew_t implements the Jones and Faddy skew-t distribution.
• scipy.stats.anderson_ksamp now supports a permutation version of the test
  using the method parameter.
• The fit methods of scipy.stats.halfcauchy, scipy.stats.halflogistic, and
  scipy.stats.halfnorm are faster and more accurate.
• scipy.stats.beta entropy accuracy has been improved for extreme values of
  distribution parameters.
• The accuracy of sf and/or isf methods have been improved for
  several distributions: scipy.stats.burr, scipy.stats.hypsecant,
  scipy.stats.kappa3, scipy.stats.loglaplace, scipy.stats.lognorm,
  scipy.stats.lomax, scipy.stats.pearson3, scipy.stats.rdist, and
  scipy.stats.pareto.
• The following functions now support parameters axis, nan_policy, and keep_dims: scipy.stats.entropy, scipy.stats.differential_entropy, scipy.stats.variation, scipy.stats.ansari, scipy.stats.bartlett, scipy.stats.levene, scipy.stats.fligner, scipy.stats.cirmean, scipy.stats.circvar, scipy.stats.circstd, scipy.stats.tmean, scipy.stats.tvar, scipy.stats.tstd, scipy.stats.tmin, scipy.stats.tmax, and scipy.stats.tsem`.
• The logpdf and fit methods of scipy.stats.skewnorm have been improved.
• The beta negative binomial distribution is implemented as scipy.stats.betanbinom.
• The speed of scipy.stats.invwishart rvs and logpdf have been improved.
• A source of intermediate overflow in scipy.stats.boxcox_normmax with method='mle' has been eliminated, and the returned value of lmbda is constrained such that the transformed data will not overflow.
• scipy.stats.nakagami stats is more accurate and reliable.
• A source of intermediate overflow in scipy.norminvgauss.pdf has been eliminated.
• Added support for masked arrays to stats.circmean, stats.circvar,
  stats.circstd, and stats.entropy.
• dirichlet has gained a new covariance (cov) method.
• Improved accuracy of multivariate_t entropy with large degrees of
  freedom.
• loggamma has an improved entropy method.

Deprecated features

• Error messages have been made clearer for objects that don't exist in the
  public namespace and warnings sharpened for private attributes that are not
  supposed to be imported at all.

• scipy.signal.cmplx_sort has been deprecated and will be removed in
  SciPy 1.14. A replacement you can use is provided in the deprecation message.

• Values the the argument initial of scipy.integrate.cumulative_trapezoid
  other than 0 and None are now deprecated.

• scipy.stats.rvs_ratio_uniforms is deprecated in favour of
  scipy.stats.sampling.RatioUniforms

• scipy.integrate.quadrature and scipy.integrate.romberg have been
  deprecated due to accuracy issues and interface shortcomings. They will
  be removed in SciPy 1.14. Please use scipy.integrate.quad instead.

• Coinciding with upcoming changes to function signatures (e.g. removal of a
  deprecated keyword), we are deprecating positional use of keyword arguments
  for the affected functions, which will raise an error starting with
  SciPy 1.14. In some cases, this has delayed the originally announced
  removal date, to give time to respond to the second part of the deprecation.
  Affected functions are:

  • linalg.{eigh, eigvalsh, pinv}
  • integrate.simpson
  • signal.{firls, firwin, firwin2, remez}
  • sparse.linalg.{bicg, bicgstab, cg, cgs, gcrotmk, gmres, lgmres, minres, qmr, tfqmr}
  • special.comb
  • stats.kendalltau

• All wavelet functions have been deprecated, as PyWavelets provides suitable
  implementations; affected functions are: signal.{daub, qmf, cascade, morlet, morlet2, ricker, cwt}

• scipy.integrate.trapz, scipy.integrate.cumtrapz, and scipy.integrate.simps have
  been deprecated in favour of scipy.integrate.trapezoid, scipy.integrate.cumulative_trapezoid,
  and scipy.integrate.simpson respectively and will be removed in SciPy 1.14.

• The tol argument of scipy.sparse.linalg.{bcg,bicstab,cg,cgs,gcrotmk,gmres,lgmres,minres,qmr,tfqmr}
  is now deprecated in favour of rtol and will be removed in SciPy 1.14.
  Furthermore, the default value of atol for these functions is due
  to change to 0.0 in SciPy 1.14.

Expired Deprecations

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

• The centered keyword of scipy.stats.qmc.LatinHypercube has been removed.
  Use scrambled=False instead of centered=True.
• scipy.stats.binom_test has been removed in favour of scipy.stats.binomtest.
• In scipy.stats.iqr, the use of scale='raw' has been removed in favour
  of scale=1.

Backwards incompatible changes

Other changes

• The arguments used to compile and link SciPy are now available via
  show_config.

Authors

• Name (commits)
• endolith (1)
• h-vetinari (32)
• Tom Adamczewski (3) +
• Anudeep Adiraju (1) +
• akeemlh (1)
• Alex Amadori (2) +
• Raja Yashwanth Avantsa (2) +
• Seth Axen (1) +
• Ross Barnowski (1)
• Dan Barzilay (1) +
• Ashish Bastola (1) +
• Christoph Baumgarten (2)
• Ben Beasley (3) +
• Doron Behar (1)
• Peter Bell (1)
• Sebastian Berg (1)
• Ben Boeckel (1) +
• David Boetius (1) +
• Matt Borland (1)
• Jake Bowhay (103)
• Larry Bradley (1) +
• Dietrich Brunn (5)
• Evgeni Burovski (102)
• Matthias Bussonnier (18)
• CJ Carey (6)
• Colin Carroll (1) +
• Aadya Chinubhai (1) +
• Luca Citi (1)
• Lucas Colley (141) +
• com3dian (1) +
• Anirudh Dagar (4)
• Danni (1) +
• Dieter Werthmüller (1)
• John Doe (2) +
• Philippe DONNAT (2) +
• drestebon (1) +
• Thomas Duvernay (1)
• elbarso (1) +
• emilfrost (2) +
• Paul Estano (8) +
• Evandro (2)
• Franz Király (1) +
• Nikita Furin (1) +
• gabrielthomsen (1) +
• Lukas Geiger (9) +
• Artem Glebov (22) +
• Caden Gobat (1)
• Ralf Gommers (126)
• Alexander Goscinski (2) +
• Rohit Goswami (2) +
• Olivier Grisel (1)
• Matt Haberland (243)
• Charles Harris (1)
• harshilkamdar (1) +
• Alon Hovav (2) +
• Gert-Ludwig Ingold (1)
• Romain Jacob (1) +
• jcwhitehead (1) +
• Julien Jerphanion (13)
• He Jia (1)
• JohnWT (1) +
• jokasimr (1) +
• Evan W Jones (1)
• Karen Róbertsdóttir (1) +
• Ganesh Kathiresan (1)
• Robert Kern (11)
• Andrew Knyazev (4)
• Uwe L. Korn (1) +
• Rishi Kulkarni (1)
• Kale Kundert (3) +
• Jozsef Kutas (2)
• Kyle0 (2) +
• Robert Langefeld (1) +
• Jeffrey Larson (1) +
• Jessy Lauer (1) +
• lciti (1) +
• Hoang Le (1) +
• Antony Lee (5)
• Thilo Leitzbach (4) +
• LemonBoy (2) +
• Ellie Litwack (8) +
• Thomas Loke (4) +
• Malte Londschien (1) +
• Christian Lorentzen (6)
• Adam Lugowski (10) +
• lutefiskhotdish (1)
• mainak33 (1) +
• Ben Mares (11) +
• mart-mihkel (2) +
• Mateusz Sokół (24) +
• Nikolay Mayorov (4)
• Nicholas McKibben (1)
• Melissa Weber Mendonça (7)
• Michał Górny (1)
• Kat Mistberg (2) +
• mkiffer (1) +
• mocquin (1) +
• Nicolas Mokus (2) +
• Sturla Molden (1)
• Roberto Pastor Muela (3) +
• Bijay Nayak (1) +
• Andrew Nelson (105)
• Praveer Nidamaluri (3) +
• Lysandros Nikolaou (2)
• Dimitri Papadopoulos Orfanos (7)
• Pablo Rodríguez Pérez (1) +
• Dimitri Papadopoulos (2)
• Tirth Patel (14)
• Kyle Paterson (1) +
• Paul (4) +
• Yann Pellegrini (2) +
• Matti Picus (4)
• Ilhan Polat (36)
• Pranav (1) +
• Bharat Raghunathan (1)
• Chris Rapson (1) +
• Matteo Raso (4)
• Tyler Reddy (201)
• Martin Reinecke (1)
• Tilo Reneau-Cardoso (1) +
• resting-dove (2) +
• Simon Segerblom Rex (4)
• Lucas Roberts (2)
• Pamphile Roy (31)
• Feras Saad (3) +
• Atsushi Sakai (3)
• Masahiro Sakai (2) +
• Omar Salman (14)
• Andrej Savikin (1) +
• Daniel Schmitz (54)
• Dan Schult (19)
• Scott Shambaugh (9)
• Sheila-nk (2) +
• Mauro Silberberg (3) +
• Maciej Skorski (1) +
• Laurent Sorber (1) +
• Albert Steppi (28)
• Kai Striega (1)
• Saswat Susmoy (1) +
• Alex Szatmary (1) +
• Søren Fuglede Jørgensen (3)
• othmane tamri (3) +
• Ewout ter Hoeven (1)
• Will Tirone (1)
• TLeitzbach (1) +
• Kevin Topolski (1) +
• Edgar Andrés Margffoy Tuay (1)
• Dipansh Uikey (1) +
• Matus Valo (3)
• Christian Veenhuis (2)
• Nicolas Vetsch (1) +
• Isaac Virshup (7)
• Hielke Walinga (2) +
• Stefan van der Walt (2)
• Warren Weckesser (7)
• Bernhard M. Wiedemann (4)
• Levi John Wolf (1)
• Xuefeng Xu (4) +
• Rory Yorke (2)
• YoussefAli1 (1) +
• Irwin Zaid (4) +
• Jinzhe Zeng (1) +
• JIMMY ZHAO (1) +

A total of 163 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.