Mailman 3 June 2021 - SciPy-Dev

New feature: fitting distributions to censored data.
by Warren Weckesser Aug. 29, 2022

Aug. 29, 2022

Hey folks, A new enhancement for fitting probability distributions to censored data by maximum likelihood estimation is in progress in https://github.com/scipy/scipy/pull/13699 This is a feature in the statistics roadmap, and is part of the work for the CZI EOSS cycle 1 grant. Censored data is data where the true value of the measurement is unknown, but there is a known bound. The common terminology is: * left-censored: The true value is greater than some known bound. * right-censored: The true value is less than some known bound. * interval-censored: The true value is between known bounds. (By allowing the bounds to be +inf and -inf, we can think of all these cases as interval-censored.) In the PR, a new class, `CensoredData`, is defined to represent censored data. The `fit` method of the univariate continuous distributions is updated to accept an instance of `CensoredData`. The `CensoredData` class constructor accepts two arrays, `lower` and `upper`, to hold the known bounds of the data. (If `lower[i] == upper[i]`, it means that data value is not censored.) Because it is quite common for data to be encountered where the only censored values in the data set are either all right-censored or all left-censored, two convenience methods, `CensoredData.right_censored(x, censored)` and `CensoredData.left_censored(x, censored)`, are provide to create a `CensoredData` instance from an array of values and a corresponding boolean array that indicates if the value is censored. Here's a quick example, with data from https://www.itl.nist.gov/div898/handbook/apr/section4/apr413.htm. The data table shows 10 regular values and 10 right-censored values. The results reported there for fitting the two-parameter Weibull distribution (location fixed at 0) to that data are shape = 1.7208 scale = 606.5280 Here's the calculation using the proposed API in SciPy: In [55]: from scipy.stats import weibull_min, CensoredData Create the `CensoredData` instance: In [56]: x = np.array([54, 187, 216, 240, 244, 335, 361, 373, 375, 386] + [500]*10) In [57]: data = CensoredData.right_censored(x, x == 500) In [58]: print(data) CensoredData(20 values: 10 not censored, 10 right-censored) Fit `weibull_min` (with the location fixed at 0) to the censored data: In [59]: shape, loc, scale = weibull_min.fit(data, floc=0) In [60]: shape Out[60]: 1.720797180719942 In [61]: scale Out[61]: 606.527565269458 Matt Haberland has already suggested quite a few improvements to the PR. Additional comments would be appreciated. Warren

4 7

Global Optimization Benchmarks
by Andrea Gavana July 11, 2021

July 11, 2021

Dear SciPy Developers & Users, long time no see :-) . I thought to start 2021 with a bit of a bang, to try and forget how bad 2020 has been... So I am happy to present you with a revamped version of the Global Optimization Benchmarks from my previous exercise in 2013. This new set of benchmarks pretty much superseeds - and greatly expands - the previous analysis that you can find at this location: http://infinity77.net/global_optimization/ . The approach I have taken this time is to select as many benchmark test suites as possible: most of them are characterized by test function *generators*, from which we can actually create almost an unlimited number of unique test problems. Biggest news are: 1. This whole exercise is made up of *6,825* test problems divided across *16* different test suites: most of these problems are of low dimensionality (2 to 6 variables) with a few benchmarks extending to 9+ variables. With all the sensitivities performed during this exercise on those benchmarks, the overall grand total number of functions evaluations stands at *3,859,786,025* - close to *4 billion*. Not bad. 2. A couple of "new" optimization algorithms I have ported to Python: - MCS: Multilevel Coordinate Search <https://www.mat.univie.ac.at/~neum/software/mcs/>, it’s my translation to Python of the original Matlab code from A. Neumaier and W. Huyer (giving then for free also GLS and MINQ) I have added a few, minor improvements compared to the original implementation. - BiteOpt: BITmask Evolution OPTimization <https://github.com/avaneev/biteopt> , I have converted the C++ code into Python and added a few, minor modifications. Enough chatting for now. The 13 tested algorithms are described here: http://infinity77.net/go_2021/ High level description & results of the 16 benchmarks: http://infinity77.net/go_2021/thebenchmarks.html Each benchmark test suite has its own dedicated page, with more detailed results and sensitivities. List of tested algorithms: 1. *AMPGO*: Adaptive Memory Programming for Global Optimization: this is my Python implementation of the algorithm described here: http://leeds-faculty.colorado.edu/glover/fred%20pubs/416%20-%20AMP%20(TS)%2… I have added a few improvements here and there based on my Master Thesis work on the standard Tunnelling Algorithm of Levy, Montalvo and Gomez. After AMPGO was integrated in lmfit <https://github.com/lmfit/lmfit-py>, I have improved it even more - in my opinion. 2. *BasinHopping*: Basin hopping is a random algorithm which attempts to find the global minimum of a smooth scalar function of one or more variables. The algorithm was originally described by David Wales: http://www-wales.ch.cam.ac.uk/ BasinHopping is now part of the standard SciPy distribution. 3. *BiteOpt*: BITmask Evolution OPTimization, based on the algorithm presented in this GitHub link: https://github.com/avaneev/biteopt I have converted the C++ code into Python and added a few, minor modifications. 4. *CMA-ES*: Covariance Matrix Adaptation Evolution Strategy, based on the following algorithm: http://www.lri.fr/~hansen/cmaesintro.html http://www.lri.fr/~hansen/cmaes_inmatlab.html#python (Python code for the algorithm) 5. *CRS2*: Controlled Random Search with Local Mutation, as implemented in the NLOpt <http://ab-initio.mit.edu/wiki/index.php/NLopt> package: http://ab-initio.mit.edu/wiki/index.php/NLopt_Algorithms#Controlled_Random_… 6. *DE*: Differential Evolution, described in the following page: http://www1.icsi.berkeley.edu/~storn/code.html DE is now part of the standard SciPy distribution, and I have taken the implementation as it stands in SciPy: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.differe… 7. *DIRECT*: the DIviding RECTangles procedure, described in: https://www.tol-project.org/export/2776/tolp/OfficialTolArchiveNetwork/NonL… http://ab-initio.mit.edu/wiki/index.php/NLopt_Algorithms#DIRECT_and_DIRECT-L (Python code for the algorithm) 8. *DualAnnealing*: the Dual Annealing algorithm, taken directly from the SciPy implementation: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.dual_an… 9. *LeapFrog*: the Leap Frog procedure, which I have been recommended for use, taken from: https://github.com/flythereddflagg/lpfgopt 10. *MCS*: Multilevel Coordinate Search, it’s my translation to Python of the original Matlab code from A. Neumaier and W. Huyer (giving then for free also GLS <https://www.mat.univie.ac.at/~neum/software/ls/> and MINQ <https://www.mat.univie.ac.at/~neum/software/minq/>): https://www.mat.univie.ac.at/~neum/software/mcs/ I have added a few, minor improvements compared to the original implementation. See the MCS <http://infinity77.net/go_2021/mcs.html#mcs> section for a quick and dirty comparison between the Matlab code and my Python conversion. 11. *PSWARM*: Particle Swarm optimization algorithm, it has been described in many online papers. I have used a compiled version of the C source code from: http://www.norg.uminho.pt/aivaz/pswarm/ 12. *SCE*: Shuffled Complex Evolution, described in: Duan, Q., S. Sorooshian, and V. Gupta, Effective and efficient global optimization for conceptual rainfall-runoff models, Water Resour. Res., 28, 1015-1031, 1992. The version I used was graciously made available by Matthias Cuntz via a personal e-mail. 13. *SHGO*: Simplicial Homology Global Optimization, taken directly from the SciPy implementation: https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.shgo.ht… List of benchmark test suites: 1. SciPy Extended <http://infinity77.net/go_2021/scipy_extended.html#scipy-extended>: 235 multivariate problems (where the number of independent variables ranges from 2 to 17), again with multiple local/global minima. I have added about 40 new functions to the standard SciPy benchmarks <https://github.com/scipy/scipy/tree/master/benchmarks/benchmarks/go_benchma…> and fixed a few bugs in the existing benchmark models in the SciPy repository. 2. GKLS <http://infinity77.net/go_2021/gkls.html#gkls>: 1,500 test functions, with dimensionality varying from 2 to 6, generated with the super famous GKLS Test Functions Generator <https://arxiv.org/abs/1103.2695>. I have taken the original C code (available at http://netlib.org/toms/) and converted it to Python. 3. GlobOpt <http://infinity77.net/go_2021/globopt.html#globopt>: 288 tough problems, with dimensionality varying from 2 to 5, created with another test function generator which I arbitrarily named “GlobOpt”: https://www.researchgate.net/publication/225566516_A_new_class_of_test_func… . The original code is in C++ and I have bridged it to Python using Cython. *Many thanks* go to Professor Marco Locatelli for providing an updated copy of the C++ source code. 4. MMTFG <http://infinity77.net/go_2021/mmtfg.html#mmtfg>: sort-of an acronym for “Multi-Modal Test Function with multiple Global minima”, this test suite implements the work of Jani Ronkkonen: https://www.researchgate.net/publication/220265526_A_Generator_for_Multimod… . It contains 981 test problems with dimensionality varying from 2 to 4. The original code is in C and I have bridge it to Python using Cython. 5. GOTPY <http://infinity77.net/go_2021/gotpy.html#gotpy>: a generator of benchmark functions using the Bocharov-Feldbaum “Method-Min”, containing 400 test problems with dimensionality varying from 2 to 5. I have taken the Python implementation from https://github.com/redb0/gotpy and improved it in terms of runtime. Original paper from http://www.mathnet.ru/php/archive.phtml?wshow=paper&jrnid=at&paperid=11985&… . 6. Huygens <http://infinity77.net/go_2021/huygens.html#huygens>: this benchmark suite is very different from the rest, as it uses a “fractal” approach to generate test functions. It is based on the work of Cara MacNish on Fractal Functions <https://www.cs.bham.ac.uk/research/projects/ecb/displayDataset.php?id=150>. The original code is in Java, and at the beginning I just converted it to Python: given it was slow as a turtle, I have re-implemented it in Fortran and wrapped it using f2py <http://www.scipy.org/F2py>, then generating 600 2-dimensional test problems out of it. 7. LGMVG <http://infinity77.net/go_2021/lgmvg.html#lgmvg>: not sure about the meaning of the acronym, but the implementation follows the “Max-Set of Gaussians Landscape Generator” described in http://boyuan.global-optimization.com/LGMVG/index.htm . Source code is given in Matlab, but it’s fairly easy to convert it to Python. This test suite contains 304 problems with dimensionality varying from 2 to 5. 8. NgLi <http://infinity77.net/go_2021/ngli.html#ngli>: Stemming from the work of Chi-Kong Ng and Duan Li, this is a test problem generator for unconstrained optimization, but it’s fairly easy to assign bound constraints to it. The methodology is described in https://www.sciencedirect.com/science/article/pii/S0305054814001774 , while the Matlab source code can be found in http://www1.se.cuhk.edu.hk/~ckng/generator/ . I have used the Matlab script to generate 240 problems with dimensionality varying from 2 to 5 by outputting the generator parameters in text files, then used Python to create the objective functions based on those parameters and the benchmark methodology. 9. MPM2 <http://infinity77.net/go_2021/mpm2.html#mpm2>: Implementing the “Multiple Peaks Model 2”, there is a Python implementation at https://github.com/jakobbossek/smoof/blob/master/inst/mpm2.py . This is a test problem generator also used in the smoof <https://github.com/jakobbossek/smoof> library, I have taken the code almost as is and generated 480 benchmark functions with dimensionality varying from 2 to 5. 10. RandomFields <http://infinity77.net/go_2021/randomfields.html#randomfields>: as described in https://www.researchgate.net/publication/301940420_Global_optimization_test… , it generates benchmark functions by “smoothing” one or more multidimensional discrete random fields and composing them. No source code is given, but the implementation is fairly straightforward from the article itself. 11. NIST <http://infinity77.net/go_2021/nist.html#nist>: not exactly the realm of Global Optimization solvers, but the NIST StRD <https://www.itl.nist.gov/div898/strd/nls/nls_main.shtml> dataset can be used to generate a single objective function as “sum of squares”. I have used the NIST dataset as implemented in lmfit <https://github.com/lmfit/lmfit-py/tree/master/NIST_STRD>, thus creating 27 test problems with dimensionality ranging from 2 to 9. 12. GlobalLib <http://infinity77.net/go_2021/globallib.html#globallib>: Arnold Neumaier maintains <https://www.mat.univie.ac.at/~neum/glopt/coconut/Benchmark/Benchmark.html> a suite of test problems termed “COCONUT Benchmark” and Sahinidis has converted the GlobalLib and PricentonLib AMPL/GAMS dataset into C/Fortran code (http://archimedes.cheme.cmu.edu/?q=dfocomp ). I have used a simple C parser to convert the benchmarks from C to Python. The global minima are taken from Sahinidis <http://thales.cheme.cmu.edu/dfo/comparison/comp.html> or from Neumaier or refined using the NEOS server <https://neos-server.org/neos/> when the accuracy of the reported minima is too low. The suite contains 181 test functions with dimensionality varying between 2 and 9. 13. CVMG <http://infinity77.net/go_2021/cvmg.html#cvmg>: another “landscape generator”, I had to dig it out using the Wayback Machine at http://web.archive.org/web/20100612044104/https://www.cs.uwyo.edu/~wspears/… , the acronym stands for “Continuous Valued Multimodality Generator”. Source code is in C++ but it’s fairly easy to port it to Python. In addition to the original implementation (that uses the Sigmoid <https://en.wikipedia.org/wiki/Sigmoid_function> as a softmax/transformation function) I have added a few others to create varied landscapes. 360 test problems have been generated, with dimensionality ranging from 2 to 5. 14. NLSE <http://infinity77.net/go_2021/nlse.html#nlse>: again, not really the realm of Global optimization solvers, but Nonlinear Systems of Equations can be transformed to single objective functions to optimize. I have drawn from many different sources (Publications <https://www.sciencedirect.com/science/article/pii/S0898122111004299>, ALIAS/COPRIN <http://www-sop.inria.fr/coprin/logiciels/ALIAS/Benches/node1.html#SECTION00…> and many others) to create 44 systems of nonlinear equations with dimensionality ranging from 2 to 8. 15. Schoen <http://infinity77.net/go_2021/schoen.html#schoen>: based on the early work of Fabio Schoen and his short note <https://link.springer.com/article/10.1007%2FBF01096734> on a simple but interesting idea on a test function generator, I have taken the C code in the note and converted it into Python, thus creating 285 benchmark functions with dimensionality ranging from 2 to 6. *Many thanks* go to Professor Fabio Schoen for providing an updated copy of the source code and for the email communications. 16. Robust <http://infinity77.net/go_2021/robust.html#robust>: the last benchmark test suite for this exercise, it is actually composed of 5 different kind-of analytical test function generators, containing deceptive, multimodal, flat functions depending on the settings. Matlab source code is available at http://www.alimirjalili.com/RO.html , I simply converted it to Python and created 420 benchmark functions with dimensionality ranging from 2 to 6. Enjoy, and Happy 2021 :-) . Andrea.

6 21

Static Typing
by Pamphile Roy July 4, 2021

July 4, 2021

Hi everyone, In a recent PR (https://github.com/scipy/scipy/pull/14284 <https://github.com/scipy/scipy/pull/14284>), we had a discussion about static typing. My understanding from previous PRs, the inclusion of MyPy in the CI and discussions during our last community meetups, was that we wanted to gradually start adding type annotations in our code base. Thanks to the great help of Bas van Beek and others, we have a few common bricks we can use to ease the process. What is your opinion about adding annotations? I expressed my position in the issue. TL;DR I am in favour of adding type annotations. This greatly helps anyone using an IDE and downstream libraries like SciKit-Learn are basically waiting for us. Lastly, I am putting here again the link to the last Python Community survey https://www.jetbrains.com/lp/python-developers-survey-2020/ <https://www.jetbrains.com/lp/python-developers-survey-2020/>, static typing is the most wanted feature. Cheers, Pamphile

8 11

GSoC: Integrating library UNU.RAN in SciPy
by Tirth Patel July 4, 2021

July 4, 2021

Hi all, I have been working on integrating UNU.RAN in scipy.stats for a few weeks on my fork (https://github.com/tirthasheshpatel/scipy/pull/6) with my mentors, Christoph and Nicholas. The design is still fairly basic but is almost ready for initial reviews. Also, it builds on Windows, macOS, and Linux. Tests pass with an exception of unrelated failures on Linux. I am planning to propose a PR on SciPy this week but before I do that, I thought it would be a good idea to summarize the progress here. The methods I propose to add and details regarding the parameters they take can be found in this excel sheet: https://docs.google.com/spreadsheets/d/1r36HypXwpit7sHt9YAe3K7yPL7HNNuQjTkb…. Feel free to comment on the sheet if you have any suggestions. The API looks something like this: import numpy as np from scipy.stats import TransformedDensityRejection pdf = lambda x: 1 - x*x dpdf = lambda x: -2*x urng = np.random.default_rng(123) rng = TransformedDensityRejection(pdf, dpdf, domain=(-1,1), seed=urng) # sample a 100,000 samples from the distribution rvs = rng.rvs(100_000) # evaluate the upper bound of the PPF at some points in the domain u = np.linspace(0, 1, num=1000) ppf_hat = rng.ppf_hat(u) Internal API ------------ For Python callbacks, I have used the `ccallback` API and used setjmp/longjmp for error handling. Using `ctypes` gives similar performance but I wasn't able to figure out a way to handle errors occurring in UNU.RAN and in the callbacks. Here is the C code I wrote to acquire and release the callbacks: https://github.com/tirthasheshpatel/scipy/blob/unuran_c_thunk/scipy/stats/u… For more details on the internal design of the API, I have attempted to create a few flowcharts on draw.io but they are very much a WIP: https://drive.google.com/file/d/1TH70SSvvc5eF6-YmDO8kFNvLqKaGROW-/view?usp=… Other Notes ----------- I think NumPy 1.19 introduced a stable interface for its Generator API. Before that the RandomState API was stable. But RandomState doesn't have a Cython Interface and its Python interface is very slow to be practically useful. For instance, it takes around 7ms to sample 100,000 samples from the normal distribution using the TDR method on NumPy >= 1.19 while it takes around 911ms on NumPy == 1.18 which is around 130 times slower! Is there a plan to drop 1.16 soon and can we use the unstable Generator API from 1.17 onwards or would it too unsafe? Maybe this discussion isn't suited here but I just thought to put it out as a note. Anyways, please feel free to comment on the design, naming convention, etc and suggest changes/ideas that would be good to incorporate before proposing a PR on SciPy. Thanks for reading this! -- Kind Regards, Tirth Patel

3 5

SciPy Community Meetups
by Pamphile Roy June 28, 2021

June 28, 2021

Hi everyone, The next SciPy community meetup (EU/AFR/USA) will be on June 25 (Friday) at 16a.m. CEST. Everyone is invited to join in and edit the work-in-progress meeting topics and notes https://hackmd.io/@tupui/scipy-meetup-3/edit <https://hackmd.io/@tupui/scipy-meetup-3/edit> You can find the previous notes https://hackmd.io/@tupui/scipy-meetup-2 <https://hackmd.io/@tupui/scipy-meetup-2> Cheers, Pamphile

4 7

Query about scipy.signal development
by Namami Shanker June 24, 2021

June 24, 2021

Hello all, I recently came across Object-oriented design of digital filtering in scipy.signal (https://link.getmailspring.com/link/231BC7A9-2408-4CD5-887C-E6156C368A0F@ge…) article on Scipy wiki. This was proposed as one of the project ideas during GSOC21 for Scipy. However, I searched through the mailing list, and it seems that no one was selected for this project. I am an Electrical Engineering undergraduate and have knowledge in signal processing. I am interested in working on this project. I have also contributed to Scipy before and I am familiar with the development environment and workflow. I have a few questions. I’ll be thankful if any maintainer can address them. Is any scipy developer currently working on this project? Does Scipy take part in any other Open Source programs for working with students other than GSoC? Thank you, Namami Shanker Github (https://link.getmailspring.com/link/231BC7A9-2408-4CD5-887C-E6156C368A0F@ge…) | LinkedIn (https://link.getmailspring.com/link/231BC7A9-2408-4CD5-887C-E6156C368A0F@ge…)

2 1

Proposal to translate hyp2f1 for complex numbers into Cython
by Steppi, Albert June 24, 2021

June 24, 2021

Hi everyone, I've submitted the PR gh-14256, which is a beginning towards moving the implementation of Gauss's hypergeometric function hyp2f1 for complex numbers from Fortran into Cython. Josh Wilson mentioned at https://github.com/scipy/scipy/pull/8151#issuecomment-845227864 that this would be appreciated, and I'd like to work on this little by little in my spare time. The current Fortran implementation has several outstanding issues gh-4894, gh-7340, gh-8054, and gh-8083. Pull requests gh-8110 and gh-8151 were submitted by GitHub user FormerPhysicist to fix some of the outstanding issues but these have languished for almost four years now due to a lack of reviewers conversant in both numerical computation of special functions and Fortran 77. This PR has a fix for gh-7430. I intend to address other defects in the implementation of hyp2f1 in future PRs. Please see my opening comment in gh-14256 for more information on the contents of this PR and plans for the future. Feel free to join the discussion of this update in gh-14256! Thanks, Albert Albert Steppi III, PhD Scientific Software Developer Laboratory of Systems Pharmacology Harvard Medical School

2 2

NumPy 1.21.0 release
by Charles R Harris June 24, 2021

June 24, 2021

Hi All, On behalf of the NumPy team I am pleased to announce the release of NumPy 1.21.0. The highlights are - continued SIMD work covering more functions and platforms, - initial work on the new dtype infrastructure and casting, - universal2 wheels for Python 3.8 and Python 3.9 on Mac, - improved documentation, - improved annotations, - new ``PCG64DXSM`` bitgenerator for random numbers. This NumPy release is the result of 581 merged pull requests contributed by 175 people. The Python versions supported for this release are 3.7-3.9, support for Python 3.10 will be added after Python 3.10 is released. Wheels can be downloaded from PyPI <https://pypi.org/project/numpy/1.21.0/>; source archives, release notes, and wheel hashes are available on Github <https://github.com/numpy/numpy/releases/tag/v1.21.0>. Linux users will need pip >= 0.19.3 in order to install manylinux2010 and manylinux2014 wheels. *Contributors* A total of 175 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - @8bitmp3 + - @DWesl + - @Endolith - @Illviljan + - @Lbogula + - @Lisa + - @Patrick + - @Scian + - @h-vetinari + - @h6197627 + - @jbCodeHub + - @legoffant + - @sfolje0 + - @tautaus + - @yetanothercheer + - Abhay Raghuvanshi + - Adrian Price-Whelan + - Aerik Pawson + - Agbonze Osazuwa + - Aitik Gupta + - Al-Baraa El-Hag - Alex Henrie - Alexander Hunt + - Alizé Papp + - Allan Haldane - Amarnath1904 + - Amrit Krishnan + - Andras Deak - AngelGris + - Anne Archibald - Anthony Vo + - Antony Lee - Atharva-Vidwans + - Ayush Verma + - Bas van Beek - Bharat Raghunathan - Bhargav V + - Brian Soto - Carl Michal + - Charles Harris - Charles Stern + - Chiara Marmo + - Chris Barnes + - Chris Vavaliaris - Christina Hedges + - Christoph Gohlke - Christopher Dahlin + - Christos Efstathiou + - Chunlin Fang - Constanza Fierro + - Daniel Evans + - Daniel Montes + - Dario Mory + - David Carlier + - David Stansby - Deepyaman Datta + - Derek Homeier - Dong Keun Oh + - Dylan Cutler + - Eric Larson - Eric Wieser - Eva Jau + - Evgeni Burovski - FX Coudert + - Faris A Chugthai + - Filip Ter + - Filip Trojan + - François Le Lay + - Ganesh Kathiresan - Giannis Zapantis + - Giulio Procopio + - Greg Lucas + - Hollow Man + - Holly Corbett + - I-Shen Leong + - Inessa Pawson - Isabela Presedo-Floyd - Ismael Jimenez + - Isuru Fernando - Jakob Jakobson - James Gerity + - Jamie Macey + - Jasmin Classen + - Jody Klymak + - Joseph Fox-Rabinovitz - Jérome Eertmans + - Jérôme Kieffer + - Kamil Choudhury + - Kasia Leszek + - Keller Meier + - Kenichi Maehashi - Kevin Sheppard - Kulin Seth + - Kumud Lakara + - Laura Kopf + - Laura Martens + - Leo Singer + - Leonardus Chen + - Lima Tango + - Lumir Balhar + - Maia Kaplan + - Mainak Debnath + - Marco Aurélio da Costa + - Marta Lemanczyk + - Marten van Kerkwijk - Mary Conley + - Marysia Winkels + - Mateusz Sokół + - Matt Haberland - Matt Hall + - Matt Ord + - Matthew Badin + - Matthias Bussonnier - Matthias Geier - Matti Picus - Matías Ríos + - Maxim Belkin + - Melissa Weber Mendonça - Meltem Eren Copur + - Michael Dubravski + - Michael Lamparski - Michal W. Tarnowski + - Michał Górny + - Mike Boyle + - Mike Toews - Misal Raj + - Mitchell Faas + - Mukulikaa Parhari + - Neil Girdhar + - Nicholas McKibben + - Nico Schlömer - Nicolas Hug + - Nilo Kruchelski + - Nirjas Jakilim + - Ohad Ravid + - Olivier Grisel - Pamphile ROY + - Panos Mavrogiorgos + - Patrick T. Komiske III + - Pearu Peterson - Peter Hawkins + - Raghuveer Devulapalli - Ralf Gommers - Raúl Montón Pinillos + - Rin Arakaki + - Robert Kern - Rohit Sanjay - Roman Yurchak - Ronan Lamy - Ross Barnowski - Ryan C Cooper - Ryan Polley + - Ryan Soklaski - Sabrina Simao + - Sayed Adel - Sebastian Berg - Shen Zhou + - Stefan van der Walt - Sylwester Arabas + - Takanori Hirano - Tania Allard + - Thomas J. Fan + - Thomas Orgis + - Tim Hoffmann - Tomoki, Karatsu + - Tong Zou + - Touqir Sajed + - Tyler Reddy - Wansoo Kim - Warren Weckesser - Weh Andreas + - Yang Hau - Yashasvi Misra + - Zolboo Erdenebaatar + - Zolisa Bleki Cheers, Charles Harris

2 1

PR: Implement higher-order SVD in scipy.linalg
by Jan Naumann June 23, 2021

June 23, 2021

Dear all, I just opened a pull request to add the higher-order SVD (HOSVD) in scipy.linalg: https://github.com/scipy/scipy/pull/14284 The HOSVD is a technique used for example in the field of tensor networks for higher dimensional structures. It generalizes the idea of the SVD to higher dimensions. The implementation is based on Ref. [1]. Best, Jan Naumann [1] https://doi.org/10.1137/S0895479896305696

2 1

Request for Information: How to Contribute?
by Alex Sherstinsky June 23, 2021

June 23, 2021

Dear SciPy-Dev: I am a new subscriber to this mailing list (I just joined) -- thank you for accepting me! I joined this mailing list, because I was interested in making a small contribution to the project. Specifically, I implemented a bootstrap based estimator with an algorithmically computed optimal number of samples. The benefit is that the developer does not have to guess the number of samples (the algorithm computes it automatically). Since I could not find an existing widely available implementation, I wanted to inquire if I could please submit my implementation. Could you please let me know what the process is for contributing? Thank you very much, and Regards. Sincerely, --Alex Sherstinsky (https://www.linkedin.com/in/alexsherstinsky/)

2 1

doc links broken (Was: ANN: SciPy 1.7.0)
by Ralf Gommers June 21, 2021

June 21, 2021

On Mon, Jun 21, 2021 at 9:20 AM Ralf Gommers <ralf.gommers(a)gmail.com> wrote: > > > On Mon, Jun 21, 2021 at 4:24 AM Juan Nunez-Iglesias <jni(a)fastmail.com> > wrote: > >> It appears that previous doc links have been broken without redirects? >> e.g.: >> >> >> https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.distance… >> >> is 404. The new link is at: >> >> >> https://docs.scipy.org/doc/scipy/reference/reference/generated/scipy.ndimag… >> >> Note the extra “reference” in the URL. Was this a conscious choice or an >> unforeseen side effect of moving to the PyData theme? There’s a *lot* of >> links to the docs out there. >> > > Argh, definitely a bug. The bug will be in the uploader, because > https://scipy.github.io/devdocs/reference/generated/scipy.linalg.solve.html… > looks fine. > > Will try to resolve that later today. > Argh, it's not an uploader bug, the structure actually changed: https://docs.scipy.org/doc/scipy-1.6.3/reference/ https://docs.scipy.org/doc/scipy-1.6.3/reference/tutorial/index.html https://docs.scipy.org/doc/scipy-1.6.3/reference/cluster.html https://docs.scipy.org/doc/scipy-1.7.0/reference/ https://docs.scipy.org/doc/scipy-1.7.0/reference/tutorial/index.html#user-g… https://docs.scipy.org/doc/scipy-1.7.0/reference/reference/cluster.html (note the double reference) Fuzzy on why we didn't notice this earlier. We also can't drop the "reference" prefer - that will fix the API doc links, but break the tutorial ones. Tracking issue at https://github.com/scipy/scipy/issues/14267 Ralf

1 0

ANN: SciPy 1.7.0
by Tyler Reddy June 21, 2021

June 21, 2021

Hi all, On behalf of the SciPy development team I'm pleased to announce the release of SciPy 1.7.0. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.7.0 One of a few ways to install this release with pip: pip install scipy==1.7.0 ===================== SciPy 1.7.0 Release Notes ===================== SciPy 1.7.0 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 1.7.x branch, and on adding new features on the master branch. This release requires Python 3.7+ and NumPy 1.16.5 or greater. For running on PyPy, PyPy3 6.0+ is required. **************************** Highlights of this release **************************** - A new submodule for quasi-Monte Carlo, `scipy.stats.qmc`, was added - The documentation design was updated to use the same PyData-Sphinx theme as NumPy and other ecosystem libraries. - We now vendor and leverage the Boost C++ library to enable numerous improvements for long-standing weaknesses in `scipy.stats` - `scipy.stats` has six new distributions, eight new (or overhauled) hypothesis tests, a new function for bootstrapping, a class that enables fast random variate sampling and percentile point function evaluation, and many other enhancements. - ``cdist`` and ``pdist`` distance calculations are faster for several metrics, especially weighted cases, thanks to a rewrite to a new C++ backend framework - A new class for radial basis function interpolation, `RBFInterpolator`, was added to address issues with the `Rbf` class. We gratefully acknowledge the Chan-Zuckerberg Initiative Essential Open Source Software for Science program for supporting many of the improvements to `scipy.stats`. *************** New features *************** `scipy.cluster` improvements ====================== An optional argument, ``seed``, has been added to ``kmeans`` and ``kmeans2`` to set the random generator and random state. `scipy.interpolate` improvements ========================= Improved input validation and error messages for ``fitpack.bispev`` and ``fitpack.parder`` for scenarios that previously caused substantial confusion for users. The class `RBFInterpolator` was added to supersede the `Rbf` class. The new class has usage that more closely follows other interpolator classes, corrects sign errors that caused unexpected smoothing behavior, includes polynomial terms in the interpolant (which are necessary for some RBF choices), and supports interpolation using only the k-nearest neighbors for memory efficiency. `scipy.linalg` improvements ===================== An LAPACK wrapper was added for access to the ``tgexc`` subroutine. `scipy.ndimage` improvements ======================= `scipy.ndimage.affine_transform` is now able to infer the ``output_shape`` from the ``out`` array. `scipy.optimize` improvements ======================= The optional parameter ``bounds`` was added to ``_minimize_neldermead`` to support bounds constraints for the Nelder-Mead solver. ``trustregion`` methods ``trust-krylov``, ``dogleg`` and ``trust-ncg`` can now estimate ``hess`` by finite difference using one of ``["2-point", "3-point", "cs"]``. ``halton`` was added as a ``sampling_method`` in `scipy.optimize.shgo`. ``sobol`` was fixed and is now using `scipy.stats.qmc.Sobol`. ``halton`` and ``sobol`` were added as ``init`` methods in `scipy.optimize.differential_evolution.` ``differential_evolution`` now accepts an ``x0`` parameter to provide an initial guess for the minimization. ``least_squares`` has a modest performance improvement when SciPy is built with Pythran transpiler enabled. When ``linprog`` is used with ``method`` ``'highs'``, ``'highs-ipm'``, or ``'highs-ds'``, the result object now reports the marginals (AKA shadow prices, dual values) and residuals associated with each constraint. `scipy.signal` improvements ===================== ``get_window`` supports ``general_cosine`` and ``general_hamming`` window functions. `scipy.signal.medfilt2d` now releases the GIL where appropriate to enable performance gains via multithreaded calculations. `scipy.sparse` improvements ====================== Addition of ``dia_matrix`` sparse matrices is now faster. `scipy.spatial` improvements ====================== ``distance.cdist`` and ``distance.pdist`` performance has greatly improved for certain weighted metrics. Namely: ``minkowski``, ``euclidean``, ``chebyshev``, ``canberra``, and ``cityblock``. Modest performance improvements for many of the unweighted ``cdist`` and ``pdist`` metrics noted above. The parameter ``seed`` was added to `scipy.spatial.vq.kmeans` and `scipy.spatial.vq.kmeans2`. The parameters ``axis`` and ``keepdims`` where added to `scipy.spatial.distance.jensenshannon`. The ``rotation`` methods ``from_rotvec`` and ``as_rotvec`` now accept a ``degrees`` argument to specify usage of degrees instead of radians. `scipy.special` improvements ====================== Wright's generalized Bessel function for positive arguments was added as `scipy.special.wright_bessel.` An implementation of the inverse of the Log CDF of the Normal Distribution is now available via `scipy.special.ndtri_exp`. `scipy.stats` improvements ==================== Hypothesis Tests ----------------------- The Mann-Whitney-Wilcoxon test, ``mannwhitneyu``, has been rewritten. It now supports n-dimensional input, an exact test method when there are no ties, and improved documentation. Please see "Other changes" for adjustments to default behavior. The new function `scipy.stats.binomtest` replaces `scipy.stats.binom_test`. The new function returns an object that calculates a confidence intervals of the proportion parameter. Also, performance was improved from O(n) to O(log(n)) by using binary search. The two-sample version of the Cramer-von Mises test is implemented in `scipy.stats.cramervonmises_2samp`. The Alexander-Govern test is implemented in the new function `scipy.stats.alexandergovern`. The new functions `scipy.stats.barnard_exact` and `scipy.stats. boschloo_exact` respectively perform Barnard's exact test and Boschloo's exact test for 2x2 contingency tables. The new function `scipy.stats.page_trend_test` performs Page's test for ordered alternatives. The new function `scipy.stats.somersd` performs Somers' D test for ordinal association between two variables. An option, ``permutations``, has been added in `scipy.stats.ttest_ind` to perform permutation t-tests. A ``trim`` option was also added to perform a trimmed (Yuen's) t-test. The ``alternative`` parameter was added to the ``skewtest``, ``kurtosistest``, ``ranksums``, ``mood``, ``ansari``, ``linregress``, and ``spearmanr`` functions to allow one-sided hypothesis testing. Sample statistics ----------------------- The new function `scipy.stats.differential_entropy` estimates the differential entropy of a continuous distribution from a sample. The ``boxcox`` and ``boxcox_normmax`` now allow the user to control the optimizer used to minimize the negative log-likelihood function. A new function `scipy.stats.contingency.relative_risk` calculates the relative risk, or risk ratio, of a 2x2 contingency table. The object returned has a method to compute the confidence interval of the relative risk. Performance improvements in the ``skew`` and ``kurtosis`` functions achieved by removal of repeated/redundant calculations. Substantial performance improvements in `scipy.stats.mstats.hdquantiles_sd`. The new function `scipy.stats.contingency.association` computes several measures of association for a contingency table: Pearsons contingency coefficient, Cramer's V, and Tschuprow's T. The parameter ``nan_policy`` was added to `scipy.stats.zmap` to provide options for handling the occurrence of ``nan`` in the input data. The parameter ``ddof`` was added to `scipy.stats.variation` and `scipy.stats.mstats.variation`. The parameter ``weights`` was added to `scipy.stats.gmean`. Statistical Distributions ------------------------------- We now vendor and leverage the Boost C++ library to address a number of previously reported issues in ``stats``. Notably, ``beta``, ``binom``, ``nbinom`` now have Boost backends, and it is straightforward to leverage the backend for additional functions. The skew Cauchy probability distribution has been implemented as `scipy.stats.skewcauchy`. The Zipfian probability distribution has been implemented as `scipy.stats.zipfian`. The new distributions ``nchypergeom_fisher`` and ``nchypergeom_wallenius`` implement the Fisher and Wallenius versions of the noncentral hypergeometric distribution, respectively. The generalized hyperbolic distribution was added in `scipy.stats.genhyperbolic`. The studentized range distribution was added in `scipy.stats.studentized_range`. `scipy.stats.argus` now has improved handling for small parameter values. Better argument handling/preparation has resulted in performance improvements for many distributions. The ``cosine`` distribution has added ufuncs for ``ppf``, ``cdf``, ``sf``, and ``isf`` methods including numerical precision improvements at the edges of the support of the distribution. An option to fit the distribution to data by the method of moments has been added to the ``fit`` method of the univariate continuous distributions. Other --------- `scipy.stats.bootstrap` has been added to allow estimation of the confidence interval and standard error of a statistic. The new function `scipy.stats.contingency.crosstab` computes a contingency table (i.e. a table of counts of unique entries) for the given data. `scipy.stats.NumericalInverseHermite` enables fast random variate sampling and percentile point function evaluation of an arbitrary univariate statistical distribution. New `scipy.stats.qmc` module ----------------------------------------- This new module provides Quasi-Monte Carlo (QMC) generators and associated helper functions. It provides a generic class `scipy.stats.qmc.QMCEngine` which defines a QMC engine/sampler. An engine is state aware: it can be continued, advanced and reset. 3 base samplers are available: - `scipy.stats.qmc.Sobol` the well known Sobol low discrepancy sequence. Several warnings have been added to guide the user into properly using this sampler. The sequence is scrambled by default. - `scipy.stats.qmc.Halton`: Halton low discrepancy sequence. The sequence is scrambled by default. - `scipy.stats.qmc.LatinHypercube`: plain LHS design. And 2 special samplers are available: - `scipy.stats.qmc.MultinomialQMC`: sampling from a multinomial distribution using any of the base `scipy.stats.qmc.QMCEngine`. - `scipy.stats.qmc.MultivariateNormalQMC`: sampling from a multivariate Normal using any of the base `scipy.stats.qmc.QMCEngine`. The module also provide the following helpers: - `scipy.stats.qmc.discrepancy`: assess the quality of a set of points in terms of space coverage. - `scipy.stats.qmc.update_discrepancy`: can be used in an optimization loop to construct a good set of points. - `scipy.stats.qmc.scale`: easily scale a set of points from (to) the unit interval to (from) a given range. *********************** Deprecated features *********************** `scipy.linalg` deprecations ==================== - `scipy.linalg.pinv2` is deprecated and its functionality is completely subsumed into `scipy.linalg.pinv` - Both ``rcond``, ``cond`` keywords of `scipy.linalg.pinv` and `scipy.linalg.pinvh` were not working and now are deprecated. They are now replaced with functioning ``atol`` and ``rtol`` keywords with clear usage. `scipy.spatial` deprecations ===================== - `scipy.spatial.distance` metrics expect 1d input vectors but will call ``np.squeeze`` on their inputs to accept any extra length-1 dimensions. That behaviour is now deprecated. ***************** Other changes ***************** We now accept and leverage performance improvements from the ahead-of-time Python-to-C++ transpiler, Pythran, which can be optionally disabled (via ``export SCIPY_USE_PYTHRAN=0``) but is enabled by default at build time. There are two changes to the default behavior of `scipy.stats.mannwhitenyu`: - For years, use of the default ``alternative=None`` was deprecated; explicit ``alternative`` specification was required. Use of the new default value of ``alternative``, "two-sided", is now permitted. - Previously, all p-values were based on an asymptotic approximation. Now, for small samples without ties, the p-values returned are exact by default. Support has been added for PEP 621 (project metadata in ``pyproject.toml``) We now support a Gitpod environment to reduce the barrier to entry for SciPy development; for more details see :ref:`quickstart-gitpod`. ********* Authors ********* * @endolith * Jelle Aalbers + * Adam + * Tania Allard + * Sven Baars + * Max Balandat + * baumgarc + * Christoph Baumgarten * Peter Bell * Lilian Besson * Robinson Besson + * Max Bolingbroke * Blair Bonnett + * Jordão Bragantini * Harm Buisman + * Evgeni Burovski * Matthias Bussonnier * Dominic C * CJ Carey * Ramón Casero + * Chachay + * charlotte12l + * Benjamin Curtice Corbett + * Falcon Dai + * Ian Dall + * Terry Davis * droussea2001 + * DWesl + * dwight200 + * Thomas J. Fan + * Joseph Fox-Rabinovitz * Max Frei + * Laura Gutierrez Funderburk + * gbonomib + * Matthias Geier + * Pradipta Ghosh + * Ralf Gommers * Evan H + * h-vetinari * Matt Haberland * Anselm Hahn + * Alex Henrie * Piet Hessenius + * Trever Hines + * Elisha Hollander + * Stephan Hoyer * Tom Hu + * Kei Ishikawa + * Julien Jerphanion * Robert Kern * Shashank KS + * Peter Mahler Larsen * Eric Larson * Cheng H. Lee + * Gregory R. Lee * Jean-Benoist Leger + * lgfunderburk + * liam-o-marsh + * Xingyu Liu + * Alex Loftus + * Christian Lorentzen + * Cong Ma * Marc + * MarkPundurs + * Markus Löning + * Liam Marsh + * Nicholas McKibben * melissawm + * Jamie Morton * Andrew Nelson * Nikola Forró * Tor Nordam + * Olivier Gauthé + * Rohit Pandey + * Avanindra Kumar Pandeya + * Tirth Patel * paugier + * Alex H. Wagner, PhD + * Jeff Plourde + * Ilhan Polat * pranavrajpal + * Vladyslav Rachek * Bharat Raghunathan * Recursing + * Tyler Reddy * Lucas Roberts * Gregor Robinson + * Pamphile Roy + * Atsushi Sakai * Benjamin Santos * Martin K. Scherer + * Thomas Schmelzer + * Daniel Scott + * Sebastian Wallkötter + * serge-sans-paille + * Namami Shanker + * Masashi Shibata + * Alexandre de Siqueira + * Albert Steppi + * Adam J. Stewart + * Kai Striega * Diana Sukhoverkhova * Søren Fuglede Jørgensen * Mike Taves * Dan Temkin + * Nicolas Tessore + * tsubota20 + * Robert Uhl * christos val + * Bas van Beek + * Ashutosh Varma + * Jose Vazquez + * Sebastiano Vigna * Aditya Vijaykumar * VNMabus * Arthur Volant + * Samuel Wallan * Stefan van der Walt * Warren Weckesser * Anreas Weh * Josh Wilson * Rory Yorke * Egor Zemlyanoy * Marc Zoeller + * zoj613 + * 秋纫 + A total of 126 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 1.7.0 ************************** * `#636 <https://github.com/scipy/scipy/issues/636>`__: Statistics Review: mannwhitneyu (Trac #109) * `#1346 <https://github.com/scipy/scipy/issues/1346>`__: signal.medfilt2d should fall back on signal.medfilt for types... * `#2118 <https://github.com/scipy/scipy/issues/2118>`__: Mann-Whitney statistic returns incorrect results (Trac #1593) * `#2158 <https://github.com/scipy/scipy/issues/2158>`__: special.chndtrix (ncx2.ppf) gives wrong results (Trac #1633) * `#3284 <https://github.com/scipy/scipy/issues/3284>`__: build_sphinx weirdness * `#3352 <https://github.com/scipy/scipy/issues/3352>`__: beta distribution sf * `#4067 <https://github.com/scipy/scipy/issues/4067>`__: Mannwhitneyu with arrays full of nan still reports significance * `#4080 <https://github.com/scipy/scipy/issues/4080>`__: entropy in Scipy * `#4641 <https://github.com/scipy/scipy/issues/4641>`__: mstats.mannwhitneyu and stats.mannwhitneyu return inconsistent... * `#5122 <https://github.com/scipy/scipy/issues/5122>`__: scipy.stats.binom.ppf Incorrect for p=0 * `#5180 <https://github.com/scipy/scipy/issues/5180>`__: Rbf interpolation - use only K nearest neighbors * `#5258 <https://github.com/scipy/scipy/issues/5258>`__: affine_transform complains about output_shape when output array... * `#5562 <https://github.com/scipy/scipy/issues/5562>`__: Wishart degrees of freedom should be $v > p-1$ instead of $v... * `#5933 <https://github.com/scipy/scipy/issues/5933>`__: mstats_basic.py - mannwhitneyu [scipy/scipy/stats/mstats_basic.py] * `#6409 <https://github.com/scipy/scipy/issues/6409>`__: _unequal_var_ttest_denom causes ZeroDivisionError in early samples * `#6682 <https://github.com/scipy/scipy/issues/6682>`__: negative binomial survival function is imprecise * `#6897 <https://github.com/scipy/scipy/issues/6897>`__: scipy.stats.mannwhitneyu of empty sets gives p=0.0 and does not... * `#7303 <https://github.com/scipy/scipy/issues/7303>`__: stats.describe with nan_policy=omit returns matrix-wide minmax... * `#7406 <https://github.com/scipy/scipy/issues/7406>`__: scipy.stats.binom.ppf returns nan for q between 0 and 1 if n... * `#7437 <https://github.com/scipy/scipy/issues/7437>`__: ENH: add skewed Cauchy distribution to stats * `#7542 <https://github.com/scipy/scipy/issues/7542>`__: DOC: stats tutorials: Questions on arcsine and Student t formulae * `#7593 <https://github.com/scipy/scipy/issues/7593>`__: Meaning of \`tol\` argument in \`scipy.optimize.minimize\` is... * `#8565 <https://github.com/scipy/scipy/issues/8565>`__: Error in SmoothSphereBivariateSpline(): "ValueError: Error code... * `#8665 <https://github.com/scipy/scipy/issues/8665>`__: \`scipy.ncx2.sf\` should be monotone decreasing * `#8836 <https://github.com/scipy/scipy/issues/8836>`__: scipy.optimize.linprog(method='simplex') needs to return duals * `#9184 <https://github.com/scipy/scipy/issues/9184>`__: Mann-Whitney implementation wrong? * `#9450 <https://github.com/scipy/scipy/issues/9450>`__: allow seeding of init methods in vq.kmeans2 * `#9704 <https://github.com/scipy/scipy/issues/9704>`__: RectSphereBivariateSpline fails for negative longitude * `#9836 <https://github.com/scipy/scipy/issues/9836>`__: scipy.stats.rice gives incorrect results when s is very low compared... * `#9904 <https://github.com/scipy/scipy/issues/9904>`__: Request/Proposal: Greatly improve scipy.interpolate.Rbf * `#9981 <https://github.com/scipy/scipy/issues/9981>`__: stats.kruskal : add a warning for an input with 2 or more columns * `#10358 <https://github.com/scipy/scipy/issues/10358>`__: DOC: linprog and linear_sum_assignment tutorials needed * `#10908 <https://github.com/scipy/scipy/issues/10908>`__: Nakami fitting doesn't converge (scipy.stats) * `#10933 <https://github.com/scipy/scipy/issues/10933>`__: Add scaled inverse chi2 distribution * `#11014 <https://github.com/scipy/scipy/issues/11014>`__: Barnard's Test for More Powerful Hypothesis Testing of 2x2 Contingency... * `#11050 <https://github.com/scipy/scipy/issues/11050>`__: Feature request: Nelder-Mead with bounds * `#11086 <https://github.com/scipy/scipy/issues/11086>`__: scipy.stats.skew doesn't work correctly for float point numbers * `#11113 <https://github.com/scipy/scipy/issues/11113>`__: inconsistent result from ttest_ind and mannwhitneyu when used... * `#11134 <https://github.com/scipy/scipy/issues/11134>`__: Wrong confidence interval for binomial distribution with p=0 * `#11325 <https://github.com/scipy/scipy/issues/11325>`__: Add axis parameter for scipy.spatial.distance.jensenshannon * `#11474 <https://github.com/scipy/scipy/issues/11474>`__: scipy.stats.skellam.cdf(0) returns 0 for large mu1 = mu2 * `#11523 <https://github.com/scipy/scipy/issues/11523>`__: scipy.stats.zipf doesn't implement zipf distribution * `#11848 <https://github.com/scipy/scipy/issues/11848>`__: How to get Lagrange / lambda multipliers out of 'linprog' optimize... * `#11909 <https://github.com/scipy/scipy/issues/11909>`__: Enable bounds for lambda in boxcox * `#12118 <https://github.com/scipy/scipy/issues/12118>`__: Docstring missing defaults * `#12132 <https://github.com/scipy/scipy/issues/12132>`__: Slow tests to be trimmed or moved to test('full') * `#12230 <https://github.com/scipy/scipy/issues/12230>`__: Dendrogram: enable leaves labelling with 'labels' when using... * `#12282 <https://github.com/scipy/scipy/issues/12282>`__: scipy.stats.chisquare test does not check that observed and expected... * `#12298 <https://github.com/scipy/scipy/issues/12298>`__: BUG: fmin_powell missing squeeze in 1.5.0rc * `#12403 <https://github.com/scipy/scipy/issues/12403>`__: Add nan_policy to stats.zmap * `#12518 <https://github.com/scipy/scipy/issues/12518>`__: Null hypothesis of Kolmogorov Smirnov test is not correctly described * `#12534 <https://github.com/scipy/scipy/issues/12534>`__: Feature request: scipy.linalg.norm to deal with 0-size array * `#12622 <https://github.com/scipy/scipy/issues/12622>`__: scipy.interpolate.interpn docstring example * `#12635 <https://github.com/scipy/scipy/issues/12635>`__: scipy.stats.beta.ppf gives unexpexted results * `#12669 <https://github.com/scipy/scipy/issues/12669>`__: Median-averaging of complex CSDs * `#12731 <https://github.com/scipy/scipy/issues/12731>`__: stats.ncx2.cdf fails for nc >> x >> 1 * `#12778 <https://github.com/scipy/scipy/issues/12778>`__: Confusing documentation of scipy.stats.weightedtau * `#12794 <https://github.com/scipy/scipy/issues/12794>`__: [Bug] The result of stats.beta.isf is inconsistent with stats.beta.sf * `#12837 <https://github.com/scipy/scipy/issues/12837>`__: stats.mannwhitneyu could support arrays * `#12868 <https://github.com/scipy/scipy/issues/12868>`__: Vector-valued interpolation in \`interp2d\` * `#12922 <https://github.com/scipy/scipy/issues/12922>`__: Minimize with trust-constr method leads to TypeError if option... * `#12929 <https://github.com/scipy/scipy/issues/12929>`__: The use of starred expressions to create data detracts from understanding... * `#12965 <https://github.com/scipy/scipy/issues/12965>`__: domain of argument of scipy.interpolate.RectSphereBivariateSpline(u,... * `#13025 <https://github.com/scipy/scipy/issues/13025>`__: Generalized Hyperbolic Distribution * `#13090 <https://github.com/scipy/scipy/issues/13090>`__: Broken link in doc for signal.max_len_seq * `#13101 <https://github.com/scipy/scipy/issues/13101>`__: MAINT: Upgrade python version in docker file * `#13158 <https://github.com/scipy/scipy/issues/13158>`__: \`signal.get_window()\` has a missing doc link and cannot get... * `#13173 <https://github.com/scipy/scipy/issues/13173>`__: Uninformative error message from bisplev function * `#13234 <https://github.com/scipy/scipy/issues/13234>`__: BUG: stats: Wrong shape of burr.moment() and fisk.moment() when... * `#13242 <https://github.com/scipy/scipy/issues/13242>`__: Does kmeans "drop" clusters? * `#13243 <https://github.com/scipy/scipy/issues/13243>`__: tgsen uses an output argument for computing a default argument * `#13245 <https://github.com/scipy/scipy/issues/13245>`__: Kurtosis returning 1 for array of same elements * `#13257 <https://github.com/scipy/scipy/issues/13257>`__: GitHub Actions test failures for MacOS * `#13272 <https://github.com/scipy/scipy/issues/13272>`__: scipy.stats.yeojohnson_llf doc mistake * `#13280 <https://github.com/scipy/scipy/issues/13280>`__: Wrong results with hypergeom cdf * `#13285 <https://github.com/scipy/scipy/issues/13285>`__: description correction in scipy.stats.t * `#13287 <https://github.com/scipy/scipy/issues/13287>`__: Generate binomial CDF with mu instead of prob * `#13294 <https://github.com/scipy/scipy/issues/13294>`__: BUG: stats: wrong bounds returned by 'support' method for distributions... * `#13299 <https://github.com/scipy/scipy/issues/13299>`__: Typing for scipy.spatial * `#13300 <https://github.com/scipy/scipy/issues/13300>`__: Add a single individual to a latinhypercube initial population... * `#13311 <https://github.com/scipy/scipy/issues/13311>`__: MAINT: pavement.py PYVER is outdated * `#13339 <https://github.com/scipy/scipy/issues/13339>`__: savemat discards dimension information if any dimension is zero * `#13341 <https://github.com/scipy/scipy/issues/13341>`__: add scipy.stats.variation with an ddof parameter * `#13353 <https://github.com/scipy/scipy/issues/13353>`__: Documentation: in scipy.stats.johnsonsu, parameter \`a\` can... * `#13405 <https://github.com/scipy/scipy/issues/13405>`__: TST: add a few tests for sparse BSR ctor * `#13410 <https://github.com/scipy/scipy/issues/13410>`__: BUG: skew for empty array raises * `#13417 <https://github.com/scipy/scipy/issues/13417>`__: 10,000 times speedup for generating random numbers from the cosine... * `#13440 <https://github.com/scipy/scipy/issues/13440>`__: python runtest.py -t path-to-test.py failed * `#13454 <https://github.com/scipy/scipy/issues/13454>`__: Scipy cosine distance can be greater than 2 * `#13459 <https://github.com/scipy/scipy/issues/13459>`__: Broken link in cramervonmises documentation * `#13494 <https://github.com/scipy/scipy/issues/13494>`__: One-word typo in the documentation of optimize.linprog_simplex * `#13501 <https://github.com/scipy/scipy/issues/13501>`__: minimize using Powell methods with Bounds leads to "TypeError:... * `#13509 <https://github.com/scipy/scipy/issues/13509>`__: signal.medfilt2d vs ndimage.median_filter * `#13511 <https://github.com/scipy/scipy/issues/13511>`__: DOC: error in description of "direc" parameter of "fmin_powell" * `#13526 <https://github.com/scipy/scipy/issues/13526>`__: TST: stats: intermittent \`test_ttest_ind_randperm_alternative2... * `#13536 <https://github.com/scipy/scipy/issues/13536>`__: \`_within_tolerance\` seems an unnecessary repetition of \`numpy.isclose\` * `#13540 <https://github.com/scipy/scipy/issues/13540>`__: missing python 3.8 manylinux wheels on scipy-wheels-nightly * `#13559 <https://github.com/scipy/scipy/issues/13559>`__: shape error in linprog with revised simplex * `#13587 <https://github.com/scipy/scipy/issues/13587>`__: binned_statistic unreliable with single precision * `#13589 <https://github.com/scipy/scipy/issues/13589>`__: Better argument preparation for distributions in stats package. * `#13602 <https://github.com/scipy/scipy/issues/13602>`__: The crystallball distribution entropy is sometimes minus infinity * `#13606 <https://github.com/scipy/scipy/issues/13606>`__: MAINT: mypy: some typing errors while running mypy + adding mypy... * `#13608 <https://github.com/scipy/scipy/issues/13608>`__: Why does stats.binned_statistic_2d convert its values argument... * `#13609 <https://github.com/scipy/scipy/issues/13609>`__: BUG: SciPy pip install -e gets unusable version spec * `#13610 <https://github.com/scipy/scipy/issues/13610>`__: Highs solver did not provide a solution nor did it report a failure * `#13614 <https://github.com/scipy/scipy/issues/13614>`__: BUG: invgauss.cdf should return the correct value when \`mu\`... * `#13628 <https://github.com/scipy/scipy/issues/13628>`__: 1-letter typo in the definition of scipy.special.spence function... * `#13634 <https://github.com/scipy/scipy/issues/13634>`__: mmwrite fails on dense, skew-symmetric array * `#13646 <https://github.com/scipy/scipy/issues/13646>`__: Sparse matrix argmax() integer overflow on Windows 10 * `#13647 <https://github.com/scipy/scipy/issues/13647>`__: \`scipy.stats.qmc.LatinHypercube\` cannot sample single sample... * `#13651 <https://github.com/scipy/scipy/issues/13651>`__: Documentation wrong in scipy.linalg.eigvalsh * `#13664 <https://github.com/scipy/scipy/issues/13664>`__: BUG: gamma distribution's inverse survival function overflows... * `#13693 <https://github.com/scipy/scipy/issues/13693>`__: BUG: sokalmichener appears to incorrectly apply weights * `#13697 <https://github.com/scipy/scipy/issues/13697>`__: BUG: stats: Spurious warning generated by arcsine.pdf at the... * `#13704 <https://github.com/scipy/scipy/issues/13704>`__: Make it possible to pass a rank cut-off value relatively to the... * `#13707 <https://github.com/scipy/scipy/issues/13707>`__: Kullback Leibler Divergence broadcasting no longer works * `#13740 <https://github.com/scipy/scipy/issues/13740>`__: Scipy.optimize x0 out of bounds when it is within bounds. * `#13744 <https://github.com/scipy/scipy/issues/13744>`__: scipy.interpolate.interp1d has inconsistent behavior for non-unique... * `#13754 <https://github.com/scipy/scipy/issues/13754>`__: optimize.minimize 'trust' methods and finite difference Hessian... * `#13762 <https://github.com/scipy/scipy/issues/13762>`__: MAINT, TST: aarch64 stats test failures showing up in wheels... * `#13769 <https://github.com/scipy/scipy/issues/13769>`__: probplot draws fit line even when fit=False * `#13791 <https://github.com/scipy/scipy/issues/13791>`__: BUG: stats: wrapcauchy.cdf does not broadcast the shape parameter... * `#13793 <https://github.com/scipy/scipy/issues/13793>`__: CI: CircleCI doc build failure * `#13840 <https://github.com/scipy/scipy/issues/13840>`__: manylinux1 builds are failing because of C99 usage in \`special/_cosine.c\` * `#13850 <https://github.com/scipy/scipy/issues/13850>`__: CI: Homebrew is failing due to bintray * `#13875 <https://github.com/scipy/scipy/issues/13875>`__: BUG: chi2_contingency with Yates correction * `#13878 <https://github.com/scipy/scipy/issues/13878>`__: BUG: \`signal.get_window\` argument handling issue * `#13880 <https://github.com/scipy/scipy/issues/13880>`__: Remove all usages of numpy.compat * `#13896 <https://github.com/scipy/scipy/issues/13896>`__: Boschloo's Test for More Powerful Hypothesis Testing of 2x2 Contingency... * `#13923 <https://github.com/scipy/scipy/issues/13923>`__: Inverse of Log CDF of Normal Distribution * `#13933 <https://github.com/scipy/scipy/issues/13933>`__: \`signal.get_window\` does not support \`general_cosine\` and... * `#13950 <https://github.com/scipy/scipy/issues/13950>`__: DOC: scipy.spatial.KDTree.query * `#13969 <https://github.com/scipy/scipy/issues/13969>`__: N=4 must not exceed M=3 * `#13970 <https://github.com/scipy/scipy/issues/13970>`__: Pearson's original paper on chi-square test could be referenced. * `#13984 <https://github.com/scipy/scipy/issues/13984>`__: Faster addition of sparse diagonal matrices * `#13988 <https://github.com/scipy/scipy/issues/13988>`__: An error occurred when using scipy.io.wavfile of scipy 1.6 version... * `#13997 <https://github.com/scipy/scipy/issues/13997>`__: BUG: sparse: Incorrect result from \`dia_matrix.diagonal()\` * `#14005 <https://github.com/scipy/scipy/issues/14005>`__: MAINT: optimize: \`curve_fit\` input error msg can be improved. * `#14038 <https://github.com/scipy/scipy/issues/14038>`__: MAINT: add type annotations for _sobol.pyx * `#14048 <https://github.com/scipy/scipy/issues/14048>`__: DOC: missing git submodule information * `#14055 <https://github.com/scipy/scipy/issues/14055>`__: linalg.solve: Unclear error when using assume_a='her' with real... * `#14093 <https://github.com/scipy/scipy/issues/14093>`__: DOC: Inconsistency in the definition of default values in the... * `#14158 <https://github.com/scipy/scipy/issues/14158>`__: TST, BUG: test_rbfinterp.py -- test_interpolation_misfit_1d fails... * `#14170 <https://github.com/scipy/scipy/issues/14170>`__: TST: signal submodule test_filtfilt_gust failing on 32-bit amd64... * `#14194 <https://github.com/scipy/scipy/issues/14194>`__: MAINT: download-wheels.py missing import * `#14199 <https://github.com/scipy/scipy/issues/14199>`__: Generated sources for biasedurn extension are broken in 1.7.0rc1 ************************** Pull requests for 1.7.0 ************************** * `#4824 <https://github.com/scipy/scipy/pull/4824>`__: Permutation Ttest (new PR) * `#4933 <https://github.com/scipy/scipy/pull/4933>`__: ENH: Update the Mann-Whitney-Wilcoxon test * `#7702 <https://github.com/scipy/scipy/pull/7702>`__: ENH: stats: Add Skewed Cauchy Distribution * `#8306 <https://github.com/scipy/scipy/pull/8306>`__: Optional Pythran support for scipy.signal.max_len_seq_inner * `#10170 <https://github.com/scipy/scipy/pull/10170>`__: MAINT: stats: Implement cdf and ppf as ufuncs for the cosine... * `#10454 <https://github.com/scipy/scipy/pull/10454>`__: ENH: Extend find_peaks_cwt to take numbers and iterables for... * `#10844 <https://github.com/scipy/scipy/pull/10844>`__: ENH: add stats.qmc module with quasi Monte Carlo functionality * `#11313 <https://github.com/scipy/scipy/pull/11313>`__: ENH: add Wright's generalized Bessel function * `#11352 <https://github.com/scipy/scipy/pull/11352>`__: ENH: stats: Add crosstab function. * `#11477 <https://github.com/scipy/scipy/pull/11477>`__: FIX: bounded parameter in cdfchn.f gives bad results * `#11695 <https://github.com/scipy/scipy/pull/11695>`__: ENH: stats: add method of moments to \`rv_continuous.fit\` * `#11911 <https://github.com/scipy/scipy/pull/11911>`__: ENH: Added bounds to boxcox and boxcox_normmax * `#12438 <https://github.com/scipy/scipy/pull/12438>`__: BUG: use ellipkm1 in elliptical filter design to prevent numerical... * `#12531 <https://github.com/scipy/scipy/pull/12531>`__: ENH: stats: add Page's L test * `#12603 <https://github.com/scipy/scipy/pull/12603>`__: ENH: stats: Add \`binomtest\` to replace \`binom_test\`. * `#12653 <https://github.com/scipy/scipy/pull/12653>`__: ENH: stats: add Somers' D test * `#12676 <https://github.com/scipy/scipy/pull/12676>`__: BUG: update median averaging in signal.csd * `#12760 <https://github.com/scipy/scipy/pull/12760>`__: BUG: special: erfinv(x<<1) loses precision * `#12801 <https://github.com/scipy/scipy/pull/12801>`__: ENH: Add single-sided p-values to remaining spearmanr and linregress * `#12873 <https://github.com/scipy/scipy/pull/12873>`__: ENH: Stats: add Alexander Govern Test * `#13008 <https://github.com/scipy/scipy/pull/13008>`__: ENH: Add 'alternative' to functions using normal CDF for p-value * `#13040 <https://github.com/scipy/scipy/pull/13040>`__: BUG: Allow RectSphereBivariateSpline to accept negative longitude * `#13048 <https://github.com/scipy/scipy/pull/13048>`__: ENH: stats: Add a function that computes the relative risk. * `#13067 <https://github.com/scipy/scipy/pull/13067>`__: ENH: Add weights parameter to stats.gmean * `#13084 <https://github.com/scipy/scipy/pull/13084>`__: ENH: fast Hankel transform * `#13104 <https://github.com/scipy/scipy/pull/13104>`__: MAINT: upgrade python version (drop python 3.6) for docker dev... * `#13153 <https://github.com/scipy/scipy/pull/13153>`__: ENH: added association measurements Pearsons Contingency Coefficient,... * `#13166 <https://github.com/scipy/scipy/pull/13166>`__: ENH: stats: Add nan_policy to zmap. * `#13175 <https://github.com/scipy/scipy/pull/13175>`__: MAINT: tests for tall cost matrices in \`linear_sum_assignment\` * `#13177 <https://github.com/scipy/scipy/pull/13177>`__: BUG: raise NotImplementedError in fourier_ellipsoid when ndim... * `#13184 <https://github.com/scipy/scipy/pull/13184>`__: BUG: stats: Fix min and max calculation of mstats.describe with... * `#13188 <https://github.com/scipy/scipy/pull/13188>`__: DOC: stats: make null and alternative hypotheses of kstest more... * `#13193 <https://github.com/scipy/scipy/pull/13193>`__: MAINT: stats: chisquare check sum of observed/expected frequencies * `#13197 <https://github.com/scipy/scipy/pull/13197>`__: ENH/MAINT: HiGHS upstream enhancements and bug fixes * `#13198 <https://github.com/scipy/scipy/pull/13198>`__: ENH: allow inference of output_shape from out array in affine_transform * `#13204 <https://github.com/scipy/scipy/pull/13204>`__: ENH: stats: add Zipfian (different from Zipf/zeta) distribution * `#13208 <https://github.com/scipy/scipy/pull/13208>`__: REL: set version to 1.7.0.dev0 * `#13216 <https://github.com/scipy/scipy/pull/13216>`__: TST: stats: break up and mark slow tests * `#13224 <https://github.com/scipy/scipy/pull/13224>`__: Update docs for the weighted τ * `#13230 <https://github.com/scipy/scipy/pull/13230>`__: ENH: linalg: Add LAPACK wrapper for tgexc. * `#13232 <https://github.com/scipy/scipy/pull/13232>`__: MAINT: stats: raise error when input to kruskal has >1 dim * `#13233 <https://github.com/scipy/scipy/pull/13233>`__: DOC: stats: fix MGF of arcsine and entropy of t in tutorial * `#13236 <https://github.com/scipy/scipy/pull/13236>`__: MAINT: reorganize shared linear assignment tests * `#13237 <https://github.com/scipy/scipy/pull/13237>`__: BENCH: Refactor stats.Distribution to easily add new distributions * `#13238 <https://github.com/scipy/scipy/pull/13238>`__: BUG: stats: fix wrong shape output of burr and fisk distributions * `#13240 <https://github.com/scipy/scipy/pull/13240>`__: MAINT: add tests of trivial cost matrices for linear sum assignment * `#13252 <https://github.com/scipy/scipy/pull/13252>`__: DOC: optimize: add \`optimize.linear_sum_assignment\` tutorial. * `#13254 <https://github.com/scipy/scipy/pull/13254>`__: BUG: Fix precision issues for constant input in skew and kurtosis * `#13262 <https://github.com/scipy/scipy/pull/13262>`__: BUG: scipy.medfilt and .medfilt2d fixes * `#13263 <https://github.com/scipy/scipy/pull/13263>`__: ENH: add Cramer-von Mises test for two samples * `#13264 <https://github.com/scipy/scipy/pull/13264>`__: fix a minor typo in \`stats.anderson\` doc * `#13268 <https://github.com/scipy/scipy/pull/13268>`__: ENH: stats: Add implementation of _entropy for the t distr. * `#13273 <https://github.com/scipy/scipy/pull/13273>`__: DOC: stats: fix typo in Yeo-Johnson LL function documentation * `#13275 <https://github.com/scipy/scipy/pull/13275>`__: MAINT: stats: Correct a comment in the _fitstart method of gamma. * `#13283 <https://github.com/scipy/scipy/pull/13283>`__: BUG: stats: fix the cdf method of rv_discrete class * `#13286 <https://github.com/scipy/scipy/pull/13286>`__: DOC: stats: clairify rv_continuous/discrete.stats example * `#13288 <https://github.com/scipy/scipy/pull/13288>`__: DOC: stats: discrete distribution shape parameter restrictions * `#13289 <https://github.com/scipy/scipy/pull/13289>`__: MAINT: fix a build warning in sigtoolsmodule.c * `#13290 <https://github.com/scipy/scipy/pull/13290>`__: DOC: Expand the discussion of the nan_policy API. * `#13291 <https://github.com/scipy/scipy/pull/13291>`__: MAINT: signal, stats: Use keepdims where appropriate. * `#13292 <https://github.com/scipy/scipy/pull/13292>`__: DOC: stats: note another common parameterization of nbinom * `#13293 <https://github.com/scipy/scipy/pull/13293>`__: DOC: Change broken link for default values to archived link * `#13295 <https://github.com/scipy/scipy/pull/13295>`__: BUG: stats: fix the support method to return correct bounds * `#13296 <https://github.com/scipy/scipy/pull/13296>`__: DOC: stats: Fix latex markup in the kstwo docstring. * `#13297 <https://github.com/scipy/scipy/pull/13297>`__: TST: mark kde.logpdf overflow test as xslow * `#13298 <https://github.com/scipy/scipy/pull/13298>`__: Generalized Hyperbolic Distribution * `#13301 <https://github.com/scipy/scipy/pull/13301>`__: DOC: cluster: Add cluster number note to the docstring of cluster.vq.kmeans * `#13302 <https://github.com/scipy/scipy/pull/13302>`__: BUG: Fix ndimage.morphology.distance_transform\_\* argument handling * `#13303 <https://github.com/scipy/scipy/pull/13303>`__: CI: prevent Codecov giving false CI failures and wrong PR annotations * `#13313 <https://github.com/scipy/scipy/pull/13313>`__: ENH: static typing for qhull * `#13316 <https://github.com/scipy/scipy/pull/13316>`__: Pythran implementation of scipy.signal._spectral * `#13317 <https://github.com/scipy/scipy/pull/13317>`__: DOC: forward port 1.6.0 relnotes * `#13319 <https://github.com/scipy/scipy/pull/13319>`__: ENH: stats: add fast numerical inversion of distribution CDF * `#13320 <https://github.com/scipy/scipy/pull/13320>`__: ENH: x0 for differential_evolution * `#13324 <https://github.com/scipy/scipy/pull/13324>`__: DOC correct linprog highs versionadded to 1.6 * `#13326 <https://github.com/scipy/scipy/pull/13326>`__: MAINT: update numpydoc to v1.1.0 * `#13327 <https://github.com/scipy/scipy/pull/13327>`__: DOC: interpolate: improved docstring examples of \`interpolate.interpn()\`... * `#13328 <https://github.com/scipy/scipy/pull/13328>`__: ENH: Boost stats distributions * `#13330 <https://github.com/scipy/scipy/pull/13330>`__: ENH: stats: add noncentral hypergeometric distributions (Fisher's... * `#13331 <https://github.com/scipy/scipy/pull/13331>`__: MAINT/ENH: resolve mypy warnings/errors * `#13332 <https://github.com/scipy/scipy/pull/13332>`__: DOC: interpolate: improved docstring of \`interpolate.interp2d\`... * `#13333 <https://github.com/scipy/scipy/pull/13333>`__: ENH: stats: Some more _sf and _isf implementations. * `#13334 <https://github.com/scipy/scipy/pull/13334>`__: MAINT: stats: Clean up a few defunct comments in _continuous_distns.py * `#13336 <https://github.com/scipy/scipy/pull/13336>`__: Pythran version of scipy.optimize._group_columns * `#13337 <https://github.com/scipy/scipy/pull/13337>`__: DOC|ENH: type hinting in scipy.integrate.simpson * `#13346 <https://github.com/scipy/scipy/pull/13346>`__: ENH: stats: add 'ddof' parameter to the 'variation' function * `#13355 <https://github.com/scipy/scipy/pull/13355>`__: ENH: stats: implement _logpdf, _sf and _isf for loggamma. * `#13360 <https://github.com/scipy/scipy/pull/13360>`__: ENH|DOC: fix docstring and input validation in interpolate.RectSphereBivariateSpline * `#13366 <https://github.com/scipy/scipy/pull/13366>`__: BUG: stats: Don't raise ZeroDivisionError in _unequal_var_ttest_denom * `#13370 <https://github.com/scipy/scipy/pull/13370>`__: ENH: fix ARGUS distribution for small parameters in stats * `#13371 <https://github.com/scipy/scipy/pull/13371>`__: ENH: stats: add \`bootstrap\` for estimating confidence interval... * `#13373 <https://github.com/scipy/scipy/pull/13373>`__: BUG: io/matlab: preserve dimensions of empty >=2D arrays * `#13374 <https://github.com/scipy/scipy/pull/13374>`__: ENH: stats: add skewed Cauchy distribution * `#13379 <https://github.com/scipy/scipy/pull/13379>`__: BUG: sparse: fix verbosity in sparse lsqr * `#13383 <https://github.com/scipy/scipy/pull/13383>`__: TST: stats: mark many dimension permutation t-test slow * `#13384 <https://github.com/scipy/scipy/pull/13384>`__: MAINT: Make keywords array static * `#13388 <https://github.com/scipy/scipy/pull/13388>`__: PERF: Avoid duplicate mean calculations in skew and kurtosis * `#13389 <https://github.com/scipy/scipy/pull/13389>`__: DOC: Fix deprecated directive syntax * `#13390 <https://github.com/scipy/scipy/pull/13390>`__: DOC: Correct line length for Parameter Section underline * `#13393 <https://github.com/scipy/scipy/pull/13393>`__: MAINT: stats: allow wishart dim - 1 < df < dim * `#13395 <https://github.com/scipy/scipy/pull/13395>`__: DOC: fix typo in setup.py warning message * `#13396 <https://github.com/scipy/scipy/pull/13396>`__: BUG: Fix MLE for Nakagami \`nakagami_gen.fit\` * `#13397 <https://github.com/scipy/scipy/pull/13397>`__: MAINT:linalg: Fix tgsen family wrapper and ordqz * `#13406 <https://github.com/scipy/scipy/pull/13406>`__: TST: add error handling tests for sparse BSR ctor * `#13413 <https://github.com/scipy/scipy/pull/13413>`__: DOC: ultra-quickstart guide * `#13418 <https://github.com/scipy/scipy/pull/13418>`__: BUG: Fix moment returning inconsistent types and shapes * `#13423 <https://github.com/scipy/scipy/pull/13423>`__: DOC: Update example for leaf_label_func/dendrogram * `#13431 <https://github.com/scipy/scipy/pull/13431>`__: ENH: stats: override _rvs for nhypergeom * `#13432 <https://github.com/scipy/scipy/pull/13432>`__: Add indicator in NDInterpolator docstring that N must be > 1 * `#13434 <https://github.com/scipy/scipy/pull/13434>`__: DOC: stats: note relationship between scaled-inv-chi2 and invgamma * `#13436 <https://github.com/scipy/scipy/pull/13436>`__: ENH: interpolate: add input validation to check input x-y is... * `#13441 <https://github.com/scipy/scipy/pull/13441>`__: ENH: add functionality \`barnard_exact\` test to scipy.stats. * `#13443 <https://github.com/scipy/scipy/pull/13443>`__: MAINT: stats: Updates for skewcauchy * `#13444 <https://github.com/scipy/scipy/pull/13444>`__: DOC: clarify range of \`a\` parameter fpr johnsonsu/johnsonsb * `#13445 <https://github.com/scipy/scipy/pull/13445>`__: DOC: fix runtests guidelines. * `#13446 <https://github.com/scipy/scipy/pull/13446>`__: MAINT: stats: Add _fitstart method to wrapcauchy. * `#13447 <https://github.com/scipy/scipy/pull/13447>`__: DEV: Update development Docker image * `#13448 <https://github.com/scipy/scipy/pull/13448>`__: ENH: Add annotations for \`scipy.spatial.distance\` * `#13451 <https://github.com/scipy/scipy/pull/13451>`__: DOC: minor formatting. * `#13458 <https://github.com/scipy/scipy/pull/13458>`__: DOC: indent see also. * `#13460 <https://github.com/scipy/scipy/pull/13460>`__: DOC: stats: Fix link to Cramer-von Mises wikipedia article. * `#13461 <https://github.com/scipy/scipy/pull/13461>`__: DOC: reorganize scipy.stats overview docs page * `#13463 <https://github.com/scipy/scipy/pull/13463>`__: DOC: misc formatting fixes * `#13466 <https://github.com/scipy/scipy/pull/13466>`__: DOC: Typo in see also s/SmoothUni/SmoothBi/g * `#13467 <https://github.com/scipy/scipy/pull/13467>`__: DOC: optimize: add description about \`tol\` argument for \`minimize\`. * `#13469 <https://github.com/scipy/scipy/pull/13469>`__: MAINT: Refactor optimization methods to use scipy.stats.qmc * `#13477 <https://github.com/scipy/scipy/pull/13477>`__: CI: pin numpy to 1.19.5 for the three macOS CI jobs * `#13478 <https://github.com/scipy/scipy/pull/13478>`__: DOC: fix typos where double :: for Sphinx directives were missing * `#13481 <https://github.com/scipy/scipy/pull/13481>`__: CI: pin numpy to 1.19.5 in the 4 parallel Windows builds on Azure * `#13482 <https://github.com/scipy/scipy/pull/13482>`__: CI: use numpy 1.20.0 again in macOS CI * `#13483 <https://github.com/scipy/scipy/pull/13483>`__: DOC: Multiple documentation syntax fixes. * `#13484 <https://github.com/scipy/scipy/pull/13484>`__: Move some pythran config from CI to setup * `#13487 <https://github.com/scipy/scipy/pull/13487>`__: DOC: add a tutorial about scipy.stats.qmc * `#13492 <https://github.com/scipy/scipy/pull/13492>`__: ENH: GH actions should not run on forks * `#13493 <https://github.com/scipy/scipy/pull/13493>`__: DEV: Enable gitpod for SciPy * `#13495 <https://github.com/scipy/scipy/pull/13495>`__: DOC One-word typo in the documentation of optimize.linprog_simplex * `#13499 <https://github.com/scipy/scipy/pull/13499>`__: DOC: describe LSAP implementation * `#13502 <https://github.com/scipy/scipy/pull/13502>`__: BUG: Bounds created with lists weren't working for Powell * `#13507 <https://github.com/scipy/scipy/pull/13507>`__: MAINT, TST: stats: centralize invalid parameters list for all... * `#13510 <https://github.com/scipy/scipy/pull/13510>`__: DOC: stats: fix small doc errors in 'multivariate_hypergeom' * `#13513 <https://github.com/scipy/scipy/pull/13513>`__: DOC: Added math notation in examples in ltisys.py * `#13514 <https://github.com/scipy/scipy/pull/13514>`__: ENH: simplify low_0_bit function for Sobol * `#13515 <https://github.com/scipy/scipy/pull/13515>`__: ENH: optimize: add bound constraint support for nelder-mead solver * `#13516 <https://github.com/scipy/scipy/pull/13516>`__: DOC: reduce LaTeX usage for johnsonb docstring * `#13519 <https://github.com/scipy/scipy/pull/13519>`__: BLD: remove build_sphinx support from setup.py * `#13527 <https://github.com/scipy/scipy/pull/13527>`__: TST: stats: xfail ttest_ind_randperm_alternative2 on 32 bit * `#13530 <https://github.com/scipy/scipy/pull/13530>`__: DOC: correct comparisons between median filter functions * `#13532 <https://github.com/scipy/scipy/pull/13532>`__: ENH: release the GIL inside medfilt2d * `#13538 <https://github.com/scipy/scipy/pull/13538>`__: DOC: optimize: fix minor doc error in 'fmin_powell' (#13511) * `#13546 <https://github.com/scipy/scipy/pull/13546>`__: DOC: fix list of "mode" options for ndimage * `#13549 <https://github.com/scipy/scipy/pull/13549>`__: ENH: stats: add 'alternative' keyword to some normality tests. * `#13551 <https://github.com/scipy/scipy/pull/13551>`__: MAINT: add git to docker env * `#13552 <https://github.com/scipy/scipy/pull/13552>`__: MAINT: stats: remove float_power shim * `#13553 <https://github.com/scipy/scipy/pull/13553>`__: DOC: use support rather than a/b in stats tutorial * `#13560 <https://github.com/scipy/scipy/pull/13560>`__: MAINT: optimize: improve linprog error message for sparse input... * `#13562 <https://github.com/scipy/scipy/pull/13562>`__: MAINT: optimize: using np.isclose instead of _within_tolerance. * `#13566 <https://github.com/scipy/scipy/pull/13566>`__: ENH: Speed up hdquantiles_sd() * `#13569 <https://github.com/scipy/scipy/pull/13569>`__: BENCH: optimize: benchmark only HiGHS methods; add bigger linprog... * `#13574 <https://github.com/scipy/scipy/pull/13574>`__: DOC: In description of cluster.hierarchy.dendrogram 'level' parameter,... * `#13576 <https://github.com/scipy/scipy/pull/13576>`__: ENH: improve discrepancy performance * `#13579 <https://github.com/scipy/scipy/pull/13579>`__: TST: Add pybind11 to tox environments * `#13583 <https://github.com/scipy/scipy/pull/13583>`__: BUG: Fix Dockerfile apt-get installs * `#13588 <https://github.com/scipy/scipy/pull/13588>`__: MAINT: forward port 1.6.1 relnotes. * `#13593 <https://github.com/scipy/scipy/pull/13593>`__: BUG: stats: preserve sample dtype for bin edges * `#13595 <https://github.com/scipy/scipy/pull/13595>`__: ENH: interpolate: add RBFInterpolator * `#13596 <https://github.com/scipy/scipy/pull/13596>`__: DOC: Fix indentation in new_stats_distribution.rst.inc * `#13601 <https://github.com/scipy/scipy/pull/13601>`__: Add dpss for get_window function * `#13604 <https://github.com/scipy/scipy/pull/13604>`__: DOC: Correct dual annealing visiting param range. * `#13605 <https://github.com/scipy/scipy/pull/13605>`__: Add Codecov badge to README * `#13607 <https://github.com/scipy/scipy/pull/13607>`__: MAINT: stats: fix crystalball entropy * `#13611 <https://github.com/scipy/scipy/pull/13611>`__: Better argument preparation for distributions in stats package. * `#13612 <https://github.com/scipy/scipy/pull/13612>`__: Add docker run command for Windows cmd * `#13613 <https://github.com/scipy/scipy/pull/13613>`__: MAINT, CI: mypy: fix typing errors + add mypy to CI * `#13616 <https://github.com/scipy/scipy/pull/13616>`__: FIX: Return correct output for invgauss.cdf when mu is very small * `#13617 <https://github.com/scipy/scipy/pull/13617>`__: MAINT: accept numbers and iterables for width in find_peaks_cwt * `#13620 <https://github.com/scipy/scipy/pull/13620>`__: CI: disable the mypy CI job (partial revert of gh-13613) * `#13621 <https://github.com/scipy/scipy/pull/13621>`__: DOC: signal: use array_like for input types * `#13622 <https://github.com/scipy/scipy/pull/13622>`__: MAINT: clean up some unused files, make \`mypy scipy\` pass * `#13623 <https://github.com/scipy/scipy/pull/13623>`__: CI: enable Mypy CI job again * `#13624 <https://github.com/scipy/scipy/pull/13624>`__: TST: test more values for \`visiting_param\` input to \`dual_annealing\` * `#13625 <https://github.com/scipy/scipy/pull/13625>`__: Rename integrate.simps to integrate.simpsons in documentation... * `#13631 <https://github.com/scipy/scipy/pull/13631>`__: ENH: add a \`stats.differential_entropy\` function * `#13633 <https://github.com/scipy/scipy/pull/13633>`__: BUG: stats.binned_statistic_2d user function expecting arrays * `#13641 <https://github.com/scipy/scipy/pull/13641>`__: ENH: Added degrees parameter to rotvec * `#13645 <https://github.com/scipy/scipy/pull/13645>`__: MAINT: mypy: don't install numpy-stubs * `#13649 <https://github.com/scipy/scipy/pull/13649>`__: BUG: sparse: csc_matrix.argmax() integer overflow * `#13650 <https://github.com/scipy/scipy/pull/13650>`__: ENH: stats: add 'alternative' parameter to ansari * `#13652 <https://github.com/scipy/scipy/pull/13652>`__: DOC: fix eigvalsh documentation (#13651) * `#13654 <https://github.com/scipy/scipy/pull/13654>`__: BUG: Fix LatinHypercubes * `#13656 <https://github.com/scipy/scipy/pull/13656>`__: DOC: Fix PCHIP references * `#13657 <https://github.com/scipy/scipy/pull/13657>`__: TST: remove IPython warning in debug session * `#13658 <https://github.com/scipy/scipy/pull/13658>`__: Remove spurious quotes in docstring * `#13661 <https://github.com/scipy/scipy/pull/13661>`__: ENH: stats: improve efficiency of / fix bug in exact permutation... * `#13667 <https://github.com/scipy/scipy/pull/13667>`__: MAINT: Make latest Docker image default * `#13668 <https://github.com/scipy/scipy/pull/13668>`__: MAINT: add .theia/ to .gitignore * `#13669 <https://github.com/scipy/scipy/pull/13669>`__: BLD: change SCIPY_USE_PYTHRAN default to \`1\` * `#13676 <https://github.com/scipy/scipy/pull/13676>`__: ENH Small improvements for LSQR with damp * `#13678 <https://github.com/scipy/scipy/pull/13678>`__: MAINT: add Pythran-generated files to .gitignore * `#13679 <https://github.com/scipy/scipy/pull/13679>`__: MAINT: move the \`conda develop .\` in the Gitpod config * `#13680 <https://github.com/scipy/scipy/pull/13680>`__: DOC: Add cKDTree note comparing it with KDTree * `#13681 <https://github.com/scipy/scipy/pull/13681>`__: DOC: build doc updates on Pythran, compiled code, and cleanups * `#13683 <https://github.com/scipy/scipy/pull/13683>`__: BUG: mmwrite correctly serializes non skew-symmetric arrays * `#13684 <https://github.com/scipy/scipy/pull/13684>`__: FIX: fix numerical overflow in gamma.isf method * `#13685 <https://github.com/scipy/scipy/pull/13685>`__: BUG: fix cosine distance range to 0-2 * `#13694 <https://github.com/scipy/scipy/pull/13694>`__: MAINT: fix warning emitted when NumPy version is incorrect * `#13696 <https://github.com/scipy/scipy/pull/13696>`__: ENH: support trimming in ttest_ind * `#13698 <https://github.com/scipy/scipy/pull/13698>`__: BUG: stats: Fix spurious warnings generated by arcsine.pdf * `#13701 <https://github.com/scipy/scipy/pull/13701>`__: DEV: scipy.interpolate b-splines (periodic case) * `#13702 <https://github.com/scipy/scipy/pull/13702>`__: DEP: Clean up spent deprecations in spatial.distance * `#13703 <https://github.com/scipy/scipy/pull/13703>`__: MAINT: fix issues found by static code analysis * `#13706 <https://github.com/scipy/scipy/pull/13706>`__: ENH: stats: Implement sf and isf for the laplace distribution. * `#13711 <https://github.com/scipy/scipy/pull/13711>`__: MAINT: stats: fix broadcasting for scipy.stats.entropy * `#13712 <https://github.com/scipy/scipy/pull/13712>`__: BUG: stats: Override _fitstart for the invweibull distribution. * `#13713 <https://github.com/scipy/scipy/pull/13713>`__: DOC: update toolchain.rst to reflect windows universal C runtime * `#13714 <https://github.com/scipy/scipy/pull/13714>`__: MAINT: stats: Remove an unused list from test_continuous_basic.py. * `#13715 <https://github.com/scipy/scipy/pull/13715>`__: MAINT: stats: No need to suppress frechet deprecation warnings. * `#13716 <https://github.com/scipy/scipy/pull/13716>`__: MAINT: use super() as described by PEP 3135 * `#13718 <https://github.com/scipy/scipy/pull/13718>`__: MAINT: new-style class, removing inheritance to object * `#13721 <https://github.com/scipy/scipy/pull/13721>`__: MAINT: add a type-ignore for mpmath (#13721) * `#13723 <https://github.com/scipy/scipy/pull/13723>`__: MAINT: mypy: ignore mpmath imports in mypy.ini * `#13724 <https://github.com/scipy/scipy/pull/13724>`__: DOC: pydata sphinx theme * `#13725 <https://github.com/scipy/scipy/pull/13725>`__: BENCH: add benchmark for Kendalltau * `#13727 <https://github.com/scipy/scipy/pull/13727>`__: CI: simplify Pythran configuration setup for Azure * `#13731 <https://github.com/scipy/scipy/pull/13731>`__: MAINT: stats: Some flake8-driven clean up. * `#13732 <https://github.com/scipy/scipy/pull/13732>`__: ENH: stats: Studentized Range Distribution * `#13735 <https://github.com/scipy/scipy/pull/13735>`__: DOC: correct Voronoi docstring * `#13738 <https://github.com/scipy/scipy/pull/13738>`__: DOC: add example to wright_bessel * `#13739 <https://github.com/scipy/scipy/pull/13739>`__: ENH: stats: Implement _sf and _isf for the chi distribution. * `#13741 <https://github.com/scipy/scipy/pull/13741>`__: MAINT: prevent overwriting of x in minimize * `#13747 <https://github.com/scipy/scipy/pull/13747>`__: DOC: Add note for interp1d for non-unique x-values * `#13749 <https://github.com/scipy/scipy/pull/13749>`__: MAINT: forward port 1.6.2 relnotes * `#13759 <https://github.com/scipy/scipy/pull/13759>`__: MAINT: simpson small performance speedups * `#13765 <https://github.com/scipy/scipy/pull/13765>`__: FIX: npymath missing causing npy_log1p to be unknown * `#13768 <https://github.com/scipy/scipy/pull/13768>`__: BENCH: Add missing pythran dependency * `#13770 <https://github.com/scipy/scipy/pull/13770>`__: ENH: stats.contingency: Add the sparse option to crosstab. * `#13774 <https://github.com/scipy/scipy/pull/13774>`__: DEP: Deprecate squeezing input vectors in spatial.distance * `#13775 <https://github.com/scipy/scipy/pull/13775>`__: Enable trust region methods to use a finite difference Hessian... * `#13777 <https://github.com/scipy/scipy/pull/13777>`__: DOC: Fix Ubuntu/Debian installation instructions * `#13778 <https://github.com/scipy/scipy/pull/13778>`__: DOC: remove references to RandomState * `#13782 <https://github.com/scipy/scipy/pull/13782>`__: MAINT: LBFGSB err msg on MAXLS changed closes #11718 * `#13785 <https://github.com/scipy/scipy/pull/13785>`__: BENCH: Add benchmark for cdist/pdist with weights * `#13786 <https://github.com/scipy/scipy/pull/13786>`__: MAINT: Prepare cdist/pdist for C++ rework * `#13787 <https://github.com/scipy/scipy/pull/13787>`__: MAINT: stats: move entropy and differential_entropy functions... * `#13790 <https://github.com/scipy/scipy/pull/13790>`__: DOC: Add some dependencies for Dockerfile doc of scipy development. * `#13792 <https://github.com/scipy/scipy/pull/13792>`__: BUG: stats: Fix broadcasting in wrapcauchy.cdf * `#13795 <https://github.com/scipy/scipy/pull/13795>`__: MAINT: stats: add hypotests to __all__ in init.py, not stats.py * `#13797 <https://github.com/scipy/scipy/pull/13797>`__: MAINT: stats: probplot: don't plot least-squares fit line unless... * `#13798 <https://github.com/scipy/scipy/pull/13798>`__: MAINT: fix incorrect code comment in \`hierarchy.to_tree\` * `#13802 <https://github.com/scipy/scipy/pull/13802>`__: DEV: add environment.yml file for development with conda/mamba * `#13803 <https://github.com/scipy/scipy/pull/13803>`__: DOC: fix doc build warning about arxiv role already being registered * `#13804 <https://github.com/scipy/scipy/pull/13804>`__: DOC+MAINT: optimize: lb and ub in the Bounds constructor are... * `#13807 <https://github.com/scipy/scipy/pull/13807>`__: MAINT: Dont use parallel Sphinx * `#13808 <https://github.com/scipy/scipy/pull/13808>`__: MAINT: cluster.to_tree: more idiomatic looping over rows of matrix... * `#13810 <https://github.com/scipy/scipy/pull/13810>`__: MAINT: add a CODEOWNERS file * `#13811 <https://github.com/scipy/scipy/pull/13811>`__: MAINT: Add ci skip to azp * `#13814 <https://github.com/scipy/scipy/pull/13814>`__: ENH/DOC: pydata sphinx theme polishing * `#13817 <https://github.com/scipy/scipy/pull/13817>`__: DOC: Misc parameter typo and casing in scipy/linalg/_decomp_ldl.py * `#13818 <https://github.com/scipy/scipy/pull/13818>`__: MAINT: stats: keep \`entropy\` importable from \`scipy.stats.distributions\` * `#13820 <https://github.com/scipy/scipy/pull/13820>`__: BUG: update _kendall_p_exact ValueError to f-string * `#13831 <https://github.com/scipy/scipy/pull/13831>`__: FIX:DEP: Allow better tolerance control for pinv and pinvh and... * `#13832 <https://github.com/scipy/scipy/pull/13832>`__: BUG: stats: Fix rvs for levy_stable when alpha=1 * `#13833 <https://github.com/scipy/scipy/pull/13833>`__: MAINT: Add inline type hintings for stats.qmc * `#13836 <https://github.com/scipy/scipy/pull/13836>`__: MAINT: Fix a couple compiler warnings. * `#13838 <https://github.com/scipy/scipy/pull/13838>`__: TST: relax test tolerances for BinomTest * `#13841 <https://github.com/scipy/scipy/pull/13841>`__: BLD: add \`-std=c99\` flag to scipy.special extensions using... * `#13845 <https://github.com/scipy/scipy/pull/13845>`__: ENH: stats: add \`method\` parameter to \`differential_entropy\`... * `#13847 <https://github.com/scipy/scipy/pull/13847>`__: TST: skip on optimize failure on macOS, mark one as xfail * `#13848 <https://github.com/scipy/scipy/pull/13848>`__: DOC: optimize: move Nelder Mead doc from Unconstrained minimization... * `#13849 <https://github.com/scipy/scipy/pull/13849>`__: DOC: Roadmap update * `#13852 <https://github.com/scipy/scipy/pull/13852>`__: CI: fix temporary wrong brew version from GitHub * `#13854 <https://github.com/scipy/scipy/pull/13854>`__: ENH: Update Scipy Gitpod * `#13859 <https://github.com/scipy/scipy/pull/13859>`__: TST: fix ultra-slow ttest permutations test * `#13860 <https://github.com/scipy/scipy/pull/13860>`__: MAINT: clean up LSAP error checking * `#13863 <https://github.com/scipy/scipy/pull/13863>`__: DOC: remove seed in examples * `#13865 <https://github.com/scipy/scipy/pull/13865>`__: DOC: optimize: The bounds param of differential_evolution is... * `#13866 <https://github.com/scipy/scipy/pull/13866>`__: MAINT: special: Remove an unused variable from _poly_approx in... * `#13867 <https://github.com/scipy/scipy/pull/13867>`__: DOC: stats: Explain meaning of alternatives for fisher_exact. * `#13868 <https://github.com/scipy/scipy/pull/13868>`__: CI: fix the failing job on linux. * `#13870 <https://github.com/scipy/scipy/pull/13870>`__: MAINT: move LSAP rectangular matrix handling into solver code * `#13871 <https://github.com/scipy/scipy/pull/13871>`__: DOC: Add Gitpod documentation * `#13876 <https://github.com/scipy/scipy/pull/13876>`__: Workflow : Add nightly release of NumPy in linux workflows * `#13877 <https://github.com/scipy/scipy/pull/13877>`__: DOC: Conform to numpydoc + uniformity. * `#13879 <https://github.com/scipy/scipy/pull/13879>`__: BUG: signal: fix get_window argument handling and add tests. * `#13881 <https://github.com/scipy/scipy/pull/13881>`__: CI: remove .travis.yml, remove codecov from CircleCI * `#13882 <https://github.com/scipy/scipy/pull/13882>`__: BLD: ensure incrementing dev version strings * `#13886 <https://github.com/scipy/scipy/pull/13886>`__: TST: optimize: skip test_network_flow_limited_capacity w/ UMFPACK... * `#13888 <https://github.com/scipy/scipy/pull/13888>`__: MAINT: Fix issues involving elif conditions * `#13891 <https://github.com/scipy/scipy/pull/13891>`__: Rename InivariateSpline to UnivariateSpline * `#13893 <https://github.com/scipy/scipy/pull/13893>`__: ENH: linprog HiGHS marginals/sensitivy analysis * `#13894 <https://github.com/scipy/scipy/pull/13894>`__: DOC: Add blank line before \`Return\` section. * `#13897 <https://github.com/scipy/scipy/pull/13897>`__: DOC: BLD: fix doc build version check, and improve build time * `#13903 <https://github.com/scipy/scipy/pull/13903>`__: MAINT: Gitpod fixes * `#13907 <https://github.com/scipy/scipy/pull/13907>`__: ENH: Rewrite minkowski metric in C++ with pybind11 * `#13909 <https://github.com/scipy/scipy/pull/13909>`__: Revert "Workflow : Add nightly release of NumPy in linux workflows" * `#13910 <https://github.com/scipy/scipy/pull/13910>`__: DOC: update Readme * `#13911 <https://github.com/scipy/scipy/pull/13911>`__: MAINT: use dict built-in rather than OrderedDict * `#13920 <https://github.com/scipy/scipy/pull/13920>`__: BUG: Reactivate conda environment in init * `#13925 <https://github.com/scipy/scipy/pull/13925>`__: BUG: stats: magnitude of Yates' correction <= abs(observed-expected)... * `#13926 <https://github.com/scipy/scipy/pull/13926>`__: DOC: correct return type in disjoint_set.subsets docstring * `#13927 <https://github.com/scipy/scipy/pull/13927>`__: DOC/MAINT: Add copyright notice to qmc.primes_from_2_to * `#13928 <https://github.com/scipy/scipy/pull/13928>`__: BUG: DOC: signal: fix need argument config and add missing doc... * `#13929 <https://github.com/scipy/scipy/pull/13929>`__: REL: add PEP 621 (project metadata in pyproject.toml) support * `#13931 <https://github.com/scipy/scipy/pull/13931>`__: MAINT: special: get rid of _logit.c.src * `#13934 <https://github.com/scipy/scipy/pull/13934>`__: ENH: signal: make \`get_window\` supports \`general_cosine\`... * `#13940 <https://github.com/scipy/scipy/pull/13940>`__: MAINT: QMCEngine d input validation * `#13941 <https://github.com/scipy/scipy/pull/13941>`__: MAINT: forward port 1.6.3 relnotes * `#13944 <https://github.com/scipy/scipy/pull/13944>`__: BUG: spatial: fix weight handling of \`distance.sokalmichener\`. * `#13947 <https://github.com/scipy/scipy/pull/13947>`__: MAINT: Remove duplicate calculations in sokalmichener * `#13949 <https://github.com/scipy/scipy/pull/13949>`__: DOC: minor grammar fixes in minimize and KDTree.query * `#13951 <https://github.com/scipy/scipy/pull/13951>`__: ENH: Add Boschloo exact test to stats * `#13956 <https://github.com/scipy/scipy/pull/13956>`__: ENH: spatial: add \`axis\` and \`keepdims\` optional argument... * `#13963 <https://github.com/scipy/scipy/pull/13963>`__: MAINT: stats: Fix unused imports and a few other issues related... * `#13971 <https://github.com/scipy/scipy/pull/13971>`__: DOC: Add Karl Pearson's reference to chi-square test * `#13972 <https://github.com/scipy/scipy/pull/13972>`__: ENH: cluster: add an optional argument \`seed\` for \`kmeans\`... * `#13973 <https://github.com/scipy/scipy/pull/13973>`__: BLD: fix build warnings for causal/anticausal pointers in ndimage * `#13975 <https://github.com/scipy/scipy/pull/13975>`__: ENH: set empty array norm to zero. * `#13977 <https://github.com/scipy/scipy/pull/13977>`__: MAINT: signal: replace distutils templating with tempita * `#13978 <https://github.com/scipy/scipy/pull/13978>`__: MAINT: improve validations and keyword only arguments for some... * `#13979 <https://github.com/scipy/scipy/pull/13979>`__: ENH: Add Inverse of Log CDF of Normal Distribution * `#13983 <https://github.com/scipy/scipy/pull/13983>`__: Fixing \`ndimage.watershed_ift\` tutorial's documentation * `#13987 <https://github.com/scipy/scipy/pull/13987>`__: DOC: Adding examples to docstrings in morphology: white_tophat,... * `#13989 <https://github.com/scipy/scipy/pull/13989>`__: DOC: interpolate: improve examples of \`RegularGridInterpolator\`... * `#13990 <https://github.com/scipy/scipy/pull/13990>`__: MAINT, DOC: optimize: Make the input validation explanation clear... * `#13992 <https://github.com/scipy/scipy/pull/13992>`__: Workflow : Add nightly release of NumPy in linux workflows * `#13995 <https://github.com/scipy/scipy/pull/13995>`__: Doc: Continuous integration information * `#14000 <https://github.com/scipy/scipy/pull/14000>`__: BUG: sparse: Fix DIA.diagonal bug and add a regression test * `#14004 <https://github.com/scipy/scipy/pull/14004>`__: ENH: Fast addition dia matrix * `#14006 <https://github.com/scipy/scipy/pull/14006>`__: MAINT: optimize: add validation to check func parameter number... * `#14008 <https://github.com/scipy/scipy/pull/14008>`__: BUG: Raise exception for inconsistent WAV header * `#14009 <https://github.com/scipy/scipy/pull/14009>`__: DEP: Remove usage of numpy.compat * `#14010 <https://github.com/scipy/scipy/pull/14010>`__: MAINT: add support for wheel DL proxy * `#14012 <https://github.com/scipy/scipy/pull/14012>`__: DOC: Broaden Exact Test Reference * `#14015 <https://github.com/scipy/scipy/pull/14015>`__: MAINT: remove brew update * `#14017 <https://github.com/scipy/scipy/pull/14017>`__: BENCH: Add more formats for sparse arithmetic * `#14018 <https://github.com/scipy/scipy/pull/14018>`__: BENCH: add benchmark for f_oneway * `#14020 <https://github.com/scipy/scipy/pull/14020>`__: MAINT: modify np.int\_ to np.int32 to make it the same for 32/64... * `#14023 <https://github.com/scipy/scipy/pull/14023>`__: MAINT: Fix clang build and remove some unicode characters * `#14025 <https://github.com/scipy/scipy/pull/14025>`__: BUG: sparse: fix DIA.setdiag issue * `#14026 <https://github.com/scipy/scipy/pull/14026>`__: TST: optimize: xfail part of test_powell * `#14029 <https://github.com/scipy/scipy/pull/14029>`__: CI: github macos fix * `#14030 <https://github.com/scipy/scipy/pull/14030>`__: MAINT: use 'yield from <expr>' (PEP 380) * `#14031 <https://github.com/scipy/scipy/pull/14031>`__: MAINT: new-style class, removing inheritance to object * `#14032 <https://github.com/scipy/scipy/pull/14032>`__: MAINT: CXXFLAGS for Pythran * `#14033 <https://github.com/scipy/scipy/pull/14033>`__: ENH: Port sqeuclidean and braycurtis to _distance_pybind * `#14034 <https://github.com/scipy/scipy/pull/14034>`__: MAINT: Clean-up 'next = __next__' * `#14045 <https://github.com/scipy/scipy/pull/14045>`__: MAINT: bump PYVER pavement.py * `#14047 <https://github.com/scipy/scipy/pull/14047>`__: DEV: initialize boost submodule in Gitpod Dockerfile * `#14051 <https://github.com/scipy/scipy/pull/14051>`__: BLD: if boost submodule content is missing, error out early * `#14052 <https://github.com/scipy/scipy/pull/14052>`__: DOC: missing submodule init information * `#14057 <https://github.com/scipy/scipy/pull/14057>`__: DOC: special: Add Examples to \`psi\` docstring * `#14058 <https://github.com/scipy/scipy/pull/14058>`__: BUG: fixed a dtype bug in linalg.solve. * `#14060 <https://github.com/scipy/scipy/pull/14060>`__: Doc: Fix typo in documentation of spence function. * `#14061 <https://github.com/scipy/scipy/pull/14061>`__: MAINT:stats: Type annotations for _sobol.pyx * `#14062 <https://github.com/scipy/scipy/pull/14062>`__: DOC: A few small fixes in quickstart_gitpod.rst * `#14063 <https://github.com/scipy/scipy/pull/14063>`__: DOC: signal: add Add Examples to \`cont2discrete\` docstring * `#14064 <https://github.com/scipy/scipy/pull/14064>`__: DOC: optimize: Add Examples to fmin_bfgs docstring * `#14065 <https://github.com/scipy/scipy/pull/14065>`__: Add example for scipy stats.trim1 under docstring * `#14066 <https://github.com/scipy/scipy/pull/14066>`__: DOC add example to scipy.special.hermite * `#14067 <https://github.com/scipy/scipy/pull/14067>`__: DOC add alpha docstring description, add example to docstring * `#14070 <https://github.com/scipy/scipy/pull/14070>`__: DOC add parameters, return, and example to docstring * `#14072 <https://github.com/scipy/scipy/pull/14072>`__: MAINT/TST: Fix tests failing with the nightly build of numpy. * `#14075 <https://github.com/scipy/scipy/pull/14075>`__: DOC Improve the code snippet in signal.hilbert docstring. * `#14076 <https://github.com/scipy/scipy/pull/14076>`__: DOC: Document Jensen-Shannon distance being accepted by cdist/pdist * `#14079 <https://github.com/scipy/scipy/pull/14079>`__: BLD: Avoid importing scipy.stats during cythonize stage * `#14082 <https://github.com/scipy/scipy/pull/14082>`__: MAINT: Remove old, commented extract_diagonal * `#14083 <https://github.com/scipy/scipy/pull/14083>`__: MAINT: sparse: Remove defunct function extract_diagonal * `#14085 <https://github.com/scipy/scipy/pull/14085>`__: ENH: Implement canberra distance in _distance_pybind * `#14086 <https://github.com/scipy/scipy/pull/14086>`__: MAINT: Clear scipy namespace of entries better imported from... * `#14088 <https://github.com/scipy/scipy/pull/14088>`__: Install Pythran from sources for python 3.10 * `#14092 <https://github.com/scipy/scipy/pull/14092>`__: BUG: Fixes issue with clang. * `#14094 <https://github.com/scipy/scipy/pull/14094>`__: DOC: Correct the inconsistence definition of Default in class... * `#14105 <https://github.com/scipy/scipy/pull/14105>`__: TST: stats: mannwhitneyu: check that mstats and stats mannwhitneyu... * `#14106 <https://github.com/scipy/scipy/pull/14106>`__: DOC: stats.mstats: mannwhitneyu: the returned statistic is the... * `#14107 <https://github.com/scipy/scipy/pull/14107>`__: ENH: stats: bootstrap: add \`vectorized\` parameter; automatically... * `#14109 <https://github.com/scipy/scipy/pull/14109>`__: BUG: fix two issues in the fblas signature files * `#14110 <https://github.com/scipy/scipy/pull/14110>`__: DOC: mailmap update * `#14113 <https://github.com/scipy/scipy/pull/14113>`__: ENH: stats: bootstrap: add \`paired\` parameter * `#14116 <https://github.com/scipy/scipy/pull/14116>`__: MAINT: fix deprecated Python C API usage in odr * `#14118 <https://github.com/scipy/scipy/pull/14118>`__: DOC: 1.7.0 release notes * `#14125 <https://github.com/scipy/scipy/pull/14125>`__: DOC: fix typo * `#14126 <https://github.com/scipy/scipy/pull/14126>`__: ENH: stats: bootstrap: add \`batch\` parameter to control batch... * `#14127 <https://github.com/scipy/scipy/pull/14127>`__: CI: upgrade pip in benchmarks CI run * `#14130 <https://github.com/scipy/scipy/pull/14130>`__: BUG: Fix trust-constr report TypeError if verbose is set to 2... * `#14133 <https://github.com/scipy/scipy/pull/14133>`__: MAINT: interpolate: raise NotImplementedError not ValueError * `#14139 <https://github.com/scipy/scipy/pull/14139>`__: FIX/DOC: lsqr doctests print failure * `#14145 <https://github.com/scipy/scipy/pull/14145>`__: MAINT: 1.7.x version pins ("backport") * `#14146 <https://github.com/scipy/scipy/pull/14146>`__: MAINT: commit count if no tag * `#14164 <https://github.com/scipy/scipy/pull/14164>`__: TST, BUG: fix rbf matrix value * `#14166 <https://github.com/scipy/scipy/pull/14166>`__: CI, MAINT: restrictions on pre-release CI * `#14171 <https://github.com/scipy/scipy/pull/14171>`__: TST: signal: Bump tolerances for a test of Gustafsson's... * `#14175 <https://github.com/scipy/scipy/pull/14175>`__: TST: stats: Loosen tolerance in some binomtest tests. * `#14182 <https://github.com/scipy/scipy/pull/14182>`__: MAINT: stats: Update ppcc_plot and ppcc_max docstring. * `#14195 <https://github.com/scipy/scipy/pull/14195>`__: MAINT: download-wheels missing import * `#14230 <https://github.com/scipy/scipy/pull/14230>`__: REL: stop shipping generated Cython sources in sdist Checksums ========= MD5 ~~~ 276042cf01da2970b83883375b036eef scipy-1.7.0-cp37-cp37m-macosx_10_9_x86_64.whl 8149ae5442d3ca11d477893b9797b565 scipy-1.7.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 32d249d21ec09fe351b471cd578a54bd scipy-1.7.0-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl 6f9b11e29d59e276729ec706c38961e2 scipy-1.7.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl c4b23f53f47888744713a25000ed73fd scipy-1.7.0-cp37-cp37m-win32.whl 767b17455eba48cbe3949a4a8609d9e7 scipy-1.7.0-cp37-cp37m-win_amd64.whl ac0f5c087893240b13a78dbc80e002e1 scipy-1.7.0-cp38-cp38-macosx_10_9_x86_64.whl e2e369078c6b7ca29c952cb9971bc154 scipy-1.7.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 2f4d2c55937133983031428405ef50e5 scipy-1.7.0-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl 092c9b3117c2acc378be46fac846b088 scipy-1.7.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl 08a560d8f936ea64d65471382d829b43 scipy-1.7.0-cp38-cp38-win32.whl 330c71d5ae61a6f1a96573ee5e2dc536 scipy-1.7.0-cp38-cp38-win_amd64.whl 535e0df93c3005acb69cf32eed57e5d7 scipy-1.7.0-cp39-cp39-macosx_10_9_x86_64.whl 003d015e6c75d683f8e27e80d731f782 scipy-1.7.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 9306001377da7b018ac0215eed2ba022 scipy-1.7.0-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl ed943492a5f97a086c96b6d158028ba4 scipy-1.7.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl 89499df789ff766d6140ab50b8a56745 scipy-1.7.0-cp39-cp39-win32.whl daf4ab11d37576bd792ece587e8f7ae6 scipy-1.7.0-cp39-cp39-win_amd64.whl 8776cb3e803f07c74ddf1045eb177904 scipy-1.7.0.tar.gz a0690bb8aa427fc0a3a59946b532763c scipy-1.7.0.tar.xz f1f1970a34948e59b37e9706a3dfca0e scipy-1.7.0.zip SHA256 ~~~~~~ 821e75f5c16cd7b0ab0ffe7eb9917e5af7b48c25306b4777287de8d792a5f7f3 scipy-1.7.0-cp37-cp37m-macosx_10_9_x86_64.whl 3e7df79b42c3015058a5554bfeab6fd4c9906c46560c9ddebb5c652840f3e182 scipy-1.7.0-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 0572256c10ddd058e3d315c555538671ddb2737f27eb56189bfbc3483391403f scipy-1.7.0-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl b77ee5e3a9507622e7f98b16122242a3903397f98d1fe3bc269d904a9025e2bc scipy-1.7.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl 53116abd5060a5b4a58489cf689bee259b779e6b7ecd4ce366e7147aa7c9626e scipy-1.7.0-cp37-cp37m-win32.whl e7b733d4d98e604109715e11f2ab9340eb45d53f803634ed730039070fc3bc11 scipy-1.7.0-cp37-cp37m-win_amd64.whl 4ef3d4df8af40cb6f4d4eaf7b02780109ebabeec334cda26a7899ec9d8de9176 scipy-1.7.0-cp38-cp38-macosx_10_9_x86_64.whl bd4399d4388ca0239a4825e312b3e61b60f743dd6daf49e5870837716502a92a scipy-1.7.0-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 80df8af7039bce92fb4cd1ceb056258631b11b3c627384e2d29bb48d44c0cae7 scipy-1.7.0-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl 6130e22bf6ee506f7cddde7e0515296d97eb6c6c94f7ef5103c2b77aec5833a7 scipy-1.7.0-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl 97ca4552ace1c313707058e774609af59644321e278c3a539322fab2fb09b943 scipy-1.7.0-cp38-cp38-win32.whl c5d012cb82cc1dcfa72609abaabb4a4ed8113e3e8ac43464508a418c146be57d scipy-1.7.0-cp38-cp38-win_amd64.whl 5eb8f054eebb351af7490bbb57465ba9662c4e16e1786655c6c7ed530eb9a74e scipy-1.7.0-cp39-cp39-macosx_10_9_x86_64.whl 7f4b89c223bd09460b52b669e2e642cab73c28855b540e6ed029692546a86f8d scipy-1.7.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 2e685fdbfa5b989af4338b29c408b9157ea6addec15d661104c437980c292be5 scipy-1.7.0-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl 3595c8b64970c9e5a3f137fa1a9eb64da417e78fb7991d0b098b18a00b776d88 scipy-1.7.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl 5a983d3cebc27294897951a494cebd78af2eae37facf75d9e4ad4f1f62229860 scipy-1.7.0-cp39-cp39-win32.whl aef6e922aea6f2e6bbb539b413c85210a9ee32757535b84204ebd22723e69704 scipy-1.7.0-cp39-cp39-win_amd64.whl 998c5e6ea649489302de2c0bc026ed34284f531df89d2bdc8df3a0d44d165739 scipy-1.7.0.tar.gz 0564d1091b8db03418356f0839cc4bf73b9bf7cd1089586eb690208e1f44bb8d scipy-1.7.0.tar.xz 3a0ec7390c491140551f6493611a30605144a4d47c0410e81f49921ada026993 scipy-1.7.0.zip

3 3

A proposal on adding new TFQMR algorithm
by 赵刚 June 20, 2021

June 20, 2021

Dear all, I have submitted an python implementation of the sparse linear iterative algorithm "Transpose-Free QMR" (https://github.com/scipy/scipy/pull/14160). This algorithm (cited by 904) is very effective to solve non-Hermitian linear systems because it has a smoother convergence curve than the other algorithms like CGS, Bi-CGSTAB, and it has been widely used in those prominent scientific computing packages such as PETSc etc. The purpose of adding the algorithm is to enrich SciPy's sparse linear library, so that users can have more/better choices when using Krylov subspace methods in SciPy to solve linear systems. I also hope that experts in this field can review the implementation of the algorithm (References are listed in "tfqmr.py"). Hope you like it. Thanks, Gang

2 1

PR: addition of Tukey's HSD test
by Sam Wallan June 17, 2021

June 17, 2021

Hello All, The PR gh-13002 <https://github.com/scipy/scipy/pull/13002> implements Tukey’s Honestly Significant Difference Test, a multiple sample test used to find pairs of means that are significantly different from each other. We’d appreciate your thoughts! The test reports the pairwise differences, p-values, and confidence intervals in separate attribute arrays of shape (n, n). This allows the client to access their desired results programmatically, which is not nearly as easy in other programs. There are a few areas with which extra input would be helpful. Specifically: - output interface - __str__ / __repr__ methods - confidence interval method More details are in the PR. Many thanks, Sam

1 0

ANN: SciPy 1.7.0rc2 -- please test
by Tyler Reddy June 14, 2021

June 14, 2021

Hi all, On behalf of the SciPy development team I'm pleased to announce the release candidate SciPy 1.7.0rc2. Please help us test this pre-release, which notably no longer includes Cython- generated C source files in the sdist. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.7.0rc2 <https://github.com/scipy/scipy/releases/tag/v1.7.0rc1> One of a few ways to install the release candidate with pip: pip install scipy==1.7.0rc2 ===================== SciPy 1.7.0 Release Notes ===================== Note: Scipy 1.7.0 is not released yet! SciPy 1.7.0 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 1.7.x branch, and on adding new features on the master branch. This release requires Python 3.7+ and NumPy 1.16.5 or greater. For running on PyPy, PyPy3 6.0+ is required. **************************** Highlights of this release **************************** - A new submodule for quasi-Monte Carlo, `scipy.stats.qmc`, was added - The documentation design was updated to use the same PyData-Sphinx theme as other NumFOCUS packages like NumPy. - We now vendor and leverage the Boost C++ library to enable numerous improvements for long-standing weaknesses in `scipy.stats` - `scipy.stats` has six new distributions, eight new (or overhauled) hypothesis tests, a new function for bootstrapping, a class that enables fast random variate sampling and percentile point function evaluation, and many other enhancements. - ``cdist`` and ``pdist`` distance calculations are faster for several metrics, especially weighted cases, thanks to a rewrite to a new C++ backend framework - A new class for radial basis function interpolation, `RBFInterpolator`, was added to address issues with the `Rbf` class. We gratefully acknowledge the Chan-Zuckerberg Initiative Essential Open Source Software for Science program for supporting many of the improvements to `scipy.stats`. *************** New features *************** `scipy.cluster` improvements ====================== An optional argument, ``seed``, has been added to ``kmeans`` and ``kmeans2`` to set the random generator and random state. `scipy.interpolate` improvements ========================= Improved input validation and error messages for ``fitpack.bispev`` and ``fitpack.parder`` for scenarios that previously caused substantial confusion for users. The class `RBFInterpolator` was added to supersede the `Rbf` class. The new class has usage that more closely follows other interpolator classes, corrects sign errors that caused unexpected smoothing behavior, includes polynomial terms in the interpolant (which are necessary for some RBF choices), and supports interpolation using only the k-nearest neighbors for memory efficiency. `scipy.linalg` improvements ===================== An LAPACK wrapper was added for access to the ``tgexc`` subroutine. `scipy.ndimage` improvements ======================== `scipy.ndimage.affine_transform` is now able to infer the ``output_shape`` from the ``out`` array. `scipy.optimize` improvements ======================= The optional parameter ``bounds`` was added to ``_minimize_neldermead`` to support bounds constraints for the Nelder-Mead solver. ``trustregion`` methods ``trust-krylov``, ``dogleg`` and ``trust-ncg`` can now estimate ``hess`` by finite difference using one of ``["2-point", "3-point", "cs"]``. ``halton`` was added as a ``sampling_method`` in `scipy.optimize.shgo`. ``sobol`` was fixed and is now using `scipy.stats.qmc.Sobol`. ``halton`` and ``sobol`` were added as ``init`` methods in `scipy.optimize.differential_evolution.` ``differential_evolution`` now accepts an ``x0`` parameter to provide an initial guess for the minimization. ``least_squares`` has a modest performance improvement when SciPy is built with Pythran transpiler enabled. When ``linprog`` is used with ``method`` ``'highs'``, ``'highs-ipm'``, or ``'highs-ds'``, the result object now reports the marginals (AKA shadow prices, dual values) and residuals associated with each constraint. `scipy.signal` improvements ====================== ``get_window`` supports ``general_cosine`` and ``general_hamming`` window functions. `scipy.signal.medfilt2d` now releases the GIL where appropriate to enable performance gains via multithreaded calculations. `scipy.sparse` improvements ====================== Addition of ``dia_matrix`` sparse matrices is now faster. `scipy.spatial` improvements ====================== ``distance.cdist`` and ``distance.pdist`` performance has greatly improved for certain weighted metrics. Namely: ``minkowski``, ``euclidean``, ``chebyshev``, ``canberra``, and ``cityblock``. Modest performance improvements for many of the unweighted ``cdist`` and ``pdist`` metrics noted above. The parameter ``seed`` was added to `scipy.spatial.vq.kmeans` and `scipy.spatial.vq.kmeans2`. The parameters ``axis`` and ``keepdims`` where added to `scipy.spatial.distance.jensenshannon`. The ``rotation`` methods ``from_rotvec`` and ``as_rotvec`` now accept a ``degrees`` argument to specify usage of degrees instead of radians. `scipy.special` improvements ====================== Wright's generalized Bessel function for positive arguments was added as `scipy.special.wright_bessel.` An implementation of the inverse of the Log CDF of the Normal Distribution is now available via `scipy.special.ndtri_exp`. `scipy.stats` improvements ==================== Hypothesis Tests ------------------------ The Mann-Whitney-Wilcoxon test, ``mannwhitneyu``, has been rewritten. It now supports n-dimensional input, an exact test method when there are no ties, and improved documentation. Please see "Other changes" for adjustments to default behavior. The new function `scipy.stats.binomtest` replaces `scipy.stats.binom_test`. The new function returns an object that calculates a confidence intervals of the proportion parameter. Also, performance was improved from O(n) to O(log(n)) by using binary search. The two-sample version of the Cramer-von Mises test is implemented in `scipy.stats.cramervonmises_2samp`. The Alexander-Govern test is implemented in the new function `scipy.stats.alexandergovern`. The new functions `scipy.stats.barnard_exact` and `scipy.stats. boschloo_exact` respectively perform Barnard's exact test and Boschloo's exact test for 2x2 contingency tables. The new function `scipy.stats.page_trend_test` performs Page's test for ordered alternatives. The new function `scipy.stats.somersd` performs Somers' D test for ordinal association between two variables. An option, ``permutations``, has been added in `scipy.stats.ttest_ind` to perform permutation t-tests. A ``trim`` option was also added to perform a trimmed (Yuen's) t-test. The ``alternative`` parameter was added to the ``skewtest``, ``kurtosistest``, ``ranksums``, ``mood``, ``ansari``, ``linregress``, and ``spearmanr`` functions to allow one-sided hypothesis testing. Sample statistics ----------------------- The new function `scipy.stats.differential_entropy` estimates the differential entropy of a continuous distribution from a sample. The ``boxcox`` and ``boxcox_normmax`` now allow the user to control the optimizer used to minimize the negative log-likelihood function. A new function `scipy.stats.contingency.relative_risk` calculates the relative risk, or risk ratio, of a 2x2 contingency table. The object returned has a method to compute the confidence interval of the relative risk. Performance improvements in the ``skew`` and ``kurtosis`` functions achieved by removal of repeated/redundant calculations. Substantial performance improvements in `scipy.stats.mstats.hdquantiles_sd`. The new function `scipy.stats.contingency.association` computes several measures of association for a contingency table: Pearsons contingency coefficient, Cramer's V, and Tschuprow's T. The parameter ``nan_policy`` was added to `scipy.stats.zmap` to provide options for handling the occurrence of ``nan`` in the input data. The parameter ``ddof`` was added to `scipy.stats.variation` and `scipy.stats.mstats.variation`. The parameter ``weights`` was added to `scipy.stats.gmean`. Statistical Distributions ------------------------------- We now vendor and leverage the Boost C++ library to address a number of previously reported issues in ``stats``. Notably, ``beta``, ``binom``, ``nbinom`` now have Boost backends, and it is straightforward to leverage the backend for additional functions. The skew Cauchy probability distribution has been implemented as `scipy.stats.skewcauchy`. The Zipfian probability distribution has been implemented as `scipy.stats.zipfian`. The new distributions ``nchypergeom_fisher`` and ``nchypergeom_wallenius`` implement the Fisher and Wallenius versions of the noncentral hypergeometric distribution, respectively. The generalized hyperbolic distribution was added in `scipy.stats.genhyperbolic`. The studentized range distribution was added in `scipy.stats.studentized_range`. `scipy.stats.argus` now has improved handling for small parameter values. Better argument handling/preparation has resulted in performance improvements for many distributions. The ``cosine`` distribution has added ufuncs for ``ppf``, ``cdf``, ``sf``, and ``isf`` methods including numerical precision improvements at the edges of the support of the distribution. An option to fit the distribution to data by the method of moments has been added to the ``fit`` method of the univariate continuous distributions. Other -------- `scipy.stats.bootstrap` has been added to allow estimation of the confidence interval and standard error of a statistic. The new function `scipy.stats.contingency.crosstab` computes a contingency table (i.e. a table of counts of unique entries) for the given data. `scipy.stats.NumericalInverseHermite` enables fast random variate sampling and percentile point function evaluation of an arbitrary univariate statistical distribution. New `scipy.stats.qmc` module ----------------------------------------- This new module provides Quasi-Monte Carlo (QMC) generators and associated helper functions. It provides a generic class `scipy.stats.qmc.QMCEngine` which defines a QMC engine/sampler. An engine is state aware: it can be continued, advanced and reset. 3 base samplers are available: - `scipy.stats.qmc.Sobol` the well known Sobol low discrepancy sequence. Several warnings have been added to guide the user into properly using this sampler. The sequence is scrambled by default. - `scipy.stats.qmc.Halton`: Halton low discrepancy sequence. The sequence is scrambled by default. - `scipy.stats.qmc.LatinHypercube`: plain LHS design. And 2 special samplers are available: - `scipy.stats.qmc.MultinomialQMC`: sampling from a multinomial distribution using any of the base `scipy.stats.qmc.QMCEngine`. - `scipy.stats.qmc.MultivariateNormalQMC`: sampling from a multivariate Normal using any of the base `scipy.stats.qmc.QMCEngine`. The module also provide the following helpers: - `scipy.stats.qmc.discrepancy`: assess the quality of a set of points in terms of space coverage. - `scipy.stats.qmc.update_discrepancy`: can be used in an optimization loop to construct a good set of points. - `scipy.stats.qmc.scale`: easily scale a set of points from (to) the unit interval to (from) a given range. ************************ Deprecated features ************************ `scipy.linalg` deprecations ==================== - `scipy.linalg.pinv2` is deprecated and its functionality is completely subsumed into `scipy.linalg.pinv` - Both ``rcond``, ``cond`` keywords of `scipy.linalg.pinv` and `scipy.linalg.pinvh` were not working and now are deprecated. They are now replaced with functioning ``atol`` and ``rtol`` keywords with clear usage. `scipy.spatial` deprecations ===================== - `scipy.spatial.distance` metrics expect 1d input vectors but will call ``np.squeeze`` on their inputs to accept any extra length-1 dimensions. That behaviour is now deprecated. ****************** Other changes ****************** We now accept and leverage performance improvements from the ahead-of-time Python-to-C++ transpiler, Pythran, which can be optionally disabled (via ``export SCIPY_USE_PYTHRAN=0``) but is enabled by default at build time. There are two changes to the default behavior of `scipy.stats.mannwhitenyu`: - For years, use of the default ``alternative=None`` was deprecated; explicit ``alternative`` specification was required. Use of the new default value of ``alternative``, "two-sided", is now permitted. - Previously, all p-values were based on an asymptotic approximation. Now, for small samples without ties, the p-values returned are exact by default. Support has been added for PEP 621 (project metadata in ``pyproject.toml``) We now support a Gitpod environment to reduce the barrier to entry for SciPy development; for more details see :ref:`quickstart-gitpod`. ********* Authors ********* * @endolith * Jelle Aalbers + * Adam + * Tania Allard + * Sven Baars + * Max Balandat + * baumgarc + * Christoph Baumgarten * Peter Bell * Lilian Besson * Robinson Besson + * Max Bolingbroke * Blair Bonnett + * Jordão Bragantini * Harm Buisman + * Evgeni Burovski * Matthias Bussonnier * Dominic C * CJ Carey * Ramón Casero + * Chachay + * charlotte12l + * Benjamin Curtice Corbett + * Falcon Dai + * Ian Dall + * Terry Davis * droussea2001 + * DWesl + * dwight200 + * Thomas J. Fan + * Joseph Fox-Rabinovitz * Max Frei + * Laura Gutierrez Funderburk + * gbonomib + * Matthias Geier + * Pradipta Ghosh + * Ralf Gommers * Evan H + * h-vetinari * Matt Haberland * Anselm Hahn + * Alex Henrie * Piet Hessenius + * Trever Hines + * Elisha Hollander + * Stephan Hoyer * Tom Hu + * Kei Ishikawa + * Julien Jerphanion * Robert Kern * Shashank KS + * Peter Mahler Larsen * Eric Larson * Cheng H. Lee + * Gregory R. Lee * Jean-Benoist Leger + * lgfunderburk + * liam-o-marsh + * Xingyu Liu + * Alex Loftus + * Christian Lorentzen + * Cong Ma * Marc + * MarkPundurs + * Markus Löning + * Liam Marsh + * Nicholas McKibben * melissawm + * Jamie Morton * Andrew Nelson * Nikola Forró * Tor Nordam + * Olivier Gauthé + * Rohit Pandey + * Avanindra Kumar Pandeya + * Tirth Patel * paugier + * Alex H. Wagner, PhD + * Jeff Plourde + * Ilhan Polat * pranavrajpal + * Vladyslav Rachek * Bharat Raghunathan * Recursing + * Tyler Reddy * Lucas Roberts * Gregor Robinson + * Pamphile Roy + * Atsushi Sakai * Benjamin Santos * Martin K. Scherer + * Thomas Schmelzer + * Daniel Scott + * Sebastian Wallkötter + * serge-sans-paille + * Namami Shanker + * Masashi Shibata + * Alexandre de Siqueira + * Albert Steppi + * Adam J. Stewart + * Kai Striega * Diana Sukhoverkhova * Søren Fuglede Jørgensen * Mike Taves * Dan Temkin + * Nicolas Tessore + * tsubota20 + * Robert Uhl * christos val + * Bas van Beek + * Ashutosh Varma + * Jose Vazquez + * Sebastiano Vigna * Aditya Vijaykumar * VNMabus * Arthur Volant + * Samuel Wallan * Stefan van der Walt * Warren Weckesser * Anreas Weh * Josh Wilson * Rory Yorke * Egor Zemlyanoy * Marc Zoeller + * zoj613 + * 秋纫 + A total of 126 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 1.7.0 ************************** * `#636 <https://github.com/scipy/scipy/issues/636>`__: Statistics Review: mannwhitneyu (Trac #109) * `#1346 <https://github.com/scipy/scipy/issues/1346>`__: signal.medfilt2d should fall back on signal.medfilt for types... * `#2118 <https://github.com/scipy/scipy/issues/2118>`__: Mann-Whitney statistic returns incorrect results (Trac #1593) * `#2158 <https://github.com/scipy/scipy/issues/2158>`__: special.chndtrix (ncx2.ppf) gives wrong results (Trac #1633) * `#3284 <https://github.com/scipy/scipy/issues/3284>`__: build_sphinx weirdness * `#3352 <https://github.com/scipy/scipy/issues/3352>`__: beta distribution sf * `#4067 <https://github.com/scipy/scipy/issues/4067>`__: Mannwhitneyu with arrays full of nan still reports significance * `#4080 <https://github.com/scipy/scipy/issues/4080>`__: entropy in Scipy * `#4641 <https://github.com/scipy/scipy/issues/4641>`__: mstats.mannwhitneyu and stats.mannwhitneyu return inconsistent... * `#5122 <https://github.com/scipy/scipy/issues/5122>`__: scipy.stats.binom.ppf Incorrect for p=0 * `#5180 <https://github.com/scipy/scipy/issues/5180>`__: Rbf interpolation - use only K nearest neighbors * `#5258 <https://github.com/scipy/scipy/issues/5258>`__: affine_transform complains about output_shape when output array... * `#5562 <https://github.com/scipy/scipy/issues/5562>`__: Wishart degrees of freedom should be $v > p-1$ instead of $v... * `#5933 <https://github.com/scipy/scipy/issues/5933>`__: mstats_basic.py - mannwhitneyu [scipy/scipy/stats/mstats_basic.py] * `#6409 <https://github.com/scipy/scipy/issues/6409>`__: _unequal_var_ttest_denom causes ZeroDivisionError in early samples * `#6682 <https://github.com/scipy/scipy/issues/6682>`__: negative binomial survival function is imprecise * `#6897 <https://github.com/scipy/scipy/issues/6897>`__: scipy.stats.mannwhitneyu of empty sets gives p=0.0 and does not... * `#7303 <https://github.com/scipy/scipy/issues/7303>`__: stats.describe with nan_policy=omit returns matrix-wide minmax... * `#7406 <https://github.com/scipy/scipy/issues/7406>`__: scipy.stats.binom.ppf returns nan for q between 0 and 1 if n... * `#7437 <https://github.com/scipy/scipy/issues/7437>`__: ENH: add skewed Cauchy distribution to stats * `#7542 <https://github.com/scipy/scipy/issues/7542>`__: DOC: stats tutorials: Questions on arcsine and Student t formulae * `#7593 <https://github.com/scipy/scipy/issues/7593>`__: Meaning of \`tol\` argument in \`scipy.optimize.minimize\` is... * `#8565 <https://github.com/scipy/scipy/issues/8565>`__: Error in SmoothSphereBivariateSpline(): "ValueError: Error code... * `#8665 <https://github.com/scipy/scipy/issues/8665>`__: \`scipy.ncx2.sf\` should be monotone decreasing * `#8836 <https://github.com/scipy/scipy/issues/8836>`__: scipy.optimize.linprog(method='simplex') needs to return duals * `#9184 <https://github.com/scipy/scipy/issues/9184>`__: Mann-Whitney implementation wrong? * `#9450 <https://github.com/scipy/scipy/issues/9450>`__: allow seeding of init methods in vq.kmeans2 * `#9704 <https://github.com/scipy/scipy/issues/9704>`__: RectSphereBivariateSpline fails for negative longitude * `#9836 <https://github.com/scipy/scipy/issues/9836>`__: scipy.stats.rice gives incorrect results when s is very low compared... * `#9904 <https://github.com/scipy/scipy/issues/9904>`__: Request/Proposal: Greatly improve scipy.interpolate.Rbf * `#9981 <https://github.com/scipy/scipy/issues/9981>`__: stats.kruskal : add a warning for an input with 2 or more columns * `#10358 <https://github.com/scipy/scipy/issues/10358>`__: DOC: linprog and linear_sum_assignment tutorials needed * `#10908 <https://github.com/scipy/scipy/issues/10908>`__: Nakami fitting doesn't converge (scipy.stats) * `#10933 <https://github.com/scipy/scipy/issues/10933>`__: Add scaled inverse chi2 distribution * `#11014 <https://github.com/scipy/scipy/issues/11014>`__: Barnard's Test for More Powerful Hypothesis Testing of 2x2 Contingency... * `#11050 <https://github.com/scipy/scipy/issues/11050>`__: Feature request: Nelder-Mead with bounds * `#11086 <https://github.com/scipy/scipy/issues/11086>`__: scipy.stats.skew doesn't work correctly for float point numbers * `#11113 <https://github.com/scipy/scipy/issues/11113>`__: inconsistent result from ttest_ind and mannwhitneyu when used... * `#11134 <https://github.com/scipy/scipy/issues/11134>`__: Wrong confidence interval for binomial distribution with p=0 * `#11325 <https://github.com/scipy/scipy/issues/11325>`__: Add axis parameter for scipy.spatial.distance.jensenshannon * `#11474 <https://github.com/scipy/scipy/issues/11474>`__: scipy.stats.skellam.cdf(0) returns 0 for large mu1 = mu2 * `#11523 <https://github.com/scipy/scipy/issues/11523>`__: scipy.stats.zipf doesn't implement zipf distribution * `#11848 <https://github.com/scipy/scipy/issues/11848>`__: How to get Lagrange / lambda multipliers out of 'linprog' optimize... * `#11909 <https://github.com/scipy/scipy/issues/11909>`__: Enable bounds for lambda in boxcox * `#12118 <https://github.com/scipy/scipy/issues/12118>`__: Docstring missing defaults * `#12132 <https://github.com/scipy/scipy/issues/12132>`__: Slow tests to be trimmed or moved to test('full') * `#12230 <https://github.com/scipy/scipy/issues/12230>`__: Dendrogram: enable leaves labelling with 'labels' when using... * `#12282 <https://github.com/scipy/scipy/issues/12282>`__: scipy.stats.chisquare test does not check that observed and expected... * `#12298 <https://github.com/scipy/scipy/issues/12298>`__: BUG: fmin_powell missing squeeze in 1.5.0rc * `#12403 <https://github.com/scipy/scipy/issues/12403>`__: Add nan_policy to stats.zmap * `#12518 <https://github.com/scipy/scipy/issues/12518>`__: Null hypothesis of Kolmogorov Smirnov test is not correctly described * `#12534 <https://github.com/scipy/scipy/issues/12534>`__: Feature request: scipy.linalg.norm to deal with 0-size array * `#12622 <https://github.com/scipy/scipy/issues/12622>`__: scipy.interpolate.interpn docstring example * `#12635 <https://github.com/scipy/scipy/issues/12635>`__: scipy.stats.beta.ppf gives unexpexted results * `#12669 <https://github.com/scipy/scipy/issues/12669>`__: Median-averaging of complex CSDs * `#12731 <https://github.com/scipy/scipy/issues/12731>`__: stats.ncx2.cdf fails for nc >> x >> 1 * `#12778 <https://github.com/scipy/scipy/issues/12778>`__: Confusing documentation of scipy.stats.weightedtau * `#12794 <https://github.com/scipy/scipy/issues/12794>`__: [Bug] The result of stats.beta.isf is inconsistent with stats.beta.sf * `#12837 <https://github.com/scipy/scipy/issues/12837>`__: stats.mannwhitneyu could support arrays * `#12868 <https://github.com/scipy/scipy/issues/12868>`__: Vector-valued interpolation in \`interp2d\` * `#12922 <https://github.com/scipy/scipy/issues/12922>`__: Minimize with trust-constr method leads to TypeError if option... * `#12929 <https://github.com/scipy/scipy/issues/12929>`__: The use of starred expressions to create data detracts from understanding... * `#12965 <https://github.com/scipy/scipy/issues/12965>`__: domain of argument of scipy.interpolate.RectSphereBivariateSpline(u,... * `#13025 <https://github.com/scipy/scipy/issues/13025>`__: Generalized Hyperbolic Distribution * `#13090 <https://github.com/scipy/scipy/issues/13090>`__: Broken link in doc for signal.max_len_seq * `#13101 <https://github.com/scipy/scipy/issues/13101>`__: MAINT: Upgrade python version in docker file * `#13158 <https://github.com/scipy/scipy/issues/13158>`__: \`signal.get_window()\` has a missing doc link and cannot get... * `#13173 <https://github.com/scipy/scipy/issues/13173>`__: Uninformative error message from bisplev function * `#13234 <https://github.com/scipy/scipy/issues/13234>`__: BUG: stats: Wrong shape of burr.moment() and fisk.moment() when... * `#13242 <https://github.com/scipy/scipy/issues/13242>`__: Does kmeans "drop" clusters? * `#13243 <https://github.com/scipy/scipy/issues/13243>`__: tgsen uses an output argument for computing a default argument * `#13245 <https://github.com/scipy/scipy/issues/13245>`__: Kurtosis returning 1 for array of same elements * `#13257 <https://github.com/scipy/scipy/issues/13257>`__: GitHub Actions test failures for MacOS * `#13272 <https://github.com/scipy/scipy/issues/13272>`__: scipy.stats.yeojohnson_llf doc mistake * `#13280 <https://github.com/scipy/scipy/issues/13280>`__: Wrong results with hypergeom cdf * `#13285 <https://github.com/scipy/scipy/issues/13285>`__: description correction in scipy.stats.t * `#13287 <https://github.com/scipy/scipy/issues/13287>`__: Generate binomial CDF with mu instead of prob * `#13294 <https://github.com/scipy/scipy/issues/13294>`__: BUG: stats: wrong bounds returned by 'support' method for distributions... * `#13299 <https://github.com/scipy/scipy/issues/13299>`__: Typing for scipy.spatial * `#13300 <https://github.com/scipy/scipy/issues/13300>`__: Add a single individual to a latinhypercube initial population... * `#13311 <https://github.com/scipy/scipy/issues/13311>`__: MAINT: pavement.py PYVER is outdated * `#13339 <https://github.com/scipy/scipy/issues/13339>`__: savemat discards dimension information if any dimension is zero * `#13341 <https://github.com/scipy/scipy/issues/13341>`__: add scipy.stats.variation with an ddof parameter * `#13353 <https://github.com/scipy/scipy/issues/13353>`__: Documentation: in scipy.stats.johnsonsu, parameter \`a\` can... * `#13405 <https://github.com/scipy/scipy/issues/13405>`__: TST: add a few tests for sparse BSR ctor * `#13410 <https://github.com/scipy/scipy/issues/13410>`__: BUG: skew for empty array raises * `#13417 <https://github.com/scipy/scipy/issues/13417>`__: 10,000 times speedup for generating random numbers from the cosine... * `#13440 <https://github.com/scipy/scipy/issues/13440>`__: python runtest.py -t path-to-test.py failed * `#13454 <https://github.com/scipy/scipy/issues/13454>`__: Scipy cosine distance can be greater than 2 * `#13459 <https://github.com/scipy/scipy/issues/13459>`__: Broken link in cramervonmises documentation * `#13494 <https://github.com/scipy/scipy/issues/13494>`__: One-word typo in the documentation of optimize.linprog_simplex * `#13501 <https://github.com/scipy/scipy/issues/13501>`__: minimize using Powell methods with Bounds leads to "TypeError:... * `#13509 <https://github.com/scipy/scipy/issues/13509>`__: signal.medfilt2d vs ndimage.median_filter * `#13511 <https://github.com/scipy/scipy/issues/13511>`__: DOC: error in description of "direc" parameter of "fmin_powell" * `#13526 <https://github.com/scipy/scipy/issues/13526>`__: TST: stats: intermittent \`test_ttest_ind_randperm_alternative2... * `#13536 <https://github.com/scipy/scipy/issues/13536>`__: \`_within_tolerance\` seems an unnecessary repetition of \`numpy.isclose\` * `#13540 <https://github.com/scipy/scipy/issues/13540>`__: missing python 3.8 manylinux wheels on scipy-wheels-nightly * `#13559 <https://github.com/scipy/scipy/issues/13559>`__: shape error in linprog with revised simplex * `#13587 <https://github.com/scipy/scipy/issues/13587>`__: binned_statistic unreliable with single precision * `#13589 <https://github.com/scipy/scipy/issues/13589>`__: Better argument preparation for distributions in stats package. * `#13602 <https://github.com/scipy/scipy/issues/13602>`__: The crystallball distribution entropy is sometimes minus infinity * `#13606 <https://github.com/scipy/scipy/issues/13606>`__: MAINT: mypy: some typing errors while running mypy + adding mypy... * `#13608 <https://github.com/scipy/scipy/issues/13608>`__: Why does stats.binned_statistic_2d convert its values argument... * `#13609 <https://github.com/scipy/scipy/issues/13609>`__: BUG: SciPy pip install -e gets unusable version spec * `#13610 <https://github.com/scipy/scipy/issues/13610>`__: Highs solver did not provide a solution nor did it report a failure * `#13614 <https://github.com/scipy/scipy/issues/13614>`__: BUG: invgauss.cdf should return the correct value when \`mu\`... * `#13628 <https://github.com/scipy/scipy/issues/13628>`__: 1-letter typo in the definition of scipy.special.spence function... * `#13634 <https://github.com/scipy/scipy/issues/13634>`__: mmwrite fails on dense, skew-symmetric array * `#13646 <https://github.com/scipy/scipy/issues/13646>`__: Sparse matrix argmax() integer overflow on Windows 10 * `#13647 <https://github.com/scipy/scipy/issues/13647>`__: \`scipy.stats.qmc.LatinHypercube\` cannot sample single sample... * `#13651 <https://github.com/scipy/scipy/issues/13651>`__: Documentation wrong in scipy.linalg.eigvalsh * `#13664 <https://github.com/scipy/scipy/issues/13664>`__: BUG: gamma distribution's inverse survival function overflows... * `#13693 <https://github.com/scipy/scipy/issues/13693>`__: BUG: sokalmichener appears to incorrectly apply weights * `#13697 <https://github.com/scipy/scipy/issues/13697>`__: BUG: stats: Spurious warning generated by arcsine.pdf at the... * `#13704 <https://github.com/scipy/scipy/issues/13704>`__: Make it possible to pass a rank cut-off value relatively to the... * `#13707 <https://github.com/scipy/scipy/issues/13707>`__: Kullback Leibler Divergence broadcasting no longer works * `#13740 <https://github.com/scipy/scipy/issues/13740>`__: Scipy.optimize x0 out of bounds when it is within bounds. * `#13744 <https://github.com/scipy/scipy/issues/13744>`__: scipy.interpolate.interp1d has inconsistent behavior for non-unique... * `#13754 <https://github.com/scipy/scipy/issues/13754>`__: optimize.minimize 'trust' methods and finite difference Hessian... * `#13762 <https://github.com/scipy/scipy/issues/13762>`__: MAINT, TST: aarch64 stats test failures showing up in wheels... * `#13769 <https://github.com/scipy/scipy/issues/13769>`__: probplot draws fit line even when fit=False * `#13791 <https://github.com/scipy/scipy/issues/13791>`__: BUG: stats: wrapcauchy.cdf does not broadcast the shape parameter... * `#13793 <https://github.com/scipy/scipy/issues/13793>`__: CI: CircleCI doc build failure * `#13840 <https://github.com/scipy/scipy/issues/13840>`__: manylinux1 builds are failing because of C99 usage in \`special/_cosine.c\` * `#13850 <https://github.com/scipy/scipy/issues/13850>`__: CI: Homebrew is failing due to bintray * `#13875 <https://github.com/scipy/scipy/issues/13875>`__: BUG: chi2_contingency with Yates correction * `#13878 <https://github.com/scipy/scipy/issues/13878>`__: BUG: \`signal.get_window\` argument handling issue * `#13880 <https://github.com/scipy/scipy/issues/13880>`__: Remove all usages of numpy.compat * `#13896 <https://github.com/scipy/scipy/issues/13896>`__: Boschloo's Test for More Powerful Hypothesis Testing of 2x2 Contingency... * `#13923 <https://github.com/scipy/scipy/issues/13923>`__: Inverse of Log CDF of Normal Distribution * `#13933 <https://github.com/scipy/scipy/issues/13933>`__: \`signal.get_window\` does not support \`general_cosine\` and... * `#13950 <https://github.com/scipy/scipy/issues/13950>`__: DOC: scipy.spatial.KDTree.query * `#13969 <https://github.com/scipy/scipy/issues/13969>`__: N=4 must not exceed M=3 * `#13970 <https://github.com/scipy/scipy/issues/13970>`__: Pearson's original paper on chi-square test could be referenced. * `#13984 <https://github.com/scipy/scipy/issues/13984>`__: Faster addition of sparse diagonal matrices * `#13988 <https://github.com/scipy/scipy/issues/13988>`__: An error occurred when using scipy.io.wavfile of scipy 1.6 version... * `#13997 <https://github.com/scipy/scipy/issues/13997>`__: BUG: sparse: Incorrect result from \`dia_matrix.diagonal()\` * `#14005 <https://github.com/scipy/scipy/issues/14005>`__: MAINT: optimize: \`curve_fit\` input error msg can be improved. * `#14038 <https://github.com/scipy/scipy/issues/14038>`__: MAINT: add type annotations for _sobol.pyx * `#14048 <https://github.com/scipy/scipy/issues/14048>`__: DOC: missing git submodule information * `#14055 <https://github.com/scipy/scipy/issues/14055>`__: linalg.solve: Unclear error when using assume_a='her' with real... * `#14093 <https://github.com/scipy/scipy/issues/14093>`__: DOC: Inconsistency in the definition of default values in the... * `#14158 <https://github.com/scipy/scipy/issues/14158>`__: TST, BUG: test_rbfinterp.py -- test_interpolation_misfit_1d fails... * `#14170 <https://github.com/scipy/scipy/issues/14170>`__: TST: signal submodule test_filtfilt_gust failing on 32-bit amd64... * `#14194 <https://github.com/scipy/scipy/issues/14194>`__: MAINT: download-wheels.py missing import * `#14199 <https://github.com/scipy/scipy/issues/14199>`__: Generated sources for biasedurn extension are broken in 1.7.0rc1 ************************** Pull requests for 1.7.0 ************************** * `#4824 <https://github.com/scipy/scipy/pull/4824>`__: Permutation Ttest (new PR) * `#4933 <https://github.com/scipy/scipy/pull/4933>`__: ENH: Update the Mann-Whitney-Wilcoxon test * `#7702 <https://github.com/scipy/scipy/pull/7702>`__: ENH: stats: Add Skewed Cauchy Distribution * `#8306 <https://github.com/scipy/scipy/pull/8306>`__: Optional Pythran support for scipy.signal.max_len_seq_inner * `#10170 <https://github.com/scipy/scipy/pull/10170>`__: MAINT: stats: Implement cdf and ppf as ufuncs for the cosine... * `#10454 <https://github.com/scipy/scipy/pull/10454>`__: ENH: Extend find_peaks_cwt to take numbers and iterables for... * `#10844 <https://github.com/scipy/scipy/pull/10844>`__: ENH: add stats.qmc module with quasi Monte Carlo functionality * `#11313 <https://github.com/scipy/scipy/pull/11313>`__: ENH: add Wright's generalized Bessel function * `#11352 <https://github.com/scipy/scipy/pull/11352>`__: ENH: stats: Add crosstab function. * `#11477 <https://github.com/scipy/scipy/pull/11477>`__: FIX: bounded parameter in cdfchn.f gives bad results * `#11695 <https://github.com/scipy/scipy/pull/11695>`__: ENH: stats: add method of moments to \`rv_continuous.fit\` * `#11911 <https://github.com/scipy/scipy/pull/11911>`__: ENH: Added bounds to boxcox and boxcox_normmax * `#12438 <https://github.com/scipy/scipy/pull/12438>`__: BUG: use ellipkm1 in elliptical filter design to prevent numerical... * `#12531 <https://github.com/scipy/scipy/pull/12531>`__: ENH: stats: add Page's L test * `#12603 <https://github.com/scipy/scipy/pull/12603>`__: ENH: stats: Add \`binomtest\` to replace \`binom_test\`. * `#12653 <https://github.com/scipy/scipy/pull/12653>`__: ENH: stats: add Somers' D test * `#12676 <https://github.com/scipy/scipy/pull/12676>`__: BUG: update median averaging in signal.csd * `#12760 <https://github.com/scipy/scipy/pull/12760>`__: BUG: special: erfinv(x<<1) loses precision * `#12801 <https://github.com/scipy/scipy/pull/12801>`__: ENH: Add single-sided p-values to remaining spearmanr and linregress * `#12873 <https://github.com/scipy/scipy/pull/12873>`__: ENH: Stats: add Alexander Govern Test * `#13008 <https://github.com/scipy/scipy/pull/13008>`__: ENH: Add 'alternative' to functions using normal CDF for p-value * `#13040 <https://github.com/scipy/scipy/pull/13040>`__: BUG: Allow RectSphereBivariateSpline to accept negative longitude * `#13048 <https://github.com/scipy/scipy/pull/13048>`__: ENH: stats: Add a function that computes the relative risk. * `#13067 <https://github.com/scipy/scipy/pull/13067>`__: ENH: Add weights parameter to stats.gmean * `#13084 <https://github.com/scipy/scipy/pull/13084>`__: ENH: fast Hankel transform * `#13104 <https://github.com/scipy/scipy/pull/13104>`__: MAINT: upgrade python version (drop python 3.6) for docker dev... * `#13153 <https://github.com/scipy/scipy/pull/13153>`__: ENH: added association measurements Pearsons Contingency Coefficient,... * `#13166 <https://github.com/scipy/scipy/pull/13166>`__: ENH: stats: Add nan_policy to zmap. * `#13175 <https://github.com/scipy/scipy/pull/13175>`__: MAINT: tests for tall cost matrices in \`linear_sum_assignment\` * `#13177 <https://github.com/scipy/scipy/pull/13177>`__: BUG: raise NotImplementedError in fourier_ellipsoid when ndim... * `#13184 <https://github.com/scipy/scipy/pull/13184>`__: BUG: stats: Fix min and max calculation of mstats.describe with... * `#13188 <https://github.com/scipy/scipy/pull/13188>`__: DOC: stats: make null and alternative hypotheses of kstest more... * `#13193 <https://github.com/scipy/scipy/pull/13193>`__: MAINT: stats: chisquare check sum of observed/expected frequencies * `#13197 <https://github.com/scipy/scipy/pull/13197>`__: ENH/MAINT: HiGHS upstream enhancements and bug fixes * `#13198 <https://github.com/scipy/scipy/pull/13198>`__: ENH: allow inference of output_shape from out array in affine_transform * `#13204 <https://github.com/scipy/scipy/pull/13204>`__: ENH: stats: add Zipfian (different from Zipf/zeta) distribution * `#13208 <https://github.com/scipy/scipy/pull/13208>`__: REL: set version to 1.7.0.dev0 * `#13216 <https://github.com/scipy/scipy/pull/13216>`__: TST: stats: break up and mark slow tests * `#13224 <https://github.com/scipy/scipy/pull/13224>`__: Update docs for the weighted τ * `#13230 <https://github.com/scipy/scipy/pull/13230>`__: ENH: linalg: Add LAPACK wrapper for tgexc. * `#13232 <https://github.com/scipy/scipy/pull/13232>`__: MAINT: stats: raise error when input to kruskal has >1 dim * `#13233 <https://github.com/scipy/scipy/pull/13233>`__: DOC: stats: fix MGF of arcsine and entropy of t in tutorial * `#13236 <https://github.com/scipy/scipy/pull/13236>`__: MAINT: reorganize shared linear assignment tests * `#13237 <https://github.com/scipy/scipy/pull/13237>`__: BENCH: Refactor stats.Distribution to easily add new distributions * `#13238 <https://github.com/scipy/scipy/pull/13238>`__: BUG: stats: fix wrong shape output of burr and fisk distributions * `#13240 <https://github.com/scipy/scipy/pull/13240>`__: MAINT: add tests of trivial cost matrices for linear sum assignment * `#13252 <https://github.com/scipy/scipy/pull/13252>`__: DOC: optimize: add \`optimize.linear_sum_assignment\` tutorial. * `#13254 <https://github.com/scipy/scipy/pull/13254>`__: BUG: Fix precision issues for constant input in skew and kurtosis * `#13262 <https://github.com/scipy/scipy/pull/13262>`__: BUG: scipy.medfilt and .medfilt2d fixes * `#13263 <https://github.com/scipy/scipy/pull/13263>`__: ENH: add Cramer-von Mises test for two samples * `#13264 <https://github.com/scipy/scipy/pull/13264>`__: fix a minor typo in \`stats.anderson\` doc * `#13268 <https://github.com/scipy/scipy/pull/13268>`__: ENH: stats: Add implementation of _entropy for the t distr. * `#13273 <https://github.com/scipy/scipy/pull/13273>`__: DOC: stats: fix typo in Yeo-Johnson LL function documentation * `#13275 <https://github.com/scipy/scipy/pull/13275>`__: MAINT: stats: Correct a comment in the _fitstart method of gamma. * `#13283 <https://github.com/scipy/scipy/pull/13283>`__: BUG: stats: fix the cdf method of rv_discrete class * `#13286 <https://github.com/scipy/scipy/pull/13286>`__: DOC: stats: clairify rv_continuous/discrete.stats example * `#13288 <https://github.com/scipy/scipy/pull/13288>`__: DOC: stats: discrete distribution shape parameter restrictions * `#13289 <https://github.com/scipy/scipy/pull/13289>`__: MAINT: fix a build warning in sigtoolsmodule.c * `#13290 <https://github.com/scipy/scipy/pull/13290>`__: DOC: Expand the discussion of the nan_policy API. * `#13291 <https://github.com/scipy/scipy/pull/13291>`__: MAINT: signal, stats: Use keepdims where appropriate. * `#13292 <https://github.com/scipy/scipy/pull/13292>`__: DOC: stats: note another common parameterization of nbinom * `#13293 <https://github.com/scipy/scipy/pull/13293>`__: DOC: Change broken link for default values to archived link * `#13295 <https://github.com/scipy/scipy/pull/13295>`__: BUG: stats: fix the support method to return correct bounds * `#13296 <https://github.com/scipy/scipy/pull/13296>`__: DOC: stats: Fix latex markup in the kstwo docstring. * `#13297 <https://github.com/scipy/scipy/pull/13297>`__: TST: mark kde.logpdf overflow test as xslow * `#13298 <https://github.com/scipy/scipy/pull/13298>`__: Generalized Hyperbolic Distribution * `#13301 <https://github.com/scipy/scipy/pull/13301>`__: DOC: cluster: Add cluster number note to the docstring of cluster.vq.kmeans * `#13302 <https://github.com/scipy/scipy/pull/13302>`__: BUG: Fix ndimage.morphology.distance_transform\_\* argument handling * `#13303 <https://github.com/scipy/scipy/pull/13303>`__: CI: prevent Codecov giving false CI failures and wrong PR annotations * `#13313 <https://github.com/scipy/scipy/pull/13313>`__: ENH: static typing for qhull * `#13316 <https://github.com/scipy/scipy/pull/13316>`__: Pythran implementation of scipy.signal._spectral * `#13317 <https://github.com/scipy/scipy/pull/13317>`__: DOC: forward port 1.6.0 relnotes * `#13319 <https://github.com/scipy/scipy/pull/13319>`__: ENH: stats: add fast numerical inversion of distribution CDF * `#13320 <https://github.com/scipy/scipy/pull/13320>`__: ENH: x0 for differential_evolution * `#13324 <https://github.com/scipy/scipy/pull/13324>`__: DOC correct linprog highs versionadded to 1.6 * `#13326 <https://github.com/scipy/scipy/pull/13326>`__: MAINT: update numpydoc to v1.1.0 * `#13327 <https://github.com/scipy/scipy/pull/13327>`__: DOC: interpolate: improved docstring examples of \`interpolate.interpn()\`... * `#13328 <https://github.com/scipy/scipy/pull/13328>`__: ENH: Boost stats distributions * `#13330 <https://github.com/scipy/scipy/pull/13330>`__: ENH: stats: add noncentral hypergeometric distributions (Fisher's... * `#13331 <https://github.com/scipy/scipy/pull/13331>`__: MAINT/ENH: resolve mypy warnings/errors * `#13332 <https://github.com/scipy/scipy/pull/13332>`__: DOC: interpolate: improved docstring of \`interpolate.interp2d\`... * `#13333 <https://github.com/scipy/scipy/pull/13333>`__: ENH: stats: Some more _sf and _isf implementations. * `#13334 <https://github.com/scipy/scipy/pull/13334>`__: MAINT: stats: Clean up a few defunct comments in _continuous_distns.py * `#13336 <https://github.com/scipy/scipy/pull/13336>`__: Pythran version of scipy.optimize._group_columns * `#13337 <https://github.com/scipy/scipy/pull/13337>`__: DOC|ENH: type hinting in scipy.integrate.simpson * `#13346 <https://github.com/scipy/scipy/pull/13346>`__: ENH: stats: add 'ddof' parameter to the 'variation' function * `#13355 <https://github.com/scipy/scipy/pull/13355>`__: ENH: stats: implement _logpdf, _sf and _isf for loggamma. * `#13360 <https://github.com/scipy/scipy/pull/13360>`__: ENH|DOC: fix docstring and input validation in interpolate.RectSphereBivariateSpline * `#13366 <https://github.com/scipy/scipy/pull/13366>`__: BUG: stats: Don't raise ZeroDivisionError in _unequal_var_ttest_denom * `#13370 <https://github.com/scipy/scipy/pull/13370>`__: ENH: fix ARGUS distribution for small parameters in stats * `#13371 <https://github.com/scipy/scipy/pull/13371>`__: ENH: stats: add \`bootstrap\` for estimating confidence interval... * `#13373 <https://github.com/scipy/scipy/pull/13373>`__: BUG: io/matlab: preserve dimensions of empty >=2D arrays * `#13374 <https://github.com/scipy/scipy/pull/13374>`__: ENH: stats: add skewed Cauchy distribution * `#13379 <https://github.com/scipy/scipy/pull/13379>`__: BUG: sparse: fix verbosity in sparse lsqr * `#13383 <https://github.com/scipy/scipy/pull/13383>`__: TST: stats: mark many dimension permutation t-test slow * `#13384 <https://github.com/scipy/scipy/pull/13384>`__: MAINT: Make keywords array static * `#13388 <https://github.com/scipy/scipy/pull/13388>`__: PERF: Avoid duplicate mean calculations in skew and kurtosis * `#13389 <https://github.com/scipy/scipy/pull/13389>`__: DOC: Fix deprecated directive syntax * `#13390 <https://github.com/scipy/scipy/pull/13390>`__: DOC: Correct line length for Parameter Section underline * `#13393 <https://github.com/scipy/scipy/pull/13393>`__: MAINT: stats: allow wishart dim - 1 < df < dim * `#13395 <https://github.com/scipy/scipy/pull/13395>`__: DOC: fix typo in setup.py warning message * `#13396 <https://github.com/scipy/scipy/pull/13396>`__: BUG: Fix MLE for Nakagami \`nakagami_gen.fit\` * `#13397 <https://github.com/scipy/scipy/pull/13397>`__: MAINT:linalg: Fix tgsen family wrapper and ordqz * `#13406 <https://github.com/scipy/scipy/pull/13406>`__: TST: add error handling tests for sparse BSR ctor * `#13413 <https://github.com/scipy/scipy/pull/13413>`__: DOC: ultra-quickstart guide * `#13418 <https://github.com/scipy/scipy/pull/13418>`__: BUG: Fix moment returning inconsistent types and shapes * `#13423 <https://github.com/scipy/scipy/pull/13423>`__: DOC: Update example for leaf_label_func/dendrogram * `#13431 <https://github.com/scipy/scipy/pull/13431>`__: ENH: stats: override _rvs for nhypergeom * `#13432 <https://github.com/scipy/scipy/pull/13432>`__: Add indicator in NDInterpolator docstring that N must be > 1 * `#13434 <https://github.com/scipy/scipy/pull/13434>`__: DOC: stats: note relationship between scaled-inv-chi2 and invgamma * `#13436 <https://github.com/scipy/scipy/pull/13436>`__: ENH: interpolate: add input validation to check input x-y is... * `#13441 <https://github.com/scipy/scipy/pull/13441>`__: ENH: add functionality \`barnard_exact\` test to scipy.stats. * `#13443 <https://github.com/scipy/scipy/pull/13443>`__: MAINT: stats: Updates for skewcauchy * `#13444 <https://github.com/scipy/scipy/pull/13444>`__: DOC: clarify range of \`a\` parameter fpr johnsonsu/johnsonsb * `#13445 <https://github.com/scipy/scipy/pull/13445>`__: DOC: fix runtests guidelines. * `#13446 <https://github.com/scipy/scipy/pull/13446>`__: MAINT: stats: Add _fitstart method to wrapcauchy. * `#13447 <https://github.com/scipy/scipy/pull/13447>`__: DEV: Update development Docker image * `#13448 <https://github.com/scipy/scipy/pull/13448>`__: ENH: Add annotations for \`scipy.spatial.distance\` * `#13451 <https://github.com/scipy/scipy/pull/13451>`__: DOC: minor formatting. * `#13458 <https://github.com/scipy/scipy/pull/13458>`__: DOC: indent see also. * `#13460 <https://github.com/scipy/scipy/pull/13460>`__: DOC: stats: Fix link to Cramer-von Mises wikipedia article. * `#13461 <https://github.com/scipy/scipy/pull/13461>`__: DOC: reorganize scipy.stats overview docs page * `#13463 <https://github.com/scipy/scipy/pull/13463>`__: DOC: misc formatting fixes * `#13466 <https://github.com/scipy/scipy/pull/13466>`__: DOC: Typo in see also s/SmoothUni/SmoothBi/g * `#13467 <https://github.com/scipy/scipy/pull/13467>`__: DOC: optimize: add description about \`tol\` argument for \`minimize\`. * `#13469 <https://github.com/scipy/scipy/pull/13469>`__: MAINT: Refactor optimization methods to use scipy.stats.qmc * `#13477 <https://github.com/scipy/scipy/pull/13477>`__: CI: pin numpy to 1.19.5 for the three macOS CI jobs * `#13478 <https://github.com/scipy/scipy/pull/13478>`__: DOC: fix typos where double :: for Sphinx directives were missing * `#13481 <https://github.com/scipy/scipy/pull/13481>`__: CI: pin numpy to 1.19.5 in the 4 parallel Windows builds on Azure * `#13482 <https://github.com/scipy/scipy/pull/13482>`__: CI: use numpy 1.20.0 again in macOS CI * `#13483 <https://github.com/scipy/scipy/pull/13483>`__: DOC: Multiple documentation syntax fixes. * `#13484 <https://github.com/scipy/scipy/pull/13484>`__: Move some pythran config from CI to setup * `#13487 <https://github.com/scipy/scipy/pull/13487>`__: DOC: add a tutorial about scipy.stats.qmc * `#13492 <https://github.com/scipy/scipy/pull/13492>`__: ENH: GH actions should not run on forks * `#13493 <https://github.com/scipy/scipy/pull/13493>`__: DEV: Enable gitpod for SciPy * `#13495 <https://github.com/scipy/scipy/pull/13495>`__: DOC One-word typo in the documentation of optimize.linprog_simplex * `#13499 <https://github.com/scipy/scipy/pull/13499>`__: DOC: describe LSAP implementation * `#13502 <https://github.com/scipy/scipy/pull/13502>`__: BUG: Bounds created with lists weren't working for Powell * `#13507 <https://github.com/scipy/scipy/pull/13507>`__: MAINT, TST: stats: centralize invalid parameters list for all... * `#13510 <https://github.com/scipy/scipy/pull/13510>`__: DOC: stats: fix small doc errors in 'multivariate_hypergeom' * `#13513 <https://github.com/scipy/scipy/pull/13513>`__: DOC: Added math notation in examples in ltisys.py * `#13514 <https://github.com/scipy/scipy/pull/13514>`__: ENH: simplify low_0_bit function for Sobol * `#13515 <https://github.com/scipy/scipy/pull/13515>`__: ENH: optimize: add bound constraint support for nelder-mead solver * `#13516 <https://github.com/scipy/scipy/pull/13516>`__: DOC: reduce LaTeX usage for johnsonb docstring * `#13519 <https://github.com/scipy/scipy/pull/13519>`__: BLD: remove build_sphinx support from setup.py * `#13527 <https://github.com/scipy/scipy/pull/13527>`__: TST: stats: xfail ttest_ind_randperm_alternative2 on 32 bit * `#13530 <https://github.com/scipy/scipy/pull/13530>`__: DOC: correct comparisons between median filter functions * `#13532 <https://github.com/scipy/scipy/pull/13532>`__: ENH: release the GIL inside medfilt2d * `#13538 <https://github.com/scipy/scipy/pull/13538>`__: DOC: optimize: fix minor doc error in 'fmin_powell' (#13511) * `#13546 <https://github.com/scipy/scipy/pull/13546>`__: DOC: fix list of "mode" options for ndimage * `#13549 <https://github.com/scipy/scipy/pull/13549>`__: ENH: stats: add 'alternative' keyword to some normality tests. * `#13551 <https://github.com/scipy/scipy/pull/13551>`__: MAINT: add git to docker env * `#13552 <https://github.com/scipy/scipy/pull/13552>`__: MAINT: stats: remove float_power shim * `#13553 <https://github.com/scipy/scipy/pull/13553>`__: DOC: use support rather than a/b in stats tutorial * `#13560 <https://github.com/scipy/scipy/pull/13560>`__: MAINT: optimize: improve linprog error message for sparse input... * `#13562 <https://github.com/scipy/scipy/pull/13562>`__: MAINT: optimize: using np.isclose instead of _within_tolerance. * `#13566 <https://github.com/scipy/scipy/pull/13566>`__: ENH: Speed up hdquantiles_sd() * `#13569 <https://github.com/scipy/scipy/pull/13569>`__: BENCH: optimize: benchmark only HiGHS methods; add bigger linprog... * `#13574 <https://github.com/scipy/scipy/pull/13574>`__: DOC: In description of cluster.hierarchy.dendrogram 'level' parameter,... * `#13576 <https://github.com/scipy/scipy/pull/13576>`__: ENH: improve discrepancy performance * `#13579 <https://github.com/scipy/scipy/pull/13579>`__: TST: Add pybind11 to tox environments * `#13583 <https://github.com/scipy/scipy/pull/13583>`__: BUG: Fix Dockerfile apt-get installs * `#13588 <https://github.com/scipy/scipy/pull/13588>`__: MAINT: forward port 1.6.1 relnotes. * `#13593 <https://github.com/scipy/scipy/pull/13593>`__: BUG: stats: preserve sample dtype for bin edges * `#13595 <https://github.com/scipy/scipy/pull/13595>`__: ENH: interpolate: add RBFInterpolator * `#13596 <https://github.com/scipy/scipy/pull/13596>`__: DOC: Fix indentation in new_stats_distribution.rst.inc * `#13601 <https://github.com/scipy/scipy/pull/13601>`__: Add dpss for get_window function * `#13604 <https://github.com/scipy/scipy/pull/13604>`__: DOC: Correct dual annealing visiting param range. * `#13605 <https://github.com/scipy/scipy/pull/13605>`__: Add Codecov badge to README * `#13607 <https://github.com/scipy/scipy/pull/13607>`__: MAINT: stats: fix crystalball entropy * `#13611 <https://github.com/scipy/scipy/pull/13611>`__: Better argument preparation for distributions in stats package. * `#13612 <https://github.com/scipy/scipy/pull/13612>`__: Add docker run command for Windows cmd * `#13613 <https://github.com/scipy/scipy/pull/13613>`__: MAINT, CI: mypy: fix typing errors + add mypy to CI * `#13616 <https://github.com/scipy/scipy/pull/13616>`__: FIX: Return correct output for invgauss.cdf when mu is very small * `#13617 <https://github.com/scipy/scipy/pull/13617>`__: MAINT: accept numbers and iterables for width in find_peaks_cwt * `#13620 <https://github.com/scipy/scipy/pull/13620>`__: CI: disable the mypy CI job (partial revert of gh-13613) * `#13621 <https://github.com/scipy/scipy/pull/13621>`__: DOC: signal: use array_like for input types * `#13622 <https://github.com/scipy/scipy/pull/13622>`__: MAINT: clean up some unused files, make \`mypy scipy\` pass * `#13623 <https://github.com/scipy/scipy/pull/13623>`__: CI: enable Mypy CI job again * `#13624 <https://github.com/scipy/scipy/pull/13624>`__: TST: test more values for \`visiting_param\` input to \`dual_annealing\` * `#13625 <https://github.com/scipy/scipy/pull/13625>`__: Rename integrate.simps to integrate.simpsons in documentation... * `#13631 <https://github.com/scipy/scipy/pull/13631>`__: ENH: add a \`stats.differential_entropy\` function * `#13633 <https://github.com/scipy/scipy/pull/13633>`__: BUG: stats.binned_statistic_2d user function expecting arrays * `#13641 <https://github.com/scipy/scipy/pull/13641>`__: ENH: Added degrees parameter to rotvec * `#13645 <https://github.com/scipy/scipy/pull/13645>`__: MAINT: mypy: don't install numpy-stubs * `#13649 <https://github.com/scipy/scipy/pull/13649>`__: BUG: sparse: csc_matrix.argmax() integer overflow * `#13650 <https://github.com/scipy/scipy/pull/13650>`__: ENH: stats: add 'alternative' parameter to ansari * `#13652 <https://github.com/scipy/scipy/pull/13652>`__: DOC: fix eigvalsh documentation (#13651) * `#13654 <https://github.com/scipy/scipy/pull/13654>`__: BUG: Fix LatinHypercubes * `#13656 <https://github.com/scipy/scipy/pull/13656>`__: DOC: Fix PCHIP references * `#13657 <https://github.com/scipy/scipy/pull/13657>`__: TST: remove IPython warning in debug session * `#13658 <https://github.com/scipy/scipy/pull/13658>`__: Remove spurious quotes in docstring * `#13661 <https://github.com/scipy/scipy/pull/13661>`__: ENH: stats: improve efficiency of / fix bug in exact permutation... * `#13667 <https://github.com/scipy/scipy/pull/13667>`__: MAINT: Make latest Docker image default * `#13668 <https://github.com/scipy/scipy/pull/13668>`__: MAINT: add .theia/ to .gitignore * `#13669 <https://github.com/scipy/scipy/pull/13669>`__: BLD: change SCIPY_USE_PYTHRAN default to \`1\` * `#13676 <https://github.com/scipy/scipy/pull/13676>`__: ENH Small improvements for LSQR with damp * `#13678 <https://github.com/scipy/scipy/pull/13678>`__: MAINT: add Pythran-generated files to .gitignore * `#13679 <https://github.com/scipy/scipy/pull/13679>`__: MAINT: move the \`conda develop .\` in the Gitpod config * `#13680 <https://github.com/scipy/scipy/pull/13680>`__: DOC: Add cKDTree note comparing it with KDTree * `#13681 <https://github.com/scipy/scipy/pull/13681>`__: DOC: build doc updates on Pythran, compiled code, and cleanups * `#13683 <https://github.com/scipy/scipy/pull/13683>`__: BUG: mmwrite correctly serializes non skew-symmetric arrays * `#13684 <https://github.com/scipy/scipy/pull/13684>`__: FIX: fix numerical overflow in gamma.isf method * `#13685 <https://github.com/scipy/scipy/pull/13685>`__: BUG: fix cosine distance range to 0-2 * `#13694 <https://github.com/scipy/scipy/pull/13694>`__: MAINT: fix warning emitted when NumPy version is incorrect * `#13696 <https://github.com/scipy/scipy/pull/13696>`__: ENH: support trimming in ttest_ind * `#13698 <https://github.com/scipy/scipy/pull/13698>`__: BUG: stats: Fix spurious warnings generated by arcsine.pdf * `#13701 <https://github.com/scipy/scipy/pull/13701>`__: DEV: scipy.interpolate b-splines (periodic case) * `#13702 <https://github.com/scipy/scipy/pull/13702>`__: DEP: Clean up spent deprecations in spatial.distance * `#13703 <https://github.com/scipy/scipy/pull/13703>`__: MAINT: fix issues found by static code analysis * `#13706 <https://github.com/scipy/scipy/pull/13706>`__: ENH: stats: Implement sf and isf for the laplace distribution. * `#13711 <https://github.com/scipy/scipy/pull/13711>`__: MAINT: stats: fix broadcasting for scipy.stats.entropy * `#13712 <https://github.com/scipy/scipy/pull/13712>`__: BUG: stats: Override _fitstart for the invweibull distribution. * `#13713 <https://github.com/scipy/scipy/pull/13713>`__: DOC: update toolchain.rst to reflect windows universal C runtime * `#13714 <https://github.com/scipy/scipy/pull/13714>`__: MAINT: stats: Remove an unused list from test_continuous_basic.py. * `#13715 <https://github.com/scipy/scipy/pull/13715>`__: MAINT: stats: No need to suppress frechet deprecation warnings. * `#13716 <https://github.com/scipy/scipy/pull/13716>`__: MAINT: use super() as described by PEP 3135 * `#13718 <https://github.com/scipy/scipy/pull/13718>`__: MAINT: new-style class, removing inheritance to object * `#13721 <https://github.com/scipy/scipy/pull/13721>`__: MAINT: add a type-ignore for mpmath (#13721) * `#13723 <https://github.com/scipy/scipy/pull/13723>`__: MAINT: mypy: ignore mpmath imports in mypy.ini * `#13724 <https://github.com/scipy/scipy/pull/13724>`__: DOC: pydata sphinx theme * `#13725 <https://github.com/scipy/scipy/pull/13725>`__: BENCH: add benchmark for Kendalltau * `#13727 <https://github.com/scipy/scipy/pull/13727>`__: CI: simplify Pythran configuration setup for Azure * `#13731 <https://github.com/scipy/scipy/pull/13731>`__: MAINT: stats: Some flake8-driven clean up. * `#13732 <https://github.com/scipy/scipy/pull/13732>`__: ENH: stats: Studentized Range Distribution * `#13735 <https://github.com/scipy/scipy/pull/13735>`__: DOC: correct Voronoi docstring * `#13738 <https://github.com/scipy/scipy/pull/13738>`__: DOC: add example to wright_bessel * `#13739 <https://github.com/scipy/scipy/pull/13739>`__: ENH: stats: Implement _sf and _isf for the chi distribution. * `#13741 <https://github.com/scipy/scipy/pull/13741>`__: MAINT: prevent overwriting of x in minimize * `#13747 <https://github.com/scipy/scipy/pull/13747>`__: DOC: Add note for interp1d for non-unique x-values * `#13749 <https://github.com/scipy/scipy/pull/13749>`__: MAINT: forward port 1.6.2 relnotes * `#13759 <https://github.com/scipy/scipy/pull/13759>`__: MAINT: simpson small performance speedups * `#13765 <https://github.com/scipy/scipy/pull/13765>`__: FIX: npymath missing causing npy_log1p to be unknown * `#13768 <https://github.com/scipy/scipy/pull/13768>`__: BENCH: Add missing pythran dependency * `#13770 <https://github.com/scipy/scipy/pull/13770>`__: ENH: stats.contingency: Add the sparse option to crosstab. * `#13774 <https://github.com/scipy/scipy/pull/13774>`__: DEP: Deprecate squeezing input vectors in spatial.distance * `#13775 <https://github.com/scipy/scipy/pull/13775>`__: Enable trust region methods to use a finite difference Hessian... * `#13777 <https://github.com/scipy/scipy/pull/13777>`__: DOC: Fix Ubuntu/Debian installation instructions * `#13778 <https://github.com/scipy/scipy/pull/13778>`__: DOC: remove references to RandomState * `#13782 <https://github.com/scipy/scipy/pull/13782>`__: MAINT: LBFGSB err msg on MAXLS changed closes #11718 * `#13785 <https://github.com/scipy/scipy/pull/13785>`__: BENCH: Add benchmark for cdist/pdist with weights * `#13786 <https://github.com/scipy/scipy/pull/13786>`__: MAINT: Prepare cdist/pdist for C++ rework * `#13787 <https://github.com/scipy/scipy/pull/13787>`__: MAINT: stats: move entropy and differential_entropy functions... * `#13790 <https://github.com/scipy/scipy/pull/13790>`__: DOC: Add some dependencies for Dockerfile doc of scipy development. * `#13792 <https://github.com/scipy/scipy/pull/13792>`__: BUG: stats: Fix broadcasting in wrapcauchy.cdf * `#13795 <https://github.com/scipy/scipy/pull/13795>`__: MAINT: stats: add hypotests to __all__ in init.py, not stats.py * `#13797 <https://github.com/scipy/scipy/pull/13797>`__: MAINT: stats: probplot: don't plot least-squares fit line unless... * `#13798 <https://github.com/scipy/scipy/pull/13798>`__: MAINT: fix incorrect code comment in \`hierarchy.to_tree\` * `#13802 <https://github.com/scipy/scipy/pull/13802>`__: DEV: add environment.yml file for development with conda/mamba * `#13803 <https://github.com/scipy/scipy/pull/13803>`__: DOC: fix doc build warning about arxiv role already being registered * `#13804 <https://github.com/scipy/scipy/pull/13804>`__: DOC+MAINT: optimize: lb and ub in the Bounds constructor are... * `#13807 <https://github.com/scipy/scipy/pull/13807>`__: MAINT: Dont use parallel Sphinx * `#13808 <https://github.com/scipy/scipy/pull/13808>`__: MAINT: cluster.to_tree: more idiomatic looping over rows of matrix... * `#13810 <https://github.com/scipy/scipy/pull/13810>`__: MAINT: add a CODEOWNERS file * `#13811 <https://github.com/scipy/scipy/pull/13811>`__: MAINT: Add ci skip to azp * `#13814 <https://github.com/scipy/scipy/pull/13814>`__: ENH/DOC: pydata sphinx theme polishing * `#13817 <https://github.com/scipy/scipy/pull/13817>`__: DOC: Misc parameter typo and casing in scipy/linalg/_decomp_ldl.py * `#13818 <https://github.com/scipy/scipy/pull/13818>`__: MAINT: stats: keep \`entropy\` importable from \`scipy.stats.distributions\` * `#13820 <https://github.com/scipy/scipy/pull/13820>`__: BUG: update _kendall_p_exact ValueError to f-string * `#13831 <https://github.com/scipy/scipy/pull/13831>`__: FIX:DEP: Allow better tolerance control for pinv and pinvh and... * `#13832 <https://github.com/scipy/scipy/pull/13832>`__: BUG: stats: Fix rvs for levy_stable when alpha=1 * `#13833 <https://github.com/scipy/scipy/pull/13833>`__: MAINT: Add inline type hintings for stats.qmc * `#13836 <https://github.com/scipy/scipy/pull/13836>`__: MAINT: Fix a couple compiler warnings. * `#13838 <https://github.com/scipy/scipy/pull/13838>`__: TST: relax test tolerances for BinomTest * `#13841 <https://github.com/scipy/scipy/pull/13841>`__: BLD: add \`-std=c99\` flag to scipy.special extensions using... * `#13845 <https://github.com/scipy/scipy/pull/13845>`__: ENH: stats: add \`method\` parameter to \`differential_entropy\`... * `#13847 <https://github.com/scipy/scipy/pull/13847>`__: TST: skip on optimize failure on macOS, mark one as xfail * `#13848 <https://github.com/scipy/scipy/pull/13848>`__: DOC: optimize: move Nelder Mead doc from Unconstrained minimization... * `#13849 <https://github.com/scipy/scipy/pull/13849>`__: DOC: Roadmap update * `#13852 <https://github.com/scipy/scipy/pull/13852>`__: CI: fix temporary wrong brew version from GitHub * `#13854 <https://github.com/scipy/scipy/pull/13854>`__: ENH: Update Scipy Gitpod * `#13859 <https://github.com/scipy/scipy/pull/13859>`__: TST: fix ultra-slow ttest permutations test * `#13860 <https://github.com/scipy/scipy/pull/13860>`__: MAINT: clean up LSAP error checking * `#13863 <https://github.com/scipy/scipy/pull/13863>`__: DOC: remove seed in examples * `#13865 <https://github.com/scipy/scipy/pull/13865>`__: DOC: optimize: The bounds param of differential_evolution is... * `#13866 <https://github.com/scipy/scipy/pull/13866>`__: MAINT: special: Remove an unused variable from _poly_approx in... * `#13867 <https://github.com/scipy/scipy/pull/13867>`__: DOC: stats: Explain meaning of alternatives for fisher_exact. * `#13868 <https://github.com/scipy/scipy/pull/13868>`__: CI: fix the failing job on linux. * `#13870 <https://github.com/scipy/scipy/pull/13870>`__: MAINT: move LSAP rectangular matrix handling into solver code * `#13871 <https://github.com/scipy/scipy/pull/13871>`__: DOC: Add Gitpod documentation * `#13876 <https://github.com/scipy/scipy/pull/13876>`__: Workflow : Add nightly release of NumPy in linux workflows * `#13877 <https://github.com/scipy/scipy/pull/13877>`__: DOC: Conform to numpydoc + uniformity. * `#13879 <https://github.com/scipy/scipy/pull/13879>`__: BUG: signal: fix get_window argument handling and add tests. * `#13881 <https://github.com/scipy/scipy/pull/13881>`__: CI: remove .travis.yml, remove codecov from CircleCI * `#13882 <https://github.com/scipy/scipy/pull/13882>`__: BLD: ensure incrementing dev version strings * `#13886 <https://github.com/scipy/scipy/pull/13886>`__: TST: optimize: skip test_network_flow_limited_capacity w/ UMFPACK... * `#13888 <https://github.com/scipy/scipy/pull/13888>`__: MAINT: Fix issues involving elif conditions * `#13891 <https://github.com/scipy/scipy/pull/13891>`__: Rename InivariateSpline to UnivariateSpline * `#13893 <https://github.com/scipy/scipy/pull/13893>`__: ENH: linprog HiGHS marginals/sensitivy analysis * `#13894 <https://github.com/scipy/scipy/pull/13894>`__: DOC: Add blank line before \`Return\` section. * `#13897 <https://github.com/scipy/scipy/pull/13897>`__: DOC: BLD: fix doc build version check, and improve build time * `#13903 <https://github.com/scipy/scipy/pull/13903>`__: MAINT: Gitpod fixes * `#13907 <https://github.com/scipy/scipy/pull/13907>`__: ENH: Rewrite minkowski metric in C++ with pybind11 * `#13909 <https://github.com/scipy/scipy/pull/13909>`__: Revert "Workflow : Add nightly release of NumPy in linux workflows" * `#13910 <https://github.com/scipy/scipy/pull/13910>`__: DOC: update Readme * `#13911 <https://github.com/scipy/scipy/pull/13911>`__: MAINT: use dict built-in rather than OrderedDict * `#13920 <https://github.com/scipy/scipy/pull/13920>`__: BUG: Reactivate conda environment in init * `#13925 <https://github.com/scipy/scipy/pull/13925>`__: BUG: stats: magnitude of Yates' correction <= abs(observed-expected)... * `#13926 <https://github.com/scipy/scipy/pull/13926>`__: DOC: correct return type in disjoint_set.subsets docstring * `#13927 <https://github.com/scipy/scipy/pull/13927>`__: DOC/MAINT: Add copyright notice to qmc.primes_from_2_to * `#13928 <https://github.com/scipy/scipy/pull/13928>`__: BUG: DOC: signal: fix need argument config and add missing doc... * `#13929 <https://github.com/scipy/scipy/pull/13929>`__: REL: add PEP 621 (project metadata in pyproject.toml) support * `#13931 <https://github.com/scipy/scipy/pull/13931>`__: MAINT: special: get rid of _logit.c.src * `#13934 <https://github.com/scipy/scipy/pull/13934>`__: ENH: signal: make \`get_window\` supports \`general_cosine\`... * `#13940 <https://github.com/scipy/scipy/pull/13940>`__: MAINT: QMCEngine d input validation * `#13941 <https://github.com/scipy/scipy/pull/13941>`__: MAINT: forward port 1.6.3 relnotes * `#13944 <https://github.com/scipy/scipy/pull/13944>`__: BUG: spatial: fix weight handling of \`distance.sokalmichener\`. * `#13947 <https://github.com/scipy/scipy/pull/13947>`__: MAINT: Remove duplicate calculations in sokalmichener * `#13949 <https://github.com/scipy/scipy/pull/13949>`__: DOC: minor grammar fixes in minimize and KDTree.query * `#13951 <https://github.com/scipy/scipy/pull/13951>`__: ENH: Add Boschloo exact test to stats * `#13956 <https://github.com/scipy/scipy/pull/13956>`__: ENH: spatial: add \`axis\` and \`keepdims\` optional argument... * `#13963 <https://github.com/scipy/scipy/pull/13963>`__: MAINT: stats: Fix unused imports and a few other issues related... * `#13971 <https://github.com/scipy/scipy/pull/13971>`__: DOC: Add Karl Pearson's reference to chi-square test * `#13972 <https://github.com/scipy/scipy/pull/13972>`__: ENH: cluster: add an optional argument \`seed\` for \`kmeans\`... * `#13973 <https://github.com/scipy/scipy/pull/13973>`__: BLD: fix build warnings for causal/anticausal pointers in ndimage * `#13975 <https://github.com/scipy/scipy/pull/13975>`__: ENH: set empty array norm to zero. * `#13977 <https://github.com/scipy/scipy/pull/13977>`__: MAINT: signal: replace distutils templating with tempita * `#13978 <https://github.com/scipy/scipy/pull/13978>`__: MAINT: improve validations and keyword only arguments for some... * `#13979 <https://github.com/scipy/scipy/pull/13979>`__: ENH: Add Inverse of Log CDF of Normal Distribution * `#13983 <https://github.com/scipy/scipy/pull/13983>`__: Fixing \`ndimage.watershed_ift\` tutorial's documentation * `#13987 <https://github.com/scipy/scipy/pull/13987>`__: DOC: Adding examples to docstrings in morphology: white_tophat,... * `#13989 <https://github.com/scipy/scipy/pull/13989>`__: DOC: interpolate: improve examples of \`RegularGridInterpolator\`... * `#13990 <https://github.com/scipy/scipy/pull/13990>`__: MAINT, DOC: optimize: Make the input validation explanation clear... * `#13992 <https://github.com/scipy/scipy/pull/13992>`__: Workflow : Add nightly release of NumPy in linux workflows * `#13995 <https://github.com/scipy/scipy/pull/13995>`__: Doc: Continuous integration information * `#14000 <https://github.com/scipy/scipy/pull/14000>`__: BUG: sparse: Fix DIA.diagonal bug and add a regression test * `#14004 <https://github.com/scipy/scipy/pull/14004>`__: ENH: Fast addition dia matrix * `#14006 <https://github.com/scipy/scipy/pull/14006>`__: MAINT: optimize: add validation to check func parameter number... * `#14008 <https://github.com/scipy/scipy/pull/14008>`__: BUG: Raise exception for inconsistent WAV header * `#14009 <https://github.com/scipy/scipy/pull/14009>`__: DEP: Remove usage of numpy.compat * `#14010 <https://github.com/scipy/scipy/pull/14010>`__: MAINT: add support for wheel DL proxy * `#14012 <https://github.com/scipy/scipy/pull/14012>`__: DOC: Broaden Exact Test Reference * `#14015 <https://github.com/scipy/scipy/pull/14015>`__: MAINT: remove brew update * `#14017 <https://github.com/scipy/scipy/pull/14017>`__: BENCH: Add more formats for sparse arithmetic * `#14018 <https://github.com/scipy/scipy/pull/14018>`__: BENCH: add benchmark for f_oneway * `#14020 <https://github.com/scipy/scipy/pull/14020>`__: MAINT: modify np.int\_ to np.int32 to make it the same for 32/64... * `#14023 <https://github.com/scipy/scipy/pull/14023>`__: MAINT: Fix clang build and remove some unicode characters * `#14025 <https://github.com/scipy/scipy/pull/14025>`__: BUG: sparse: fix DIA.setdiag issue * `#14026 <https://github.com/scipy/scipy/pull/14026>`__: TST: optimize: xfail part of test_powell * `#14029 <https://github.com/scipy/scipy/pull/14029>`__: CI: github macos fix * `#14030 <https://github.com/scipy/scipy/pull/14030>`__: MAINT: use 'yield from <expr>' (PEP 380) * `#14031 <https://github.com/scipy/scipy/pull/14031>`__: MAINT: new-style class, removing inheritance to object * `#14032 <https://github.com/scipy/scipy/pull/14032>`__: MAINT: CXXFLAGS for Pythran * `#14033 <https://github.com/scipy/scipy/pull/14033>`__: ENH: Port sqeuclidean and braycurtis to _distance_pybind * `#14034 <https://github.com/scipy/scipy/pull/14034>`__: MAINT: Clean-up 'next = __next__' * `#14045 <https://github.com/scipy/scipy/pull/14045>`__: MAINT: bump PYVER pavement.py * `#14047 <https://github.com/scipy/scipy/pull/14047>`__: DEV: initialize boost submodule in Gitpod Dockerfile * `#14051 <https://github.com/scipy/scipy/pull/14051>`__: BLD: if boost submodule content is missing, error out early * `#14052 <https://github.com/scipy/scipy/pull/14052>`__: DOC: missing submodule init information * `#14057 <https://github.com/scipy/scipy/pull/14057>`__: DOC: special: Add Examples to \`psi\` docstring * `#14058 <https://github.com/scipy/scipy/pull/14058>`__: BUG: fixed a dtype bug in linalg.solve. * `#14060 <https://github.com/scipy/scipy/pull/14060>`__: Doc: Fix typo in documentation of spence function. * `#14061 <https://github.com/scipy/scipy/pull/14061>`__: MAINT:stats: Type annotations for _sobol.pyx * `#14062 <https://github.com/scipy/scipy/pull/14062>`__: DOC: A few small fixes in quickstart_gitpod.rst * `#14063 <https://github.com/scipy/scipy/pull/14063>`__: DOC: signal: add Add Examples to \`cont2discrete\` docstring * `#14064 <https://github.com/scipy/scipy/pull/14064>`__: DOC: optimize: Add Examples to fmin_bfgs docstring * `#14065 <https://github.com/scipy/scipy/pull/14065>`__: Add example for scipy stats.trim1 under docstring * `#14066 <https://github.com/scipy/scipy/pull/14066>`__: DOC add example to scipy.special.hermite * `#14067 <https://github.com/scipy/scipy/pull/14067>`__: DOC add alpha docstring description, add example to docstring * `#14070 <https://github.com/scipy/scipy/pull/14070>`__: DOC add parameters, return, and example to docstring * `#14072 <https://github.com/scipy/scipy/pull/14072>`__: MAINT/TST: Fix tests failing with the nightly build of numpy. * `#14075 <https://github.com/scipy/scipy/pull/14075>`__: DOC Improve the code snippet in signal.hilbert docstring. * `#14076 <https://github.com/scipy/scipy/pull/14076>`__: DOC: Document Jensen-Shannon distance being accepted by cdist/pdist * `#14079 <https://github.com/scipy/scipy/pull/14079>`__: BLD: Avoid importing scipy.stats during cythonize stage * `#14082 <https://github.com/scipy/scipy/pull/14082>`__: MAINT: Remove old, commented extract_diagonal * `#14083 <https://github.com/scipy/scipy/pull/14083>`__: MAINT: sparse: Remove defunct function extract_diagonal * `#14085 <https://github.com/scipy/scipy/pull/14085>`__: ENH: Implement canberra distance in _distance_pybind * `#14086 <https://github.com/scipy/scipy/pull/14086>`__: MAINT: Clear scipy namespace of entries better imported from... * `#14088 <https://github.com/scipy/scipy/pull/14088>`__: Install Pythran from sources for python 3.10 * `#14092 <https://github.com/scipy/scipy/pull/14092>`__: BUG: Fixes issue with clang. * `#14094 <https://github.com/scipy/scipy/pull/14094>`__: DOC: Correct the inconsistence definition of Default in class... * `#14105 <https://github.com/scipy/scipy/pull/14105>`__: TST: stats: mannwhitneyu: check that mstats and stats mannwhitneyu... * `#14106 <https://github.com/scipy/scipy/pull/14106>`__: DOC: stats.mstats: mannwhitneyu: the returned statistic is the... * `#14107 <https://github.com/scipy/scipy/pull/14107>`__: ENH: stats: bootstrap: add \`vectorized\` parameter; automatically... * `#14109 <https://github.com/scipy/scipy/pull/14109>`__: BUG: fix two issues in the fblas signature files * `#14110 <https://github.com/scipy/scipy/pull/14110>`__: DOC: mailmap update * `#14113 <https://github.com/scipy/scipy/pull/14113>`__: ENH: stats: bootstrap: add \`paired\` parameter * `#14116 <https://github.com/scipy/scipy/pull/14116>`__: MAINT: fix deprecated Python C API usage in odr * `#14118 <https://github.com/scipy/scipy/pull/14118>`__: DOC: 1.7.0 release notes * `#14125 <https://github.com/scipy/scipy/pull/14125>`__: DOC: fix typo * `#14126 <https://github.com/scipy/scipy/pull/14126>`__: ENH: stats: bootstrap: add \`batch\` parameter to control batch... * `#14127 <https://github.com/scipy/scipy/pull/14127>`__: CI: upgrade pip in benchmarks CI run * `#14130 <https://github.com/scipy/scipy/pull/14130>`__: BUG: Fix trust-constr report TypeError if verbose is set to 2... * `#14133 <https://github.com/scipy/scipy/pull/14133>`__: MAINT: interpolate: raise NotImplementedError not ValueError * `#14139 <https://github.com/scipy/scipy/pull/14139>`__: FIX/DOC: lsqr doctests print failure * `#14145 <https://github.com/scipy/scipy/pull/14145>`__: MAINT: 1.7.x version pins ("backport") * `#14146 <https://github.com/scipy/scipy/pull/14146>`__: MAINT: commit count if no tag * `#14164 <https://github.com/scipy/scipy/pull/14164>`__: TST, BUG: fix rbf matrix value * `#14166 <https://github.com/scipy/scipy/pull/14166>`__: CI, MAINT: restrictions on pre-release CI * `#14171 <https://github.com/scipy/scipy/pull/14171>`__: TST: signal: Bump tolerances for a test of Gustafsson's... * `#14175 <https://github.com/scipy/scipy/pull/14175>`__: TST: stats: Loosen tolerance in some binomtest tests. * `#14182 <https://github.com/scipy/scipy/pull/14182>`__: MAINT: stats: Update ppcc_plot and ppcc_max docstring. * `#14195 <https://github.com/scipy/scipy/pull/14195>`__: MAINT: download-wheels missing import * `#14230 <https://github.com/scipy/scipy/pull/14230>`__: REL: stop shipping generated Cython sources in sdist Checksums ========= MD5 ~~~ 723fe734dc1f49274454819c3082b02b scipy-1.7.0rc2-cp37-cp37m-macosx_10_9_x86_64.whl 3d9eac78e03298a51196d02458d1d49c scipy-1.7.0rc2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 050de4e379b55f7af52bc7415fe92a3b scipy-1.7.0rc2-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl 92322931a3ac5fe03f4f4242c866c524 scipy-1.7.0rc2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl f49bf61bfab4b248638f2b1cae361ed9 scipy-1.7.0rc2-cp37-cp37m-win32.whl 37f6762a03375501f9f62a42a7630427 scipy-1.7.0rc2-cp37-cp37m-win_amd64.whl bf461a9bd869e12d506ec13c2af5bb82 scipy-1.7.0rc2-cp38-cp38-macosx_10_9_x86_64.whl 96b0a804ceaf6e66e036f9adb680f18d scipy-1.7.0rc2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 347f567129061863b4c97a27da78baa4 scipy-1.7.0rc2-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl de88ecccaad1c36ccc98e0a6c2fc826a scipy-1.7.0rc2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl 7a4041bfb2c7efb25cd1a8aaca3341c8 scipy-1.7.0rc2-cp38-cp38-win32.whl aa65d3cee38ee58dc51c02e8efc7a740 scipy-1.7.0rc2-cp38-cp38-win_amd64.whl 7e4625f35b18fd5fe583fdb7ce537804 scipy-1.7.0rc2-cp39-cp39-macosx_10_9_x86_64.whl d0a394d3a5f84e8b72738173f8a56a68 scipy-1.7.0rc2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl c93d965330fe34a671c9f849a5976309 scipy-1.7.0rc2-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl 1ed5be440f58786ad79b5e22d8e0832b scipy-1.7.0rc2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl ecbffc705d0354294e789c9342a96758 scipy-1.7.0rc2-cp39-cp39-win32.whl 23ddd7d8cf958ecbbae4dd25569db2f5 scipy-1.7.0rc2-cp39-cp39-win_amd64.whl c5df87bb977974cc58d0b303760567c8 scipy-1.7.0rc2.tar.gz 6f085abd8063212c4d093991e7e296cf scipy-1.7.0rc2.tar.xz d7e0fd0116747993ab49c2cd7b50f917 scipy-1.7.0rc2.zip SHA256 ~~~~~~ 243f285cf6421a71e4061efba0bb816d4d22501231cb600862878dead9f4039d scipy-1.7.0rc2-cp37-cp37m-macosx_10_9_x86_64.whl 04aae1cb78fd914ee854ac2d81c71fc8582a08f43f83659c46f57c9c51d2387d scipy-1.7.0rc2-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 4e524b5cadb762b623898261f0715f1f9b93a5272850cbfc9c333997f6f71f55 scipy-1.7.0rc2-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl 545ccf90903e2f75fbadad01824f7b806d457be0146eea2a7e14a7a0c130ca37 scipy-1.7.0rc2-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl 40d7b9a60ef0cdbcce4e51166c6a1df02b6b7c38a5a6324148a305db416ef597 scipy-1.7.0rc2-cp37-cp37m-win32.whl ce5f28458f7118b927b32187fdd42398ecb6a7777a0894e84a7726581257d5cf scipy-1.7.0rc2-cp37-cp37m-win_amd64.whl 47d375a4085adcf0d42a4499810be403323b6d01a3c049036e1c1c5d689887fd scipy-1.7.0rc2-cp38-cp38-macosx_10_9_x86_64.whl f4beec4562f944f3e583c3c0c2a40ec13731588383b18b63e2ee9bf89e9d56ac scipy-1.7.0rc2-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl d29dce260e4933ef858ff7f645b6440312982bb23067a175952654f55967c208 scipy-1.7.0rc2-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl c9efb79e6dd4563eafa59708d3a90b69d89a55b5f6afe28d018d74497cdc08c3 scipy-1.7.0rc2-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl db75e54adb7359b29254e144cf1e9190be6dcc9d29b7b423f3b3c5c7c2306bc1 scipy-1.7.0rc2-cp38-cp38-win32.whl a0f89ba9f674ab696cb2cd463f344b870c81299b966d30196bc6237c68734e8b scipy-1.7.0rc2-cp38-cp38-win_amd64.whl f0b3beb9bf332a031a49259dcc4d4cb3f425bd7429e646783fa8dea2ae1eee63 scipy-1.7.0rc2-cp39-cp39-macosx_10_9_x86_64.whl 7fe5bd2f126545667bc8f59773bf5140dedc6cc457a6543d0cf7bb94138411e6 scipy-1.7.0rc2-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl f6dc2287afcb02607a84e687c4d9e597d1916830836356129b0ce3bf0798b9d2 scipy-1.7.0rc2-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl d597c6ff7624b6a387ce3ac6cda95e1ed23b2346a5e35ca655790bf4133c1dc3 scipy-1.7.0rc2-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl 842b23d45aed8dbed3b6df02209a7154be4744ae57b3f3ce3f724b79871352d7 scipy-1.7.0rc2-cp39-cp39-win32.whl 55d19c4fa237a47f9314618977664527f0260a205e7de3a9b8c9403686afdf0a scipy-1.7.0rc2-cp39-cp39-win_amd64.whl bb5598f8e349e77a9f05d2be605a75b5752648669a0886379b257a449fce244b scipy-1.7.0rc2.tar.gz 48bdd6fbe46aa4c75948ae1e2acefcf2ceaa548b12575fa29ebcc999eb314a8f scipy-1.7.0rc2.tar.xz 886ea7c4aa98d1b46ba64d1928217219db4fc790dd0b07cb62af0e736cc8aa6c scipy-1.7.0rc2.zip

1 0

Adding Wigner-Ville distribution and related methods to scipy.signal
by Leander Claes June 14, 2021

June 14, 2021

Dear SciPy developers, I recently submitted a pull request to add the Wigner-Ville distribution (wvd) to scipy.signal (https://github.com/scipy/scipy/pull/14141). To oversimplify the description of the wvd: It is a method for time-frequency analysis similar to the short-time Fourier-transform or the wavelet transform with some really interesting properties that makes it useful in many applications (e.g. detecting gravitational waves). We often use it in our group and we teach it to students in our lecture on signal processing with python. It was kindly suggested that I send a mail to this list first to check if there was need for such a function. So here I am: Do you think that Wigner-Ville distribution (and maybe later some the derived methods) should be added scipy? Thank you for the consideration. Best regards, Leander (lndr)

1 0

ANN: SciPy 1.7.0rc1 -- please test
by Tyler Reddy June 9, 2021

June 9, 2021

Hi all, On behalf of the SciPy development team I'm pleased to announce the release candidate SciPy 1.7.0rc1. Please help us test this pre-release. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.7.0rc1 One of a few ways to install the release candidate with pip: pip install scipy==1.7.0rc1 ===================== SciPy 1.7.0 Release Notes ===================== Note: Scipy 1.7.0 is not released yet! SciPy 1.7.0 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 1.7.x branch, and on adding new features on the master branch. This release requires Python 3.7+ and NumPy 1.16.5 or greater. For running on PyPy, PyPy3 6.0+ is required. **************************** Highlights of this release **************************** - A new submodule for quasi-Monte Carlo, `scipy.stats.qmc`, was added - The documentation design was updated to use the same PyData-Sphinx theme as other NumFOCUS packages like NumPy. - We now vendor and leverage the Boost C++ library to enable numerous improvements for long-standing weaknesses in `scipy.stats` - `scipy.stats` has six new distributions, eight new (or overhauled) hypothesis tests, a new function for bootstrapping, a class that enables fast random variate sampling and percentile point function evaluation, and many other enhancements. - ``cdist`` and ``pdist`` distance calculations are faster for several metrics, especially weighted cases, thanks to a rewrite to a new C++ backend framework - A new class for radial basis function interpolation, `RBFInterpolator`, was added to address issues with the `Rbf` class. We gratefully acknowledge the Chan-Zuckerberg Initiative Essential Open Source Software for Science program for supporting many of the improvements to `scipy.stats`. *************** New features *************** `scipy.cluster` improvements ====================== An optional argument, ``seed``, has been added to ``kmeans`` and ``kmeans2`` to set the random generator and random state. `scipy.interpolate` improvements ========================= Improved input validation and error messages for ``fitpack.bispev`` and ``fitpack.parder`` for scenarios that previously caused substantial confusion for users. The class `RBFInterpolator` was added to supersede the `Rbf` class. The new class has usage that more closely follows other interpolator classes, corrects sign errors that caused unexpected smoothing behavior, includes polynomial terms in the interpolant (which are necessary for some RBF choices), and supports interpolation using only the k-nearest neighbors for memory efficiency. `scipy.linalg` improvements ===================== An LAPACK wrapper was added for access to the ``tgexc`` subroutine. `scipy.ndimage` improvements ======================= `scipy.ndimage.affine_transform` is now able to infer the ``output_shape`` from the ``out`` array. `scipy.optimize` improvements ======================= The optional parameter ``bounds`` was added to ``_minimize_neldermead`` to support bounds constraints for the Nelder-Mead solver. ``trustregion`` methods ``trust-krylov``, ``dogleg`` and ``trust-ncg`` can now estimate ``hess`` by finite difference using one of ``["2-point", "3-point", "cs"]``. ``halton`` was added as a ``sampling_method`` in `scipy.optimize.shgo`. ``sobol`` was fixed and is now using `scipy.stats.qmc.Sobol`. ``halton`` and ``sobol`` were added as ``init`` methods in `scipy.optimize.differential_evolution.` ``differential_evolution`` now accepts an ``x0`` parameter to provide an initial guess for the minimization. ``least_squares`` has a modest performance improvement when SciPy is built with Pythran transpiler enabled. When ``linprog`` is used with ``method`` ``'highs'``, ``'highs-ipm'``, or ``'highs-ds'``, the result object now reports the marginals (AKA shadow prices, dual values) and residuals associated with each constraint. `scipy.signal` improvements ===================== ``get_window`` supports ``general_cosine`` and ``general_hamming`` window functions. `scipy.signal.medfilt2d` now releases the GIL where appropriate to enable performance gains via multithreaded calculations. `scipy.sparse` improvements ====================== Addition of ``dia_matrix`` sparse matrices is now faster. `scipy.spatial` improvements ====================== ``distance.cdist`` and ``distance.pdist`` performance has greatly improved for certain weighted metrics. Namely: ``minkowski``, ``euclidean``, ``chebyshev``, ``canberra``, and ``cityblock``. Modest performance improvements for many of the unweighted ``cdist`` and ``pdist`` metrics noted above. The parameter ``seed`` was added to `scipy.spatial.vq.kmeans` and `scipy.spatial.vq.kmeans2`. The parameters ``axis`` and ``keepdims`` where added to `scipy.spatial.distance.jensenshannon`. The ``rotation`` methods ``from_rotvec`` and ``as_rotvec`` now accept a ``degrees`` argument to specify usage of degrees instead of radians. `scipy.special` improvements ====================== Wright's generalized Bessel function for positive arguments was added as `scipy.special.wright_bessel.` An implementation of the inverse of the Log CDF of the Normal Distribution is now available via `scipy.special.ndtri_exp`. `scipy.stats` improvements ==================== Hypothesis Tests ----------------------- The Mann-Whitney-Wilcoxon test, ``mannwhitneyu``, has been rewritten. It now supports n-dimensional input, an exact test method when there are no ties, and improved documentation. Please see "Other changes" for adjustments to default behavior. The new function `scipy.stats.binomtest` replaces `scipy.stats.binom_test`. The new function returns an object that calculates a confidence intervals of the proportion parameter. Also, performance was improved from O(n) to O(log(n)) by using binary search. The two-sample version of the Cramer-von Mises test is implemented in `scipy.stats.cramervonmises_2samp`. The Alexander-Govern test is implemented in the new function `scipy.stats.alexandergovern`. The new functions `scipy.stats.barnard_exact` and `scipy.stats. boschloo_exact` respectively perform Barnard's exact test and Boschloo's exact test for 2x2 contingency tables. The new function `scipy.stats.page_trend_test` performs Page's test for ordered alternatives. The new function `scipy.stats.somersd` performs Somers' D test for ordinal association between two variables. An option, ``permutations``, has been added in `scipy.stats.ttest_ind` to perform permutation t-tests. A ``trim`` option was also added to perform a trimmed (Yuen's) t-test. The ``alternative`` parameter was added to the ``skewtest``, ``kurtosistest``, ``ranksums``, ``mood``, ``ansari``, ``linregress``, and ``spearmanr`` functions to allow one-sided hypothesis testing. Sample statistics ----------------------- The new function `scipy.stats.differential_entropy` estimates the differential entropy of a continuous distribution from a sample. The ``boxcox`` and ``boxcox_normmax`` now allow the user to control the optimizer used to minimize the negative log-likelihood function. A new function `scipy.stats.contingency.relative_risk` calculates the relative risk, or risk ratio, of a 2x2 contingency table. The object returned has a method to compute the confidence interval of the relative risk. Performance improvements in the ``skew`` and ``kurtosis`` functions achieved by removal of repeated/redundant calculations. Substantial performance improvements in `scipy.stats.mstats.hdquantiles_sd`. The new function `scipy.stats.contingency.association` computes several measures of association for a contingency table: Pearsons contingency coefficient, Cramer's V, and Tschuprow's T. The parameter ``nan_policy`` was added to `scipy.stats.zmap` to provide options for handling the occurrence of ``nan`` in the input data. The parameter ``ddof`` was added to `scipy.stats.variation` and `scipy.stats.mstats.variation`. The parameter ``weights`` was added to `scipy.stats.gmean`. Statistical Distributions ------------------------------- We now vendor and leverage the Boost C++ library to address a number of previously reported issues in ``stats``. Notably, ``beta``, ``binom``, ``nbinom`` now have Boost backends, and it is straightforward to leverage the backend for additional functions. The skew Cauchy probability distribution has been implemented as `scipy.stats.skewcauchy`. The Zipfian probability distribution has been implemented as `scipy.stats.zipfian`. The new distributions ``nchypergeom_fisher`` and ``nchypergeom_wallenius`` implement the Fisher and Wallenius versions of the noncentral hypergeometric distribution, respectively. The generalized hyperbolic distribution was added in `scipy.stats.genhyperbolic`. The studentized range distribution was added in `scipy.stats.studentized_range`. `scipy.stats.argus` now has improved handling for small parameter values. Better argument handling/preparation has resulted in performance improvements for many distributions. The ``cosine`` distribution has added ufuncs for ``ppf``, ``cdf``, ``sf``, and ``isf`` methods including numerical precision improvements at the edges of the support of the distribution. An option to fit the distribution to data by the method of moments has been added to the ``fit`` method of the univariate continuous distributions. Other -------- `scipy.stats.bootstrap` has been added to allow estimation of the confidence interval and standard error of a statistic. The new function `scipy.stats.contingency.crosstab` computes a contingency table (i.e. a table of counts of unique entries) for the given data. `scipy.stats.NumericalInverseHermite` enables fast random variate sampling and percentile point function evaluation of an arbitrary univariate statistical distribution. New `scipy.stats.qmc` module ---------------------------------------- This new module provides Quasi-Monte Carlo (QMC) generators and associated helper functions. It provides a generic class `scipy.stats.qmc.QMCEngine` which defines a QMC engine/sampler. An engine is state aware: it can be continued, advanced and reset. 3 base samplers are available: - `scipy.stats.qmc.Sobol` the well known Sobol low discrepancy sequence. Several warnings have been added to guide the user into properly using this sampler. The sequence is scrambled by default. - `scipy.stats.qmc.Halton`: Halton low discrepancy sequence. The sequence is scrambled by default. - `scipy.stats.qmc.LatinHypercube`: plain LHS design. And 2 special samplers are available: - `scipy.stats.qmc.MultinomialQMC`: sampling from a multinomial distribution using any of the base `scipy.stats.qmc.QMCEngine`. - `scipy.stats.qmc.MultivariateNormalQMC`: sampling from a multivariate Normal using any of the base `scipy.stats.qmc.QMCEngine`. The module also provide the following helpers: - `scipy.stats.qmc.discrepancy`: assess the quality of a set of points in terms of space coverage. - `scipy.stats.qmc.update_discrepancy`: can be used in an optimization loop to construct a good set of points. - `scipy.stats.qmc.scale`: easily scale a set of points from (to) the unit interval to (from) a given range. *********************** Deprecated features *********************** `scipy.linalg` deprecations ==================== - `scipy.linalg.pinv2` is deprecated and its functionality is completely subsumed into `scipy.linalg.pinv` - Both ``rcond``, ``cond`` keywords of `scipy.linalg.pinv` and `scipy.linalg.pinvh` were not working and now are deprecated. They are now replaced with functioning ``atol`` and ``rtol`` keywords with clear usage. `scipy.spatial` deprecations ===================== - `scipy.spatial.distance` metrics expect 1d input vectors but will call ``np.squeeze`` on their inputs to accept any extra length-1 dimensions. That behaviour is now deprecated. ************************************** Backwards incompatible changes ************************************** ***************** Other changes ***************** We now accept and leverage performance improvements from the ahead-of-time Python-to-C++ transpiler, Pythran, which can be optionally disabled (via ``export SCIPY_USE_PYTHRAN=0``) but is enabled by default at build time. There are two changes to the default behavior of `scipy.stats.mannwhitenyu`: - For years, use of the default ``alternative=None`` was deprecated; explicit ``alternative`` specification was required. Use of the new default value of ``alternative``, "two-sided", is now permitted. - Previously, all p-values were based on an asymptotic approximation. Now, for small samples without ties, the p-values returned are exact by default. Support has been added for PEP 621 (project metadata in ``pyproject.toml``) We now support a Gitpod environment to reduce the barrier to entry for SciPy development; for more details see :ref:`quickstart-gitpod`. ********* Authors ********* * @endolith * Jelle Aalbers + * Adam + * Tania Allard + * Sven Baars + * Max Balandat + * baumgarc + * Christoph Baumgarten * Peter Bell * Lilian Besson * Robinson Besson + * Max Bolingbroke * Blair Bonnett + * Jordão Bragantini * Harm Buisman + * Evgeni Burovski * Matthias Bussonnier * Dominic C * CJ Carey * Ramón Casero + * Chachay + * charlotte12l + * Benjamin Curtice Corbett + * Falcon Dai + * Ian Dall + * Terry Davis * droussea2001 + * DWesl + * dwight200 + * Thomas J. Fan + * Joseph Fox-Rabinovitz * Max Frei + * Laura Gutierrez Funderburk + * gbonomib + * Matthias Geier + * Pradipta Ghosh + * Ralf Gommers * Evan H + * h-vetinari * Matt Haberland * Anselm Hahn + * Alex Henrie * Piet Hessenius + * Trever Hines + * Elisha Hollander + * Stephan Hoyer * Tom Hu + * Kei Ishikawa + * Julien Jerphanion * Robert Kern * Shashank KS + * Peter Mahler Larsen * Eric Larson * Cheng H. Lee + * Gregory R. Lee * Jean-Benoist Leger + * lgfunderburk + * liam-o-marsh + * Xingyu Liu + * Alex Loftus + * Christian Lorentzen + * Cong Ma * Marc + * MarkPundurs + * Markus Löning + * Liam Marsh + * Nicholas McKibben * melissawm + * Jamie Morton * Andrew Nelson * Nikola Forró * Tor Nordam + * Olivier Gauthé + * Rohit Pandey + * Avanindra Kumar Pandeya + * Tirth Patel * paugier + * Alex H. Wagner, PhD + * Jeff Plourde + * Ilhan Polat * pranavrajpal + * Vladyslav Rachek * Bharat Raghunathan * Recursing + * Tyler Reddy * Lucas Roberts * Gregor Robinson + * Pamphile Roy + * Atsushi Sakai * Benjamin Santos * Martin K. Scherer + * Thomas Schmelzer + * Daniel Scott + * Sebastian Wallkötter + * serge-sans-paille + * Namami Shanker + * Masashi Shibata + * Alexandre de Siqueira + * Albert Steppi + * Adam J. Stewart + * Kai Striega * Diana Sukhoverkhova * Søren Fuglede Jørgensen * Mike Taves * Dan Temkin + * Nicolas Tessore + * tsubota20 + * Robert Uhl * christos val + * Bas van Beek + * Ashutosh Varma + * Jose Vazquez + * Sebastiano Vigna * Aditya Vijaykumar * VNMabus * Arthur Volant + * Samuel Wallan * Stefan van der Walt * Warren Weckesser * Anreas Weh * Josh Wilson * Rory Yorke * Egor Zemlyanoy * Marc Zoeller + * zoj613 + * 秋纫 + A total of 126 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 1.7.0 ************************** * `#636 <https://github.com/scipy/scipy/issues/636>`__: Statistics Review: mannwhitneyu (Trac #109) * `#1346 <https://github.com/scipy/scipy/issues/1346>`__: signal.medfilt2d should fall back on signal.medfilt for types... * `#2118 <https://github.com/scipy/scipy/issues/2118>`__: Mann-Whitney statistic returns incorrect results (Trac #1593) * `#2158 <https://github.com/scipy/scipy/issues/2158>`__: special.chndtrix (ncx2.ppf) gives wrong results (Trac #1633) * `#3284 <https://github.com/scipy/scipy/issues/3284>`__: build_sphinx weirdness * `#3352 <https://github.com/scipy/scipy/issues/3352>`__: beta distribution sf * `#4067 <https://github.com/scipy/scipy/issues/4067>`__: Mannwhitneyu with arrays full of nan still reports significance * `#4080 <https://github.com/scipy/scipy/issues/4080>`__: entropy in Scipy * `#4641 <https://github.com/scipy/scipy/issues/4641>`__: mstats.mannwhitneyu and stats.mannwhitneyu return inconsistent... * `#5122 <https://github.com/scipy/scipy/issues/5122>`__: scipy.stats.binom.ppf Incorrect for p=0 * `#5180 <https://github.com/scipy/scipy/issues/5180>`__: Rbf interpolation - use only K nearest neighbors * `#5258 <https://github.com/scipy/scipy/issues/5258>`__: affine_transform complains about output_shape when output array... * `#5562 <https://github.com/scipy/scipy/issues/5562>`__: Wishart degrees of freedom should be $v > p-1$ instead of $v... * `#5933 <https://github.com/scipy/scipy/issues/5933>`__: mstats_basic.py - mannwhitneyu [scipy/scipy/stats/mstats_basic.py] * `#6409 <https://github.com/scipy/scipy/issues/6409>`__: _unequal_var_ttest_denom causes ZeroDivisionError in early samples * `#6682 <https://github.com/scipy/scipy/issues/6682>`__: negative binomial survival function is imprecise * `#6897 <https://github.com/scipy/scipy/issues/6897>`__: scipy.stats.mannwhitneyu of empty sets gives p=0.0 and does not... * `#7303 <https://github.com/scipy/scipy/issues/7303>`__: stats.describe with nan_policy=omit returns matrix-wide minmax... * `#7406 <https://github.com/scipy/scipy/issues/7406>`__: scipy.stats.binom.ppf returns nan for q between 0 and 1 if n... * `#7437 <https://github.com/scipy/scipy/issues/7437>`__: ENH: add skewed Cauchy distribution to stats * `#7542 <https://github.com/scipy/scipy/issues/7542>`__: DOC: stats tutorials: Questions on arcsine and Student t formulae * `#7593 <https://github.com/scipy/scipy/issues/7593>`__: Meaning of \`tol\` argument in \`scipy.optimize.minimize\` is... * `#8565 <https://github.com/scipy/scipy/issues/8565>`__: Error in SmoothSphereBivariateSpline(): "ValueError: Error code... * `#8665 <https://github.com/scipy/scipy/issues/8665>`__: \`scipy.ncx2.sf\` should be monotone decreasing * `#8836 <https://github.com/scipy/scipy/issues/8836>`__: scipy.optimize.linprog(method='simplex') needs to return duals * `#9184 <https://github.com/scipy/scipy/issues/9184>`__: Mann-Whitney implementation wrong? * `#9450 <https://github.com/scipy/scipy/issues/9450>`__: allow seeding of init methods in vq.kmeans2 * `#9704 <https://github.com/scipy/scipy/issues/9704>`__: RectSphereBivariateSpline fails for negative longitude * `#9836 <https://github.com/scipy/scipy/issues/9836>`__: scipy.stats.rice gives incorrect results when s is very low compared... * `#9904 <https://github.com/scipy/scipy/issues/9904>`__: Request/Proposal: Greatly improve scipy.interpolate.Rbf * `#9981 <https://github.com/scipy/scipy/issues/9981>`__: stats.kruskal : add a warning for an input with 2 or more columns * `#10358 <https://github.com/scipy/scipy/issues/10358>`__: DOC: linprog and linear_sum_assignment tutorials needed * `#10908 <https://github.com/scipy/scipy/issues/10908>`__: Nakami fitting doesn't converge (scipy.stats) * `#10933 <https://github.com/scipy/scipy/issues/10933>`__: Add scaled inverse chi2 distribution * `#11014 <https://github.com/scipy/scipy/issues/11014>`__: Barnard's Test for More Powerful Hypothesis Testing of 2x2 Contingency... * `#11050 <https://github.com/scipy/scipy/issues/11050>`__: Feature request: Nelder-Mead with bounds * `#11086 <https://github.com/scipy/scipy/issues/11086>`__: scipy.stats.skew doesn't work correctly for float point numbers * `#11113 <https://github.com/scipy/scipy/issues/11113>`__: inconsistent result from ttest_ind and mannwhitneyu when used... * `#11134 <https://github.com/scipy/scipy/issues/11134>`__: Wrong confidence interval for binomial distribution with p=0 * `#11325 <https://github.com/scipy/scipy/issues/11325>`__: Add axis parameter for scipy.spatial.distance.jensenshannon * `#11474 <https://github.com/scipy/scipy/issues/11474>`__: scipy.stats.skellam.cdf(0) returns 0 for large mu1 = mu2 * `#11523 <https://github.com/scipy/scipy/issues/11523>`__: scipy.stats.zipf doesn't implement zipf distribution * `#11848 <https://github.com/scipy/scipy/issues/11848>`__: How to get Lagrange / lambda multipliers out of 'linprog' optimize... * `#11909 <https://github.com/scipy/scipy/issues/11909>`__: Enable bounds for lambda in boxcox * `#12118 <https://github.com/scipy/scipy/issues/12118>`__: Docstring missing defaults * `#12132 <https://github.com/scipy/scipy/issues/12132>`__: Slow tests to be trimmed or moved to test('full') * `#12230 <https://github.com/scipy/scipy/issues/12230>`__: Dendrogram: enable leaves labelling with 'labels' when using... * `#12282 <https://github.com/scipy/scipy/issues/12282>`__: scipy.stats.chisquare test does not check that observed and expected... * `#12298 <https://github.com/scipy/scipy/issues/12298>`__: BUG: fmin_powell missing squeeze in 1.5.0rc * `#12403 <https://github.com/scipy/scipy/issues/12403>`__: Add nan_policy to stats.zmap * `#12518 <https://github.com/scipy/scipy/issues/12518>`__: Null hypothesis of Kolmogorov Smirnov test is not correctly described * `#12534 <https://github.com/scipy/scipy/issues/12534>`__: Feature request: scipy.linalg.norm to deal with 0-size array * `#12622 <https://github.com/scipy/scipy/issues/12622>`__: scipy.interpolate.interpn docstring example * `#12635 <https://github.com/scipy/scipy/issues/12635>`__: scipy.stats.beta.ppf gives unexpexted results * `#12669 <https://github.com/scipy/scipy/issues/12669>`__: Median-averaging of complex CSDs * `#12731 <https://github.com/scipy/scipy/issues/12731>`__: stats.ncx2.cdf fails for nc >> x >> 1 * `#12778 <https://github.com/scipy/scipy/issues/12778>`__: Confusing documentation of scipy.stats.weightedtau * `#12794 <https://github.com/scipy/scipy/issues/12794>`__: [Bug] The result of stats.beta.isf is inconsistent with stats.beta.sf * `#12837 <https://github.com/scipy/scipy/issues/12837>`__: stats.mannwhitneyu could support arrays * `#12868 <https://github.com/scipy/scipy/issues/12868>`__: Vector-valued interpolation in \`interp2d\` * `#12922 <https://github.com/scipy/scipy/issues/12922>`__: Minimize with trust-constr method leads to TypeError if option... * `#12929 <https://github.com/scipy/scipy/issues/12929>`__: The use of starred expressions to create data detracts from understanding... * `#12965 <https://github.com/scipy/scipy/issues/12965>`__: domain of argument of scipy.interpolate.RectSphereBivariateSpline(u,... * `#13025 <https://github.com/scipy/scipy/issues/13025>`__: Generalized Hyperbolic Distribution * `#13090 <https://github.com/scipy/scipy/issues/13090>`__: Broken link in doc for signal.max_len_seq * `#13101 <https://github.com/scipy/scipy/issues/13101>`__: MAINT: Upgrade python version in docker file * `#13158 <https://github.com/scipy/scipy/issues/13158>`__: \`signal.get_window()\` has a missing doc link and cannot get... * `#13173 <https://github.com/scipy/scipy/issues/13173>`__: Uninformative error message from bisplev function * `#13234 <https://github.com/scipy/scipy/issues/13234>`__: BUG: stats: Wrong shape of burr.moment() and fisk.moment() when... * `#13242 <https://github.com/scipy/scipy/issues/13242>`__: Does kmeans "drop" clusters? * `#13243 <https://github.com/scipy/scipy/issues/13243>`__: tgsen uses an output argument for computing a default argument * `#13245 <https://github.com/scipy/scipy/issues/13245>`__: Kurtosis returning 1 for array of same elements * `#13257 <https://github.com/scipy/scipy/issues/13257>`__: GitHub Actions test failures for MacOS * `#13272 <https://github.com/scipy/scipy/issues/13272>`__: scipy.stats.yeojohnson_llf doc mistake * `#13280 <https://github.com/scipy/scipy/issues/13280>`__: Wrong results with hypergeom cdf * `#13285 <https://github.com/scipy/scipy/issues/13285>`__: description correction in scipy.stats.t * `#13287 <https://github.com/scipy/scipy/issues/13287>`__: Generate binomial CDF with mu instead of prob * `#13294 <https://github.com/scipy/scipy/issues/13294>`__: BUG: stats: wrong bounds returned by 'support' method for distributions... * `#13299 <https://github.com/scipy/scipy/issues/13299>`__: Typing for scipy.spatial * `#13300 <https://github.com/scipy/scipy/issues/13300>`__: Add a single individual to a latinhypercube initial population... * `#13311 <https://github.com/scipy/scipy/issues/13311>`__: MAINT: pavement.py PYVER is outdated * `#13339 <https://github.com/scipy/scipy/issues/13339>`__: savemat discards dimension information if any dimension is zero * `#13341 <https://github.com/scipy/scipy/issues/13341>`__: add scipy.stats.variation with an ddof parameter * `#13353 <https://github.com/scipy/scipy/issues/13353>`__: Documentation: in scipy.stats.johnsonsu, parameter \`a\` can... * `#13405 <https://github.com/scipy/scipy/issues/13405>`__: TST: add a few tests for sparse BSR ctor * `#13410 <https://github.com/scipy/scipy/issues/13410>`__: BUG: skew for empty array raises * `#13417 <https://github.com/scipy/scipy/issues/13417>`__: 10,000 times speedup for generating random numbers from the cosine... * `#13440 <https://github.com/scipy/scipy/issues/13440>`__: python runtest.py -t path-to-test.py failed * `#13454 <https://github.com/scipy/scipy/issues/13454>`__: Scipy cosine distance can be greater than 2 * `#13459 <https://github.com/scipy/scipy/issues/13459>`__: Broken link in cramervonmises documentation * `#13494 <https://github.com/scipy/scipy/issues/13494>`__: One-word typo in the documentation of optimize.linprog_simplex * `#13501 <https://github.com/scipy/scipy/issues/13501>`__: minimize using Powell methods with Bounds leads to "TypeError:... * `#13509 <https://github.com/scipy/scipy/issues/13509>`__: signal.medfilt2d vs ndimage.median_filter * `#13511 <https://github.com/scipy/scipy/issues/13511>`__: DOC: error in description of "direc" parameter of "fmin_powell" * `#13526 <https://github.com/scipy/scipy/issues/13526>`__: TST: stats: intermittent \`test_ttest_ind_randperm_alternative2... * `#13536 <https://github.com/scipy/scipy/issues/13536>`__: \`_within_tolerance\` seems an unnecessary repetition of \`numpy.isclose\` * `#13540 <https://github.com/scipy/scipy/issues/13540>`__: missing python 3.8 manylinux wheels on scipy-wheels-nightly * `#13559 <https://github.com/scipy/scipy/issues/13559>`__: shape error in linprog with revised simplex * `#13587 <https://github.com/scipy/scipy/issues/13587>`__: binned_statistic unreliable with single precision * `#13589 <https://github.com/scipy/scipy/issues/13589>`__: Better argument preparation for distributions in stats package. * `#13602 <https://github.com/scipy/scipy/issues/13602>`__: The crystallball distribution entropy is sometimes minus infinity * `#13606 <https://github.com/scipy/scipy/issues/13606>`__: MAINT: mypy: some typing errors while running mypy + adding mypy... * `#13608 <https://github.com/scipy/scipy/issues/13608>`__: Why does stats.binned_statistic_2d convert its values argument... * `#13609 <https://github.com/scipy/scipy/issues/13609>`__: BUG: SciPy pip install -e gets unusable version spec * `#13610 <https://github.com/scipy/scipy/issues/13610>`__: Highs solver did not provide a solution nor did it report a failure * `#13614 <https://github.com/scipy/scipy/issues/13614>`__: BUG: invgauss.cdf should return the correct value when \`mu\`... * `#13628 <https://github.com/scipy/scipy/issues/13628>`__: 1-letter typo in the definition of scipy.special.spence function... * `#13634 <https://github.com/scipy/scipy/issues/13634>`__: mmwrite fails on dense, skew-symmetric array * `#13646 <https://github.com/scipy/scipy/issues/13646>`__: Sparse matrix argmax() integer overflow on Windows 10 * `#13647 <https://github.com/scipy/scipy/issues/13647>`__: \`scipy.stats.qmc.LatinHypercube\` cannot sample single sample... * `#13651 <https://github.com/scipy/scipy/issues/13651>`__: Documentation wrong in scipy.linalg.eigvalsh * `#13664 <https://github.com/scipy/scipy/issues/13664>`__: BUG: gamma distribution's inverse survival function overflows... * `#13693 <https://github.com/scipy/scipy/issues/13693>`__: BUG: sokalmichener appears to incorrectly apply weights * `#13697 <https://github.com/scipy/scipy/issues/13697>`__: BUG: stats: Spurious warning generated by arcsine.pdf at the... * `#13704 <https://github.com/scipy/scipy/issues/13704>`__: Make it possible to pass a rank cut-off value relatively to the... * `#13707 <https://github.com/scipy/scipy/issues/13707>`__: Kullback Leibler Divergence broadcasting no longer works * `#13740 <https://github.com/scipy/scipy/issues/13740>`__: Scipy.optimize x0 out of bounds when it is within bounds. * `#13744 <https://github.com/scipy/scipy/issues/13744>`__: scipy.interpolate.interp1d has inconsistent behavior for non-unique... * `#13754 <https://github.com/scipy/scipy/issues/13754>`__: optimize.minimize 'trust' methods and finite difference Hessian... * `#13762 <https://github.com/scipy/scipy/issues/13762>`__: MAINT, TST: aarch64 stats test failures showing up in wheels... * `#13769 <https://github.com/scipy/scipy/issues/13769>`__: probplot draws fit line even when fit=False * `#13791 <https://github.com/scipy/scipy/issues/13791>`__: BUG: stats: wrapcauchy.cdf does not broadcast the shape parameter... * `#13793 <https://github.com/scipy/scipy/issues/13793>`__: CI: CircleCI doc build failure * `#13840 <https://github.com/scipy/scipy/issues/13840>`__: manylinux1 builds are failing because of C99 usage in \`special/_cosine.c\` * `#13850 <https://github.com/scipy/scipy/issues/13850>`__: CI: Homebrew is failing due to bintray * `#13875 <https://github.com/scipy/scipy/issues/13875>`__: BUG: chi2_contingency with Yates correction * `#13878 <https://github.com/scipy/scipy/issues/13878>`__: BUG: \`signal.get_window\` argument handling issue * `#13880 <https://github.com/scipy/scipy/issues/13880>`__: Remove all usages of numpy.compat * `#13896 <https://github.com/scipy/scipy/issues/13896>`__: Boschloo's Test for More Powerful Hypothesis Testing of 2x2 Contingency... * `#13923 <https://github.com/scipy/scipy/issues/13923>`__: Inverse of Log CDF of Normal Distribution * `#13933 <https://github.com/scipy/scipy/issues/13933>`__: \`signal.get_window\` does not support \`general_cosine\` and... * `#13950 <https://github.com/scipy/scipy/issues/13950>`__: DOC: scipy.spatial.KDTree.query * `#13969 <https://github.com/scipy/scipy/issues/13969>`__: N=4 must not exceed M=3 * `#13970 <https://github.com/scipy/scipy/issues/13970>`__: Pearson's original paper on chi-square test could be referenced. * `#13984 <https://github.com/scipy/scipy/issues/13984>`__: Faster addition of sparse diagonal matrices * `#13988 <https://github.com/scipy/scipy/issues/13988>`__: An error occurred when using scipy.io.wavfile of scipy 1.6 version... * `#13997 <https://github.com/scipy/scipy/issues/13997>`__: BUG: sparse: Incorrect result from \`dia_matrix.diagonal()\` * `#14005 <https://github.com/scipy/scipy/issues/14005>`__: MAINT: optimize: \`curve_fit\` input error msg can be improved. * `#14038 <https://github.com/scipy/scipy/issues/14038>`__: MAINT: add type annotations for _sobol.pyx * `#14048 <https://github.com/scipy/scipy/issues/14048>`__: DOC: missing git submodule information * `#14055 <https://github.com/scipy/scipy/issues/14055>`__: linalg.solve: Unclear error when using assume_a='her' with real... * `#14093 <https://github.com/scipy/scipy/issues/14093>`__: DOC: Inconsistency in the definition of default values in the... * `#14158 <https://github.com/scipy/scipy/issues/14158>`__: TST, BUG: test_rbfinterp.py -- test_interpolation_misfit_1d fails... * `#14170 <https://github.com/scipy/scipy/issues/14170>`__: TST: signal submodule test_filtfilt_gust failing on 32-bit amd64... ************************** Pull requests for 1.7.0 ************************** * `#4824 <https://github.com/scipy/scipy/pull/4824>`__: Permutation Ttest (new PR) * `#4933 <https://github.com/scipy/scipy/pull/4933>`__: ENH: Update the Mann-Whitney-Wilcoxon test * `#7702 <https://github.com/scipy/scipy/pull/7702>`__: ENH: stats: Add Skewed Cauchy Distribution * `#8306 <https://github.com/scipy/scipy/pull/8306>`__: Optional Pythran support for scipy.signal.max_len_seq_inner * `#10170 <https://github.com/scipy/scipy/pull/10170>`__: MAINT: stats: Implement cdf and ppf as ufuncs for the cosine... * `#10454 <https://github.com/scipy/scipy/pull/10454>`__: ENH: Extend find_peaks_cwt to take numbers and iterables for... * `#10844 <https://github.com/scipy/scipy/pull/10844>`__: ENH: add stats.qmc module with quasi Monte Carlo functionality * `#11313 <https://github.com/scipy/scipy/pull/11313>`__: ENH: add Wright's generalized Bessel function * `#11352 <https://github.com/scipy/scipy/pull/11352>`__: ENH: stats: Add crosstab function. * `#11477 <https://github.com/scipy/scipy/pull/11477>`__: FIX: bounded parameter in cdfchn.f gives bad results * `#11695 <https://github.com/scipy/scipy/pull/11695>`__: ENH: stats: add method of moments to \`rv_continuous.fit\` * `#11911 <https://github.com/scipy/scipy/pull/11911>`__: ENH: Added bounds to boxcox and boxcox_normmax * `#12438 <https://github.com/scipy/scipy/pull/12438>`__: BUG: use ellipkm1 in elliptical filter design to prevent numerical... * `#12531 <https://github.com/scipy/scipy/pull/12531>`__: ENH: stats: add Page's L test * `#12603 <https://github.com/scipy/scipy/pull/12603>`__: ENH: stats: Add \`binomtest\` to replace \`binom_test\`. * `#12653 <https://github.com/scipy/scipy/pull/12653>`__: ENH: stats: add Somers' D test * `#12676 <https://github.com/scipy/scipy/pull/12676>`__: BUG: update median averaging in signal.csd * `#12760 <https://github.com/scipy/scipy/pull/12760>`__: BUG: special: erfinv(x<<1) loses precision * `#12801 <https://github.com/scipy/scipy/pull/12801>`__: ENH: Add single-sided p-values to remaining spearmanr and linregress * `#12873 <https://github.com/scipy/scipy/pull/12873>`__: ENH: Stats: add Alexander Govern Test * `#13008 <https://github.com/scipy/scipy/pull/13008>`__: ENH: Add 'alternative' to functions using normal CDF for p-value * `#13040 <https://github.com/scipy/scipy/pull/13040>`__: BUG: Allow RectSphereBivariateSpline to accept negative longitude * `#13048 <https://github.com/scipy/scipy/pull/13048>`__: ENH: stats: Add a function that computes the relative risk. * `#13067 <https://github.com/scipy/scipy/pull/13067>`__: ENH: Add weights parameter to stats.gmean * `#13084 <https://github.com/scipy/scipy/pull/13084>`__: ENH: fast Hankel transform * `#13104 <https://github.com/scipy/scipy/pull/13104>`__: MAINT: upgrade python version (drop python 3.6) for docker dev... * `#13153 <https://github.com/scipy/scipy/pull/13153>`__: ENH: added association measurements Pearsons Contingency Coefficient,... * `#13166 <https://github.com/scipy/scipy/pull/13166>`__: ENH: stats: Add nan_policy to zmap. * `#13175 <https://github.com/scipy/scipy/pull/13175>`__: MAINT: tests for tall cost matrices in \`linear_sum_assignment\` * `#13177 <https://github.com/scipy/scipy/pull/13177>`__: BUG: raise NotImplementedError in fourier_ellipsoid when ndim... * `#13184 <https://github.com/scipy/scipy/pull/13184>`__: BUG: stats: Fix min and max calculation of mstats.describe with... * `#13188 <https://github.com/scipy/scipy/pull/13188>`__: DOC: stats: make null and alternative hypotheses of kstest more... * `#13193 <https://github.com/scipy/scipy/pull/13193>`__: MAINT: stats: chisquare check sum of observed/expected frequencies * `#13197 <https://github.com/scipy/scipy/pull/13197>`__: ENH/MAINT: HiGHS upstream enhancements and bug fixes * `#13198 <https://github.com/scipy/scipy/pull/13198>`__: ENH: allow inference of output_shape from out array in affine_transform * `#13204 <https://github.com/scipy/scipy/pull/13204>`__: ENH: stats: add Zipfian (different from Zipf/zeta) distribution * `#13208 <https://github.com/scipy/scipy/pull/13208>`__: REL: set version to 1.7.0.dev0 * `#13216 <https://github.com/scipy/scipy/pull/13216>`__: TST: stats: break up and mark slow tests * `#13224 <https://github.com/scipy/scipy/pull/13224>`__: Update docs for the weighted τ * `#13230 <https://github.com/scipy/scipy/pull/13230>`__: ENH: linalg: Add LAPACK wrapper for tgexc. * `#13232 <https://github.com/scipy/scipy/pull/13232>`__: MAINT: stats: raise error when input to kruskal has >1 dim * `#13233 <https://github.com/scipy/scipy/pull/13233>`__: DOC: stats: fix MGF of arcsine and entropy of t in tutorial * `#13236 <https://github.com/scipy/scipy/pull/13236>`__: MAINT: reorganize shared linear assignment tests * `#13237 <https://github.com/scipy/scipy/pull/13237>`__: BENCH: Refactor stats.Distribution to easily add new distributions * `#13238 <https://github.com/scipy/scipy/pull/13238>`__: BUG: stats: fix wrong shape output of burr and fisk distributions * `#13240 <https://github.com/scipy/scipy/pull/13240>`__: MAINT: add tests of trivial cost matrices for linear sum assignment * `#13252 <https://github.com/scipy/scipy/pull/13252>`__: DOC: optimize: add \`optimize.linear_sum_assignment\` tutorial. * `#13254 <https://github.com/scipy/scipy/pull/13254>`__: BUG: Fix precision issues for constant input in skew and kurtosis * `#13262 <https://github.com/scipy/scipy/pull/13262>`__: BUG: scipy.medfilt and .medfilt2d fixes * `#13263 <https://github.com/scipy/scipy/pull/13263>`__: ENH: add Cramer-von Mises test for two samples * `#13264 <https://github.com/scipy/scipy/pull/13264>`__: fix a minor typo in \`stats.anderson\` doc * `#13268 <https://github.com/scipy/scipy/pull/13268>`__: ENH: stats: Add implementation of _entropy for the t distr. * `#13273 <https://github.com/scipy/scipy/pull/13273>`__: DOC: stats: fix typo in Yeo-Johnson LL function documentation * `#13275 <https://github.com/scipy/scipy/pull/13275>`__: MAINT: stats: Correct a comment in the _fitstart method of gamma. * `#13283 <https://github.com/scipy/scipy/pull/13283>`__: BUG: stats: fix the cdf method of rv_discrete class * `#13286 <https://github.com/scipy/scipy/pull/13286>`__: DOC: stats: clairify rv_continuous/discrete.stats example * `#13288 <https://github.com/scipy/scipy/pull/13288>`__: DOC: stats: discrete distribution shape parameter restrictions * `#13289 <https://github.com/scipy/scipy/pull/13289>`__: MAINT: fix a build warning in sigtoolsmodule.c * `#13290 <https://github.com/scipy/scipy/pull/13290>`__: DOC: Expand the discussion of the nan_policy API. * `#13291 <https://github.com/scipy/scipy/pull/13291>`__: MAINT: signal, stats: Use keepdims where appropriate. * `#13292 <https://github.com/scipy/scipy/pull/13292>`__: DOC: stats: note another common parameterization of nbinom * `#13293 <https://github.com/scipy/scipy/pull/13293>`__: DOC: Change broken link for default values to archived link * `#13295 <https://github.com/scipy/scipy/pull/13295>`__: BUG: stats: fix the support method to return correct bounds * `#13296 <https://github.com/scipy/scipy/pull/13296>`__: DOC: stats: Fix latex markup in the kstwo docstring. * `#13297 <https://github.com/scipy/scipy/pull/13297>`__: TST: mark kde.logpdf overflow test as xslow * `#13298 <https://github.com/scipy/scipy/pull/13298>`__: Generalized Hyperbolic Distribution * `#13301 <https://github.com/scipy/scipy/pull/13301>`__: DOC: cluster: Add cluster number note to the docstring of cluster.vq.kmeans * `#13302 <https://github.com/scipy/scipy/pull/13302>`__: BUG: Fix ndimage.morphology.distance_transform\_\* argument handling * `#13303 <https://github.com/scipy/scipy/pull/13303>`__: CI: prevent Codecov giving false CI failures and wrong PR annotations * `#13313 <https://github.com/scipy/scipy/pull/13313>`__: ENH: static typing for qhull * `#13316 <https://github.com/scipy/scipy/pull/13316>`__: Pythran implementation of scipy.signal._spectral * `#13317 <https://github.com/scipy/scipy/pull/13317>`__: DOC: forward port 1.6.0 relnotes * `#13319 <https://github.com/scipy/scipy/pull/13319>`__: ENH: stats: add fast numerical inversion of distribution CDF * `#13320 <https://github.com/scipy/scipy/pull/13320>`__: ENH: x0 for differential_evolution * `#13324 <https://github.com/scipy/scipy/pull/13324>`__: DOC correct linprog highs versionadded to 1.6 * `#13326 <https://github.com/scipy/scipy/pull/13326>`__: MAINT: update numpydoc to v1.1.0 * `#13327 <https://github.com/scipy/scipy/pull/13327>`__: DOC: interpolate: improved docstring examples of \`interpolate.interpn()\`... * `#13328 <https://github.com/scipy/scipy/pull/13328>`__: ENH: Boost stats distributions * `#13330 <https://github.com/scipy/scipy/pull/13330>`__: ENH: stats: add noncentral hypergeometric distributions (Fisher's... * `#13331 <https://github.com/scipy/scipy/pull/13331>`__: MAINT/ENH: resolve mypy warnings/errors * `#13332 <https://github.com/scipy/scipy/pull/13332>`__: DOC: interpolate: improved docstring of \`interpolate.interp2d\`... * `#13333 <https://github.com/scipy/scipy/pull/13333>`__: ENH: stats: Some more _sf and _isf implementations. * `#13334 <https://github.com/scipy/scipy/pull/13334>`__: MAINT: stats: Clean up a few defunct comments in _continuous_distns.py * `#13336 <https://github.com/scipy/scipy/pull/13336>`__: Pythran version of scipy.optimize._group_columns * `#13337 <https://github.com/scipy/scipy/pull/13337>`__: DOC|ENH: type hinting in scipy.integrate.simpson * `#13346 <https://github.com/scipy/scipy/pull/13346>`__: ENH: stats: add 'ddof' parameter to the 'variation' function * `#13355 <https://github.com/scipy/scipy/pull/13355>`__: ENH: stats: implement _logpdf, _sf and _isf for loggamma. * `#13360 <https://github.com/scipy/scipy/pull/13360>`__: ENH|DOC: fix docstring and input validation in interpolate.RectSphereBivariateSpline * `#13366 <https://github.com/scipy/scipy/pull/13366>`__: BUG: stats: Don't raise ZeroDivisionError in _unequal_var_ttest_denom * `#13370 <https://github.com/scipy/scipy/pull/13370>`__: ENH: fix ARGUS distribution for small parameters in stats * `#13371 <https://github.com/scipy/scipy/pull/13371>`__: ENH: stats: add \`bootstrap\` for estimating confidence interval... * `#13373 <https://github.com/scipy/scipy/pull/13373>`__: BUG: io/matlab: preserve dimensions of empty >=2D arrays * `#13374 <https://github.com/scipy/scipy/pull/13374>`__: ENH: stats: add skewed Cauchy distribution * `#13379 <https://github.com/scipy/scipy/pull/13379>`__: BUG: sparse: fix verbosity in sparse lsqr * `#13383 <https://github.com/scipy/scipy/pull/13383>`__: TST: stats: mark many dimension permutation t-test slow * `#13384 <https://github.com/scipy/scipy/pull/13384>`__: MAINT: Make keywords array static * `#13388 <https://github.com/scipy/scipy/pull/13388>`__: PERF: Avoid duplicate mean calculations in skew and kurtosis * `#13389 <https://github.com/scipy/scipy/pull/13389>`__: DOC: Fix deprecated directive syntax * `#13390 <https://github.com/scipy/scipy/pull/13390>`__: DOC: Correct line length for Parameter Section underline * `#13393 <https://github.com/scipy/scipy/pull/13393>`__: MAINT: stats: allow wishart dim - 1 < df < dim * `#13395 <https://github.com/scipy/scipy/pull/13395>`__: DOC: fix typo in setup.py warning message * `#13396 <https://github.com/scipy/scipy/pull/13396>`__: BUG: Fix MLE for Nakagami \`nakagami_gen.fit\` * `#13397 <https://github.com/scipy/scipy/pull/13397>`__: MAINT:linalg: Fix tgsen family wrapper and ordqz * `#13406 <https://github.com/scipy/scipy/pull/13406>`__: TST: add error handling tests for sparse BSR ctor * `#13413 <https://github.com/scipy/scipy/pull/13413>`__: DOC: ultra-quickstart guide * `#13418 <https://github.com/scipy/scipy/pull/13418>`__: BUG: Fix moment returning inconsistent types and shapes * `#13423 <https://github.com/scipy/scipy/pull/13423>`__: DOC: Update example for leaf_label_func/dendrogram * `#13431 <https://github.com/scipy/scipy/pull/13431>`__: ENH: stats: override _rvs for nhypergeom * `#13432 <https://github.com/scipy/scipy/pull/13432>`__: Add indicator in NDInterpolator docstring that N must be > 1 * `#13434 <https://github.com/scipy/scipy/pull/13434>`__: DOC: stats: note relationship between scaled-inv-chi2 and invgamma * `#13436 <https://github.com/scipy/scipy/pull/13436>`__: ENH: interpolate: add input validation to check input x-y is... * `#13441 <https://github.com/scipy/scipy/pull/13441>`__: ENH: add functionality \`barnard_exact\` test to scipy.stats. * `#13443 <https://github.com/scipy/scipy/pull/13443>`__: MAINT: stats: Updates for skewcauchy * `#13444 <https://github.com/scipy/scipy/pull/13444>`__: DOC: clarify range of \`a\` parameter fpr johnsonsu/johnsonsb * `#13445 <https://github.com/scipy/scipy/pull/13445>`__: DOC: fix runtests guidelines. * `#13446 <https://github.com/scipy/scipy/pull/13446>`__: MAINT: stats: Add _fitstart method to wrapcauchy. * `#13447 <https://github.com/scipy/scipy/pull/13447>`__: DEV: Update development Docker image * `#13448 <https://github.com/scipy/scipy/pull/13448>`__: ENH: Add annotations for \`scipy.spatial.distance\` * `#13451 <https://github.com/scipy/scipy/pull/13451>`__: DOC: minor formatting. * `#13458 <https://github.com/scipy/scipy/pull/13458>`__: DOC: indent see also. * `#13460 <https://github.com/scipy/scipy/pull/13460>`__: DOC: stats: Fix link to Cramer-von Mises wikipedia article. * `#13461 <https://github.com/scipy/scipy/pull/13461>`__: DOC: reorganize scipy.stats overview docs page * `#13463 <https://github.com/scipy/scipy/pull/13463>`__: DOC: misc formatting fixes * `#13466 <https://github.com/scipy/scipy/pull/13466>`__: DOC: Typo in see also s/SmoothUni/SmoothBi/g * `#13467 <https://github.com/scipy/scipy/pull/13467>`__: DOC: optimize: add description about \`tol\` argument for \`minimize\`. * `#13469 <https://github.com/scipy/scipy/pull/13469>`__: MAINT: Refactor optimization methods to use scipy.stats.qmc * `#13477 <https://github.com/scipy/scipy/pull/13477>`__: CI: pin numpy to 1.19.5 for the three macOS CI jobs * `#13478 <https://github.com/scipy/scipy/pull/13478>`__: DOC: fix typos where double :: for Sphinx directives were missing * `#13481 <https://github.com/scipy/scipy/pull/13481>`__: CI: pin numpy to 1.19.5 in the 4 parallel Windows builds on Azure * `#13482 <https://github.com/scipy/scipy/pull/13482>`__: CI: use numpy 1.20.0 again in macOS CI * `#13483 <https://github.com/scipy/scipy/pull/13483>`__: DOC: Multiple documentation syntax fixes. * `#13484 <https://github.com/scipy/scipy/pull/13484>`__: Move some pythran config from CI to setup * `#13487 <https://github.com/scipy/scipy/pull/13487>`__: DOC: add a tutorial about scipy.stats.qmc * `#13492 <https://github.com/scipy/scipy/pull/13492>`__: ENH: GH actions should not run on forks * `#13493 <https://github.com/scipy/scipy/pull/13493>`__: DEV: Enable gitpod for SciPy * `#13495 <https://github.com/scipy/scipy/pull/13495>`__: DOC One-word typo in the documentation of optimize.linprog_simplex * `#13499 <https://github.com/scipy/scipy/pull/13499>`__: DOC: describe LSAP implementation * `#13502 <https://github.com/scipy/scipy/pull/13502>`__: BUG: Bounds created with lists weren't working for Powell * `#13507 <https://github.com/scipy/scipy/pull/13507>`__: MAINT, TST: stats: centralize invalid parameters list for all... * `#13510 <https://github.com/scipy/scipy/pull/13510>`__: DOC: stats: fix small doc errors in 'multivariate_hypergeom' * `#13513 <https://github.com/scipy/scipy/pull/13513>`__: DOC: Added math notation in examples in ltisys.py * `#13514 <https://github.com/scipy/scipy/pull/13514>`__: ENH: simplify low_0_bit function for Sobol * `#13515 <https://github.com/scipy/scipy/pull/13515>`__: ENH: optimize: add bound constraint support for nelder-mead solver * `#13516 <https://github.com/scipy/scipy/pull/13516>`__: DOC: reduce LaTeX usage for johnsonb docstring * `#13519 <https://github.com/scipy/scipy/pull/13519>`__: BLD: remove build_sphinx support from setup.py * `#13527 <https://github.com/scipy/scipy/pull/13527>`__: TST: stats: xfail ttest_ind_randperm_alternative2 on 32 bit * `#13530 <https://github.com/scipy/scipy/pull/13530>`__: DOC: correct comparisons between median filter functions * `#13532 <https://github.com/scipy/scipy/pull/13532>`__: ENH: release the GIL inside medfilt2d * `#13538 <https://github.com/scipy/scipy/pull/13538>`__: DOC: optimize: fix minor doc error in 'fmin_powell' (#13511) * `#13546 <https://github.com/scipy/scipy/pull/13546>`__: DOC: fix list of "mode" options for ndimage * `#13549 <https://github.com/scipy/scipy/pull/13549>`__: ENH: stats: add 'alternative' keyword to some normality tests. * `#13551 <https://github.com/scipy/scipy/pull/13551>`__: MAINT: add git to docker env * `#13552 <https://github.com/scipy/scipy/pull/13552>`__: MAINT: stats: remove float_power shim * `#13553 <https://github.com/scipy/scipy/pull/13553>`__: DOC: use support rather than a/b in stats tutorial * `#13560 <https://github.com/scipy/scipy/pull/13560>`__: MAINT: optimize: improve linprog error message for sparse input... * `#13562 <https://github.com/scipy/scipy/pull/13562>`__: MAINT: optimize: using np.isclose instead of _within_tolerance. * `#13566 <https://github.com/scipy/scipy/pull/13566>`__: ENH: Speed up hdquantiles_sd() * `#13569 <https://github.com/scipy/scipy/pull/13569>`__: BENCH: optimize: benchmark only HiGHS methods; add bigger linprog... * `#13574 <https://github.com/scipy/scipy/pull/13574>`__: DOC: In description of cluster.hierarchy.dendrogram 'level' parameter,... * `#13576 <https://github.com/scipy/scipy/pull/13576>`__: ENH: improve discrepancy performance * `#13579 <https://github.com/scipy/scipy/pull/13579>`__: TST: Add pybind11 to tox environments * `#13583 <https://github.com/scipy/scipy/pull/13583>`__: BUG: Fix Dockerfile apt-get installs * `#13588 <https://github.com/scipy/scipy/pull/13588>`__: MAINT: forward port 1.6.1 relnotes. * `#13593 <https://github.com/scipy/scipy/pull/13593>`__: BUG: stats: preserve sample dtype for bin edges * `#13595 <https://github.com/scipy/scipy/pull/13595>`__: ENH: interpolate: add RBFInterpolator * `#13596 <https://github.com/scipy/scipy/pull/13596>`__: DOC: Fix indentation in new_stats_distribution.rst.inc * `#13601 <https://github.com/scipy/scipy/pull/13601>`__: Add dpss for get_window function * `#13604 <https://github.com/scipy/scipy/pull/13604>`__: DOC: Correct dual annealing visiting param range. * `#13605 <https://github.com/scipy/scipy/pull/13605>`__: Add Codecov badge to README * `#13607 <https://github.com/scipy/scipy/pull/13607>`__: MAINT: stats: fix crystalball entropy * `#13611 <https://github.com/scipy/scipy/pull/13611>`__: Better argument preparation for distributions in stats package. * `#13612 <https://github.com/scipy/scipy/pull/13612>`__: Add docker run command for Windows cmd * `#13613 <https://github.com/scipy/scipy/pull/13613>`__: MAINT, CI: mypy: fix typing errors + add mypy to CI * `#13616 <https://github.com/scipy/scipy/pull/13616>`__: FIX: Return correct output for invgauss.cdf when mu is very small * `#13617 <https://github.com/scipy/scipy/pull/13617>`__: MAINT: accept numbers and iterables for width in find_peaks_cwt * `#13620 <https://github.com/scipy/scipy/pull/13620>`__: CI: disable the mypy CI job (partial revert of gh-13613) * `#13621 <https://github.com/scipy/scipy/pull/13621>`__: DOC: signal: use array_like for input types * `#13622 <https://github.com/scipy/scipy/pull/13622>`__: MAINT: clean up some unused files, make \`mypy scipy\` pass * `#13623 <https://github.com/scipy/scipy/pull/13623>`__: CI: enable Mypy CI job again * `#13624 <https://github.com/scipy/scipy/pull/13624>`__: TST: test more values for \`visiting_param\` input to \`dual_annealing\` * `#13625 <https://github.com/scipy/scipy/pull/13625>`__: Rename integrate.simps to integrate.simpsons in documentation... * `#13631 <https://github.com/scipy/scipy/pull/13631>`__: ENH: add a \`stats.differential_entropy\` function * `#13633 <https://github.com/scipy/scipy/pull/13633>`__: BUG: stats.binned_statistic_2d user function expecting arrays * `#13641 <https://github.com/scipy/scipy/pull/13641>`__: ENH: Added degrees parameter to rotvec * `#13645 <https://github.com/scipy/scipy/pull/13645>`__: MAINT: mypy: don't install numpy-stubs * `#13649 <https://github.com/scipy/scipy/pull/13649>`__: BUG: sparse: csc_matrix.argmax() integer overflow * `#13650 <https://github.com/scipy/scipy/pull/13650>`__: ENH: stats: add 'alternative' parameter to ansari * `#13652 <https://github.com/scipy/scipy/pull/13652>`__: DOC: fix eigvalsh documentation (#13651) * `#13654 <https://github.com/scipy/scipy/pull/13654>`__: BUG: Fix LatinHypercubes * `#13656 <https://github.com/scipy/scipy/pull/13656>`__: DOC: Fix PCHIP references * `#13657 <https://github.com/scipy/scipy/pull/13657>`__: TST: remove IPython warning in debug session * `#13658 <https://github.com/scipy/scipy/pull/13658>`__: Remove spurious quotes in docstring * `#13661 <https://github.com/scipy/scipy/pull/13661>`__: ENH: stats: improve efficiency of / fix bug in exact permutation... * `#13667 <https://github.com/scipy/scipy/pull/13667>`__: MAINT: Make latest Docker image default * `#13668 <https://github.com/scipy/scipy/pull/13668>`__: MAINT: add .theia/ to .gitignore * `#13669 <https://github.com/scipy/scipy/pull/13669>`__: BLD: change SCIPY_USE_PYTHRAN default to \`1\` * `#13676 <https://github.com/scipy/scipy/pull/13676>`__: ENH Small improvements for LSQR with damp * `#13678 <https://github.com/scipy/scipy/pull/13678>`__: MAINT: add Pythran-generated files to .gitignore * `#13679 <https://github.com/scipy/scipy/pull/13679>`__: MAINT: move the \`conda develop .\` in the Gitpod config * `#13680 <https://github.com/scipy/scipy/pull/13680>`__: DOC: Add cKDTree note comparing it with KDTree * `#13681 <https://github.com/scipy/scipy/pull/13681>`__: DOC: build doc updates on Pythran, compiled code, and cleanups * `#13683 <https://github.com/scipy/scipy/pull/13683>`__: BUG: mmwrite correctly serializes non skew-symmetric arrays * `#13684 <https://github.com/scipy/scipy/pull/13684>`__: FIX: fix numerical overflow in gamma.isf method * `#13685 <https://github.com/scipy/scipy/pull/13685>`__: BUG: fix cosine distance range to 0-2 * `#13694 <https://github.com/scipy/scipy/pull/13694>`__: MAINT: fix warning emitted when NumPy version is incorrect * `#13696 <https://github.com/scipy/scipy/pull/13696>`__: ENH: support trimming in ttest_ind * `#13698 <https://github.com/scipy/scipy/pull/13698>`__: BUG: stats: Fix spurious warnings generated by arcsine.pdf * `#13701 <https://github.com/scipy/scipy/pull/13701>`__: DEV: scipy.interpolate b-splines (periodic case) * `#13702 <https://github.com/scipy/scipy/pull/13702>`__: DEP: Clean up spent deprecations in spatial.distance * `#13703 <https://github.com/scipy/scipy/pull/13703>`__: MAINT: fix issues found by static code analysis * `#13706 <https://github.com/scipy/scipy/pull/13706>`__: ENH: stats: Implement sf and isf for the laplace distribution. * `#13711 <https://github.com/scipy/scipy/pull/13711>`__: MAINT: stats: fix broadcasting for scipy.stats.entropy * `#13712 <https://github.com/scipy/scipy/pull/13712>`__: BUG: stats: Override _fitstart for the invweibull distribution. * `#13713 <https://github.com/scipy/scipy/pull/13713>`__: DOC: update toolchain.rst to reflect windows universal C runtime * `#13714 <https://github.com/scipy/scipy/pull/13714>`__: MAINT: stats: Remove an unused list from test_continuous_basic.py. * `#13715 <https://github.com/scipy/scipy/pull/13715>`__: MAINT: stats: No need to suppress frechet deprecation warnings. * `#13716 <https://github.com/scipy/scipy/pull/13716>`__: MAINT: use super() as described by PEP 3135 * `#13718 <https://github.com/scipy/scipy/pull/13718>`__: MAINT: new-style class, removing inheritance to object * `#13721 <https://github.com/scipy/scipy/pull/13721>`__: MAINT: add a type-ignore for mpmath (#13721) * `#13723 <https://github.com/scipy/scipy/pull/13723>`__: MAINT: mypy: ignore mpmath imports in mypy.ini * `#13724 <https://github.com/scipy/scipy/pull/13724>`__: DOC: pydata sphinx theme * `#13725 <https://github.com/scipy/scipy/pull/13725>`__: BENCH: add benchmark for Kendalltau * `#13727 <https://github.com/scipy/scipy/pull/13727>`__: CI: simplify Pythran configuration setup for Azure * `#13731 <https://github.com/scipy/scipy/pull/13731>`__: MAINT: stats: Some flake8-driven clean up. * `#13732 <https://github.com/scipy/scipy/pull/13732>`__: ENH: stats: Studentized Range Distribution * `#13735 <https://github.com/scipy/scipy/pull/13735>`__: DOC: correct Voronoi docstring * `#13738 <https://github.com/scipy/scipy/pull/13738>`__: DOC: add example to wright_bessel * `#13739 <https://github.com/scipy/scipy/pull/13739>`__: ENH: stats: Implement _sf and _isf for the chi distribution. * `#13741 <https://github.com/scipy/scipy/pull/13741>`__: MAINT: prevent overwriting of x in minimize * `#13747 <https://github.com/scipy/scipy/pull/13747>`__: DOC: Add note for interp1d for non-unique x-values * `#13749 <https://github.com/scipy/scipy/pull/13749>`__: MAINT: forward port 1.6.2 relnotes * `#13759 <https://github.com/scipy/scipy/pull/13759>`__: MAINT: simpson small performance speedups * `#13765 <https://github.com/scipy/scipy/pull/13765>`__: FIX: npymath missing causing npy_log1p to be unknown * `#13768 <https://github.com/scipy/scipy/pull/13768>`__: BENCH: Add missing pythran dependency * `#13770 <https://github.com/scipy/scipy/pull/13770>`__: ENH: stats.contingency: Add the sparse option to crosstab. * `#13774 <https://github.com/scipy/scipy/pull/13774>`__: DEP: Deprecate squeezing input vectors in spatial.distance * `#13775 <https://github.com/scipy/scipy/pull/13775>`__: Enable trust region methods to use a finite difference Hessian... * `#13777 <https://github.com/scipy/scipy/pull/13777>`__: DOC: Fix Ubuntu/Debian installation instructions * `#13778 <https://github.com/scipy/scipy/pull/13778>`__: DOC: remove references to RandomState * `#13782 <https://github.com/scipy/scipy/pull/13782>`__: MAINT: LBFGSB err msg on MAXLS changed closes #11718 * `#13785 <https://github.com/scipy/scipy/pull/13785>`__: BENCH: Add benchmark for cdist/pdist with weights * `#13786 <https://github.com/scipy/scipy/pull/13786>`__: MAINT: Prepare cdist/pdist for C++ rework * `#13787 <https://github.com/scipy/scipy/pull/13787>`__: MAINT: stats: move entropy and differential_entropy functions... * `#13790 <https://github.com/scipy/scipy/pull/13790>`__: DOC: Add some dependencies for Dockerfile doc of scipy development. * `#13792 <https://github.com/scipy/scipy/pull/13792>`__: BUG: stats: Fix broadcasting in wrapcauchy.cdf * `#13795 <https://github.com/scipy/scipy/pull/13795>`__: MAINT: stats: add hypotests to __all__ in init.py, not stats.py * `#13797 <https://github.com/scipy/scipy/pull/13797>`__: MAINT: stats: probplot: don't plot least-squares fit line unless... * `#13798 <https://github.com/scipy/scipy/pull/13798>`__: MAINT: fix incorrect code comment in \`hierarchy.to_tree\` * `#13802 <https://github.com/scipy/scipy/pull/13802>`__: DEV: add environment.yml file for development with conda/mamba * `#13803 <https://github.com/scipy/scipy/pull/13803>`__: DOC: fix doc build warning about arxiv role already being registered * `#13804 <https://github.com/scipy/scipy/pull/13804>`__: DOC+MAINT: optimize: lb and ub in the Bounds constructor are... * `#13807 <https://github.com/scipy/scipy/pull/13807>`__: MAINT: Dont use parallel Sphinx * `#13808 <https://github.com/scipy/scipy/pull/13808>`__: MAINT: cluster.to_tree: more idiomatic looping over rows of matrix... * `#13810 <https://github.com/scipy/scipy/pull/13810>`__: MAINT: add a CODEOWNERS file * `#13811 <https://github.com/scipy/scipy/pull/13811>`__: MAINT: Add ci skip to azp * `#13814 <https://github.com/scipy/scipy/pull/13814>`__: ENH/DOC: pydata sphinx theme polishing * `#13817 <https://github.com/scipy/scipy/pull/13817>`__: DOC: Misc parameter typo and casing in scipy/linalg/_decomp_ldl.py * `#13818 <https://github.com/scipy/scipy/pull/13818>`__: MAINT: stats: keep \`entropy\` importable from \`scipy.stats.distributions\` * `#13820 <https://github.com/scipy/scipy/pull/13820>`__: BUG: update _kendall_p_exact ValueError to f-string * `#13831 <https://github.com/scipy/scipy/pull/13831>`__: FIX:DEP: Allow better tolerance control for pinv and pinvh and... * `#13832 <https://github.com/scipy/scipy/pull/13832>`__: BUG: stats: Fix rvs for levy_stable when alpha=1 * `#13833 <https://github.com/scipy/scipy/pull/13833>`__: MAINT: Add inline type hintings for stats.qmc * `#13836 <https://github.com/scipy/scipy/pull/13836>`__: MAINT: Fix a couple compiler warnings. * `#13838 <https://github.com/scipy/scipy/pull/13838>`__: TST: relax test tolerances for BinomTest * `#13841 <https://github.com/scipy/scipy/pull/13841>`__: BLD: add \`-std=c99\` flag to scipy.special extensions using... * `#13845 <https://github.com/scipy/scipy/pull/13845>`__: ENH: stats: add \`method\` parameter to \`differential_entropy\`... * `#13847 <https://github.com/scipy/scipy/pull/13847>`__: TST: skip on optimize failure on macOS, mark one as xfail * `#13848 <https://github.com/scipy/scipy/pull/13848>`__: DOC: optimize: move Nelder Mead doc from Unconstrained minimization... * `#13849 <https://github.com/scipy/scipy/pull/13849>`__: DOC: Roadmap update * `#13852 <https://github.com/scipy/scipy/pull/13852>`__: CI: fix temporary wrong brew version from GitHub * `#13854 <https://github.com/scipy/scipy/pull/13854>`__: ENH: Update Scipy Gitpod * `#13859 <https://github.com/scipy/scipy/pull/13859>`__: TST: fix ultra-slow ttest permutations test * `#13860 <https://github.com/scipy/scipy/pull/13860>`__: MAINT: clean up LSAP error checking * `#13863 <https://github.com/scipy/scipy/pull/13863>`__: DOC: remove seed in examples * `#13865 <https://github.com/scipy/scipy/pull/13865>`__: DOC: optimize: The bounds param of differential_evolution is... * `#13866 <https://github.com/scipy/scipy/pull/13866>`__: MAINT: special: Remove an unused variable from _poly_approx in... * `#13867 <https://github.com/scipy/scipy/pull/13867>`__: DOC: stats: Explain meaning of alternatives for fisher_exact. * `#13868 <https://github.com/scipy/scipy/pull/13868>`__: CI: fix the failing job on linux. * `#13870 <https://github.com/scipy/scipy/pull/13870>`__: MAINT: move LSAP rectangular matrix handling into solver code * `#13871 <https://github.com/scipy/scipy/pull/13871>`__: DOC: Add Gitpod documentation * `#13876 <https://github.com/scipy/scipy/pull/13876>`__: Workflow : Add nightly release of NumPy in linux workflows * `#13877 <https://github.com/scipy/scipy/pull/13877>`__: DOC: Conform to numpydoc + uniformity. * `#13879 <https://github.com/scipy/scipy/pull/13879>`__: BUG: signal: fix get_window argument handling and add tests. * `#13881 <https://github.com/scipy/scipy/pull/13881>`__: CI: remove .travis.yml, remove codecov from CircleCI * `#13882 <https://github.com/scipy/scipy/pull/13882>`__: BLD: ensure incrementing dev version strings * `#13886 <https://github.com/scipy/scipy/pull/13886>`__: TST: optimize: skip test_network_flow_limited_capacity w/ UMFPACK... * `#13888 <https://github.com/scipy/scipy/pull/13888>`__: MAINT: Fix issues involving elif conditions * `#13891 <https://github.com/scipy/scipy/pull/13891>`__: Rename InivariateSpline to UnivariateSpline * `#13893 <https://github.com/scipy/scipy/pull/13893>`__: ENH: linprog HiGHS marginals/sensitivy analysis * `#13894 <https://github.com/scipy/scipy/pull/13894>`__: DOC: Add blank line before \`Return\` section. * `#13897 <https://github.com/scipy/scipy/pull/13897>`__: DOC: BLD: fix doc build version check, and improve build time * `#13903 <https://github.com/scipy/scipy/pull/13903>`__: MAINT: Gitpod fixes * `#13907 <https://github.com/scipy/scipy/pull/13907>`__: ENH: Rewrite minkowski metric in C++ with pybind11 * `#13909 <https://github.com/scipy/scipy/pull/13909>`__: Revert "Workflow : Add nightly release of NumPy in linux workflows" * `#13910 <https://github.com/scipy/scipy/pull/13910>`__: DOC: update Readme * `#13911 <https://github.com/scipy/scipy/pull/13911>`__: MAINT: use dict built-in rather than OrderedDict * `#13920 <https://github.com/scipy/scipy/pull/13920>`__: BUG: Reactivate conda environment in init * `#13925 <https://github.com/scipy/scipy/pull/13925>`__: BUG: stats: magnitude of Yates' correction <= abs(observed-expected)... * `#13926 <https://github.com/scipy/scipy/pull/13926>`__: DOC: correct return type in disjoint_set.subsets docstring * `#13927 <https://github.com/scipy/scipy/pull/13927>`__: DOC/MAINT: Add copyright notice to qmc.primes_from_2_to * `#13928 <https://github.com/scipy/scipy/pull/13928>`__: BUG: DOC: signal: fix need argument config and add missing doc... * `#13929 <https://github.com/scipy/scipy/pull/13929>`__: REL: add PEP 621 (project metadata in pyproject.toml) support * `#13931 <https://github.com/scipy/scipy/pull/13931>`__: MAINT: special: get rid of _logit.c.src * `#13934 <https://github.com/scipy/scipy/pull/13934>`__: ENH: signal: make \`get_window\` supports \`general_cosine\`... * `#13940 <https://github.com/scipy/scipy/pull/13940>`__: MAINT: QMCEngine d input validation * `#13941 <https://github.com/scipy/scipy/pull/13941>`__: MAINT: forward port 1.6.3 relnotes * `#13944 <https://github.com/scipy/scipy/pull/13944>`__: BUG: spatial: fix weight handling of \`distance.sokalmichener\`. * `#13947 <https://github.com/scipy/scipy/pull/13947>`__: MAINT: Remove duplicate calculations in sokalmichener * `#13949 <https://github.com/scipy/scipy/pull/13949>`__: DOC: minor grammar fixes in minimize and KDTree.query * `#13951 <https://github.com/scipy/scipy/pull/13951>`__: ENH: Add Boschloo exact test to stats * `#13956 <https://github.com/scipy/scipy/pull/13956>`__: ENH: spatial: add \`axis\` and \`keepdims\` optional argument... * `#13963 <https://github.com/scipy/scipy/pull/13963>`__: MAINT: stats: Fix unused imports and a few other issues related... * `#13971 <https://github.com/scipy/scipy/pull/13971>`__: DOC: Add Karl Pearson's reference to chi-square test * `#13972 <https://github.com/scipy/scipy/pull/13972>`__: ENH: cluster: add an optional argument \`seed\` for \`kmeans\`... * `#13973 <https://github.com/scipy/scipy/pull/13973>`__: BLD: fix build warnings for causal/anticausal pointers in ndimage * `#13975 <https://github.com/scipy/scipy/pull/13975>`__: ENH: set empty array norm to zero. * `#13977 <https://github.com/scipy/scipy/pull/13977>`__: MAINT: signal: replace distutils templating with tempita * `#13978 <https://github.com/scipy/scipy/pull/13978>`__: MAINT: improve validations and keyword only arguments for some... * `#13979 <https://github.com/scipy/scipy/pull/13979>`__: ENH: Add Inverse of Log CDF of Normal Distribution * `#13983 <https://github.com/scipy/scipy/pull/13983>`__: Fixing \`ndimage.watershed_ift\` tutorial's documentation * `#13987 <https://github.com/scipy/scipy/pull/13987>`__: DOC: Adding examples to docstrings in morphology: white_tophat,... * `#13989 <https://github.com/scipy/scipy/pull/13989>`__: DOC: interpolate: improve examples of \`RegularGridInterpolator\`... * `#13990 <https://github.com/scipy/scipy/pull/13990>`__: MAINT, DOC: optimize: Make the input validation explanation clear... * `#13992 <https://github.com/scipy/scipy/pull/13992>`__: Workflow : Add nightly release of NumPy in linux workflows * `#13995 <https://github.com/scipy/scipy/pull/13995>`__: Doc: Continuous integration information * `#14000 <https://github.com/scipy/scipy/pull/14000>`__: BUG: sparse: Fix DIA.diagonal bug and add a regression test * `#14004 <https://github.com/scipy/scipy/pull/14004>`__: ENH: Fast addition dia matrix * `#14006 <https://github.com/scipy/scipy/pull/14006>`__: MAINT: optimize: add validation to check func parameter number... * `#14008 <https://github.com/scipy/scipy/pull/14008>`__: BUG: Raise exception for inconsistent WAV header * `#14009 <https://github.com/scipy/scipy/pull/14009>`__: DEP: Remove usage of numpy.compat * `#14010 <https://github.com/scipy/scipy/pull/14010>`__: MAINT: add support for wheel DL proxy * `#14012 <https://github.com/scipy/scipy/pull/14012>`__: DOC: Broaden Exact Test Reference * `#14015 <https://github.com/scipy/scipy/pull/14015>`__: MAINT: remove brew update * `#14017 <https://github.com/scipy/scipy/pull/14017>`__: BENCH: Add more formats for sparse arithmetic * `#14018 <https://github.com/scipy/scipy/pull/14018>`__: BENCH: add benchmark for f_oneway * `#14020 <https://github.com/scipy/scipy/pull/14020>`__: MAINT: modify np.int\_ to np.int32 to make it the same for 32/64... * `#14023 <https://github.com/scipy/scipy/pull/14023>`__: MAINT: Fix clang build and remove some unicode characters * `#14025 <https://github.com/scipy/scipy/pull/14025>`__: BUG: sparse: fix DIA.setdiag issue * `#14026 <https://github.com/scipy/scipy/pull/14026>`__: TST: optimize: xfail part of test_powell * `#14029 <https://github.com/scipy/scipy/pull/14029>`__: CI: github macos fix * `#14030 <https://github.com/scipy/scipy/pull/14030>`__: MAINT: use 'yield from <expr>' (PEP 380) * `#14031 <https://github.com/scipy/scipy/pull/14031>`__: MAINT: new-style class, removing inheritance to object * `#14032 <https://github.com/scipy/scipy/pull/14032>`__: MAINT: CXXFLAGS for Pythran * `#14033 <https://github.com/scipy/scipy/pull/14033>`__: ENH: Port sqeuclidean and braycurtis to _distance_pybind * `#14034 <https://github.com/scipy/scipy/pull/14034>`__: MAINT: Clean-up 'next = __next__' * `#14045 <https://github.com/scipy/scipy/pull/14045>`__: MAINT: bump PYVER pavement.py * `#14047 <https://github.com/scipy/scipy/pull/14047>`__: DEV: initialize boost submodule in Gitpod Dockerfile * `#14051 <https://github.com/scipy/scipy/pull/14051>`__: BLD: if boost submodule content is missing, error out early * `#14052 <https://github.com/scipy/scipy/pull/14052>`__: DOC: missing submodule init information * `#14057 <https://github.com/scipy/scipy/pull/14057>`__: DOC: special: Add Examples to \`psi\` docstring * `#14058 <https://github.com/scipy/scipy/pull/14058>`__: BUG: fixed a dtype bug in linalg.solve. * `#14060 <https://github.com/scipy/scipy/pull/14060>`__: Doc: Fix typo in documentation of spence function. * `#14061 <https://github.com/scipy/scipy/pull/14061>`__: MAINT:stats: Type annotations for _sobol.pyx * `#14062 <https://github.com/scipy/scipy/pull/14062>`__: DOC: A few small fixes in quickstart_gitpod.rst * `#14063 <https://github.com/scipy/scipy/pull/14063>`__: DOC: signal: add Add Examples to \`cont2discrete\` docstring * `#14064 <https://github.com/scipy/scipy/pull/14064>`__: DOC: optimize: Add Examples to fmin_bfgs docstring * `#14065 <https://github.com/scipy/scipy/pull/14065>`__: Add example for scipy stats.trim1 under docstring * `#14066 <https://github.com/scipy/scipy/pull/14066>`__: DOC add example to scipy.special.hermite * `#14067 <https://github.com/scipy/scipy/pull/14067>`__: DOC add alpha docstring description, add example to docstring * `#14070 <https://github.com/scipy/scipy/pull/14070>`__: DOC add parameters, return, and example to docstring * `#14072 <https://github.com/scipy/scipy/pull/14072>`__: MAINT/TST: Fix tests failing with the nightly build of numpy. * `#14075 <https://github.com/scipy/scipy/pull/14075>`__: DOC Improve the code snippet in signal.hilbert docstring. * `#14076 <https://github.com/scipy/scipy/pull/14076>`__: DOC: Document Jensen-Shannon distance being accepted by cdist/pdist * `#14079 <https://github.com/scipy/scipy/pull/14079>`__: BLD: Avoid importing scipy.stats during cythonize stage * `#14082 <https://github.com/scipy/scipy/pull/14082>`__: MAINT: Remove old, commented extract_diagonal * `#14083 <https://github.com/scipy/scipy/pull/14083>`__: MAINT: sparse: Remove defunct function extract_diagonal * `#14085 <https://github.com/scipy/scipy/pull/14085>`__: ENH: Implement canberra distance in _distance_pybind * `#14086 <https://github.com/scipy/scipy/pull/14086>`__: MAINT: Clear scipy namespace of entries better imported from... * `#14088 <https://github.com/scipy/scipy/pull/14088>`__: Install Pythran from sources for python 3.10 * `#14092 <https://github.com/scipy/scipy/pull/14092>`__: BUG: Fixes issue with clang. * `#14094 <https://github.com/scipy/scipy/pull/14094>`__: DOC: Correct the inconsistence definition of Default in class... * `#14105 <https://github.com/scipy/scipy/pull/14105>`__: TST: stats: mannwhitneyu: check that mstats and stats mannwhitneyu... * `#14106 <https://github.com/scipy/scipy/pull/14106>`__: DOC: stats.mstats: mannwhitneyu: the returned statistic is the... * `#14107 <https://github.com/scipy/scipy/pull/14107>`__: ENH: stats: bootstrap: add \`vectorized\` parameter; automatically... * `#14109 <https://github.com/scipy/scipy/pull/14109>`__: BUG: fix two issues in the fblas signature files * `#14110 <https://github.com/scipy/scipy/pull/14110>`__: DOC: mailmap update * `#14113 <https://github.com/scipy/scipy/pull/14113>`__: ENH: stats: bootstrap: add \`paired\` parameter * `#14116 <https://github.com/scipy/scipy/pull/14116>`__: MAINT: fix deprecated Python C API usage in odr * `#14118 <https://github.com/scipy/scipy/pull/14118>`__: DOC: 1.7.0 release notes * `#14125 <https://github.com/scipy/scipy/pull/14125>`__: DOC: fix typo * `#14126 <https://github.com/scipy/scipy/pull/14126>`__: ENH: stats: bootstrap: add \`batch\` parameter to control batch... * `#14127 <https://github.com/scipy/scipy/pull/14127>`__: CI: upgrade pip in benchmarks CI run * `#14130 <https://github.com/scipy/scipy/pull/14130>`__: BUG: Fix trust-constr report TypeError if verbose is set to 2... * `#14133 <https://github.com/scipy/scipy/pull/14133>`__: MAINT: interpolate: raise NotImplementedError not ValueError * `#14139 <https://github.com/scipy/scipy/pull/14139>`__: FIX/DOC: lsqr doctests print failure * `#14145 <https://github.com/scipy/scipy/pull/14145>`__: MAINT: 1.7.x version pins ("backport") * `#14146 <https://github.com/scipy/scipy/pull/14146>`__: MAINT: commit count if no tag * `#14164 <https://github.com/scipy/scipy/pull/14164>`__: TST, BUG: fix rbf matrix value * `#14166 <https://github.com/scipy/scipy/pull/14166>`__: CI, MAINT: restrictions on pre-release CI * `#14171 <https://github.com/scipy/scipy/pull/14171>`__: TST: signal: Bump tolerances for a test of Gustafsson's... * `#14175 <https://github.com/scipy/scipy/pull/14175>`__: TST: stats: Loosen tolerance in some binomtest tests. * `#14182 <https://github.com/scipy/scipy/pull/14182>`__: MAINT: stats: Update ppcc_plot and ppcc_max docstring. Checksums ========= MD5 ~~~ 5663523db409564ca11c6c94ab9a00b3 scipy-1.7.0rc1-cp37-cp37m-macosx_10_9_x86_64.whl 06e0143578cef69fc985bdd7ab534f59 scipy-1.7.0rc1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 60b46d37358c9e335c1711a3c82b8a4a scipy-1.7.0rc1-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl 12b18e8398d5c592991d35ed008e42a4 scipy-1.7.0rc1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl 1e4fddc62dbfdd29a8f5ef1954c54fb4 scipy-1.7.0rc1-cp37-cp37m-win32.whl d85a6d7a2289388d5d96c760859bb28f scipy-1.7.0rc1-cp37-cp37m-win_amd64.whl 2874082c4ce7422d7c7bd7f9397392e5 scipy-1.7.0rc1-cp38-cp38-macosx_10_9_x86_64.whl 22241402415519c0a80b7001ef9e36d2 scipy-1.7.0rc1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 8cb156b7e3e73d2f2bfddc817837d72a scipy-1.7.0rc1-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl 2180d0318a077ceaf48c314547887a76 scipy-1.7.0rc1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl 0bb8de89e1ef51adf050fe0c13cf00fe scipy-1.7.0rc1-cp38-cp38-win32.whl 18ec67e0939f2c4f66848a0073812ec5 scipy-1.7.0rc1-cp38-cp38-win_amd64.whl 95297e327369dcca2166d99d918f98cc scipy-1.7.0rc1-cp39-cp39-macosx_10_9_x86_64.whl dfc5f5cf5f93be60ef05aaa4d99b746b scipy-1.7.0rc1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 56e99e317b4063f85d6f7cb5fd820e32 scipy-1.7.0rc1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl 732ef2146805dbd422e920326d398841 scipy-1.7.0rc1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl fc568ac1d23edd9c61f5e53c53d69345 scipy-1.7.0rc1-cp39-cp39-win32.whl 4b019e5de3638b28ba19e987b18e703c scipy-1.7.0rc1-cp39-cp39-win_amd64.whl 651c79b44fc23d7403b7b4ff3146386c scipy-1.7.0rc1.tar.gz 9c353986615f93ad9d00ac44670fad1b scipy-1.7.0rc1.tar.xz 74032e20717d678cd67740215f2e8f6b scipy-1.7.0rc1.zip SHA256 ~~~~~~ 3e17adcbcf58a14890f6987f8b0cf13cf6c44258588ae9915912854a503ab937 scipy-1.7.0rc1-cp37-cp37m-macosx_10_9_x86_64.whl 250533a064b006d992dd5f80b9327396c2e09e62611c68acb5b15dd7e104c40b scipy-1.7.0rc1-cp37-cp37m-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 8f30ca6bafbacc905c3ef20b74e662177896209f279c0adff263c522593b8799 scipy-1.7.0rc1-cp37-cp37m-manylinux_2_5_i686.manylinux1_i686.whl ccacb1f0bda3f46608e1a721f6ab6107a978c27e88918dfc5d2e9afae3187dbd scipy-1.7.0rc1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl c41ec0521729cfe2a1c1e0e9b487e45f5c42957b77bb9bb97dcb3df53321cc26 scipy-1.7.0rc1-cp37-cp37m-win32.whl af341027b6937ef24346b342c511dbf517ab3d671c2e3c43c194592793d20789 scipy-1.7.0rc1-cp37-cp37m-win_amd64.whl f76d26beeb0963b3560d1bb20911ae97552d442c46a73df46006b018d2543079 scipy-1.7.0rc1-cp38-cp38-macosx_10_9_x86_64.whl 67b61dedddba2084819f284280f7d84eaacdf67b7b44ab21a6c17eb3ea4176fc scipy-1.7.0rc1-cp38-cp38-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 32819afdb42d70cca3b1b638d43fafc958d9b6e81ecf4fc2495fdc8134d357a9 scipy-1.7.0rc1-cp38-cp38-manylinux_2_5_i686.manylinux1_i686.whl 96459118025a540a13fbb3118eae3a9e5157335bb8612979f3d4443e0ca1d97d scipy-1.7.0rc1-cp38-cp38-manylinux_2_5_x86_64.manylinux1_x86_64.whl e945a4f33d5141d8c62074206ca23c3d822053a55a941b28fb37daaac9f3ca74 scipy-1.7.0rc1-cp38-cp38-win32.whl 093017be12146a8125e564877bb2d66dacc77387542b834b20dd111664ce3116 scipy-1.7.0rc1-cp38-cp38-win_amd64.whl e3c39cb0117f48c4c52bb6590bb8a508f76a47a6248b01ff535ce048dafdcd79 scipy-1.7.0rc1-cp39-cp39-macosx_10_9_x86_64.whl 3af0a29260b2dba983c31b7d90ccec06dd88afc0365a4b4ccbe71d7b343597d0 scipy-1.7.0rc1-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl a39b3afc90a12cb541ca0d6cec70b0ceb0c9212334a3356bae143fd6ca7c29aa scipy-1.7.0rc1-cp39-cp39-manylinux_2_5_i686.manylinux1_i686.whl a3c13a99e3b90abd189a22ebf51f1c4cc826fa0b8338711b55bb10243657a4ac scipy-1.7.0rc1-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl d31d9e1dd16e26c2e298b7118c2c115fdb248cf11b3164f68bdb808f19928ecc scipy-1.7.0rc1-cp39-cp39-win32.whl 50b9a9c5740035d7ce4771d82ccecc73f931ad12dce3212ba9310dc3aca78119 scipy-1.7.0rc1-cp39-cp39-win_amd64.whl b24ce88245397126bb64005ed4a9c00d916ea4c5ba8383d85a2ddbaac4805f06 scipy-1.7.0rc1.tar.gz 6e10f3083428bc8190fafb0a5c854f04dfcf705be605c598f651ab423fee4d59 scipy-1.7.0rc1.tar.xz ff18329dae5510c528c997e907c821165c8c5b034dbf43277f12130d6be0eb9a scipy-1.7.0rc1.zip

3 2

Enhancement Request: SuperLU_dist/SuperLU_mt replace current scipy.sparse.superLU
by Neil Godber June 9, 2021

June 9, 2021

Hi dev-list, I've logged an enhancement request on github to bring the parallel versions of SuperLU into scipy. As requested I'm circulating the enhancement here to solicit comment/feedback/engagement. Content of request is as follows (with light editing and links): "Is your feature request related to a problem? Please describe. The direct solution of sparse matrices is a common problem that arises across many domains. Current scipy.sparse.linalg provides spsolve and splu to solve such classes of problems. Neither solution appears to utilise more than one or two threads leaving a lot of the available compute on modern machines unused. Other solutions (MUMPS, Pardiso) exploit multicore processors but are either minimally supported and/or locked behind proprietary libraries. Describe the solution you'd like Fortunately SuperLU has two multithreaded implementations superLU_mt and superLU_dt, both actively maintained (SuperLU: Home Page (nersc.gov) <https://portal.nersc.gov/project/sparse/superlu/>). Ideally SciPy would replace the current sequential implementation with one of the parallel implementations to yield large performance improvements. Describe alternatives you've considered pyMKL (Pardiso dwfmarchant/pyMKL: Python wrappers to Intel MKL routines (github.com) <https://github.com/dwfmarchant/pyMKL>) - MKL with issues associated with that for non Intel processors, unmaintained relatively to scipy, PyTrilinos (implements all three superLU types but only available on osx and linux PyTrilinos | Trilinos <https://trilinos.github.io/pytrilinos.html>), petsc (petsc4py PETSc / petsc · GitLab <https://gitlab.com/petsc/petsc>) (implements all three superLU types but only available on osx and linux). All are relatively inaccessible compared to ubiquity and accessibility of scipy. Additional context (e.g. screenshots) Anecdotally large number of projects use various non scipy sparse solvers to achieve high level of performance. This comes with considerable time and maintenance investment. It would be fantastic for scipy to provide a 'performance competitive' sparse direct solver out of the hood as it does for dense matrices." Cheers, Neil

2 7

NumPy 1.21.0rc2 released
by Charles R Harris June 8, 2021

June 8, 2021

Hi All, On behalf of the NumPy team I am pleased to announce the release of NumPy 1.21.0rc2. The highlights are - continued SIMD work covering more functions and platforms, - initial work on the new dtype infrastructure and casting, - universal2 wheels for Python 3.8 and Python 3.9 on Mac, - improved documentation, - improved annotations, - new ``PCG64DXSM`` bitgenerator for random numbers. This NumPy release is the result of 571 merged pull requests contributed by 173 people. The Python versions supported for this release are 3.7-3.9, support for Python 3.10 will be added after Python 3.10 is released. Wheels can be downloaded from PyPI <https://pypi.org/project/numpy/1.21.0rc2/>; source archives, release notes, and wheel hashes are available on Github <https://github.com/numpy/numpy/releases/tag/v1.21.0rc2>. Linux users will need pip >= 0.19.3 in order to install manylinux2010 and manylinux2014 wheels. *Contributors* A total of 171 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - @8bitmp3 + - @DWesl + - @Endolith - @Illviljan + - @Lbogula + - @Lisa + - @Patrick + - @Scian + - @h-vetinari + - @h6197627 + - @jbCodeHub + - @legoffant + - @sfolje0 + - @tautaus + - @yetanothercheer + - Abhay Raghuvanshi + - Adrian Price-Whelan + - Aerik Pawson + - Agbonze Osazuwa + - Aitik Gupta + - Al-Baraa El-Hag - Alex Henrie - Alexander Hunt + - Alizé Papp + - Allan Haldane - Amarnath1904 + - Amrit Krishnan + - Andras Deak - AngelGris + - Anne Archibald - Anthony Vo + - Antony Lee - Atharva-Vidwans + - Ayush Verma + - Bas van Beek - Bharat Raghunathan - Bhargav V + - Brian Soto - Carl Michal + - Charles Harris - Charles Stern + - Chiara Marmo + - Chris Barnes + - Chris Vavaliaris - Christina Hedges + - Christoph Gohlke - Christopher Dahlin + - Christos Efstathiou + - Chunlin Fang - Constanza Fierro + - Daniel Evans + - Daniel Montes + - Dario Mory + - David Carlier + - David Stansby - Deepyaman Datta + - Derek Homeier - Dong Keun Oh + - Dylan Cutler + - Eric Larson - Eric Wieser - Eva Jau + - Evgeni Burovski - FX Coudert + - Faris A Chugthai + - Filip Ter + - Filip Trojan + - François Le Lay + - Ganesh Kathiresan - Giannis Zapantis + - Giulio Procopio + - Greg Lucas + - Hollow Man + - Holly Corbett + - I-Shen Leong + - Inessa Pawson - Isabela Presedo-Floyd - Ismael Jimenez + - Isuru Fernando - Jakob Jakobson - James Gerity + - Jamie Macey + - Jasmin Classen + - Jody Klymak + - Joseph Fox-Rabinovitz - Jérome Eertmans + - Jérôme Kieffer + - Kamil Choudhury + - Kasia Leszek + - Keller Meier + - Kevin Sheppard - Kulin Seth + - Kumud Lakara + - Laura Kopf + - Laura Martens + - Leo Singer + - Leonardus Chen + - Lima Tango + - Lumir Balhar + - Maia Kaplan + - Mainak Debnath + - Marco Aurélio da Costa + - Marta Lemanczyk + - Marten van Kerkwijk - Mary Conley + - Marysia Winkels + - Mateusz Sokół + - Matt Haberland - Matt Hall + - Matt Ord + - Matthew Badin + - Matthias Bussonnier - Matthias Geier - Matti Picus - Matías Ríos + - Maxim Belkin + - Melissa Weber Mendonça - Meltem Eren Copur + - Michael Dubravski + - Michael Lamparski - Michal W. Tarnowski + - Michał Górny + - Mike Boyle + - Mike Toews - Misal Raj + - Mitchell Faas + - Mukulikaa Parhari + - Neil Girdhar + - Nicholas McKibben + - Nico Schlömer - Nicolas Hug + - Nilo Kruchelski + - Nirjas Jakilim + - Ohad Ravid + - Olivier Grisel - Pamphile ROY + - Panos Mavrogiorgos + - Patrick T. Komiske III + - Pearu Peterson - Raghuveer Devulapalli - Ralf Gommers - Raúl Montón Pinillos + - Rin Arakaki + - Robert Kern - Rohit Sanjay - Roman Yurchak - Ronan Lamy - Ross Barnowski - Ryan C Cooper - Ryan Polley + - Ryan Soklaski - Sabrina Simao + - Sayed Adel - Sebastian Berg - Shen Zhou + - Stefan van der Walt - Sylwester Arabas + - Takanori Hirano - Tania Allard + - Thomas J. Fan + - Thomas Orgis + - Tim Hoffmann - Tomoki, Karatsu + - Tong Zou + - Touqir Sajed + - Tyler Reddy - Wansoo Kim - Warren Weckesser - Weh Andreas + - Yang Hau - Yashasvi Misra + - Zolboo Erdenebaatar + - Zolisa Bleki Cheers, Charles Harris Reply allReplyForward

1 0

Minimal sparse array interface
by Stefan van der Walt June 4, 2021

June 4, 2021

Hi everyone, Several times now, I've needed exactly what is available in scipy.sparse but with an array interface, instead of a matrix interface. Having such an interface would also simplify matters for libraries such as NetworkX and scikit-learn. I am aware of pydata.sparse, but that seems like quite a bit more than is needed here (higher dimensions, optimizations via numba; I'm not clear on the linear algebra status). Would it make sense to add a minimal interface on top of the SciPy sparse matrices that exposes a NumPy array interface? Eventually that could become the default (although it probably implies a larger refactor of the underlying classes). Best regards, Stéfan

3 6