scipy/scipy: SciPy 1.10.0rc2

SciPy 1.10.0 Release Notes

Note: SciPy 1.10.0 is not released yet!

SciPy 1.10.0 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 1.10.x branch, and on adding new features on the main branch.

This release requires Python 3.8+ and NumPy 1.19.5 or greater.

For running on PyPy, PyPy3 6.0+ is required.

Highlights of this release

• A new dedicated datasets submodule (scipy.datasets) has been added, and is now preferred over usage of scipy.misc for dataset retrieval.
• A new scipy.interpolate.make_smoothing_spline function was added. This function constructs a smoothing cubic spline from noisy data, using the generalized cross-validation (GCV) criterion to find the tradeoff between smoothness and proximity to data points.
• scipy.stats has three new distributions, two new hypothesis tests, three new sample statistics, a class for greater control over calculations involving covariance matrices, and many other enhancements.

New features scipy.datasets introduction

• A new dedicated datasets submodule has been added. The submodules is meant for datasets that are relevant to other SciPy submodules ands content (tutorials, examples, tests), as well as contain a curated set of datasets that are of wider interest. As of this release, all the datasets from scipy.misc have been added to scipy.datasets (and deprecated in scipy.misc).
• The submodule is based on Pooch (a new optional dependency for SciPy), a Python package to simplify fetching data files. This move will, in a subsequent release, facilitate SciPy to trim down the sdist/wheel sizes, by decoupling the data files and moving them out of the SciPy repository, hosting them externally and downloading them when requested. After downloading the datasets once, the files are cached to avoid network dependence and repeated usage.
• Added datasets from scipy.misc: scipy.datasets.face, scipy.datasets.ascent, scipy.datasets.electrocardiogram

• Added download and caching functionality:

  • scipy.datasets.download_all: a function to download all the scipy.datasets associated files at once.
  • scipy.datasets.clear_cache: a simple utility function to clear cached dataset files from the file system.
  • scipy/datasets/_download_all.py can be run as a standalone script for packaging purposes to avoid any external dependency at build or test time. This can be used by SciPy packagers (e.g., for Linux distros) which may have to adhere to rules that forbid downloading sources from external repositories at package build time.

scipy.integrate improvements

• Added scipy.integrate.qmc_quad, which performs quadrature using Quasi-Monte Carlo points.
• Added parameter complex_func to scipy.integrate.quad, which can be set True to integrate a complex integrand.

scipy.interpolate improvements

• scipy.interpolate.interpn now supports tensor-product interpolation methods (slinear, cubic, quintic and pchip)
• Tensor-product interpolation methods (slinear, cubic, quintic and pchip) in scipy.interpolate.interpn and scipy.interpolate.RegularGridInterpolator now allow values with trailing dimensions.
• scipy.interpolate.RegularGridInterpolator has a new fast path for method="linear" with 2D data, and RegularGridInterpolator is now easier to subclass
• scipy.interpolate.interp1d now can take a single value for non-spline methods.
• A new extrapolate argument is available to scipy.interpolate.BSpline.design_matrix, allowing extrapolation based on the first and last intervals.
• A new function scipy.interpolate.make_smoothing_spline has been added. It is an implementation of the generalized cross-validation spline smoothing algorithm. The lam=None (default) mode of this function is a clean-room reimplementation of the classic gcvspl.f Fortran algorithm for constructing GCV splines.
• A new method="pchip" mode was aded to scipy.interpolate.RegularGridInterpolator. This mode constructs an interpolator using tensor products of C1-continuous monotone splines (essentially, a scipy.interpolate.PchipInterpolator instance per dimension).

scipy.sparse.linalg improvements

• The spectral 2-norm is now available in scipy.sparse.linalg.norm.
• The performance of scipy.sparse.linalg.norm for the default case (Frobenius norm) has been improved.
• LAPACK wrappers were added for trexc and trsen.

• The scipy.sparse.linalg.lobpcg algorithm was rewritten, yielding the following improvements:

  • a simple tunable restart potentially increases the attainable accuracy for edge cases,
  • internal postprocessing runs one final exact Rayleigh-Ritz method giving more accurate and orthonormal eigenvectors,
  • output the computed iterate with the smallest max norm of the residual and drop the history of subsequent iterations,
  • remove the check for LinearOperator format input and thus allow a simple function handle of a callable object as an input,
  • better handling of common user errors with input data, rather than letting the algorithm fail.

scipy.linalg improvements

• scipy.linalg.lu_factor now accepts rectangular arrays instead of being restricted to square arrays.

scipy.ndimage improvements

• The new scipy.ndimage.value_indices function provides a time-efficient method to search for the locations of individual values with an array of image data.
• A new radius argument is supported by scipy.ndimage.gaussian_filter1d and scipy.ndimage.gaussian_filter for adjusting the kernel size of the filter.

scipy.optimize improvements

• scipy.optimize.brute now coerces non-iterable/single-value args into a tuple.
• scipy.optimize.least_squares and scipy.optimize.curve_fit now accept scipy.optimize.Bounds for bounds constraints.
• Added a tutorial for scipy.optimize.milp.
• Improved the pretty-printing of scipy.optimize.OptimizeResult objects.
• Additional options (parallel, threads, mip_rel_gap) can now be passed to scipy.optimize.linprog with method='highs'.

scipy.signal improvements

• The new window function scipy.signal.windows.lanczos was added to compute a Lanczos window, also known as a sinc window.

scipy.sparse.csgraph improvements

• the performance of scipy.sparse.csgraph.dijkstra has been improved, and star graphs in particular see a marked performance improvement

scipy.special improvements

• The new function scipy.special.powm1, a ufunc with signature powm1(x, y), computes x**y - 1. The function avoids the loss of precision that can result when y is close to 0 or when x is close to 1.
• scipy.special.erfinv is now more accurate as it leverages the Boost equivalent under the hood.

scipy.stats improvements

• Added scipy.stats.goodness_of_fit, a generalized goodness-of-fit test for use with any univariate distribution, any combination of known and unknown parameters, and several choices of test statistic (Kolmogorov-Smirnov, Cramer-von Mises, and Anderson-Darling).
• Improved scipy.stats.bootstrap: Default method 'BCa' now supports multi-sample statistics. Also, the bootstrap distribution is returned in the result object, and the result object can be passed into the function as parameter bootstrap_result to add additional resamples or change the confidence interval level and type.
• Added maximum spacing estimation to scipy.stats.fit.
• Added the Poisson means test ("E-test") as scipy.stats.poisson_means_test.

• Added new sample statistics.

  • Added scipy.stats.contingency.odds_ratio to compute both the conditional and unconditional odds ratios and corresponding confidence intervals for 2x2 contingency tables.
  • Added scipy.stats.directional_stats to compute sample statistics of n-dimensional directional data.
  • Added scipy.stats.expectile, which generalizes the expected value in the same way as quantiles are a generalization of the median.

• Added new statistical distributions.

  • Added scipy.stats.uniform_direction, a multivariate distribution to sample uniformly from the surface of a hypersphere.
  • Added scipy.stats.random_table, a multivariate distribution to sample uniformly from m x n contingency tables with provided marginals.
  • Added scipy.stats.truncpareto, the truncated Pareto distribution.

• Improved the fit method of several distributions.

  • scipy.stats.skewnorm and scipy.stats.weibull_min now use an analytical solution when method='mm', which also serves a starting guess to improve the performance of method='mle'.
  • scipy.stats.gumbel_r and scipy.stats.gumbel_l: analytical maximum likelihood estimates have been extended to the cases in which location or scale are fixed by the user.
  • Analytical maximum likelihood estimates have been added for scipy.stats.powerlaw.

• Improved random variate sampling of several distributions.

  • Drawing multiple samples from scipy.stats.matrix_normal, scipy.stats.ortho_group, scipy.stats.special_ortho_group, and scipy.stats.unitary_group is faster.
  • The rvs method of scipy.stats.vonmises now wraps to the interval [-np.pi, np.pi].
  • Improved the reliability of scipy.stats.loggamma rvs method for small values of the shape parameter.

• Improved the speed and/or accuracy of functions of several statistical distributions.

  • Added scipy.stats.Covariance for better speed, accuracy, and user control in multivariate normal calculations.
  • scipy.stats.skewnorm methods cdf, sf, ppf, and isf methods now use the implementations from Boost, improving speed while maintaining accuracy. The calculation of higher-order moments is also faster and more accurate.
  • scipy.stats.invgauss methods ppf and isf methods now use the implementations from Boost, improving speed and accuracy.
  • scipy.stats.invweibull methods sf and isf are more accurate for small probability masses.
  • scipy.stats.nct and scipy.stats.ncx2 now rely on the implementations from Boost, improving speed and accuracy.
  • Implemented the logpdf method of scipy.stats.vonmises for reliability in extreme tails.
  • Implemented the isf method of scipy.stats.levy for speed and accuracy.
  • Improved the robustness of scipy.stats.studentized_range for large df by adding an infinite degree-of-freedom approximation.
  • Added a parameter lower_limit to scipy.stats.multivariate_normal, allowing the user to change the integration limit from -inf to a desired value.
  • Improved the robustness of entropy of scipy.stats.vonmises for large concentration values.

• Enhanced scipy.stats.gaussian_kde.

  • Added scipy.stats.gaussian_kde.marginal, which returns the desired marginal distribution of the original kernel density estimate distribution.
  • The cdf method of scipy.stats.gaussian_kde now accepts a lower_limit parameter for integrating the PDF over a rectangular region.
  • Moved calculations for scipy.stats.gaussian_kde.logpdf to Cython, improving speed.
  • The global interpreter lock is released by the pdf method of scipy.stats.gaussian_kde for improved multithreading performance.
  • Replaced explicit matrix inversion with Cholesky decomposition for speed and accuracy.

• Enhanced the result objects returned by many scipy.stats functions

  • Added a confidence_interval method to the result object returned by scipy.stats.ttest_1samp and scipy.stats.ttest_rel.
  • The scipy.stats functions combine_pvalues, fisher_exact, chi2_contingency, median_test and mood now return bunch objects rather than plain tuples, allowing attributes to be accessed by name.
  • Attributes of the result objects returned by multiscale_graphcorr, anderson_ksamp, binomtest, crosstab, pointbiserialr, spearmanr, kendalltau, and weightedtau have been renamed to statistic and pvalue for consistency throughout scipy.stats. Old attribute names are still allowed for backward compatibility.
  • scipy.stats.anderson now returns the parameters of the fitted distribution in a scipy.stats._result_classes.FitResult object.
  • The plot method of scipy.stats._result_classes.FitResult now accepts a plot_type parameter; the options are 'hist' (histogram, default), 'qq' (Q-Q plot), 'pp' (P-P plot), and 'cdf' (empirical CDF plot).
  • Kolmogorov-Smirnov tests (e.g. scipy.stats.kstest) now return the location (argmax) at which the statistic is calculated and the variant of the statistic used.

• Improved the performance of several scipy.stats functions.

  • Improved the performance of scipy.stats.cramervonmises_2samp and scipy.stats.ks_2samp with method='exact'.
  • Improved the performance of scipy.stats.siegelslopes.
  • Improved the performance of scipy.stats.mstats.hdquantile_sd.
  • Improved the performance of scipy.stats.binned_statistic_dd for several NumPy statistics, and binned statistics methods now support complex data.

• Added the scramble optional argument to scipy.stats.qmc.LatinHypercube. It replaces centered, which is now deprecated.

• Added a parameter optimization to all scipy.stats.qmc.QMCEngine subclasses to improve characteristics of the quasi-random variates.
• Added tie correction to scipy.stats.mood.
• Added tutorials for resampling methods in scipy.stats.
• scipy.stats.bootstrap, scipy.stats.permutation_test, and scipy.stats.monte_carlo_test now automatically detect whether the provided statistic is vectorized, so passing the vectorized argument explicitly is no longer required to take advantage of vectorized statistics.
• Improved the speed of scipy.stats.permutation_test for permutation types 'samples' and 'pairings'.
• Added axis, nan_policy, and masked array support to scipy.stats.jarque_bera.
• Added the nan_policy optional argument to scipy.stats.rankdata.

Deprecated features

• scipy.misc module and all the methods in misc are deprecated in v1.10 and will be completely removed in SciPy v2.0.0. Users are suggested to utilize the scipy.datasets module instead for the dataset methods.
• scipy.stats.qmc.LatinHypercube parameter centered has been deprecated. It is replaced by the scramble argument for more consistency with other QMC engines.
• scipy.interpolate.interp2d class has been deprecated. The docstring of the deprecated routine lists recommended replacements.

Expired Deprecations

• There is an ongoing effort to follow through on long-standing deprecations.

• The following previously deprecated features are affected:

  • Removed cond & rcond kwargs in linalg.pinv
  • Removed wrappers scipy.linalg.blas.{clapack, flapack}
  • Removed scipy.stats.NumericalInverseHermite and removed tol & max_intervals kwargs from scipy.stats.sampling.NumericalInverseHermite
  • Removed local_search_options kwarg frrom scipy.optimize.dual_annealing.

Other changes

• scipy.stats.bootstrap, scipy.stats.permutation_test, and scipy.stats.monte_carlo_test now automatically detect whether the provided statistic is vectorized by looking for an axis parameter in the signature of statistic. If an axis parameter is present in statistic but should not be relied on for vectorized calls, users must pass option vectorized==False explicitly.
• scipy.stats.multivariate_normal will now raise a ValueError when the covariance matrix is not positive semidefinite, regardless of which method is called.

Authors

• Name (commits)
• h-vetinari (10)
• Jelle Aalbers (1)
• Oriol Abril-Pla (1) +
• Alan-Hung (1) +
• Tania Allard (7)
• Oren Amsalem (1) +
• Sven Baars (10)
• Balthasar (1) +
• Ross Barnowski (1)
• Christoph Baumgarten (2)
• Peter Bell (2)
• Sebastian Berg (1)
• Aaron Berk (1) +
• boatwrong (1) +
• boeleman (1) +
• Jake Bowhay (50)
• Matthew Brett (4)
• Evgeni Burovski (93)
• Matthias Bussonnier (6)
• Dominic C (2)
• Mingbo Cai (1) +
• James Campbell (2) +
• CJ Carey (4)
• cesaregarza (1) +
• charlie0389 (1) +
• Hood Chatham (5)
• Andrew Chin (1) +
• Daniel Ching (1) +
• Leo Chow (1) +
• chris (3) +
• John Clow (1) +
• cm7S (1) +
• cmgodwin (1) +
• Christopher Cowden (2) +
• Henry Cuzco (2) +
• Anirudh Dagar (12)
• Hans Dembinski (2) +
• Jaiden di Lanzo (24) +
• Felipe Dias (1) +
• Dieter Werthmüller (1)
• Giuseppe Dilillo (1) +
• dpoerio (1) +
• drpeteb (1) +
• Christopher Dupuis (1) +
• Jordan Edmunds (1) +
• Pieter Eendebak (1) +
• Jérome Eertmans (1) +
• Fabian Egli (2) +
• Sebastian Ehlert (2) +
• Kian Eliasi (1) +
• Tomohiro Endo (1) +
• Stefan Endres (1)
• Zeb Engberg (4) +
• Jonas Eschle (1) +
• Thomas J. Fan (9)
• fiveseven (1) +
• Neil Flood (1) +
• Franz Forstmayr (1)
• Sara Fridovich-Keil (1)
• David Gilbertson (1) +
• Ralf Gommers (251)
• Marco Gorelli (2) +
• Matt Haberland (383)
• Andrew Hawryluk (2) +
• Christoph Hohnerlein (2) +
• Loïc Houpert (2) +
• Shamus Husheer (1) +
• ideasrule (1) +
• imoiwm (1) +
• Lakshaya Inani (1) +
• Joseph T. Iosue (1)
• iwbc-mzk (1) +
• Nathan Jacobi (3) +
• Julien Jerphanion (5)
• He Jia (1)
• jmkuebler (1) +
• Johannes Müller (1) +
• Vedant Jolly (1) +
• Juan Luis Cano Rodríguez (2)
• Justin (1) +
• jvavrek (1) +
• jyuv (2)
• Kai Mühlbauer (1) +
• Nikita Karetnikov (3) +
• Reinert Huseby Karlsen (1) +
• kaspar (2) +
• Toshiki Kataoka (1)
• Robert Kern (3)
• Joshua Klein (1) +
• Andrew Knyazev (7)
• Jozsef Kutas (16) +
• Eric Larson (4)
• Lechnio (1) +
• Antony Lee (2)
• Aditya Limaye (1) +
• Xingyu Liu (2)
• Christian Lorentzen (4)
• Loïc Estève (2)
• Thibaut Lunet (2) +
• Peter Lysakovski (1)
• marianasalamoni (2) +
• mariprudencio (1) +
• Paige Martin (1) +
• Arno Marty (1) +
• matthewborish (3) +
• Damon McDougall (1)
• Nicholas McKibben (22)
• McLP (1) +
• mdmahendri (1) +
• Melissa Weber Mendonça (9)
• Jarrod Millman (1)
• Naoto Mizuno (2)
• Shashaank N (1)
• Pablo S Naharro (1) +
• nboudrie (2) +
• Andrew Nelson (52)
• Nico Schlömer (1)
• NiMlr (1) +
• o-alexandre-felipe (1) +
• Maureen Ononiwu (1) +
• Dimitri Papadopoulos (2) +
• partev (1) +
• Tirth Patel (10)
• Paulius Šarka (1) +
• Josef Perktold (1)
• Giacomo Petrillo (3) +
• Matti Picus (1)
• Rafael Pinto (1) +
• PKNaveen (1) +
• Ilhan Polat (6)
• Akshita Prasanth (2) +
• Sean Quinn (1)
• Tyler Reddy (142)
• Martin Reinecke (1)
• Ned Richards (1)
• Marie Roald (1) +
• Sam Rosen (4) +
• Pamphile Roy (105)
• sabonerune (2) +
• Atsushi Sakai (94)
• Daniel Schmitz (27)
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• Eli Schwartz (11)
• serge-sans-paille (2)
• JEEVANSHI SHARMA (1) +
• ehsan shirvanian (2) +
• siddhantwahal (2)
• Mathieu Dutour Sikiric (1) +
• Sourav Singh (1)
• Alexander Soare (1) +
• Bjørge Solli (2) +
• Scott Staniewicz (1)
• Albert Steppi (3)
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• Kai Striega (4)
• Tartopohm (1) +
• Mamoru TASAKA (2) +
• Ewout ter Hoeven (5)
• TianyiQ (1) +
• Tiger (1) +
• Will Tirone (1)
• Edgar Andrés Margffoy Tuay (1) +
• Dmitry Ulyumdzhiev (1) +
• Hari Vamsi (1) +
• VitalyChait (1) +
• Rik Voorhaar (1) +
• Samuel Wallan (4)
• Stefan van der Walt (2)
• Warren Weckesser (145)
• wei2222 (1) +
• windows-server-2003 (3) +
• Marek Wojciechowski (2) +
• Niels Wouda (1) +
• WRKampi (1) +
• Yeonjoo Yoo (1) +
• Rory Yorke (1)
• Xiao Yuan (2) +
• Meekail Zain (2) +
• Fabio Zanini (1) +
• Steffen Zeile (1) +
• Egor Zemlyanoy (19)
• Gavin Zhang (3) +

A total of 182 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.