From sebastian at sipsolutions.net Mon Dec 2 14:13:23 2019 From: sebastian at sipsolutions.net (Sebastian Berg) Date: Mon, 02 Dec 2019 13:13:23 -0600 Subject: [Numpy-discussion] [API] (minor change) Allow multiple axes in `expand_dims` Message-ID: Hi all, Pull request 14051: https://github.com/numpy/numpy/pull/14051 means that `np.expand_dims` now accepts multiple axes in the `axis` argument. As before, the axis signal where a new axis is in the output array. From the new tests: a = np.empty((3, 3, 3)) np.expand_dims(a, axis=(0, 1, 2)).shape == (1, 1, 1, 3, 3, 3) np.expand_dims(a, axis=(0, -1, -2)).shape == (1, 3, 3, 3, 1, 1) np.expand_dims(a, axis=(0, 3, 5)).shape == (1, 3, 3, 1, 3, 1) np.expand_dims(a, axis=(0, -3, -5)).shape == (1, 1, 3, 1, 3, 3) We believe this is an uncontroversial generalization, but pinging the mailing list since it is an API change. If anyone is concerned please I will be happy to revert, otherwise this is expected to be included in 1.18. Cheers, Sebastian -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part URL: From shoyer at gmail.com Mon Dec 2 14:40:10 2019 From: shoyer at gmail.com (Stephan Hoyer) Date: Mon, 2 Dec 2019 11:40:10 -0800 Subject: [Numpy-discussion] [API] (minor change) Allow multiple axes in `expand_dims` In-Reply-To: References: Message-ID: This looks good to me! On Mon, Dec 2, 2019 at 11:13 AM Sebastian Berg wrote: > Hi all, > > Pull request 14051: > > https://github.com/numpy/numpy/pull/14051 > > means that `np.expand_dims` now accepts multiple axes in the `axis` > argument. As before, the axis signal where a new axis is in the output > array. From the new tests: > > a = np.empty((3, 3, 3)) > np.expand_dims(a, axis=(0, 1, 2)).shape == (1, 1, 1, 3, 3, 3) > np.expand_dims(a, axis=(0, -1, -2)).shape == (1, 3, 3, 3, 1, 1) > np.expand_dims(a, axis=(0, 3, 5)).shape == (1, 3, 3, 1, 3, 1) > np.expand_dims(a, axis=(0, -3, -5)).shape == (1, 1, 3, 1, 3, 3) > > We believe this is an uncontroversial generalization, but pinging the > mailing list since it is an API change. If anyone is concerned please I > will be happy to revert, otherwise this is expected to be included in > 1.18. > > Cheers, > > Sebastian > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Mon Dec 2 22:29:43 2019 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Mon, 2 Dec 2019 19:29:43 -0800 Subject: [Numpy-discussion] Triage-review and Triaged labels & triage meeting Message-ID: Hi all, We now have "Triage-review" and "Triaged" labels, to go with the bi-weekly meeting we will start with this week. For those that missed it in the notes from the sprint: the idea is to change from the weekly "community call" meetings to: 1. a bi-weekly community call with higher-level topics (roadmap, docs, website, funding, the bigger NEPs, etc.) that should be interesting and accessible to anyone with an interest in where NumPy is going, and 2. a bi-weekly triage meeting, where we can discuss specific issues, blocked PRs, discuss whether some issue or idea should be high-prio or not, etc. The first triage meeting will be this Wednesday. To prepare for that, we created the new labels. It will take some time to figure out how to make these meetings most effective, and we'll discuss that in the meeting. One of the main topics on the agenda will be the actual issues and PRs that maintainers have labeled with "Triage-review". So if you have specific issues in mind that you think are high-prio or important to discuss for some other reason, please add that tag. After discussion, we aim to change the tag to "Triaged" with some summary and possibly the high-prio tag. Please feel free to put other things on the agenda ([1]) as well. Cheers, Ralf [1] https://hackmd.io/76o-IxCjQX2mOXO_wwkcpg?both -------------- next part -------------- An HTML attachment was scrubbed... URL: From warren.weckesser at gmail.com Tue Dec 3 14:33:21 2019 From: warren.weckesser at gmail.com (Warren Weckesser) Date: Tue, 3 Dec 2019 14:33:21 -0500 Subject: [Numpy-discussion] numpy/windows-wheel-builder repository Message-ID: It looks like the repo https://github.com/numpy/windows-wheel-builder is defunct. Could someone with the appropriate access privileges merge Matti's pull request to update README.rst (https://github.com/numpy/windows-wheel-builder/pull/7), and add a one-line description to the main repo page that says something like "INACTIVE - this repo is no longer maintained"? Thanks, Warren From ralf.gommers at gmail.com Tue Dec 3 14:44:58 2019 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 3 Dec 2019 11:44:58 -0800 Subject: [Numpy-discussion] numpy/windows-wheel-builder repository In-Reply-To: References: Message-ID: On Tue, Dec 3, 2019 at 11:33 AM Warren Weckesser wrote: > It looks like the repo https://github.com/numpy/windows-wheel-builder > is defunct. Could someone with the appropriate access privileges > merge Matti's pull request to update README.rst > (https://github.com/numpy/windows-wheel-builder/pull/7), and add a > one-line description to the main repo page that says something like > "INACTIVE - this repo is no longer maintained"? > Thanks, done. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Tue Dec 3 15:52:31 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 3 Dec 2019 13:52:31 -0700 Subject: [Numpy-discussion] numpy/windows-wheel-builder repository In-Reply-To: References: Message-ID: On Tue, Dec 3, 2019 at 12:45 PM Ralf Gommers wrote: > > > On Tue, Dec 3, 2019 at 11:33 AM Warren Weckesser < > warren.weckesser at gmail.com> wrote: > >> It looks like the repo https://github.com/numpy/windows-wheel-builder >> is defunct. Could someone with the appropriate access privileges >> merge Matti's pull request to update README.rst >> (https://github.com/numpy/windows-wheel-builder/pull/7), and add a >> one-line description to the main repo page that says something like >> "INACTIVE - this repo is no longer maintained"? >> > > Thanks, done. > > It is still used charris at fc [numpy-wheels.git (v1.17.x)]$ find . -name 'windows-wheel*' ./.git/modules/windows-wheel-builder Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Tue Dec 3 15:55:29 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 3 Dec 2019 13:55:29 -0700 Subject: [Numpy-discussion] numpy/windows-wheel-builder repository In-Reply-To: References: Message-ID: On Tue, Dec 3, 2019 at 1:52 PM Charles R Harris wrote: > > > On Tue, Dec 3, 2019 at 12:45 PM Ralf Gommers > wrote: > >> >> >> On Tue, Dec 3, 2019 at 11:33 AM Warren Weckesser < >> warren.weckesser at gmail.com> wrote: >> >>> It looks like the repo https://github.com/numpy/windows-wheel-builder >>> is defunct. Could someone with the appropriate access privileges >>> merge Matti's pull request to update README.rst >>> (https://github.com/numpy/windows-wheel-builder/pull/7), and add a >>> one-line description to the main repo page that says something like >>> "INACTIVE - this repo is no longer maintained"? >>> >> >> Thanks, done. >> >> > It is still used > > charris at fc [numpy-wheels.git (v1.17.x)]$ find . -name 'windows-wheel*' > ./.git/modules/windows-wheel-builder > > But not currently. charris at fc [numpy-wheels.git (v1.16.x)]$ git submodule e9764d0a8f4e3adcd385c319e7742177193484c7 gfortran-install (heads/master) +643d202b6f20827d31c45c709de490d0ccd810c1 multibuild (heads/devel) 9e419a0359cb5dbb9ae0b2711ab7a59b121a98cf numpy (pre-removal-numpybook-6032-g9e419a035) Chuck > Chuck > -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Tue Dec 3 15:58:39 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 3 Dec 2019 13:58:39 -0700 Subject: [Numpy-discussion] numpy/windows-wheel-builder repository In-Reply-To: References: Message-ID: On Tue, Dec 3, 2019 at 1:55 PM Charles R Harris wrote: > > > On Tue, Dec 3, 2019 at 1:52 PM Charles R Harris > wrote: > >> >> >> On Tue, Dec 3, 2019 at 12:45 PM Ralf Gommers >> wrote: >> >>> >>> >>> On Tue, Dec 3, 2019 at 11:33 AM Warren Weckesser < >>> warren.weckesser at gmail.com> wrote: >>> >>>> It looks like the repo https://github.com/numpy/windows-wheel-builder >>>> is defunct. Could someone with the appropriate access privileges >>>> merge Matti's pull request to update README.rst >>>> (https://github.com/numpy/windows-wheel-builder/pull/7), and add a >>>> one-line description to the main repo page that says something like >>>> "INACTIVE - this repo is no longer maintained"? >>>> >>> >>> Thanks, done. >>> >>> >> It is still used >> >> charris at fc [numpy-wheels.git (v1.17.x)]$ find . -name 'windows-wheel*' >> ./.git/modules/windows-wheel-builder >> >> > But not currently. > > charris at fc [numpy-wheels.git (v1.16.x)]$ git submodule > e9764d0a8f4e3adcd385c319e7742177193484c7 gfortran-install (heads/master) > +643d202b6f20827d31c45c709de490d0ccd810c1 multibuild (heads/devel) > 9e419a0359cb5dbb9ae0b2711ab7a59b121a98cf numpy > (pre-removal-numpybook-6032-g9e419a035) > > Chuck > > Was removed in from the wheels build in 2018. charris at fc [numpy-wheels.git (master)]$ git log --grep 'windows-wheel' commit 31aa52821df7436ecc5b7199d0071531c67be6ec Author: Charles Harris Date: Sun Feb 11 10:50:52 2018 -070 Chuck 0 MAINT: Remove now unused windows-wheel-builder submodule. Chuck > > >> Chuck >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Tue Dec 3 16:01:51 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 3 Dec 2019 14:01:51 -0700 Subject: [Numpy-discussion] NumPy 1.18 branch Message-ID: Hi All, I will be branching 1.18 this evening or tomorrow unless someone objects. There is still one last minute change to be merged. Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From kannanaswinvenu at gmail.com Tue Dec 3 16:47:33 2019 From: kannanaswinvenu at gmail.com (Aswin Venu) Date: Wed, 4 Dec 2019 03:17:33 +0530 Subject: [Numpy-discussion] We Message-ID: Ssszezr ss?ez -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.sipocz+numpylist at gmail.com Tue Dec 3 20:48:27 2019 From: b.sipocz+numpylist at gmail.com (Brigitta Sipocz) Date: Tue, 3 Dec 2019 17:48:27 -0800 Subject: [Numpy-discussion] numpy/windows-wheel-builder repository In-Reply-To: References: Message-ID: Hi, You could consider archiving the repository (bottom at the Settings page for folks with admin access), too. That makes it ever more visible that it's no longer maintained or in fact to be used. Cheers, Brigitta On Tue, 3 Dec 2019 at 11:33, Warren Weckesser wrote: > > It looks like the repo https://github.com/numpy/windows-wheel-builder > is defunct. Could someone with the appropriate access privileges > merge Matti's pull request to update README.rst > (https://github.com/numpy/windows-wheel-builder/pull/7), and add a > one-line description to the main repo page that says something like > "INACTIVE - this repo is no longer maintained"? > > Thanks, > > Warren > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion From charlesr.harris at gmail.com Tue Dec 3 21:07:48 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 3 Dec 2019 19:07:48 -0700 Subject: [Numpy-discussion] NumPy 1.19.0-dev is open. Message-ID: Hi All, The 1.18.x branch has been made and the master branch is open for 1.19.0 development. Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Tue Dec 3 22:37:37 2019 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 3 Dec 2019 19:37:37 -0800 Subject: [Numpy-discussion] numpy/windows-wheel-builder repository In-Reply-To: References: Message-ID: On Tue, Dec 3, 2019 at 5:49 PM Brigitta Sipocz wrote: > Hi, > > You could consider archiving the repository (bottom at the Settings > page for folks with admin access), too. That makes it ever more > visible that it's no longer maintained or in fact to be used. > Good idea, thanks Brigitta. Done. Cheers, Ralf > Cheers, > Brigitta > > On Tue, 3 Dec 2019 at 11:33, Warren Weckesser > wrote: > > > > It looks like the repo https://github.com/numpy/windows-wheel-builder > > is defunct. Could someone with the appropriate access privileges > > merge Matti's pull request to update README.rst > > (https://github.com/numpy/windows-wheel-builder/pull/7), and add a > > one-line description to the main repo page that says something like > > "INACTIVE - this repo is no longer maintained"? > > > > Thanks, > > > > Warren > > _______________________________________________ > > NumPy-Discussion mailing list > > NumPy-Discussion at python.org > > https://mail.python.org/mailman/listinfo/numpy-discussion > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Thu Dec 5 21:40:55 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Thu, 5 Dec 2019 19:40:55 -0700 Subject: [Numpy-discussion] NumPy 1.18.0rc1 released. Message-ID: Hi All, On behalf of the NumPy team I am pleased to announce that NumPy 1.18.0rc1 has been released. In addition to the usual bug fixes, this NumPy release cleans up and documents the new random C-API, expires a large number of old deprecations, and improves the appearance and organization of the documentation. The Python versions supported are 3.5-3.8. This is the last NumPy release series that will support Python 3.5. The highlights of this release are: - the C-API for ``numpy.random`` has been defined and documented, - basic infrastructure for linking with 64 bit BLAS and LAPACK libraries, - many documentation improvements. Downstream developers should use Cython >= 0.29.14 for Python 3.8 support and OpenBLAS >= 3.7 to avoid wrong results on the Skylake architecture. The NumPy Wheels for this release can be downloaded from PyPI , source archives and release notes are available from Github . *Highlights* - The C-API for ``numpy.random`` has been defined and documented. - Basic infrastructure for linking with 64 bit BLAS and LAPACK libraries. - Many documentation improvements. *Contributors* A total of 113 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Abhinav Sagar - Alex Henrie + - Alexander Jung + - Allan Haldane - Andrea Pattori - Andrew Liu + - Anis Ladram + - Anne Bonner + - Antoine Dechaume + - Aryan Naraghi + - Bastian Eichenberger + - Brian Wignall + - Brigitta Sipocz - CakeWithSteak + - Charles Harris - Chris Barker - Chris Burr + - Chris Markiewicz + - Christoph Gohlke - Christopher Whelan - Colin Snyder - Dan Allan - Daniel Ching - David Stansby + - David Zwicker + - Dieter Werthm?ller - Disconnect3d + - Dmytro + - Doug Davis + - Eric Larson - Eric Wieser - Esben Haabendal + - Eugene Prilepin + - Felix Divo + - Gary Gurlaskie - Gina + - Giuseppe Cuccu + - Grzegorz Bokota + - Guanqun Lu + - Guilherme Leobas + - Guillaume Horel - G?raud Le Falher + - Hameer Abbasi - Harmon - Hiroyuki V. Yamazaki - Huang, Guangtai + - Hugo + - Hyeonguk Ryu + - Ilhan Polat + - Isaac Virshup - Jack J. Woehr + - Jack Woehr + - Jackie Leng - Jaime Fernandez - Jeff Hale + - Johann Faouzi + - Jon Dufresne + - Joseph Fox-Rabinovitz - Joseph R. Fox-Rabinovitz + - Jo?o Marcos Gris + - Justus Magin + - J?r?mie du Boisberranger - Kai Striega - Kevin Sheppard - Kexuan Sun - Kmol Yuan + - Kriti Singh - Larry Bradley + - Lars Grueter - Luis Pedro Coelho - MSeifert04 - Magdalena Proszewska + - Manny + - Mark Harfouche - Martin Reinecke - Martin Thoma - Matt Haberland + - Matt McCormick + - Matthias Bussonnier - Matti Picus - Max Bolingbroke + - Maxwell Aladago + - Michael Hudson-Doyle + - Oleksandr Pavlyk - Omar Merghany + - Pauli Virtanen - Peter Andreas Entschev - Peter Bell - Peter Cock + - Pradeep Reddy Raamana + - Qiming Sun + - Raghuveer Devulapalli - Ralf Gommers - Samesh + - Samesh Lakhotia + - Sebastian Berg - Sergei Lebedev - Seth Troisi + - Siddhesh Poyarekar + - Simon + - Simon Notley + - Stefan van der Walt - Stephan Hoyer - Steve Stagg - Thomas A Caswell - Thomas Kluyver - Tim Hoffmann + - Tyler Reddy - Vladimir Pershin + - Warren Weckesser - Yadong Zhang + - Zieji Pohz + - Zolisa Bleki + Cheers, Charles Harris -------------- next part -------------- An HTML attachment was scrubbed... URL: From p4j at j4d.net Fri Dec 6 01:56:31 2019 From: p4j at j4d.net (Pankaj Jangid) Date: Fri, 6 Dec 2019 06:56:31 +0000 Subject: [Numpy-discussion] NumPy 1.18.0rc1 released. In-Reply-To: (Charles R. Harris's message of "Thu, 5 Dec 2019 19:40:55 -0700") References: Message-ID: <0100016ed9fee777-5ac1667e-fe5c-4b85-ba13-bb88e238fec3-000000@email.amazonses.com> Charles R Harris writes: > *Contributors* > > A total of 113 people contributed to this release. People with a "+" > by their names contributed a patch for the first time. The list has so many new names. Cheers for the growing community. Congratulations All. From tyler.je.reddy at gmail.com Sun Dec 8 15:53:51 2019 From: tyler.je.reddy at gmail.com (Tyler Reddy) Date: Sun, 8 Dec 2019 13:53:51 -0700 Subject: [Numpy-discussion] ANN: SciPy 1.4.0rc2 -- please test Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi all, On behalf of the SciPy development team I'm pleased to announce the release candidate SciPy 1.4.0rc2. Please help us test this pre-release. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.4.0rc2 One of a few ways to install the release candidate with pip: pip install scipy==1.4.0rc2 ========================== SciPy 1.4.0 Release Notes ========================== Note: Scipy 1.4.0 is not released yet! SciPy 1.4.0 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 1.4.x branch, and on adding new features on the master branch. This release requires Python 3.5+ and NumPy >=1.13.3 (for Python 3.5, 3.6), >=1.14.5 (for Python 3.7), >= 1.17.3 (for Python 3.8) For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. Highlights of this release ----------------------------------- - a new submodule, `scipy.fft`, now supersedes `scipy.fftpack`; this means support for ``long double`` transforms, faster multi-dimensional transforms, improved algorithm time complexity, release of the global intepreter lock, and control over threading behavior - support for ``pydata/sparse`` arrays in `scipy.sparse.linalg` - substantial improvement to the documentation and functionality of several `scipy.special` functions, and some new additions - the generalized inverse Gaussian distribution has been added to `scipy.stats` - an implementation of the Edmonds-Karp algorithm in `scipy.sparse.csgraph.maximum_flow` - `scipy.spatial.SphericalVoronoi` now supports n-dimensional input, has linear memory complexity, improved performance, and supports single-hemisphere generators New features ============ Infrastructure -------------------- Documentation can now be built with ``runtests.py --doc`` A ``Dockerfile`` is now available in the ``scipy/scipy-dev`` repository to facilitate getting started with SciPy development. `scipy.constants` improvements ---------------------------------------------- `scipy.constants` has been updated with the CODATA 2018 constants. `scipy.fft` added ----------------------- `scipy.fft` is a new submodule that supersedes the `scipy.fftpack` submodule. For the most part, this is a drop-in replacement for ``numpy.fft`` and `scipy.fftpack` alike. With some important differences, `scipy.fft`: - uses NumPy's conventions for real transforms (``rfft``). This means the return value is a complex array, half the size of the full ``fft`` output. This is different from the output of ``fftpack`` which returned a real array representing complex components packed together. - the inverse real to real transforms (``idct`` and ``idst``) are normalized for ``norm=None`` in thesame way as ``ifft``. This means the identity ``idct(dct(x)) == x`` is now ``True`` for all norm modes. - does not include the convolutions or pseudo-differential operators from ``fftpack``. This submodule is based on the ``pypocketfft`` library, developed by the author of ``pocketfft`` which was recently adopted by NumPy as well. ``pypocketfft`` offers a number of advantages over fortran ``FFTPACK``: - support for long double (``np.longfloat``) precision transforms. - faster multi-dimensional transforms using vectorisation - Bluestein?s algorithm removes the worst-case ``O(n^2)`` complexity of ``FFTPACK`` - the global interpreter lock (``GIL``) is released during transforms - optional multithreading of multi-dimensional transforms via the ``workers`` argument Note that `scipy.fftpack` has not been deprecated and will continue to be maintained but is now considered legacy. New code is recommended to use `scipy.fft` instead, where possible. `scipy.fftpack` improvements ---------------------------------------- `scipy.fftpack` now uses pypocketfft to perform its FFTs, offering the same speed and accuracy benefits listed for scipy.fft above but without the improved API. `scipy.integrate` improvements ------------------------------------------- The function `scipy.integrate.solve_ivp` now has an ``args`` argument. This allows the user-defined functions passed to the function to have additional parameters without having to create wrapper functions or lambda expressions for them. `scipy.integrate.solve_ivp` can now return a ``y_events`` attribute representing the solution of the ODE at event times New ``OdeSolver`` is implemented --- ``DOP853``. This is a high-order explicit Runge-Kutta method originally implemented in Fortran. Now we provide a pure Python implementation usable through ``solve_ivp`` with all its features. `scipy.integrate.quad` provides better user feedback when break points are specified with a weighted integrand. `scipy.integrate.quad_vec` is now available for general purpose integration of vector-valued functions `scipy.interpolate` improvements -------------------------------------------- `scipy.interpolate.pade` now handles complex input data gracefully `scipy.interpolate.Rbf` can now interpolate multi-dimensional functions `scipy.io` improvements --------------------------------- `scipy.io.wavfile.read` can now read data from a `WAV` file that has a malformed header, similar to other modern `WAV` file parsers `scipy.io.FortranFile` now has an expanded set of available ``Exception`` classes for handling poorly-formatted files `scipy.linalg` improvements -------------------------------------- The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct results for complex-valued matrices. Before this, the function only returned correct values for real-valued matrices. New boolean keyword argument ``check_finite`` for `scipy.linalg.norm`; whether to check that the input matrix contains only finite numbers. Disabling may give a performance gain, but may result in problems (crashes, non-termination) if the inputs do contain infinities or NaNs. `scipy.linalg.solve_triangular` has improved performance for a C-ordered triangular matrix ``LAPACK`` wrappers have been added for ``?geequ``, ``?geequb``, ``?syequb``, and ``?heequb`` Some performance improvements may be observed due to an internal optimization in operations involving LAPACK routines via ``_compute_lwork``. This is particularly true for operations on small arrays. Block ``QR`` wrappers are now available in `scipy.linalg.lapack` `scipy.ndimage` improvements ------------------------------------------ `scipy.optimize` improvements ------------------------------------------ It is now possible to use linear and non-linear constraints with `scipy.optimize.differential_evolution`. `scipy.optimize.linear_sum_assignment` has been re-written in C++ to improve performance, and now allows input costs to be infinite. A ``ScalarFunction.fun_and_grad`` method was added for convenient simultaneous retrieval of a function and gradient evaluation `scipy.optimize.minimize` ``BFGS`` method has improved performance by avoiding duplicate evaluations in some cases Better user feedback is provided when an objective function returns an array instead of a scalar. `scipy.signal` improvements --------------------------------------- Added a new function to calculate convolution using the overlap-add method, named `scipy.signal.oaconvolve`. Like `scipy.signal.fftconvolve`, this function supports specifying dimensions along which to do the convolution. `scipy.signal.cwt` now supports complex wavelets. The implementation of ``choose_conv_method`` has been updated to reflect the new FFT implementation. In addition, the performance has been significantly improved (with rather drastic improvements in edge cases). The function ``upfirdn`` now has a ``mode`` keyword argument that can be used to select the signal extension mode used at the signal boundaries. These modes are also available for use in ``resample_poly`` via a newly added ``padtype`` argument. `scipy.signal.sosfilt` now benefits from Cython code for improved performance `scipy.signal.resample` should be more efficient by leveraging ``rfft`` when possible `scipy.sparse` improvements ---------------------------------------- It is now possible to use the LOBPCG method in `scipy.sparse.linalg.svds`. `scipy.sparse.linalg.LinearOperator` now supports the operation ``rmatmat`` for adjoint matrix-matrix multiplication, in addition to ``rmatvec``. Multiple stability updates enable float32 support in the LOBPCG eigenvalue solver for symmetric and Hermitian eigenvalues problems in ``scipy.sparse.linalg.lobpcg``. A solver for the maximum flow problem has been added as `scipy.sparse.csgraph.maximum_flow`. `scipy.sparse.csgraph.maximum_bipartite_matching` now allows non-square inputs, no longer requires a perfect matching to exist, and has improved performance. `scipy.sparse.lil_matrix` conversions now perform better in some scenarios Basic support is available for ``pydata/sparse`` arrays in `scipy.sparse.linalg` `scipy.sparse.linalg.spsolve_triangular` now supports the ``unit_diagonal`` argument to improve call signature similarity with its dense counterpart, `scipy.linalg.solve_triangular` ``assertAlmostEqual`` may now be used with sparse matrices, which have added support for ``__round__`` `scipy.spatial` improvements -------------------------------------- The bundled Qhull library was upgraded to version 2019.1, fixing several issues. Scipy-specific patches are no longer applied to it. `scipy.spatial.SphericalVoronoi` now has linear memory complexity, improved performance, and supports single-hemisphere generators. Support has also been added for handling generators that lie on a great circle arc (geodesic input) and for generators in n-dimensions. `scipy.spatial.transform.Rotation` now includes functions for calculation of a mean rotation, generation of the 3D rotation groups, and reduction of rotations with rotational symmetries. `scipy.spatial.transform.Slerp` is now callable with a scalar argument `scipy.spatial.voronoi_plot_2d` now supports furthest site Voronoi diagrams `scipy.spatial.Delaunay` and `scipy.spatial.Voronoi` now have attributes for tracking whether they are furthest site diagrams `scipy.special` improvements --------------------------------------- The Voigt profile has been added as `scipy.special.voigt_profile`. A real dispatch has been added for the Wright Omega function (`scipy.special.wrightomega`). The analytic continuation of the Riemann zeta function has been added. (The Riemann zeta function is the one-argument variant of `scipy.special.zeta`.) The complete elliptic integral of the first kind (`scipy.special.ellipk`) is now available in `scipy.special.cython_special`. The accuracy of `scipy.special.hyp1f1` for real arguments has been improved. The documentation of many functions has been improved. `scipy.stats` improvements ------------------------------------- `scipy.stats.multiscale_graphcorr` added as an independence test that operates on high dimensional and nonlinear data sets. It has higher statistical power than other `scipy.stats` tests while being the only one that operates on multivariate data. The generalized inverse Gaussian distribution (`scipy.stats.geninvgauss`) has been added. It is now possible to efficiently reuse `scipy.stats.binned_statistic_dd` with new values by providing the result of a previous call to the function. `scipy.stats.hmean` now handles input with zeros more gracefully. The beta-binomial distribution is now available in `scipy.stats.betabinom`. `scipy.stats.zscore`, `scipy.stats.circmean`, `scipy.stats.circstd`, and `scipy.stats.circvar` now support the ``nan_policy`` argument for enhanced handling of ``NaN`` values `scipy.stats.entropy` now accepts an ``axis`` argument `scipy.stats.gaussian_kde.resample` now accepts a ``seed`` argument to empower reproducibility `scipy.stats.kendalltau` performance has improved, especially for large inputs, due to improved cache usage `scipy.stats.truncnorm` distribution has been rewritten to support much wider tails Deprecated features =================== `scipy` deprecations ---------------------------- Support for NumPy functions exposed via the root SciPy namespace is deprecated and will be removed in 2.0.0. For example, if you use ``scipy.rand`` or ``scipy.diag``, you should change your code to directly use ``numpy.random.default_rng`` or ``numpy.diag``, respectively. They remain available in the currently continuing Scipy 1.x release series. The exception to this rule is using ``scipy.fft`` as a function -- :mod:`scipy.fft` is now meant to be used only as a module, so the ability to call ``scipy.fft(...)`` will be removed in SciPy 1.5.0. In `scipy.spatial.Rotation` methods ``from_dcm``, ``as_dcm`` were renamed to ``from_matrix``, ``as_matrix`` respectively. The old names will be removed in SciPy 1.6.0. Method ``Rotation.match_vectors`` was deprecated in favor of ``Rotation.align_vectors``, which provides a more logical and general API to the same functionality. The old method will be removed in SciPy 1.6.0. Backwards incompatible changes ============================== `scipy.special` changes -------------------------------- The deprecated functions ``hyp2f0``, ``hyp1f2``, and ``hyp3f0`` have been removed. The deprecated function ``bessel_diff_formula`` has been removed. The function ``i0`` is no longer registered with ``numpy.dual``, so that ``numpy.dual.i0`` will unconditionally refer to the NumPy version regardless of whether `scipy.special` is imported. The function ``expn`` has been changed to return ``nan`` outside of its domain of definition (``x, n < 0``) instead of ``inf``. `scipy.sparse` changes -------------------------------- Sparse matrix reshape now raises an error if shape is not two-dimensional, rather than guessing what was meant. The behavior is now the same as before SciPy 1.1.0. ``CSR`` and ``CSC`` sparse matrix classes should now return empty matrices of the same type when indexed out of bounds. Previously, for some versions of SciPy, this would raise an ``IndexError``. The change is largely motivated by greater consistency with ``ndarray`` and ``numpy.matrix`` semantics. `scipy.signal` changes ------------------------------ `scipy.signal.resample` behavior for length-1 signal inputs has been fixed to output a constant (DC) value rather than an impulse, consistent with the assumption of signal periodicity in the FFT method. `scipy.signal.cwt` now performs complex conjugation and time-reversal of wavelet data, which is a backwards-incompatible bugfix for time-asymmetric wavelets. `scipy.stats` changes ----------------------------- `scipy.stats.loguniform` added with better documentation as (an alias for ``scipy.stats.reciprocal``). ``loguniform`` generates random variables that are equally likely in the log space; e.g., ``1``, ``10`` and ``100`` are all equally likely if ``loguniform(10 ** 0, 10 ** 2).rvs()`` is used. Other changes ============= The ``LSODA`` method of `scipy.integrate.solve_ivp` now correctly detects stiff problems. `scipy.spatial.cKDTree` now accepts and correctly handles empty input data `scipy.stats.binned_statistic_dd` now calculates the standard deviation statistic in a numerically stable way. `scipy.stats.binned_statistic_dd` now throws an error if the input data contains either ``np.nan`` or ``np.inf``. Similarly, in `scipy.stats` now all continuous distributions' ``.fit()`` methods throw an error if the input data contain any instance of either ``np.nan`` or ``np.inf``. Authors ======= * @endolith * @wenhui-prudencemed + * Abhinav + * Anne Archibald * ashwinpathak20nov1996 + * Danilo Augusto + * Nelson Auner + * aypiggott + * Christoph Baumgarten * Peter Bell * Sebastian Berg * Arman Bilge + * Benedikt Boecking + * Christoph Boeddeker + * Daniel Bunting * Evgeni Burovski * Angeline Burrell + * Angeline G. Burrell + * CJ Carey * Carlos Ramos Carre?o + * Mak Sze Chun + * Malayaja Chutani + * Christian Clauss + * Jonathan Conroy + * Stephen P Cook + * Dylan Cutler + * Anirudh Dagar + * Aidan Dang + * dankleeman + * Brandon David + * Tyler Dawson + * Dieter Werthm?ller * Joe Driscoll + * Jakub Dyczek + * D?vid Bodn?r * Fletcher Easton + * Stefan Endres * etienne + * Johann Faouzi * Yu Feng * Isuru Fernando + * Matthew H Flamm * Martin Gauch + * Gabriel Gerlero + * Ralf Gommers * Chris Gorgolewski + * Domen Gorjup + * Edouard Goudenhoofdt + * Jan Gwinner + * Maja Gwozdz + * Matt Haberland * hadshirt + * Pierre Haessig + * David Hagen * Charles Harris * Gina Helfrich + * Alex Henrie + * Francisco J. Hernandez Heras + * Andreas Hilboll * Lindsey Hiltner * Thomas Hisch * Min ho Kim + * Gert-Ludwig Ingold * jakobjakobson13 + * Todd Jennings * He Jia * Muhammad Firmansyah Kasim + * Andrew Knyazev + * Holger Kohr + * Mateusz Konieczny + * Krzysztof Pi?ro + * Philipp Lang + * Peter Mahler Larsen + * Eric Larson * Antony Lee * Gregory R. Lee * Chelsea Liu + * Jesse Livezey * Peter Lysakovski + * Jason Manley + * Michael Marien + * Nikolay Mayorov * G. D. McBain + * Sam McCormack + * Melissa Weber Mendon?a + * Kevin Michel + * mikeWShef + * Sturla Molden * Eric Moore * Peyton Murray + * Andrew Nelson * Clement Ng + * Juan Nunez-Iglesias * Renee Otten + * Kellie Ottoboni + * Ayappan P * Sambit Panda + * Tapasweni Pathak + * Oleksandr Pavlyk * Fabian Pedregosa * Petar Mlinari? * Matti Picus * Marcel Plch + * Christoph Pohl + * Ilhan Polat * Siddhesh Poyarekar + * Ioannis Prapas + * James Alan Preiss + * Yisheng Qiu + * Eric Quintero * Bharat Raghunathan + * Tyler Reddy * Joscha Reimer * Antonio Horta Ribeiro * Lucas Roberts * rtshort + * Josua Sassen * Kevin Sheppard * Scott Sievert * Leo Singer * Kai Striega * S?ren Fuglede J?rgensen * tborisow + * ?tienne Tremblay + * tuxcell + * Miguel de Val-Borro * Andrew Valentine + * Hugo van Kemenade * Paul van Mulbregt * Sebastiano Vigna * Pauli Virtanen * Dany Vohl + * Ben Walsh + * Huize Wang + * Warren Weckesser * Anreas Weh + * Joseph Weston + * Adrian Wijaya + * Timothy Willard + * Josh Wilson * Kentaro Yamamoto + * Dave Zbarsky + A total of 142 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 1.4.0 -------------------------------- * `#1255 `__: maxiter broken for Scipy.sparse.linalg gmres, in addition to... * `#1301 `__: consolidate multipack.h from interpolate and integrate packages... * `#1739 `__: Single precision FFT insufficiently accurate. (Trac #1212) * `#1795 `__: stats test_distributions.py: replace old fuzz tests (Trac #1269) * `#2233 `__: fftpack segfault with big arrays (Trac #1714) * `#2434 `__: rmatmat and the sophistication of linear operator objects * `#2477 `__: stats.truncnorm.rvs() does not give symmetric results for negative... * `#2629 `__: FFTpack is unacceptably slow on non power of 2 * `#2883 `__: UnboundLocalError in scipy.interpolate.splrep * `#2956 `__: Feature Request: axis argument for stats.entropy function * `#3528 `__: Segfault on test_djbfft (possibly MKL-related?) * `#3793 `__: cwt should also return complex array * `#4464 `__: TST: residue/residuez/invres/invresz don't have any tests * `#4561 `__: BUG: tf filter trailing and leading zeros in residuez * `#4669 `__: Rewrite sosfilt to make a single loop over the input? * `#5040 `__: BUG: Empty data handling of (c)KDTrees * `#5112 `__: boxcox transform edge cases could use more care * `#5441 `__: scipy.stats.ncx2 fails for nc=0 * `#5502 `__: args keyword not handled in optimize.curve_fit * `#6484 `__: Qhull segmentation fault * `#6900 `__: linear_sum_assignment with infinite weights * `#6966 `__: Hypergeometric Functions documentation is lacking * `#6999 `__: possible false positive corruption check in compressed loadmat() * `#7018 `__: ydata that needs broadcasting renders curve_fit unable to compute... * `#7140 `__: trouble with documentation for windows * `#7327 `__: interpolate.ndgriddata.griddata causes Python to crash rather... * `#7396 `__: MatrixLinearOperator implements _adjoint(), but not _transpose() * `#7400 `__: BUG(?): special: factorial and factorial2 return a 0-dimensional... * `#7434 `__: Testing of scipy.stats continuous distributions misses 25 distributions * `#7491 `__: Several scipy.stats distributions (fisk, burr, burr12, f) return... * `#7759 `__: Overflow in stats.kruskal for large samples * `#7906 `__: Wrong result from scipy.interpolate.UnivariateSpline.integral... * `#8165 `__: ENH: match functionality of R for hmean * `#8417 `__: optimimze.minimize(method='L-BFGS-B', options={'disp': True})... * `#8535 `__: Strictly increasing requirement in UnivariateSpline * `#8815 `__: [BUG] GMRES: number of iteration is only increased if callback... * `#9207 `__: scipy.linalg.solve_triangular speed after scipy.linalg.lu_factor * `#9275 `__: new feature: adding LOBPCG solver in svds in addition to ARPACK * `#9403 `__: range of truncnorm.logpdf could be extended * `#9429 `__: gaussian_kde not working with numpy matrix * `#9515 `__: ndimage implementation relies on undefined behavior * `#9643 `__: arpack returns singular values in ascending order * `#9669 `__: DOC: matthew-brett/build-openblas has been retired * `#9852 `__: scipy.spatial.ConvexHull exit with code 134, free(): invalid... * `#9902 `__: scipy.stats.truncnorm second moment may be wrong * `#9943 `__: Custom sampling methods in shgo do not work * `#9947 `__: DOC: Incorrect documentation for \`nan_policy='propagate\` in... * `#9994 `__: BUG: sparse: reshape method allows a shape containing an arbitrary... * `#10036 `__: Official Nelder mead tutorial uses xtol instead of xatol, which... * `#10078 `__: possible to get a better error message when objective function... * `#10092 `__: overflow in truncnorm.rvs * `#10121 `__: A little spelling mistake * `#10126 `__: inaccurate std implementation in binned_statistic * `#10161 `__: Error in documentation scipy.special.modstruve * `#10195 `__: Derivative of spline with 'const' extrapolation is also extrapolted... * `#10206 `__: sparse matrices indexing with scipy 1.3 * `#10236 `__: Non-descriptive error on type mismatch for functions of scipy.optimize... * `#10258 `__: LOBPCG convergence failure if guess provided * `#10262 `__: distance matrix lacks dtype checks / warnings * `#10271 `__: BUG: optimize failure on wheels * `#10277 `__: scipy.special.zeta(0) = NAN * `#10292 `__: DOC/REL: Some sections of the release notes are not nested correctly. * `#10300 `__: scipy.stats.rv_continuous.fit throws empty RuntimeError when... * `#10319 `__: events in scipy.integrate.solve_ivp: How do I setup an events... * `#10323 `__: Adding more low-level LAPACK wrappers * `#10360 `__: firwin2 inadvertently modifies input and may result in undefined... * `#10388 `__: BLD: TestHerd::test_hetrd core dumps with Python-dbg * `#10395 `__: Remove warning about output shape of zoom * `#10403 `__: DOC: scipy.signal.resample ignores t parameter * `#10421 `__: Yeo-Johnson power transformation fails with integer input data * `#10422 `__: BUG: scipy.fft does not support multiprocessing * `#10427 `__: ENH: convolve numbers should be updated * `#10444 `__: BUG: scipy.spatial.transform.Rotation.match_vectors returns improper... * `#10488 `__: ENH: DCTs/DSTs for scipy.fft * `#10501 `__: BUG: scipy.spatial.HalfspaceIntersection works incorrectly * `#10514 `__: BUG: cKDTree GIL handling is incorrect * `#10535 `__: TST: master branch CI failures * `#10588 `__: scipy.fft and numpy.fft inconsistency when axes=None and shape... * `#10628 `__: Scipy python>3.6 Windows wheels don't ship msvcp\*.dll * `#10733 `__: DOC/BUG: min_only result does not match documentation * `#10774 `__: min_only=true djisktra infinite loop with duplicate indices * `#10775 `__: UnboundLocalError in Radau when given a NaN * `#10835 `__: io.wavfile.read unnecessarily raises an error for a bad wav header * `#10838 `__: Error in documentation for scipy.linalg.lu_factor * `#10875 `__: DOC: Graphical guides (using TikZ) * `#10880 `__: setting verbose > 2 in minimize with trust-constr method leads... * `#10887 `__: scipy.signal.signaltools._fftconv_faster has incorrect estimates * `#10948 `__: gammainc(0,x) = nan but should be 1, gammaincc(0,x) = nan but... * `#10952 `__: TestQRdelete_F.test_delete_last_p_col test failure * `#10968 `__: API: Change normalized=False to normalize=True in Rotation * `#10987 `__: Memory leak in shgo triangulation * `#10991 `__: Error running openBlas probably missing a step * `#11033 `__: deadlock on osx for python 3.8 * `#11041 `__: Test failure in wheel builds for TestTf2zpk.test_simple * `#11089 `__: Regression in scipy.stats where distribution will not accept loc and scale parameters * `#11100 `__: BUG: multiscale_graphcorr random state seeding and parallel use * `#11121 `__: Calls to `scipy.interpolate.splprep` increase RAM usage. * `#11125 `__: BUG: segfault when slicing a CSR or CSC sparse matrix with slice start index > stop index Pull requests for 1.4.0 ------------------------------- * `#4591 `__: BUG, TST: Several issues with scipy.signal.residue * `#6629 `__: ENH: sparse: canonicalize on initialization * `#7076 `__: ENH: add complex wavelet support to scipy.signal.cwt. * `#8681 `__: ENH add generalized inverse Gaussian distribution to scipy.stats * `#9064 `__: BUG/ENH: Added default _transpose into LinearOperator. Fixes... * `#9215 `__: ENH: Rbf interpolation of large multi-dimensional data * `#9311 `__: ENH: Added voigt in scipy.special. * `#9642 `__: ENH: integrate: quad() for vector-valued functions * `#9679 `__: DOC: expand docstring of exponweib distribution * `#9684 `__: TST: add ppc64le ci testing * `#9800 `__: WIP : ENH: Refactored _hungarian.py for speed and added a minimize/maximize? * `#9847 `__: DOC: Change integrate tutorial to use solve_ivp instead of odeint * `#9876 `__: ENH: Use rfft when possible in resampling * `#9998 `__: BUG: Do not remove 1s when calling sparse: reshape method #9994 * `#10002 `__: ENH: adds constraints for differential evolution * `#10098 `__: ENH: integrate: add args argument to solve_ivp. * `#10099 `__: DOC: Add missing docs for linprog unknown_options * `#10104 `__: BUG: Rewrite of stats.truncnorm distribution. * `#10105 `__: MAINT improve efficiency of rvs_ratio_uniforms in scipy.stats * `#10107 `__: TST: dual_annealing set seed * `#10108 `__: ENH: stats: improve kendall_tau cache usage * `#10110 `__: MAINT: _lib: Fix a build warning. * `#10114 `__: FIX: only print bounds when supported by minimizer (shgo) * `#10115 `__: TST: Add a test with an almost singular design matrix for lsq_linear * `#10118 `__: MAINT: fix rdist methods in scipy.stats * `#10119 `__: MAINT: improve rvs of randint in scipy.stats * `#10127 `__: Fix typo in record array field name (spatial-ckdtree-sparse_distance? * `#10130 `__: MAINT: ndimage: Fix some compiler warnings. * `#10131 `__: DOC: Note the solve_ivp args enhancement in the 1.4.0 release... * `#10133 `__: MAINT: add rvs for semicircular in scipy.stats * `#10138 `__: BUG: special: Invalid arguments to ellip_harm can crash Python. * `#10139 `__: MAINT: spatial: Fix some compiler warnings in the file distance_wrap.c. * `#10140 `__: ENH: add handling of NaN in RuntimeWarning except clause * `#10142 `__: DOC: return value of scipy.special.comb * `#10143 `__: MAINT: Loosen linprog tol * `#10152 `__: BUG: Fix custom sampling input for shgo, add unittest * `#10154 `__: MAINT: add moments and improve doc of mielke in scipy.stats * `#10158 `__: Issue #6999: read zlib checksum before checking bytes read. * `#10166 `__: BUG: Correctly handle broadcasted ydata in curve_fit pcov computation. * `#10167 `__: DOC: special: Add missing factor of \`i\` to \`modstruve\` docstring * `#10168 `__: MAINT: stats: Fix an incorrect comment. * `#10169 `__: ENH: optimize: Clarify error when objective function returns... * `#10172 `__: DEV: Run tests in parallel when --parallel flag is passed to... * `#10173 `__: ENH: Implement DOP853 ODE integrator * `#10176 `__: Fixed typo * `#10182 `__: TST: fix test issue for stats.pearsonr * `#10184 `__: MAINT: stats: Simplify zmap and zscore (we can use keepdims now). * `#10191 `__: DOC: fix a formatting issue in the scipy.spatial module docstring. * `#10193 `__: DOC: Updated docstring for optimize.nnls * `#10198 `__: DOC, ENH: special: Make \`hyp2f1\` references more specific * `#10202 `__: DOC: Format DST and DCT definitions as latex equations * `#10207 `__: BUG: Compressed matrix indexing should return a scalar * `#10210 `__: DOC: Update docs for connection='weak' in connected_components * `#10225 `__: DOC: Clarify new interfaces for legacy functions in 'optimize' * `#10231 `__: DOC, MAINT: gpg2 updates to release docs / pavement * `#10235 `__: LICENSE: split license file in standard BSD 3-clause and bundled. * `#10238 `__: ENH: Add new scipy.fft module using pocketfft * `#10243 `__: BUG: fix ARFF reader regression with quoted values. * `#10248 `__: DOC: update README file * `#10255 `__: CI: bump OpenBLAS to match wheels * `#10264 `__: TST: add tests for stats.tvar with unflattened arrays * `#10280 `__: MAINT: stats: Use a constant value for sqrt(2/PI). * `#10286 `__: Development Documentation Overhaul * `#10290 `__: MAINT: Deprecate NumPy functions in SciPy root * `#10291 `__: FIX: Avoid importing xdist when checking for availability * `#10295 `__: Disable deprecated Numpy API in __odrpack.c * `#10296 `__: ENH: C++ extension for linear assignment problem * `#10298 `__: ENH: Made pade function work with complex inputs * `#10301 `__: DOC: Fix critical value significance levels in stats.anderson_ksamp * `#10307 `__: Minkowski Distance Type Fix (issue #10262) * `#10309 `__: BUG: Pass jac=None directly to lsoda * `#10310 `__: BUG: interpolate: UnivariateSpline.derivative.ext is 'zeros'... * `#10312 `__: FIX: Fixing a typo in a comment * `#10314 `__: scipy.spatial enhancement request * `#10315 `__: DOC: Update integration tutorial to solve_ivp * `#10318 `__: DOC: update the example for PPoly.solve * `#10333 `__: TST: add tests for stats.tvar with unflattened arrays * `#10334 `__: MAINT: special: Remove deprecated \`hyp2f0\`, \`hyp1f2\`, and... * `#10336 `__: BUG: linalg/interpolative: fix interp_decomp modifying input * `#10341 `__: BUG: sparse.linalg/gmres: deprecate effect of callback on semantics... * `#10344 `__: DOC: improve wording of mathematical formulation * `#10345 `__: ENH: Tiled QR wrappers for scipy.linalg.lapack * `#10350 `__: MAINT: linalg: Use the new fft subpackage in linalg.dft test... * `#10351 `__: BUG: Fix unstable standard deviation calculation in histogram * `#10353 `__: Bug: interpolate.NearestNDInterpolator (issue #10352) * `#10357 `__: DOC: linalg: Refer to scipy.fft.fft (not fftpack) in the dft... * `#10359 `__: DOC: Update roadmap now scipy.fft has been merged * `#10361 `__: ENH: Prefer scipy.fft to scipy.fftpack in scipy.signal * `#10371 `__: DOC: Tweaks to fft documentation * `#10372 `__: DOC: Fix typos * `#10377 `__: TST, MAINT: adjustments for pytest 5.0 * `#10378 `__: ENH: _lib: allow new np.random.Generator in check_random_state * `#10379 `__: BUG: sparse: set writeability to be forward-compatible with numpy>=1.17 * `#10381 `__: BUG: Fixes gh-7491, pdf at x=0 of fisk/burr/burr12/f distributions. * `#10387 `__: ENH: optimize/bfgs: don't evaluate twice at initial point for... * `#10392 `__: [DOC] Add an example for _binned_statistic_dd * `#10396 `__: Remove warning about output shape of zoom * `#10397 `__: ENH: Add check_finite to sp.linalg.norm * `#10399 `__: ENH: Add __round__ method to sparse matrix * `#10407 `__: MAINT: drop pybind11 from install_requires, it's only build-time... * `#10408 `__: TST: use pytest.raises, not numpy assert_raises * `#10409 `__: CI: uninstall nose on Travis * `#10410 `__: [ENH] ncx2 dispatch to chi2 when nc=0 * `#10411 `__: TST: optimize: test should use assert_allclose for fp comparisons * `#10414 `__: DOC: add pybind11 to the other part of quickstart guides * `#10417 `__: DOC: special: don't mark non-ufuncs with a \`[+]\` * `#10423 `__: FIX: Use pybind11::isinstace to check array dtypes * `#10424 `__: DOC: add doctest example for binary data for ttest_ind_from_stats * `#10425 `__: ENH: Add missing Hermitian transforms to scipy.fft * `#10426 `__: MAINT: Fix doc build bugs * `#10431 `__: Update numpy version for AIX * `#10433 `__: MAINT: Minor fixes for the stats * `#10434 `__: BUG: special: make \`ndtri\` return NaN outside domain of definition * `#10435 `__: BUG: Allow integer input data in scipy.stats.yeojohnson * `#10438 `__: [DOC] Add example for kurtosis * `#10440 `__: ENH: special: make \`ellipk\` a ufunc * `#10443 `__: MAINT: ndimage: malloc fail check * `#10447 `__: BLD: Divert output from test compiles into a temporary directory * `#10451 `__: MAINT: signal: malloc fail check * `#10455 `__: BUG: special: fix values of \`hyperu\` for negative \`x\` * `#10456 `__: DOC: Added comment clarifying the call for dcsrch.f in lbfgsb.f * `#10457 `__: BUG: Allow ckdtree to accept empty data input * `#10459 `__: BUG:TST: Compute lwork safely * `#10460 `__: [DOC] Add example to entropy * `#10461 `__: DOC: Quickstart Guide updates * `#10462 `__: TST: special: only show max atol/rtol for test points that failed * `#10465 `__: BUG: Correctly align fft inputs * `#10467 `__: ENH: lower-memory duplicate generator checking in spatial.SphericalVoronoi * `#10470 `__: ENH: Normalise the inverse DCT/DST in scipy.fft * `#10472 `__: BENCH: adjust timeout for slow setup_cache * `#10475 `__: CI: include python debug for Travis-ci * `#10476 `__: TST: special: use \`__tracebackhide__\` to get better error messages * `#10477 `__: ENH: faster region building in spatial.SphericalVoronoi * `#10479 `__: BUG: stats: Fix a few issues with the distributions' fit method. * `#10480 `__: Add RuntimeError in _distn_infrastructure.py in fit() method * `#10481 `__: BENCH, MAINT: wheel_cache_size has been renamed build_cache_size * `#10494 `__: ENH: faster circumcenter calculation in spatial.SphericalVoronoi * `#10500 `__: Splrep _curfit_cache global variable bugfix * `#10503 `__: BUG: spatial/qhull: get HalfspaceIntersection.dual_points from... * `#10506 `__: DOC: interp2d, note nearest neighbor extrapolation * `#10507 `__: MAINT: Remove fortran fftpack library in favour of pypocketfft * `#10508 `__: TST: fix a bug in the circular import test. * `#10509 `__: MAINT: Set up _build_utils as subpackage * `#10516 `__: BUG: Use nogil contexts in cKDTree * `#10517 `__: ENH: fftconvolve should not FFT broadcastable axes * `#10518 `__: ENH: Speedup fftconvolve * `#10520 `__: DOC: Proper .rst formatting for deprecated features and Backwards... * `#10523 `__: DOC: Improve scipy.signal.resample documentation * `#10524 `__: ENH: Add MGC to scipy.stats * `#10525 `__: [ENH] ncx2.ppf dispatch to chi2 when nc=0 * `#10526 `__: DOC: clarify laplacian normalization * `#10528 `__: API: Rename scipy.fft DCT/DST shape argument to s * `#10531 `__: BUG: fixed improper rotations in spatial.transform.rotation.match_vectors * `#10533 `__: [DOC] Add example for winsorize function * `#10539 `__: MAINT: special: don't register \`i0\` with \`numpy.dual\` * `#10540 `__: MAINT: Fix Travis and Circle * `#10542 `__: MAINT: interpolate: use cython_lapack * `#10547 `__: Feature request. Add furthest site Voronoi diagrams to scipy.spatial.plotutils. * `#10549 `__: [BUG] Fix bug in trimr when inclusive=False * `#10552 `__: add scipy.signal.upfirdn signal extension modes * `#10555 `__: MAINT: special: move \`c_misc\` into Cephes * `#10556 `__: [DOC] Add example for trima * `#10562 `__: [DOC] Fix triple string fo trimmed so that __doc__ can show... * `#10563 `__: improve least_squares error msg for mismatched shape * `#10564 `__: ENH: linalg: memoize get_lapack/blas_funcs to speed it up * `#10566 `__: ENH: add implementation of solver for the maximum flow problem * `#10567 `__: BUG: spatial: use c++11 construct for getting start of vector... * `#10568 `__: DOC: special: small tweaks to the \`zetac\` docstring * `#10571 `__: [ENH] Gaussian_kde can accept matrix dataset * `#10574 `__: ENH: linalg: speed up _compute_lwork by avoiding numpy constructs * `#10582 `__: Fix typos with typos in bundled libraries reverted * `#10583 `__: ENH: special: add the analytic continuation of Riemann zeta * `#10584 `__: MAINT: special: clean up \`special.__all__\` * `#10586 `__: BUG: multidimensional scipy.fft functions should accept 's' rather... * `#10587 `__: BUG: integrate/lsoda: never abort run, set error istate instead * `#10594 `__: API: Replicate numpy's fftn behaviour when s is given but not... * `#10599 `__: DOC: dev: update documentation vs. github pull request workflow... * `#10603 `__: MAINT: installer scripts removed * `#10604 `__: MAINT: Change c\*np.ones(...) to np.full(..., c, ...) in many... * `#10608 `__: Univariate splines should require x to be strictly increasing... * `#10613 `__: ENH: Add seed option for gaussian_kde.resample * `#10614 `__: ENH: Add parallel computation to scipy.fft * `#10615 `__: MAINT: interpolate: remove unused header file * `#10616 `__: MAINT: Clean up 32-bit platform xfail markers * `#10618 `__: BENCH: Added 'trust-constr' to minimize benchmarks * `#10621 `__: [MRG] multiple stability updates in lobpcg * `#10622 `__: MAINT: forward port 1.3.1 release notes * `#10624 `__: DOC: stats: Fix spelling of 'support'. * `#10627 `__: DOC: stats: Add references for the alpha distribution. * `#10629 `__: MAINT: special: avoid overflow longer in \`zeta\` for negative... * `#10630 `__: TST: GH10271, relax test assertion, fixes #10271 * `#10631 `__: DOC: nelder-mean uses xatol fixes #10036 * `#10633 `__: BUG: interpolate: integral(a, b) should be zero when both limits... * `#10635 `__: DOC: special: complete hypergeometric functions documentation * `#10636 `__: BUG: special: use series for \`hyp1f1\` when it converges rapidly * `#10641 `__: ENH: allow matching of general bipartite graphs * `#10643 `__: ENH: scipy.sparse.linalg.spsolve triangular unit diagonal * `#10650 `__: ENH: Cythonize sosfilt * `#10654 `__: DOC: Vertical alignment of table entries * `#10655 `__: ENH: Dockerfile for scipy development * `#10660 `__: TST: clean up tests for rvs in scipy.stats * `#10664 `__: Throw error on non-finite input for binned_statistic_dd() * `#10665 `__: DOC: special: improve the docstrings for \`gamma\` and \`gammasgn\` * `#10669 `__: TST: Update scipy.fft real transform tests * `#10670 `__: DOC: Clarify docs and error messages for scipy.signal.butter * `#10672 `__: ENH: return solution attribute when using events in solve_ivp * `#10675 `__: MAINT: special: add an explicit NaN check for \`iv\` arguments * `#10679 `__: DOC: special: Add documentation for \`beta\` function * `#10681 `__: TST: sparse.linalg: fix arnoldi test seed * `#10682 `__: DOC: special: Add documentation for \`betainc\` function * `#10684 `__: TST: special: require Mpmath 1.1.0 for \`test_hyperu_around_0\` * `#10686 `__: FIX: sphinx isattributedescriptor is not available in sphinx... * `#10687 `__: DOC: added Docker quickstart guide by @andyfaff * `#10689 `__: DOC: special: clarify format of parameters/returns sections for... * `#10690 `__: DOC: special: improve docstrings of incomplete gamma functions * `#10692 `__: ENH: higher-dimensional input in \`spatial.SphericalVoronoi\` * `#10694 `__: ENH: ScalarFunction.fun_and_grad * `#10698 `__: DOC: special: Add documentation for \`betaincinv\` * `#10699 `__: MAINT: remove time print lbfgsb fixes #8417 * `#10701 `__: TST, MAINT: bump OpenBLAS to 0.3.7 stable * `#10702 `__: DOC: clarify iterations consume multiple function calls * `#10703 `__: DOC: iprint doc lbfgsb closes #5482 * `#10708 `__: TST: test suggested in gh1758 * `#10710 `__: ENH: Added nan_policy to circ functions in \`stats\` * `#10712 `__: ENH: add axis parameter to stats.entropy * `#10714 `__: DOC: Formatting fix rv_continuous.expect docs * `#10715 `__: DOC: BLD: update doc Makefile for python version; add scipy version... * `#10717 `__: MAINT: modernize doc/Makefile * `#10719 `__: Enable setting minres initial vector * `#10720 `__: DOC: silence random warning in doc build for \`stats.binned_statistic_dd\` * `#10724 `__: DEV: Add doc option to runtests.py * `#10728 `__: MAINT: get rid of gramA, gramB text files that lobpcg tests leave... * `#10732 `__: DOC: add min_only to docstring for Dijkstra's algorithm * `#10734 `__: DOC: spell out difference between source and target in shortest... * `#10735 `__: Fix for Python 4 * `#10739 `__: BUG: optimize/slsqp: deal with singular BFGS update * `#10741 `__: ENH: LAPACK wrappers for ?geequ, ?geequb, ?syequb, ?heequb * `#10742 `__: DOC: special: add to the docstring of \`gammaln\` * `#10743 `__: ENH: special: add a real dispatch for \`wrightomega\` * `#10746 `__: MAINT: Fix typos in comments, docs and test name * `#10747 `__: Remove spurious quotes * `#10750 `__: MAINT: make cython code more precise * `#10751 `__: MAINT: Check that scipy.linalg.lapack functions are documented * `#10752 `__: MAINT: special: use \`sf_error\` in Cephes * `#10755 `__: DOC: cluster: Add 'See Also' and 'Examples' for kmeans2. * `#10763 `__: MAINT: list of minimize methods * `#10768 `__: BUG: Fix corner case for sos2zpk * `#10773 `__: Fix error type for complex input to scipy.fftpack.rfft and irfft * `#10776 `__: ENH: handle geodesic input in \`spatial.SphericalVoronoi\` * `#10777 `__: MAINT: minimizer-->custom should handle the kinds of bounds/constrain?... * `#10781 `__: ENH: solve_triangular C order improvement * `#10787 `__: Fix behavior of \`exp1\` on branch cut and add docstring * `#10789 `__: DOC: special: add parameters/returns doc sections for erfc/erfcx/erfi * `#10790 `__: Travis CI: sudo is deprecated and Xenial is default distro * `#10792 `__: DOC: special: add full docstring for \`expi\` * `#10799 `__: DOC: special: add a complete docstring for \`expn\` * `#10800 `__: Docs edits (GSoD) * `#10802 `__: BUG: fix UnboundLocalError in Radau (scipy#10775) * `#10804 `__: ENH: Speed up next_fast_len with LRU cache * `#10805 `__: DOC: Fix unbalanced quotes in signal.place_poles * `#10809 `__: ENH: Speed up next_fast_len * `#10810 `__: ENH: Raise catchable exceptions for bad Fortran files * `#10811 `__: MAINT: optimize: Remove extra variable from _remove_redundancy_dense * `#10813 `__: MAINT: special: Remove unused variables from _kolmogi and _smirnovi * `#10815 `__: DOC, API: scipy.stats.reciprocal is "log-uniform" * `#10816 `__: MAINT: special: remove deprecated \`bessel_diff_formula\` * `#10817 `__: DOC: special: complete the docstring for \`fresnel\` * `#10820 `__: Fixed compiler_helper.py to allow compilation with ICC on Linux * `#10823 `__: DOC: updated reference guide text for consistency in writing... * `#10825 `__: MAINT: special: change some features of the Voigt function * `#10828 `__: MAINT: integrate: Remove unused variable from init_callback * `#10830 `__: Adding LOBPCG solver in svds in addition to ARPACK * `#10837 `__: WIP: ENH: reduction function for \`spatial.tranform.Rotation\`... * `#10843 `__: ENH: Adding optional parameter to stats.zscores to allow for... * `#10845 `__: Rebase kruskal fix * `#10847 `__: remove redundant __getitem__ from scipy.sparse.lil * `#10848 `__: Better handling of empty (not missing) docstrings * `#10849 `__: ENH: implement rmatmat for LinearOperator * `#10850 `__: MAINT : Refactoring lil List of Lists * `#10851 `__: DOC: add a generative art example to the scipy.spatial tutorial. * `#10852 `__: DOC: linalg: fixed gh-10838 unused imports in example deleted * `#10854 `__: DOC: special: add a full docstring for \`pdtr\` * `#10861 `__: ENH: option to reuse binnumbers in stats.binned_statistic_dd * `#10863 `__: DOC: partial standardization and validation of scipy.stats reference... * `#10865 `__: BUG: special: fix incomplete gamma functions for infinite \`a\` * `#10866 `__: ENH: calculation of mean in spatial.transform.Rotation * `#10867 `__: MAINT: Also store latex directory * `#10869 `__: ENH: Implement overlap-add convolution * `#10870 `__: ENH: Do not raise EOF error if wavfile data read * `#10876 `__: ENH: Add beta-binomial distribution to scipy.stats * `#10878 `__: MAINT: Update R project URL * `#10883 `__: MAINT: (ndimage) More robust check for output being a numpy dtype * `#10884 `__: DOC: Added instructions on adding a new distribution to scipy.stats. * `#10885 `__: [BUG] fix lobpcg with maxiter=None results in Exception * `#10899 `__: ENH: Match R functionality for hmean * `#10900 `__: MAINT: stats: Use keepdims to simplify a few lines in power_divergence. * `#10901 `__: ENH: sparse/linalg: support pydata/sparse matrices * `#10907 `__: Check whether \`maxiter\` is integer * `#10912 `__: ENH: warn user that quad() ignores \`points=...\` when \`weight=...\`... * `#10918 `__: CI: fix Travis CI py3.8 build * `#10920 `__: MAINT: Update constants to codata 2018 values (second try) * `#10921 `__: ENH: scipy.sparse.lil: tocsr accelerated * `#10924 `__: BUG: Forbid passing 'args' as kwarg in scipy.optimize.curve_fit * `#10928 `__: DOC: Add examples to io.wavfile docstrings * `#10934 `__: typo fix * `#10935 `__: BUG: Avoid undefined behaviour on float to unsigned conversion * `#10936 `__: DOC: Added missing example to stats.mstats.variation * `#10939 `__: ENH: scipy.sparse.lil: tocsr accelerated depending on density * `#10946 `__: BUG: setting verbose > 2 in minimize with trust-constr method... * `#10947 `__: DOC: special: small improvements to the \`poch\` docstring * `#10949 `__: BUG: fix return type of erlang_gen._argcheck * `#10951 `__: DOC: fixed Ricker wavelet formula * `#10954 `__: BUG: special: fix \`factorial\` return type for 0-d inputs * `#10955 `__: MAINT: Relax the assert_unitary atol value * `#10956 `__: WIP: make pdtr(int, double) be pdtr(double, double) * `#10957 `__: BUG: Ensure full binary compatibility of long double test data * `#10964 `__: ENH: Make Slerp callable with a scalar argument * `#10972 `__: BUG: Handle complex gains in zpk2sos * `#10975 `__: TST: skip test_kendalltau ppc64le * `#10978 `__: BUG: boxcox data dimension and constancy check #5112 * `#10979 `__: API: Rename dcm to (rotation) matrix in Rotation class * `#10981 `__: MAINT: add support for a==0 and x>0 edge case to igam and igamc * `#10986 `__: MAINT: Remove direct imports from numpy in signaltools.py * `#10988 `__: BUG: signal: fixed issue #10360 * `#10989 `__: FIX binned_statistic_dd Mac wheel test fails * `#10990 `__: BUG: Fix memory leak in shgo triangulation * `#10992 `__: TST: Relax tolerance in upfirdn test_modes * `#10993 `__: TST: bump tolerance in optimize tests * `#10997 `__: MAINT: Rework residue and residuez * `#11001 `__: DOC: Updated Windows build tutorial * `#11004 `__: BUG: integrate/quad_vec: fix several bugs in quad_vec * `#11005 `__: TST: add Python 3.8 Win CI * `#11006 `__: DOC: special: add a reference for \`kl_div\` * `#11012 `__: MAINT: Rework invres and invresz * `#11015 `__: DOC: special: add references for \`rel_entr\` * `#11017 `__: DOC: numpydoc validation of morestats.py * `#11018 `__: MAINT: Filter unrelated warning * `#11031 `__: MAINT: update choose_conv_method for pocketfft implementation * `#11034 `__: MAINT: TST: Skip tests with multiprocessing that use "spawn"... * `#11036 `__: DOC: update doc/README with some more useful content. * `#11037 `__: DOC: special: add a complete docstring for \`rgamma\` * `#11038 `__: DOC: special: add a reference for the polygamma function * `#11042 `__: TST: fix tf2zpk test failure due to incorrect complex sorting. * `#11044 `__: MAINT: choose_conv_method can choose fftconvolution for longcomplex * `#11046 `__: TST: Reduce tolerance for ppc64le with reference lapack * `#11048 `__: DOC: special: add reference for orthogonal polynomial functions * `#11049 `__: MAINT: proper random number initialization and readability fix * `#11051 `__: MAINT: pep8 cleanup * `#11054 `__: TST: bump test precision for dual_annealing SLSQP test * `#11055 `__: DOC: special: add a reference for \`zeta\` * `#11056 `__: API: Deprecated normalized keyword in Rotation * `#11065 `__: DOC: Ubuntu Development Environment Quickstart should not modify... * `#11066 `__: BUG: skip deprecation for numpy top-level types * `#11067 `__: DOC: updated documentation for consistency in writing style * `#11070 `__: DOC: Amendment to Ubuntu Development Environment Quickstart should... * `#11073 `__: DOC: fix 1.4.0 release notes * `#11081 `__: API: Replace Rotation.match_vectors with align_vectors * `#11083 `__: DOC: more 1.4.0 release note fixes * `#11092 `__: BUG: stats: fix freezing of some distributions * `#11096 `__: BUG: scipy.sparse.csgraph: fixed issue #10774 * `#11124 `__: fix Cython warnings related to _stats.pyx * `#11126 `__: BUG: interpolate/fitpack: fix memory leak in splprep * `#11127 `__: Avoid potential segfault in CSR and CSC matrix indexing * `#11152 `__: BUG: Fix random state bug multiscale_graphcorr * `#11166 `__: BUG: empty sparse slice shapes * `#11167 `__: BUG: redundant fft in signal.resample Checksums ========= MD5 ~~~ 3ab6ebe868c3b16a748ba483d4f6cec3 scipy-1.4.0rc2-cp35-cp35m-macosx_10_6_intel.whl bc542c69def16b92b3900c851e7491b0 scipy-1.4.0rc2-cp35-cp35m-manylinux1_i686.whl 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URL: From tcaswell at gmail.com Mon Dec 9 12:23:20 2019 From: tcaswell at gmail.com (Thomas Caswell) Date: Mon, 9 Dec 2019 12:23:20 -0500 Subject: [Numpy-discussion] Matplotlib Research Software Engineering Fellow Message-ID: Hi folks, Matplotlib has received a grant from the Chan Zuckerberg Initiative to fund maintenance! As part of the grant, we have 1 year of funding for a Research Software Engineering Fellow to carry out this work. If you are interested in working on Matplotlib full time, please apply! See below for a link to the full job description and application instructions. The timeline on this is rather short, so applications are due Jan 3. https://discourse.matplotlib.org/t/now-hiring-matplotlib-research-software-engineering-fellow/20701 Tom and Hannah -- Thomas Caswell tcaswell at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From poh.zijie at gmail.com Tue Dec 10 13:43:52 2019 From: poh.zijie at gmail.com (Zijie Poh) Date: Tue, 10 Dec 2019 10:43:52 -0800 Subject: [Numpy-discussion] Adding keepdims to linspace / logspace / geomspace Message-ID: Hi all, We've created a PR (#14922 ) on adding keepdims to linspace / logspace / geomspace, which enables linspace to directly take the output of min and max with keepdims = True as the start and stop arguments. That is, the following two linspace calls return the same result. np.linspace( arr.min(axis=ax), arr.max(axis=ax), axis=ax ) np.linspace( arr.min(axis=ax, keepdims=True), arr.max(axis=ax, keepdims=True), axis=ax, keepdims=True ) Please let me know if you have any questions / suggestions. Regards, ZJ -------------- next part -------------- An HTML attachment was scrubbed... URL: From sebastian at sipsolutions.net Tue Dec 10 14:54:35 2019 From: sebastian at sipsolutions.net (Sebastian Berg) Date: Tue, 10 Dec 2019 13:54:35 -0600 Subject: [Numpy-discussion] Adding keepdims to linspace / logspace / geomspace In-Reply-To: References: Message-ID: <53a5048eb5b1bf6c94d34f32e23379a974632488.camel@sipsolutions.net> On Tue, 2019-12-10 at 10:43 -0800, Zijie Poh wrote: > Hi all, > > We've created a PR (#14922) on > adding keepdims to linspace / logspace / geomspace, which > enables linspace to directly take the output > of min and max with keepdims = True as the start and stop arguments. > That is, the following two linspace calls return the same result. > > np.linspace( > arr.min(axis=ax), > arr.max(axis=ax), > axis=ax > ) > > np.linspace( > arr.min(axis=ax, keepdims=True), > arr.max(axis=ax, keepdims=True), > axis=ax, keepdims=True > ) > I am a bit hesitant about the name `keepdims` being the best one. I realize it is nice to have the pattern to use the same name for symmetry. But on the other hand, there is no axes being "kept" here. In fact, `keepdims=True` returns fewer dims than `keepdims=False` :). Not sure I have a better idea though, `expand_axis` (or axis) might be closer to what happens? `keepdims` is currently used entirely for reduction-like operations (including complex reduce-like behaviour in `percentile`). However, the closest to an opposite of reduce-like operations are maybe broadcasts (they expand axis), but I cannot think of a way to use that for a parameter name ;). The change itself is small enough and I am good with adding it, I have some doubts it will be used much. But it is like a very natural thing to give input with the same number of dimensions/axis as the output will have. Maybe we should have had `new_axis=` and `expand_axis=` and you can only use one ;). - Sebastian > Please let me know if you have any questions / suggestions. > > Regards, > ZJ > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part URL: From shoyer at gmail.com Tue Dec 10 14:58:25 2019 From: shoyer at gmail.com (Stephan Hoyer) Date: Tue, 10 Dec 2019 11:58:25 -0800 Subject: [Numpy-discussion] Adding keepdims to linspace / logspace / geomspace In-Reply-To: <53a5048eb5b1bf6c94d34f32e23379a974632488.camel@sipsolutions.net> References: <53a5048eb5b1bf6c94d34f32e23379a974632488.camel@sipsolutions.net> Message-ID: I'm not sure I understand the motivation here. Is the idea that you want to reuse min/max values computed with keepdims that you also want to use for other purposes? If so, this could be achieved with squeeze(), e.g., np.linspace( arr.min(axis=ax, keepdims=True).squeeze(ax), arr.max(axis=ax, keepdims=True).squeeze(ax), axis=ax, ) This is not the most elegant code, but it seems better than adding a new keyword argument, and the resulting code is likely about as efficient. On Tue, Dec 10, 2019 at 11:54 AM Sebastian Berg wrote: > On Tue, 2019-12-10 at 10:43 -0800, Zijie Poh wrote: > > Hi all, > > > > We've created a PR (#14922) on > > adding keepdims to linspace / logspace / geomspace, which > > enables linspace to directly take the output > > of min and max with keepdims = True as the start and stop arguments. > > That is, the following two linspace calls return the same result. > > > > np.linspace( > > arr.min(axis=ax), > > arr.max(axis=ax), > > axis=ax > > ) > > > > np.linspace( > > arr.min(axis=ax, keepdims=True), > > arr.max(axis=ax, keepdims=True), > > axis=ax, keepdims=True > > ) > > > > I am a bit hesitant about the name `keepdims` being the best one. I > realize it is nice to have the pattern to use the same name for > symmetry. But on the other hand, there is no axes being "kept" here. In > fact, `keepdims=True` returns fewer dims than `keepdims=False` :). > > Not sure I have a better idea though, `expand_axis` (or axis) might be > closer to what happens? > > `keepdims` is currently used entirely for reduction-like operations > (including complex reduce-like behaviour in `percentile`). However, the > closest to an opposite of reduce-like operations are maybe broadcasts > (they expand axis), but I cannot think of a way to use that for a > parameter name ;). > > The change itself is small enough and I am good with adding it, I have > some doubts it will be used much. But it is like a very natural thing > to give input with the same number of dimensions/axis as the output > will have. > > Maybe we should have had `new_axis=` and `expand_axis=` and you can > only use one ;). > > - Sebastian > > > > Please let me know if you have any questions / suggestions. > > > > Regards, > > ZJ > > _______________________________________________ > > NumPy-Discussion mailing list > > NumPy-Discussion at python.org > > https://mail.python.org/mailman/listinfo/numpy-discussion > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From efiring at hawaii.edu Tue Dec 10 17:04:02 2019 From: efiring at hawaii.edu (Eric Firing) Date: Tue, 10 Dec 2019 12:04:02 -1000 Subject: [Numpy-discussion] Adding keepdims to linspace / logspace / geomspace In-Reply-To: References: Message-ID: <0aefb77b-8ab9-ba8d-d876-aaa7e7e05bba@hawaii.edu> I wasn't sure whether the discussion would be on the list or on Github, so I posted to the latter: https://github.com/numpy/numpy/pull/14922#issuecomment-564211192 Eric On 2019/12/10 8:43 AM, Zijie Poh wrote: > Hi all, > > We've created a PR (#14922 ) > on adding keepdims?to linspace?/ logspace?/ geomspace, which enables > linspace?to directly take the output of min?and max?with keepdims = > True?as the start and stop arguments. That is, the following two > linspace calls return the same result. > > np.linspace( > ? ? arr.min(axis=ax), > ? ? arr.max(axis=ax), > ? ? axis=ax > ) > > np.linspace( > ? ? arr.min(axis=ax, keepdims=True), > ? ? arr.max(axis=ax, keepdims=True), > ? ? axis=ax, keepdims=True > ) > > Please let me know if you have any questions / suggestions. > > Regards, > ZJ > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion > From sebastian at sipsolutions.net Tue Dec 10 23:26:46 2019 From: sebastian at sipsolutions.net (Sebastian Berg) Date: Tue, 10 Dec 2019 22:26:46 -0600 Subject: [Numpy-discussion] NumPy Community Meeting Wednesday, Dec. 11 Message-ID: <230b55558dc7b222f244111b7e6a51fea820c56d.camel@sipsolutions.net> Hi all, There will be a NumPy Community meeting Wednesday December 11 at 11 am Pacific Time. Everyone is invited to join in and edit the work-in- progress meeting topics and notes: https://hackmd.io/76o-IxCjQX2mOXO_wwkcpg?both Best wishes Sebastian -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part URL: From poh.zijie at gmail.com Wed Dec 11 11:35:14 2019 From: poh.zijie at gmail.com (Zijie Poh) Date: Wed, 11 Dec 2019 08:35:14 -0800 Subject: [Numpy-discussion] Adding keepdims to linspace / logspace / geomspace In-Reply-To: <0aefb77b-8ab9-ba8d-d876-aaa7e7e05bba@hawaii.edu> References: <0aefb77b-8ab9-ba8d-d876-aaa7e7e05bba@hawaii.edu> Message-ID: I agree with Stephan and Eric especially it when can be done with existing method. I'll add it to the PR and close it. Thanks for the suggestions / comments! Regards, ZJ On Tue, Dec 10, 2019 at 2:05 PM Eric Firing wrote: > I wasn't sure whether the discussion would be on the list or on Github, > so I posted to the latter: > > https://github.com/numpy/numpy/pull/14922#issuecomment-564211192 > > Eric > > On 2019/12/10 8:43 AM, Zijie Poh wrote: > > Hi all, > > > > We've created a PR (#14922 ) > > on adding keepdims to linspace / logspace / geomspace, which enables > > linspace to directly take the output of min and max with keepdims = > > True as the start and stop arguments. That is, the following two > > linspace calls return the same result. > > > > np.linspace( > > arr.min(axis=ax), > > arr.max(axis=ax), > > axis=ax > > ) > > > > np.linspace( > > arr.min(axis=ax, keepdims=True), > > arr.max(axis=ax, keepdims=True), > > axis=ax, keepdims=True > > ) > > > > Please let me know if you have any questions / suggestions. > > > > Regards, > > ZJ > > > > _______________________________________________ > > NumPy-Discussion mailing list > > NumPy-Discussion at python.org > > https://mail.python.org/mailman/listinfo/numpy-discussion > > > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matti.picus at gmail.com Mon Dec 16 14:01:04 2019 From: matti.picus at gmail.com (Matti Picus) Date: Mon, 16 Dec 2019 21:01:04 +0200 Subject: [Numpy-discussion] removing undocumented use of __array__(dtype, context) Message-ID: <636b0506-6599-5e41-7283-91b906c5cc7c@gmail.com> A code path and test have been in the code since NumPy 0.4 for a two-argument variant of ``__array__(dtype=None, context=None)``. It was activated when calling ``ufunc(op)`` or ``ufunc.reduce(op)`` if ``op.__array__`` existed. However that variant is not documented, and it is not clear what the intention was for its use. The code was something like try: ??? op.__array__(dtype, context) except TypeError: ??? op.__array__(dtype) In PR 15118 https://github.com/numpy/numpy/pull/15118 I proposed to remove this, so the call is now simply op.__array__(dtype) or `op.__array__()` if there is no dtype Does anyone need the undocumented two-argument variant? Matti From sebastian at sipsolutions.net Mon Dec 16 14:41:37 2019 From: sebastian at sipsolutions.net (Sebastian Berg) Date: Mon, 16 Dec 2019 13:41:37 -0600 Subject: [Numpy-discussion] removing undocumented use of __array__(dtype, context) In-Reply-To: <636b0506-6599-5e41-7283-91b906c5cc7c@gmail.com> References: <636b0506-6599-5e41-7283-91b906c5cc7c@gmail.com> Message-ID: <490b70ed24d63c459ce5d774a50f01030f03a76e.camel@sipsolutions.net> On Mon, 2019-12-16 at 21:01 +0200, Matti Picus wrote: > A code path and test have been in the code since NumPy 0.4 for a > two-argument variant of ``__array__(dtype=None, context=None)``. It > was > activated when calling ``ufunc(op)`` or ``ufunc.reduce(op)`` if > ``op.__array__`` existed. However that variant is not documented, and > it > is not clear what the intention was for its use. > > > The code was something like > > > try: > > op.__array__(dtype, context) > > except TypeError: > > op.__array__(dtype) > > > In PR 15118 https://github.com/numpy/numpy/pull/15118 I proposed to > remove this, so the call is now simply > > > op.__array__(dtype) > > > or `op.__array__()` if there is no dtype > > > Does anyone need the undocumented two-argument variant? > I agree, if nobody knows any usecase, I am for trying to remove it. It seems like a Deprecation will not be super simple here. And since there are no known use-cases, and any new use-case is better covered by `__array_ufunc__` (and probably also `__array_wrap__`), removing this simplifies an already tricky enough corner of NumPy. Best, Sebastian > > Matti > > > > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part URL: From tyler.je.reddy at gmail.com Mon Dec 16 19:37:05 2019 From: tyler.je.reddy at gmail.com (Tyler Reddy) Date: Mon, 16 Dec 2019 17:37:05 -0700 Subject: [Numpy-discussion] ANN: SciPy 1.4.0 Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi all, On behalf of the SciPy development team I'm pleased to announce the release of SciPy 1.4.0. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.4.0 One of a few ways to install this release with pip: pip install scipy==1.4.0 ========================== SciPy 1.4.0 Release Notes ========================== SciPy 1.4.0 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 1.4.x branch, and on adding new features on the master branch. This release requires Python 3.5+ and NumPy >=1.13.3 (for Python 3.5, 3.6), >=1.14.5 (for Python 3.7), >= 1.17.3 (for Python 3.8) For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. Highlights of this release ---------------------------------- - a new submodule, `scipy.fft`, now supersedes `scipy.fftpack`; this means support for ``long double`` transforms, faster multi-dimensional transforms, improved algorithm time complexity, release of the global intepreter lock, and control over threading behavior - support for ``pydata/sparse`` arrays in `scipy.sparse.linalg` - substantial improvement to the documentation and functionality of several `scipy.special` functions, and some new additions - the generalized inverse Gaussian distribution has been added to `scipy.stats` - an implementation of the Edmonds-Karp algorithm in `scipy.sparse.csgraph.maximum_flow` - `scipy.spatial.SphericalVoronoi` now supports n-dimensional input, has linear memory complexity, improved performance, and supports single-hemisphere generators New features ============ Infrastructure -------------------- Documentation can now be built with ``runtests.py --doc`` A ``Dockerfile`` is now available in the ``scipy/scipy-dev`` repository to facilitate getting started with SciPy development. `scipy.constants` improvements --------------------------------------------- `scipy.constants` has been updated with the CODATA 2018 constants. `scipy.fft` added ------------------------ `scipy.fft` is a new submodule that supersedes the `scipy.fftpack` submodule. For the most part, this is a drop-in replacement for ``numpy.fft`` and `scipy.fftpack` alike. With some important differences, `scipy.fft`: - uses NumPy's conventions for real transforms (``rfft``). This means the return value is a complex array, half the size of the full ``fft`` output. This is different from the output of ``fftpack`` which returned a real array representing complex components packed together. - the inverse real to real transforms (``idct`` and ``idst``) are normalized for ``norm=None`` in thesame way as ``ifft``. This means the identity ``idct(dct(x)) == x`` is now ``True`` for all norm modes. - does not include the convolutions or pseudo-differential operators from ``fftpack``. This submodule is based on the ``pypocketfft`` library, developed by the author of ``pocketfft`` which was recently adopted by NumPy as well. ``pypocketfft`` offers a number of advantages over fortran ``FFTPACK``: - support for long double (``np.longfloat``) precision transforms. - faster multi-dimensional transforms using vectorisation - Bluestein?s algorithm removes the worst-case ``O(n^2)`` complexity of ``FFTPACK`` - the global interpreter lock (``GIL``) is released during transforms - optional multithreading of multi-dimensional transforms via the ``workers`` argument Note that `scipy.fftpack` has not been deprecated and will continue to be maintained but is now considered legacy. New code is recommended to use `scipy.fft` instead, where possible. `scipy.fftpack` improvements ---------------------------------------- `scipy.fftpack` now uses pypocketfft to perform its FFTs, offering the same speed and accuracy benefits listed for scipy.fft above but without the improved API. `scipy.integrate` improvements ------------------------------------------- The function `scipy.integrate.solve_ivp` now has an ``args`` argument. This allows the user-defined functions passed to the function to have additional parameters without having to create wrapper functions or lambda expressions for them. `scipy.integrate.solve_ivp` can now return a ``y_events`` attribute representing the solution of the ODE at event times New ``OdeSolver`` is implemented --- ``DOP853``. This is a high-order explicit Runge-Kutta method originally implemented in Fortran. Now we provide a pure Python implementation usable through ``solve_ivp`` with all its features. `scipy.integrate.quad` provides better user feedback when break points are specified with a weighted integrand. `scipy.integrate.quad_vec` is now available for general purpose integration of vector-valued functions `scipy.interpolate` improvements --------------------------------------------- `scipy.interpolate.pade` now handles complex input data gracefully `scipy.interpolate.Rbf` can now interpolate multi-dimensional functions `scipy.io` improvements --------------------------------- `scipy.io.wavfile.read` can now read data from a `WAV` file that has a malformed header, similar to other modern `WAV` file parsers `scipy.io.FortranFile` now has an expanded set of available ``Exception`` classes for handling poorly-formatted files `scipy.linalg` improvements ------------------------------------- The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct results for complex-valued matrices. Before this, the function only returned correct values for real-valued matrices. New boolean keyword argument ``check_finite`` for `scipy.linalg.norm`; whether to check that the input matrix contains only finite numbers. Disabling may give a performance gain, but may result in problems (crashes, non-termination) if the inputs do contain infinities or NaNs. `scipy.linalg.solve_triangular` has improved performance for a C-ordered triangular matrix ``LAPACK`` wrappers have been added for ``?geequ``, ``?geequb``, ``?syequb``, and ``?heequb`` Some performance improvements may be observed due to an internal optimization in operations involving LAPACK routines via ``_compute_lwork``. This is particularly true for operations on small arrays. Block ``QR`` wrappers are now available in `scipy.linalg.lapack` `scipy.ndimage` improvements ------------------------------------------ `scipy.optimize` improvements ------------------------------------------ It is now possible to use linear and non-linear constraints with `scipy.optimize.differential_evolution`. `scipy.optimize.linear_sum_assignment` has been re-written in C++ to improve performance, and now allows input costs to be infinite. A ``ScalarFunction.fun_and_grad`` method was added for convenient simultaneous retrieval of a function and gradient evaluation `scipy.optimize.minimize` ``BFGS`` method has improved performance by avoiding duplicate evaluations in some cases Better user feedback is provided when an objective function returns an array instead of a scalar. `scipy.signal` improvements -------------------------------------- Added a new function to calculate convolution using the overlap-add method, named `scipy.signal.oaconvolve`. Like `scipy.signal.fftconvolve`, this function supports specifying dimensions along which to do the convolution. `scipy.signal.cwt` now supports complex wavelets. The implementation of ``choose_conv_method`` has been updated to reflect the new FFT implementation. In addition, the performance has been significantly improved (with rather drastic improvements in edge cases). The function ``upfirdn`` now has a ``mode`` keyword argument that can be used to select the signal extension mode used at the signal boundaries. These modes are also available for use in ``resample_poly`` via a newly added ``padtype`` argument. `scipy.signal.sosfilt` now benefits from Cython code for improved performance `scipy.signal.resample` should be more efficient by leveraging ``rfft`` when possible `scipy.sparse` improvements --------------------------------------- It is now possible to use the LOBPCG method in `scipy.sparse.linalg.svds`. `scipy.sparse.linalg.LinearOperator` now supports the operation ``rmatmat`` for adjoint matrix-matrix multiplication, in addition to ``rmatvec``. Multiple stability updates enable float32 support in the LOBPCG eigenvalue solver for symmetric and Hermitian eigenvalues problems in ``scipy.sparse.linalg.lobpcg``. A solver for the maximum flow problem has been added as `scipy.sparse.csgraph.maximum_flow`. `scipy.sparse.csgraph.maximum_bipartite_matching` now allows non-square inputs, no longer requires a perfect matching to exist, and has improved performance. `scipy.sparse.lil_matrix` conversions now perform better in some scenarios Basic support is available for ``pydata/sparse`` arrays in `scipy.sparse.linalg` `scipy.sparse.linalg.spsolve_triangular` now supports the ``unit_diagonal`` argument to improve call signature similarity with its dense counterpart, `scipy.linalg.solve_triangular` ``assertAlmostEqual`` may now be used with sparse matrices, which have added support for ``__round__`` `scipy.spatial` improvements --------------------------------------- The bundled Qhull library was upgraded to version 2019.1, fixing several issues. Scipy-specific patches are no longer applied to it. `scipy.spatial.SphericalVoronoi` now has linear memory complexity, improved performance, and supports single-hemisphere generators. Support has also been added for handling generators that lie on a great circle arc (geodesic input) and for generators in n-dimensions. `scipy.spatial.transform.Rotation` now includes functions for calculation of a mean rotation, generation of the 3D rotation groups, and reduction of rotations with rotational symmetries. `scipy.spatial.transform.Slerp` is now callable with a scalar argument `scipy.spatial.voronoi_plot_2d` now supports furthest site Voronoi diagrams `scipy.spatial.Delaunay` and `scipy.spatial.Voronoi` now have attributes for tracking whether they are furthest site diagrams `scipy.special` improvements ----------------------------------------- The Voigt profile has been added as `scipy.special.voigt_profile`. A real dispatch has been added for the Wright Omega function (`scipy.special.wrightomega`). The analytic continuation of the Riemann zeta function has been added. (The Riemann zeta function is the one-argument variant of `scipy.special.zeta`.) The complete elliptic integral of the first kind (`scipy.special.ellipk`) is now available in `scipy.special.cython_special`. The accuracy of `scipy.special.hyp1f1` for real arguments has been improved. The documentation of many functions has been improved. `scipy.stats` improvements ------------------------------------- `scipy.stats.multiscale_graphcorr` added as an independence test that operates on high dimensional and nonlinear data sets. It has higher statistical power than other `scipy.stats` tests while being the only one that operates on multivariate data. The generalized inverse Gaussian distribution (`scipy.stats.geninvgauss`) has been added. It is now possible to efficiently reuse `scipy.stats.binned_statistic_dd` with new values by providing the result of a previous call to the function. `scipy.stats.hmean` now handles input with zeros more gracefully. The beta-binomial distribution is now available in `scipy.stats.betabinom`. `scipy.stats.zscore`, `scipy.stats.circmean`, `scipy.stats.circstd`, and `scipy.stats.circvar` now support the ``nan_policy`` argument for enhanced handling of ``NaN`` values `scipy.stats.entropy` now accepts an ``axis`` argument `scipy.stats.gaussian_kde.resample` now accepts a ``seed`` argument to empower reproducibility `scipy.stats.kendalltau` performance has improved, especially for large inputs, due to improved cache usage `scipy.stats.truncnorm` distribution has been rewritten to support much wider tails Deprecated features =================== `scipy` deprecations ----------------------------- Support for NumPy functions exposed via the root SciPy namespace is deprecated and will be removed in 2.0.0. For example, if you use ``scipy.rand`` or ``scipy.diag``, you should change your code to directly use ``numpy.random.default_rng`` or ``numpy.diag``, respectively. They remain available in the currently continuing Scipy 1.x release series. The exception to this rule is using ``scipy.fft`` as a function -- :mod:`scipy.fft` is now meant to be used only as a module, so the ability to call ``scipy.fft(...)`` will be removed in SciPy 1.5.0. In `scipy.spatial.Rotation` methods ``from_dcm``, ``as_dcm`` were renamed to ``from_matrix``, ``as_matrix`` respectively. The old names will be removed in SciPy 1.6.0. Method ``Rotation.match_vectors`` was deprecated in favor of ``Rotation.align_vectors``, which provides a more logical and general API to the same functionality. The old method will be removed in SciPy 1.6.0. Backwards incompatible changes ========================== `scipy.special` changes --------------------------------- The deprecated functions ``hyp2f0``, ``hyp1f2``, and ``hyp3f0`` have been removed. The deprecated function ``bessel_diff_formula`` has been removed. The function ``i0`` is no longer registered with ``numpy.dual``, so that ``numpy.dual.i0`` will unconditionally refer to the NumPy version regardless of whether `scipy.special` is imported. The function ``expn`` has been changed to return ``nan`` outside of its domain of definition (``x, n < 0``) instead of ``inf``. `scipy.sparse` changes -------------------------------- Sparse matrix reshape now raises an error if shape is not two-dimensional, rather than guessing what was meant. The behavior is now the same as before SciPy 1.1.0. ``CSR`` and ``CSC`` sparse matrix classes should now return empty matrices of the same type when indexed out of bounds. Previously, for some versions of SciPy, this would raise an ``IndexError``. The change is largely motivated by greater consistency with ``ndarray`` and ``numpy.matrix`` semantics. `scipy.signal` changes ------------------------------- `scipy.signal.resample` behavior for length-1 signal inputs has been fixed to output a constant (DC) value rather than an impulse, consistent with the assumption of signal periodicity in the FFT method. `scipy.signal.cwt` now performs complex conjugation and time-reversal of wavelet data, which is a backwards-incompatible bugfix for time-asymmetric wavelets. `scipy.stats` changes ------------------------------ `scipy.stats.loguniform` added with better documentation as (an alias for ``scipy.stats.reciprocal``). ``loguniform`` generates random variables that are equally likely in the log space; e.g., ``1``, ``10`` and ``100`` are all equally likely if ``loguniform(10 ** 0, 10 ** 2).rvs()`` is used. Other changes ============= The ``LSODA`` method of `scipy.integrate.solve_ivp` now correctly detects stiff problems. `scipy.spatial.cKDTree` now accepts and correctly handles empty input data `scipy.stats.binned_statistic_dd` now calculates the standard deviation statistic in a numerically stable way. `scipy.stats.binned_statistic_dd` now throws an error if the input data contains either ``np.nan`` or ``np.inf``. Similarly, in `scipy.stats` now all continuous distributions' ``.fit()`` methods throw an error if the input data contain any instance of either ``np.nan`` or ``np.inf``. Authors ======= * @endolith * @wenhui-prudencemed + * Abhinav + * Anne Archibald * ashwinpathak20nov1996 + * Danilo Augusto + * Nelson Auner + * aypiggott + * Christoph Baumgarten * Peter Bell * Sebastian Berg * Arman Bilge + * Benedikt Boecking + * Christoph Boeddeker + * Daniel Bunting * Evgeni Burovski * Angeline Burrell + * Angeline G. Burrell + * CJ Carey * Carlos Ramos Carre?o + * Mak Sze Chun + * Malayaja Chutani + * Christian Clauss + * Jonathan Conroy + * Stephen P Cook + * Dylan Cutler + * Anirudh Dagar + * Aidan Dang + * dankleeman + * Brandon David + * Tyler Dawson + * Dieter Werthm?ller * Joe Driscoll + * Jakub Dyczek + * D?vid Bodn?r * Fletcher Easton + * Stefan Endres * etienne + * Johann Faouzi * Yu Feng * Isuru Fernando + * Matthew H Flamm * Martin Gauch + * Gabriel Gerlero + * Ralf Gommers * Chris Gorgolewski + * Domen Gorjup + * Edouard Goudenhoofdt + * Jan Gwinner + * Maja Gwozdz + * Matt Haberland * hadshirt + * Pierre Haessig + * David Hagen * Charles Harris * Gina Helfrich + * Alex Henrie + * Francisco J. Hernandez Heras + * Andreas Hilboll * Lindsey Hiltner * Thomas Hisch * Min ho Kim + * Gert-Ludwig Ingold * jakobjakobson13 + * Todd Jennings * He Jia * Muhammad Firmansyah Kasim + * Andrew Knyazev + * Holger Kohr + * Mateusz Konieczny + * Krzysztof Pi?ro + * Philipp Lang + * Peter Mahler Larsen + * Eric Larson * Antony Lee * Gregory R. Lee * Chelsea Liu + * Jesse Livezey * Peter Lysakovski + * Jason Manley + * Michael Marien + * Nikolay Mayorov * G. D. McBain + * Sam McCormack + * Melissa Weber Mendon?a + * Kevin Michel + * mikeWShef + * Sturla Molden * Eric Moore * Peyton Murray + * Andrew Nelson * Clement Ng + * Juan Nunez-Iglesias * Renee Otten + * Kellie Ottoboni + * Ayappan P * Sambit Panda + * Tapasweni Pathak + * Oleksandr Pavlyk * Fabian Pedregosa * Petar Mlinari? * Matti Picus * Marcel Plch + * Christoph Pohl + * Ilhan Polat * Siddhesh Poyarekar + * Ioannis Prapas + * James Alan Preiss + * Yisheng Qiu + * Eric Quintero * Bharat Raghunathan + * Tyler Reddy * Joscha Reimer * Antonio Horta Ribeiro * Lucas Roberts * rtshort + * Josua Sassen * Kevin Sheppard * Scott Sievert * Leo Singer * Kai Striega * S?ren Fuglede J?rgensen * tborisow + * ?tienne Tremblay + * tuxcell + * Miguel de Val-Borro * Andrew Valentine + * Hugo van Kemenade * Paul van Mulbregt * Sebastiano Vigna * Pauli Virtanen * Dany Vohl + * Ben Walsh + * Huize Wang + * Warren Weckesser * Anreas Weh + * Joseph Weston + * Adrian Wijaya + * Timothy Willard + * Josh Wilson * Kentaro Yamamoto + * Dave Zbarsky + A total of 142 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 1.4.0 -------------------------------- * `#1255 `__: maxiter broken for Scipy.sparse.linalg gmres, in addition to... * `#1301 `__: consolidate multipack.h from interpolate and integrate packages... * `#1739 `__: Single precision FFT insufficiently accurate. (Trac #1212) * `#1795 `__: stats test_distributions.py: replace old fuzz tests (Trac #1269) * `#2233 `__: fftpack segfault with big arrays (Trac #1714) * `#2434 `__: rmatmat and the sophistication of linear operator objects * `#2477 `__: stats.truncnorm.rvs() does not give symmetric results for negative... * `#2629 `__: FFTpack is unacceptably slow on non power of 2 * `#2883 `__: UnboundLocalError in scipy.interpolate.splrep * `#2956 `__: Feature Request: axis argument for stats.entropy function * `#3528 `__: Segfault on test_djbfft (possibly MKL-related?) * `#3793 `__: cwt should also return complex array * `#4464 `__: TST: residue/residuez/invres/invresz don't have any tests * `#4561 `__: BUG: tf filter trailing and leading zeros in residuez * `#4669 `__: Rewrite sosfilt to make a single loop over the input? * `#5040 `__: BUG: Empty data handling of (c)KDTrees * `#5112 `__: boxcox transform edge cases could use more care * `#5441 `__: scipy.stats.ncx2 fails for nc=0 * `#5502 `__: args keyword not handled in optimize.curve_fit * `#6484 `__: Qhull segmentation fault * `#6900 `__: linear_sum_assignment with infinite weights * `#6966 `__: Hypergeometric Functions documentation is lacking * `#6999 `__: possible false positive corruption check in compressed loadmat() * `#7018 `__: ydata that needs broadcasting renders curve_fit unable to compute... * `#7140 `__: trouble with documentation for windows * `#7327 `__: interpolate.ndgriddata.griddata causes Python to crash rather... * `#7396 `__: MatrixLinearOperator implements _adjoint(), but not _transpose() * `#7400 `__: BUG(?): special: factorial and factorial2 return a 0-dimensional... * `#7434 `__: Testing of scipy.stats continuous distributions misses 25 distributions * `#7491 `__: Several scipy.stats distributions (fisk, burr, burr12, f) return... * `#7759 `__: Overflow in stats.kruskal for large samples * `#7906 `__: Wrong result from scipy.interpolate.UnivariateSpline.integral... * `#8165 `__: ENH: match functionality of R for hmean * `#8417 `__: optimimze.minimize(method='L-BFGS-B', options={'disp': True})... * `#8535 `__: Strictly increasing requirement in UnivariateSpline * `#8815 `__: [BUG] GMRES: number of iteration is only increased if callback... * `#9207 `__: scipy.linalg.solve_triangular speed after scipy.linalg.lu_factor * `#9275 `__: new feature: adding LOBPCG solver in svds in addition to ARPACK * `#9403 `__: range of truncnorm.logpdf could be extended * `#9429 `__: gaussian_kde not working with numpy matrix * `#9515 `__: ndimage implementation relies on undefined behavior * `#9643 `__: arpack returns singular values in ascending order * `#9669 `__: DOC: matthew-brett/build-openblas has been retired * `#9852 `__: scipy.spatial.ConvexHull exit with code 134, free(): invalid... * `#9902 `__: scipy.stats.truncnorm second moment may be wrong * `#9943 `__: Custom sampling methods in shgo do not work * `#9947 `__: DOC: Incorrect documentation for \`nan_policy='propagate\` in... * `#9994 `__: BUG: sparse: reshape method allows a shape containing an arbitrary... * `#10036 `__: Official Nelder mead tutorial uses xtol instead of xatol, which... * `#10078 `__: possible to get a better error message when objective function... * `#10092 `__: overflow in truncnorm.rvs * `#10121 `__: A little spelling mistake * `#10126 `__: inaccurate std implementation in binned_statistic * `#10161 `__: Error in documentation scipy.special.modstruve * `#10195 `__: Derivative of spline with 'const' extrapolation is also extrapolted... * `#10206 `__: sparse matrices indexing with scipy 1.3 * `#10236 `__: Non-descriptive error on type mismatch for functions of scipy.optimize... * `#10258 `__: LOBPCG convergence failure if guess provided * `#10262 `__: distance matrix lacks dtype checks / warnings * `#10271 `__: BUG: optimize failure on wheels * `#10277 `__: scipy.special.zeta(0) = NAN * `#10292 `__: DOC/REL: Some sections of the release notes are not nested correctly. * `#10300 `__: scipy.stats.rv_continuous.fit throws empty RuntimeError when... * `#10319 `__: events in scipy.integrate.solve_ivp: How do I setup an events... * `#10323 `__: Adding more low-level LAPACK wrappers * `#10360 `__: firwin2 inadvertently modifies input and may result in undefined... * `#10388 `__: BLD: TestHerd::test_hetrd core dumps with Python-dbg * `#10395 `__: Remove warning about output shape of zoom * `#10403 `__: DOC: scipy.signal.resample ignores t parameter * `#10421 `__: Yeo-Johnson power transformation fails with integer input data * `#10422 `__: BUG: scipy.fft does not support multiprocessing * `#10427 `__: ENH: convolve numbers should be updated * `#10444 `__: BUG: scipy.spatial.transform.Rotation.match_vectors returns improper... * `#10488 `__: ENH: DCTs/DSTs for scipy.fft * `#10501 `__: BUG: scipy.spatial.HalfspaceIntersection works incorrectly * `#10514 `__: BUG: cKDTree GIL handling is incorrect * `#10535 `__: TST: master branch CI failures * `#10588 `__: scipy.fft and numpy.fft inconsistency when axes=None and shape... * `#10628 `__: Scipy python>3.6 Windows wheels don't ship msvcp\*.dll * `#10733 `__: DOC/BUG: min_only result does not match documentation * `#10774 `__: min_only=true djisktra infinite loop with duplicate indices * `#10775 `__: UnboundLocalError in Radau when given a NaN * `#10835 `__: io.wavfile.read unnecessarily raises an error for a bad wav header * `#10838 `__: Error in documentation for scipy.linalg.lu_factor * `#10875 `__: DOC: Graphical guides (using TikZ) * `#10880 `__: setting verbose > 2 in minimize with trust-constr method leads... * `#10887 `__: scipy.signal.signaltools._fftconv_faster has incorrect estimates * `#10948 `__: gammainc(0,x) = nan but should be 1, gammaincc(0,x) = nan but... * `#10952 `__: TestQRdelete_F.test_delete_last_p_col test failure * `#10968 `__: API: Change normalized=False to normalize=True in Rotation * `#10987 `__: Memory leak in shgo triangulation * `#10991 `__: Error running openBlas probably missing a step * `#11033 `__: deadlock on osx for python 3.8 * `#11041 `__: Test failure in wheel builds for TestTf2zpk.test_simple * `#11089 `__: Regression in scipy.stats where distribution will not accept loc and scale parameters * `#11100 `__: BUG: multiscale_graphcorr random state seeding and parallel use * `#11121 `__: Calls to `scipy.interpolate.splprep` increase RAM usage. * `#11125 `__: BUG: segfault when slicing a CSR or CSC sparse matrix with slice start index > stop index * `#11198 `__: BUG: sparse eigs (arpack) shift-invert drops the smallest eigenvalue for some k Pull requests for 1.4.0 ------------------------------- * `#4591 `__: BUG, TST: Several issues with scipy.signal.residue * `#6629 `__: ENH: sparse: canonicalize on initialization * `#7076 `__: ENH: add complex wavelet support to scipy.signal.cwt. * `#8681 `__: ENH add generalized inverse Gaussian distribution to scipy.stats * `#9064 `__: BUG/ENH: Added default _transpose into LinearOperator. Fixes... * `#9215 `__: ENH: Rbf interpolation of large multi-dimensional data * `#9311 `__: ENH: Added voigt in scipy.special. * `#9642 `__: ENH: integrate: quad() for vector-valued functions * `#9679 `__: DOC: expand docstring of exponweib distribution * `#9684 `__: TST: add ppc64le ci testing * `#9800 `__: WIP : ENH: Refactored _hungarian.py for speed and added a minimize/maximize? * `#9847 `__: DOC: Change integrate tutorial to use solve_ivp instead of odeint * `#9876 `__: ENH: Use rfft when possible in resampling * `#9998 `__: BUG: Do not remove 1s when calling sparse: reshape method #9994 * `#10002 `__: ENH: adds constraints for differential evolution * `#10098 `__: ENH: integrate: add args argument to solve_ivp. * `#10099 `__: DOC: Add missing docs for linprog unknown_options * `#10104 `__: BUG: Rewrite of stats.truncnorm distribution. * `#10105 `__: MAINT improve efficiency of rvs_ratio_uniforms in scipy.stats * `#10107 `__: TST: dual_annealing set seed * `#10108 `__: ENH: stats: improve kendall_tau cache usage * `#10110 `__: MAINT: _lib: Fix a build warning. * `#10114 `__: FIX: only print bounds when supported by minimizer (shgo) * `#10115 `__: TST: Add a test with an almost singular design matrix for lsq_linear * `#10118 `__: MAINT: fix rdist methods in scipy.stats * `#10119 `__: MAINT: improve rvs of randint in scipy.stats * `#10127 `__: Fix typo in record array field name (spatial-ckdtree-sparse_distance? * `#10130 `__: MAINT: ndimage: Fix some compiler warnings. * `#10131 `__: DOC: Note the solve_ivp args enhancement in the 1.4.0 release... * `#10133 `__: MAINT: add rvs for semicircular in scipy.stats * `#10138 `__: BUG: special: Invalid arguments to ellip_harm can crash Python. * `#10139 `__: MAINT: spatial: Fix some compiler warnings in the file distance_wrap.c. * `#10140 `__: ENH: add handling of NaN in RuntimeWarning except clause * `#10142 `__: DOC: return value of scipy.special.comb * `#10143 `__: MAINT: Loosen linprog tol * `#10152 `__: BUG: Fix custom sampling input for shgo, add unittest * `#10154 `__: MAINT: add moments and improve doc of mielke in scipy.stats * `#10158 `__: Issue #6999: read zlib checksum before checking bytes read. * `#10166 `__: BUG: Correctly handle broadcasted ydata in curve_fit pcov computation. * `#10167 `__: DOC: special: Add missing factor of \`i\` to \`modstruve\` docstring * `#10168 `__: MAINT: stats: Fix an incorrect comment. * `#10169 `__: ENH: optimize: Clarify error when objective function returns... * `#10172 `__: DEV: Run tests in parallel when --parallel flag is passed to... * `#10173 `__: ENH: Implement DOP853 ODE integrator * `#10176 `__: Fixed typo * `#10182 `__: TST: fix test issue for stats.pearsonr * `#10184 `__: MAINT: stats: Simplify zmap and zscore (we can use keepdims now). * `#10191 `__: DOC: fix a formatting issue in the scipy.spatial module docstring. * `#10193 `__: DOC: Updated docstring for optimize.nnls * `#10198 `__: DOC, ENH: special: Make \`hyp2f1\` references more specific * `#10202 `__: DOC: Format DST and DCT definitions as latex equations * `#10207 `__: BUG: Compressed matrix indexing should return a scalar * `#10210 `__: DOC: Update docs for connection='weak' in connected_components * `#10225 `__: DOC: Clarify new interfaces for legacy functions in 'optimize' * `#10231 `__: DOC, MAINT: gpg2 updates to release docs / pavement * `#10235 `__: LICENSE: split license file in standard BSD 3-clause and bundled. * `#10238 `__: ENH: Add new scipy.fft module using pocketfft * `#10243 `__: BUG: fix ARFF reader regression with quoted values. * `#10248 `__: DOC: update README file * `#10255 `__: CI: bump OpenBLAS to match wheels * `#10264 `__: TST: add tests for stats.tvar with unflattened arrays * `#10280 `__: MAINT: stats: Use a constant value for sqrt(2/PI). * `#10286 `__: Development Documentation Overhaul * `#10290 `__: MAINT: Deprecate NumPy functions in SciPy root * `#10291 `__: FIX: Avoid importing xdist when checking for availability * `#10295 `__: Disable deprecated Numpy API in __odrpack.c * `#10296 `__: ENH: C++ extension for linear assignment problem * `#10298 `__: ENH: Made pade function work with complex inputs * `#10301 `__: DOC: Fix critical value significance levels in stats.anderson_ksamp * `#10307 `__: Minkowski Distance Type Fix (issue #10262) * `#10309 `__: BUG: Pass jac=None directly to lsoda * `#10310 `__: BUG: interpolate: UnivariateSpline.derivative.ext is 'zeros'... * `#10312 `__: FIX: Fixing a typo in a comment * `#10314 `__: scipy.spatial enhancement request * `#10315 `__: DOC: Update integration tutorial to solve_ivp * `#10318 `__: DOC: update the example for PPoly.solve * `#10333 `__: TST: add tests for stats.tvar with unflattened arrays * `#10334 `__: MAINT: special: Remove deprecated \`hyp2f0\`, \`hyp1f2\`, and... * `#10336 `__: BUG: linalg/interpolative: fix interp_decomp modifying input * `#10341 `__: BUG: sparse.linalg/gmres: deprecate effect of callback on semantics... * `#10344 `__: DOC: improve wording of mathematical formulation * `#10345 `__: ENH: Tiled QR wrappers for scipy.linalg.lapack * `#10350 `__: MAINT: linalg: Use the new fft subpackage in linalg.dft test... * `#10351 `__: BUG: Fix unstable standard deviation calculation in histogram * `#10353 `__: Bug: interpolate.NearestNDInterpolator (issue #10352) * `#10357 `__: DOC: linalg: Refer to scipy.fft.fft (not fftpack) in the dft... * `#10359 `__: DOC: Update roadmap now scipy.fft has been merged * `#10361 `__: ENH: Prefer scipy.fft to scipy.fftpack in scipy.signal * `#10371 `__: DOC: Tweaks to fft documentation * `#10372 `__: DOC: Fix typos * `#10377 `__: TST, MAINT: adjustments for pytest 5.0 * `#10378 `__: ENH: _lib: allow new np.random.Generator in check_random_state * `#10379 `__: BUG: sparse: set writeability to be forward-compatible with numpy>=1.17 * `#10381 `__: BUG: Fixes gh-7491, pdf at x=0 of fisk/burr/burr12/f distributions. * `#10387 `__: ENH: optimize/bfgs: don't evaluate twice at initial point for... * `#10392 `__: [DOC] Add an example for _binned_statistic_dd * `#10396 `__: Remove warning about output shape of zoom * `#10397 `__: ENH: Add check_finite to sp.linalg.norm * `#10399 `__: ENH: Add __round__ method to sparse matrix * `#10407 `__: MAINT: drop pybind11 from install_requires, it's only build-time... * `#10408 `__: TST: use pytest.raises, not numpy assert_raises * `#10409 `__: CI: uninstall nose on Travis * `#10410 `__: [ENH] ncx2 dispatch to chi2 when nc=0 * `#10411 `__: TST: optimize: test should use assert_allclose for fp comparisons * `#10414 `__: DOC: add pybind11 to the other part of quickstart guides * `#10417 `__: DOC: special: don't mark non-ufuncs with a \`[+]\` * `#10423 `__: FIX: Use pybind11::isinstace to check array dtypes * `#10424 `__: DOC: add doctest example for binary data for ttest_ind_from_stats * `#10425 `__: ENH: Add missing Hermitian transforms to scipy.fft * `#10426 `__: MAINT: Fix doc build bugs * `#10431 `__: Update numpy version for AIX * `#10433 `__: MAINT: Minor fixes for the stats * `#10434 `__: BUG: special: make \`ndtri\` return NaN outside domain of definition * `#10435 `__: BUG: Allow integer input data in scipy.stats.yeojohnson * `#10438 `__: [DOC] Add example for kurtosis * `#10440 `__: ENH: special: make \`ellipk\` a ufunc * `#10443 `__: MAINT: ndimage: malloc fail check * `#10447 `__: BLD: Divert output from test compiles into a temporary directory * `#10451 `__: MAINT: signal: malloc fail check * `#10455 `__: BUG: special: fix values of \`hyperu\` for negative \`x\` * `#10456 `__: DOC: Added comment clarifying the call for dcsrch.f in lbfgsb.f * `#10457 `__: BUG: Allow ckdtree to accept empty data input * `#10459 `__: BUG:TST: Compute lwork safely * `#10460 `__: [DOC] Add example to entropy * `#10461 `__: DOC: Quickstart Guide updates * `#10462 `__: TST: special: only show max atol/rtol for test points that failed * `#10465 `__: BUG: Correctly align fft inputs * `#10467 `__: ENH: lower-memory duplicate generator checking in spatial.SphericalVoronoi * `#10470 `__: ENH: Normalise the inverse DCT/DST in scipy.fft * `#10472 `__: BENCH: adjust timeout for slow setup_cache * `#10475 `__: CI: include python debug for Travis-ci * `#10476 `__: TST: special: use \`__tracebackhide__\` to get better error messages * `#10477 `__: ENH: faster region building in spatial.SphericalVoronoi * `#10479 `__: BUG: stats: Fix a few issues with the distributions' fit method. * `#10480 `__: Add RuntimeError in _distn_infrastructure.py in fit() method * `#10481 `__: BENCH, MAINT: wheel_cache_size has been renamed build_cache_size * `#10494 `__: ENH: faster circumcenter calculation in spatial.SphericalVoronoi * `#10500 `__: Splrep _curfit_cache global variable bugfix * `#10503 `__: BUG: spatial/qhull: get HalfspaceIntersection.dual_points from... * `#10506 `__: DOC: interp2d, note nearest neighbor extrapolation * `#10507 `__: MAINT: Remove fortran fftpack library in favour of pypocketfft * `#10508 `__: TST: fix a bug in the circular import test. * `#10509 `__: MAINT: Set up _build_utils as subpackage * `#10516 `__: BUG: Use nogil contexts in cKDTree * `#10517 `__: ENH: fftconvolve should not FFT broadcastable axes * `#10518 `__: ENH: Speedup fftconvolve * `#10520 `__: DOC: Proper .rst formatting for deprecated features and Backwards... * `#10523 `__: DOC: Improve scipy.signal.resample documentation * `#10524 `__: ENH: Add MGC to scipy.stats * `#10525 `__: [ENH] ncx2.ppf dispatch to chi2 when nc=0 * `#10526 `__: DOC: clarify laplacian normalization * `#10528 `__: API: Rename scipy.fft DCT/DST shape argument to s * `#10531 `__: BUG: fixed improper rotations in spatial.transform.rotation.match_vectors * `#10533 `__: [DOC] Add example for winsorize function * `#10539 `__: MAINT: special: don't register \`i0\` with \`numpy.dual\` * `#10540 `__: MAINT: Fix Travis and Circle * `#10542 `__: MAINT: interpolate: use cython_lapack * `#10547 `__: Feature request. Add furthest site Voronoi diagrams to scipy.spatial.plotutils. * `#10549 `__: [BUG] Fix bug in trimr when inclusive=False * `#10552 `__: add scipy.signal.upfirdn signal extension modes * `#10555 `__: MAINT: special: move \`c_misc\` into Cephes * `#10556 `__: [DOC] Add example for trima * `#10562 `__: [DOC] Fix triple string fo trimmed so that __doc__ can show... * `#10563 `__: improve least_squares error msg for mismatched shape * `#10564 `__: ENH: linalg: memoize get_lapack/blas_funcs to speed it up * `#10566 `__: ENH: add implementation of solver for the maximum flow problem * `#10567 `__: BUG: spatial: use c++11 construct for getting start of vector... * `#10568 `__: DOC: special: small tweaks to the \`zetac\` docstring * `#10571 `__: [ENH] Gaussian_kde can accept matrix dataset * `#10574 `__: ENH: linalg: speed up _compute_lwork by avoiding numpy constructs * `#10582 `__: Fix typos with typos in bundled libraries reverted * `#10583 `__: ENH: special: add the analytic continuation of Riemann zeta * `#10584 `__: MAINT: special: clean up \`special.__all__\` * `#10586 `__: BUG: multidimensional scipy.fft functions should accept 's' rather... * `#10587 `__: BUG: integrate/lsoda: never abort run, set error istate instead * `#10594 `__: API: Replicate numpy's fftn behaviour when s is given but not... * `#10599 `__: DOC: dev: update documentation vs. github pull request workflow... * `#10603 `__: MAINT: installer scripts removed * `#10604 `__: MAINT: Change c\*np.ones(...) to np.full(..., c, ...) in many... * `#10608 `__: Univariate splines should require x to be strictly increasing... * `#10613 `__: ENH: Add seed option for gaussian_kde.resample * `#10614 `__: ENH: Add parallel computation to scipy.fft * `#10615 `__: MAINT: interpolate: remove unused header file * `#10616 `__: MAINT: Clean up 32-bit platform xfail markers * `#10618 `__: BENCH: Added 'trust-constr' to minimize benchmarks * `#10621 `__: [MRG] multiple stability updates in lobpcg * `#10622 `__: MAINT: forward port 1.3.1 release notes * `#10624 `__: DOC: stats: Fix spelling of 'support'. * `#10627 `__: DOC: stats: Add references for the alpha distribution. * `#10629 `__: MAINT: special: avoid overflow longer in \`zeta\` for negative... * `#10630 `__: TST: GH10271, relax test assertion, fixes #10271 * `#10631 `__: DOC: nelder-mean uses xatol fixes #10036 * `#10633 `__: BUG: interpolate: integral(a, b) should be zero when both limits... * `#10635 `__: DOC: special: complete hypergeometric functions documentation * `#10636 `__: BUG: special: use series for \`hyp1f1\` when it converges rapidly * `#10641 `__: ENH: allow matching of general bipartite graphs * `#10643 `__: ENH: scipy.sparse.linalg.spsolve triangular unit diagonal * `#10650 `__: ENH: Cythonize sosfilt * `#10654 `__: DOC: Vertical alignment of table entries * `#10655 `__: ENH: Dockerfile for scipy development * `#10660 `__: TST: clean up tests for rvs in scipy.stats * `#10664 `__: Throw error on non-finite input for binned_statistic_dd() * `#10665 `__: DOC: special: improve the docstrings for \`gamma\` and \`gammasgn\` * `#10669 `__: TST: Update scipy.fft real transform tests * `#10670 `__: DOC: Clarify docs and error messages for scipy.signal.butter * `#10672 `__: ENH: return solution attribute when using events in solve_ivp * `#10675 `__: MAINT: special: add an explicit NaN check for \`iv\` arguments * `#10679 `__: DOC: special: Add documentation for \`beta\` function * `#10681 `__: TST: sparse.linalg: fix arnoldi test seed * `#10682 `__: DOC: special: Add documentation for \`betainc\` function * `#10684 `__: TST: special: require Mpmath 1.1.0 for \`test_hyperu_around_0\` * `#10686 `__: FIX: sphinx isattributedescriptor is not available in sphinx... * `#10687 `__: DOC: added Docker quickstart guide by @andyfaff * `#10689 `__: DOC: special: clarify format of parameters/returns sections for... * `#10690 `__: DOC: special: improve docstrings of incomplete gamma functions * `#10692 `__: ENH: higher-dimensional input in \`spatial.SphericalVoronoi\` * `#10694 `__: ENH: ScalarFunction.fun_and_grad * `#10698 `__: DOC: special: Add documentation for \`betaincinv\` * `#10699 `__: MAINT: remove time print lbfgsb fixes #8417 * `#10701 `__: TST, MAINT: bump OpenBLAS to 0.3.7 stable * `#10702 `__: DOC: clarify iterations consume multiple function calls * `#10703 `__: DOC: iprint doc lbfgsb closes #5482 * `#10708 `__: TST: test suggested in gh1758 * `#10710 `__: ENH: Added nan_policy to circ functions in \`stats\` * `#10712 `__: ENH: add axis parameter to stats.entropy * `#10714 `__: DOC: Formatting fix rv_continuous.expect docs * `#10715 `__: DOC: BLD: update doc Makefile for python version; add scipy version... * `#10717 `__: MAINT: modernize doc/Makefile * `#10719 `__: Enable setting minres initial vector * `#10720 `__: DOC: silence random warning in doc build for \`stats.binned_statistic_dd\` * `#10724 `__: DEV: Add doc option to runtests.py * `#10728 `__: MAINT: get rid of gramA, gramB text files that lobpcg tests leave... * `#10732 `__: DOC: add min_only to docstring for Dijkstra's algorithm * `#10734 `__: DOC: spell out difference between source and target in shortest... * `#10735 `__: Fix for Python 4 * `#10739 `__: BUG: optimize/slsqp: deal with singular BFGS update * `#10741 `__: ENH: LAPACK wrappers for ?geequ, ?geequb, ?syequb, ?heequb * `#10742 `__: DOC: special: add to the docstring of \`gammaln\` * `#10743 `__: ENH: special: add a real dispatch for \`wrightomega\` * `#10746 `__: MAINT: Fix typos in comments, docs and test name * `#10747 `__: Remove spurious quotes * `#10750 `__: MAINT: make cython code more precise * `#10751 `__: MAINT: Check that scipy.linalg.lapack functions are documented * `#10752 `__: MAINT: special: use \`sf_error\` in Cephes * `#10755 `__: DOC: cluster: Add 'See Also' and 'Examples' for kmeans2. * `#10763 `__: MAINT: list of minimize methods * `#10768 `__: BUG: Fix corner case for sos2zpk * `#10773 `__: Fix error type for complex input to scipy.fftpack.rfft and irfft * `#10776 `__: ENH: handle geodesic input in \`spatial.SphericalVoronoi\` * `#10777 `__: MAINT: minimizer-->custom should handle the kinds of bounds/constrain?... * `#10781 `__: ENH: solve_triangular C order improvement * `#10787 `__: Fix behavior of \`exp1\` on branch cut and add docstring * `#10789 `__: DOC: special: add parameters/returns doc sections for erfc/erfcx/erfi * `#10790 `__: Travis CI: sudo is deprecated and Xenial is default distro * `#10792 `__: DOC: special: add full docstring for \`expi\` * `#10799 `__: DOC: special: add a complete docstring for \`expn\` * `#10800 `__: Docs edits (GSoD) * `#10802 `__: BUG: fix UnboundLocalError in Radau (scipy#10775) * `#10804 `__: ENH: Speed up next_fast_len with LRU cache * `#10805 `__: DOC: Fix unbalanced quotes in signal.place_poles * `#10809 `__: ENH: Speed up next_fast_len * `#10810 `__: ENH: Raise catchable exceptions for bad Fortran files * `#10811 `__: MAINT: optimize: Remove extra variable from _remove_redundancy_dense * `#10813 `__: MAINT: special: Remove unused variables from _kolmogi and _smirnovi * `#10815 `__: DOC, API: scipy.stats.reciprocal is "log-uniform" * `#10816 `__: MAINT: special: remove deprecated \`bessel_diff_formula\` * `#10817 `__: DOC: special: complete the docstring for \`fresnel\` * `#10820 `__: Fixed compiler_helper.py to allow compilation with ICC on Linux * `#10823 `__: DOC: updated reference guide text for consistency in writing... * `#10825 `__: MAINT: special: change some features of the Voigt function * `#10828 `__: MAINT: integrate: Remove unused variable from init_callback * `#10830 `__: Adding LOBPCG solver in svds in addition to ARPACK * `#10837 `__: WIP: ENH: reduction function for \`spatial.tranform.Rotation\`... * `#10843 `__: ENH: Adding optional parameter to stats.zscores to allow for... * `#10845 `__: Rebase kruskal fix * `#10847 `__: remove redundant __getitem__ from scipy.sparse.lil * `#10848 `__: Better handling of empty (not missing) docstrings * `#10849 `__: ENH: implement rmatmat for LinearOperator * `#10850 `__: MAINT : Refactoring lil List of Lists * `#10851 `__: DOC: add a generative art example to the scipy.spatial tutorial. * `#10852 `__: DOC: linalg: fixed gh-10838 unused imports in example deleted * `#10854 `__: DOC: special: add a full docstring for \`pdtr\` * `#10861 `__: ENH: option to reuse binnumbers in stats.binned_statistic_dd * `#10863 `__: DOC: partial standardization and validation of scipy.stats reference... * `#10865 `__: BUG: special: fix incomplete gamma functions for infinite \`a\` * `#10866 `__: ENH: calculation of mean in spatial.transform.Rotation * `#10867 `__: MAINT: Also store latex directory * `#10869 `__: ENH: Implement overlap-add convolution * `#10870 `__: ENH: Do not raise EOF error if wavfile data read * `#10876 `__: ENH: Add beta-binomial distribution to scipy.stats * `#10878 `__: MAINT: Update R project URL * `#10883 `__: MAINT: (ndimage) More robust check for output being a numpy dtype * `#10884 `__: DOC: Added instructions on adding a new distribution to scipy.stats. * `#10885 `__: [BUG] fix lobpcg with maxiter=None results in Exception * `#10899 `__: ENH: Match R functionality for hmean * `#10900 `__: MAINT: stats: Use keepdims to simplify a few lines in power_divergence. * `#10901 `__: ENH: sparse/linalg: support pydata/sparse matrices * `#10907 `__: Check whether \`maxiter\` is integer * `#10912 `__: ENH: warn user that quad() ignores \`points=...\` when \`weight=...\`... * `#10918 `__: CI: fix Travis CI py3.8 build * `#10920 `__: MAINT: Update constants to codata 2018 values (second try) * `#10921 `__: ENH: scipy.sparse.lil: tocsr accelerated * `#10924 `__: BUG: Forbid passing 'args' as kwarg in scipy.optimize.curve_fit * `#10928 `__: DOC: Add examples to io.wavfile docstrings * `#10934 `__: typo fix * `#10935 `__: BUG: Avoid undefined behaviour on float to unsigned conversion * `#10936 `__: DOC: Added missing example to stats.mstats.variation * `#10939 `__: ENH: scipy.sparse.lil: tocsr accelerated depending on density * `#10946 `__: BUG: setting verbose > 2 in minimize with trust-constr method... * `#10947 `__: DOC: special: small improvements to the \`poch\` docstring * `#10949 `__: BUG: fix return type of erlang_gen._argcheck * `#10951 `__: DOC: fixed Ricker wavelet formula * `#10954 `__: BUG: special: fix \`factorial\` return type for 0-d inputs * `#10955 `__: MAINT: Relax the assert_unitary atol value * `#10956 `__: WIP: make pdtr(int, double) be pdtr(double, double) * `#10957 `__: BUG: Ensure full binary compatibility of long double test data * `#10964 `__: ENH: Make Slerp callable with a scalar argument * `#10972 `__: BUG: Handle complex gains in zpk2sos * `#10975 `__: TST: skip test_kendalltau ppc64le * `#10978 `__: BUG: boxcox data dimension and constancy check #5112 * `#10979 `__: API: Rename dcm to (rotation) matrix in Rotation class * `#10981 `__: MAINT: add support for a==0 and x>0 edge case to igam and igamc * `#10986 `__: MAINT: Remove direct imports from numpy in signaltools.py * `#10988 `__: BUG: signal: fixed issue #10360 * `#10989 `__: FIX binned_statistic_dd Mac wheel test fails * `#10990 `__: BUG: Fix memory leak in shgo triangulation * `#10992 `__: TST: Relax tolerance in upfirdn test_modes * `#10993 `__: TST: bump tolerance in optimize tests * `#10997 `__: MAINT: Rework residue and residuez * `#11001 `__: DOC: Updated Windows build tutorial * `#11004 `__: BUG: integrate/quad_vec: fix several bugs in quad_vec * `#11005 `__: TST: add Python 3.8 Win CI * `#11006 `__: DOC: special: add a reference for \`kl_div\` * `#11012 `__: MAINT: Rework invres and invresz * `#11015 `__: DOC: special: add references for \`rel_entr\` * `#11017 `__: DOC: numpydoc validation of morestats.py * `#11018 `__: MAINT: Filter unrelated warning * `#11031 `__: MAINT: update choose_conv_method for pocketfft implementation * `#11034 `__: MAINT: TST: Skip tests with multiprocessing that use "spawn"... * `#11036 `__: DOC: update doc/README with some more useful content. * `#11037 `__: DOC: special: add a complete docstring for \`rgamma\` * `#11038 `__: DOC: special: add a reference for the polygamma function * `#11042 `__: TST: fix tf2zpk test failure due to incorrect complex sorting. * `#11044 `__: MAINT: choose_conv_method can choose fftconvolution for longcomplex * `#11046 `__: TST: Reduce tolerance for ppc64le with reference lapack * `#11048 `__: DOC: special: add reference for orthogonal polynomial functions * `#11049 `__: MAINT: proper random number initialization and readability fix * `#11051 `__: MAINT: pep8 cleanup * `#11054 `__: TST: bump test precision for dual_annealing SLSQP test * `#11055 `__: DOC: special: add a reference for \`zeta\` * `#11056 `__: API: Deprecated normalized keyword in Rotation * `#11065 `__: DOC: Ubuntu Development Environment Quickstart should not modify... * `#11066 `__: BUG: skip deprecation for numpy top-level types * `#11067 `__: DOC: updated documentation for consistency in writing style * `#11070 `__: DOC: Amendment to Ubuntu Development Environment Quickstart should... * `#11073 `__: DOC: fix 1.4.0 release notes * `#11081 `__: API: Replace Rotation.match_vectors with align_vectors * `#11083 `__: DOC: more 1.4.0 release note fixes * `#11092 `__: BUG: stats: fix freezing of some distributions * `#11096 `__: BUG: scipy.sparse.csgraph: fixed issue #10774 * `#11124 `__: fix Cython warnings related to _stats.pyx * `#11126 `__: BUG: interpolate/fitpack: fix memory leak in splprep * `#11127 `__: Avoid potential segfault in CSR and CSC matrix indexing * `#11152 `__: BUG: Fix random state bug multiscale_graphcorr * `#11166 `__: BUG: empty sparse slice shapes * `#11167 `__: BUG: redundant fft in signal.resample * `#11181 `__: TST: Fix tolerance of tests for aarch64 * `#11182 `__: TST: Bump up tolerance for test_maxiter_worsening * `#11199 `__: BUG: sparse.linalg: mistake in unsymm. real shift-invert ARPACK eigenvalue 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URL: From warren.weckesser at gmail.com Mon Dec 16 20:13:07 2019 From: warren.weckesser at gmail.com (Warren Weckesser) Date: Mon, 16 Dec 2019 20:13:07 -0500 Subject: [Numpy-discussion] [SciPy-Dev] ANN: SciPy 1.4.0 In-Reply-To: References: Message-ID: On 12/16/19, Tyler Reddy wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA256 > > Hi all, > > On behalf of the SciPy development team I'm pleased to announce > the release of SciPy 1.4.0. Fantastic, thanks Tyler! Warren > > Sources and binary wheels can be found at: > https://pypi.org/project/scipy/ > and at: > https://github.com/scipy/scipy/releases/tag/v1.4.0 > > One of a few ways to install this release with pip: > > pip install scipy==1.4.0 > > ========================== > SciPy 1.4.0 Release Notes > ========================== > > SciPy 1.4.0 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 > 1.4.x branch, and on adding new features on the master branch. > > This release requires Python 3.5+ and NumPy >=1.13.3 (for Python 3.5, 3.6), >>=1.14.5 (for Python 3.7), >= 1.17.3 (for Python 3.8) > > For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. > > Highlights of this release > ---------------------------------- > > - a new submodule, `scipy.fft`, now supersedes `scipy.fftpack`; this > means support for ``long double`` transforms, faster multi-dimensional > transforms, improved algorithm time complexity, release of the global > intepreter lock, and control over threading behavior > - support for ``pydata/sparse`` arrays in `scipy.sparse.linalg` > - substantial improvement to the documentation and functionality of > several `scipy.special` functions, and some new additions > - the generalized inverse Gaussian distribution has been added to > `scipy.stats` > - an implementation of the Edmonds-Karp algorithm in > `scipy.sparse.csgraph.maximum_flow` > - `scipy.spatial.SphericalVoronoi` now supports n-dimensional input, > has linear memory complexity, improved performance, and > supports single-hemisphere generators > > > New features > ============ > > Infrastructure > -------------------- > Documentation can now be built with ``runtests.py --doc`` > > A ``Dockerfile`` is now available in the ``scipy/scipy-dev`` repository to > facilitate getting started with SciPy development. > > `scipy.constants` improvements > --------------------------------------------- > `scipy.constants` has been updated with the CODATA 2018 constants. > > > `scipy.fft` added > ------------------------ > `scipy.fft` is a new submodule that supersedes the `scipy.fftpack` > submodule. > For the most part, this is a drop-in replacement for ``numpy.fft`` and > `scipy.fftpack` alike. With some important differences, `scipy.fft`: > - uses NumPy's conventions for real transforms (``rfft``). This means the > return value is a complex array, half the size of the full ``fft`` output. > This is different from the output of ``fftpack`` which returned a real > array > representing complex components packed together. > - the inverse real to real transforms (``idct`` and ``idst``) are > normalized > for ``norm=None`` in thesame way as ``ifft``. This means the identity > ``idct(dct(x)) == x`` is now ``True`` for all norm modes. > - does not include the convolutions or pseudo-differential operators > from ``fftpack``. > > This submodule is based on the ``pypocketfft`` library, developed by the > author of ``pocketfft`` which was recently adopted by NumPy as well. > ``pypocketfft`` offers a number of advantages over fortran ``FFTPACK``: > - support for long double (``np.longfloat``) precision transforms. > - faster multi-dimensional transforms using vectorisation > - Bluestein?s algorithm removes the worst-case ``O(n^2)`` complexity of > ``FFTPACK`` > - the global interpreter lock (``GIL``) is released during transforms > - optional multithreading of multi-dimensional transforms via the > ``workers`` > argument > > Note that `scipy.fftpack` has not been deprecated and will continue to be > maintained but is now considered legacy. New code is recommended to use > `scipy.fft` instead, where possible. > > `scipy.fftpack` improvements > ---------------------------------------- > `scipy.fftpack` now uses pypocketfft to perform its FFTs, offering the same > speed and accuracy benefits listed for scipy.fft above but without the > improved API. > > `scipy.integrate` improvements > ------------------------------------------- > > The function `scipy.integrate.solve_ivp` now has an ``args`` argument. > This allows the user-defined functions passed to the function to have > additional parameters without having to create wrapper functions or > lambda expressions for them. > > `scipy.integrate.solve_ivp` can now return a ``y_events`` attribute > representing the solution of the ODE at event times > > New ``OdeSolver`` is implemented --- ``DOP853``. This is a high-order > explicit > Runge-Kutta method originally implemented in Fortran. Now we provide a pure > Python implementation usable through ``solve_ivp`` with all its features. > > `scipy.integrate.quad` provides better user feedback when break points are > specified with a weighted integrand. > > `scipy.integrate.quad_vec` is now available for general purpose integration > of vector-valued functions > > > `scipy.interpolate` improvements > --------------------------------------------- > `scipy.interpolate.pade` now handles complex input data gracefully > > `scipy.interpolate.Rbf` can now interpolate multi-dimensional functions > > `scipy.io` improvements > --------------------------------- > > `scipy.io.wavfile.read` can now read data from a `WAV` file that has a > malformed header, similar to other modern `WAV` file parsers > > `scipy.io.FortranFile` now has an expanded set of available ``Exception`` > classes for handling poorly-formatted files > > > `scipy.linalg` improvements > ------------------------------------- > The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct > results for complex-valued matrices. Before this, the function only > returned > correct values for real-valued matrices. > > New boolean keyword argument ``check_finite`` for `scipy.linalg.norm`; > whether > to check that the input matrix contains only finite numbers. Disabling may > give a performance gain, but may result in problems (crashes, > non-termination) > if the inputs do contain infinities or NaNs. > > `scipy.linalg.solve_triangular` has improved performance for a C-ordered > triangular matrix > > ``LAPACK`` wrappers have been added for ``?geequ``, ``?geequb``, > ``?syequb``, > and ``?heequb`` > > Some performance improvements may be observed due to an internal > optimization > in operations involving LAPACK routines via ``_compute_lwork``. This is > particularly true for operations on small arrays. > > Block ``QR`` wrappers are now available in `scipy.linalg.lapack` > > > `scipy.ndimage` improvements > ------------------------------------------ > > > `scipy.optimize` improvements > ------------------------------------------ > It is now possible to use linear and non-linear constraints with > `scipy.optimize.differential_evolution`. > > `scipy.optimize.linear_sum_assignment` has been re-written in C++ to > improve > performance, and now allows input costs to be infinite. > > A ``ScalarFunction.fun_and_grad`` method was added for convenient > simultaneous > retrieval of a function and gradient evaluation > > `scipy.optimize.minimize` ``BFGS`` method has improved performance by > avoiding > duplicate evaluations in some cases > > Better user feedback is provided when an objective function returns an > array > instead of a scalar. > > > `scipy.signal` improvements > -------------------------------------- > > Added a new function to calculate convolution using the overlap-add method, > named `scipy.signal.oaconvolve`. Like `scipy.signal.fftconvolve`, this > function supports specifying dimensions along which to do the convolution. > > `scipy.signal.cwt` now supports complex wavelets. > > The implementation of ``choose_conv_method`` has been updated to reflect > the > new FFT implementation. In addition, the performance has been significantly > improved (with rather drastic improvements in edge cases). > > The function ``upfirdn`` now has a ``mode`` keyword argument that can be > used > to select the signal extension mode used at the signal boundaries. These > modes > are also available for use in ``resample_poly`` via a newly added > ``padtype`` > argument. > > `scipy.signal.sosfilt` now benefits from Cython code for improved > performance > > `scipy.signal.resample` should be more efficient by leveraging ``rfft`` > when > possible > > `scipy.sparse` improvements > --------------------------------------- > It is now possible to use the LOBPCG method in `scipy.sparse.linalg.svds`. > > `scipy.sparse.linalg.LinearOperator` now supports the operation ``rmatmat`` > for adjoint matrix-matrix multiplication, in addition to ``rmatvec``. > > Multiple stability updates enable float32 support in the LOBPCG eigenvalue > solver for symmetric and Hermitian eigenvalues problems in > ``scipy.sparse.linalg.lobpcg``. > > A solver for the maximum flow problem has been added as > `scipy.sparse.csgraph.maximum_flow`. > > `scipy.sparse.csgraph.maximum_bipartite_matching` now allows non-square > inputs, > no longer requires a perfect matching to exist, and has improved > performance. > > `scipy.sparse.lil_matrix` conversions now perform better in some scenarios > > Basic support is available for ``pydata/sparse`` arrays in > `scipy.sparse.linalg` > > `scipy.sparse.linalg.spsolve_triangular` now supports the ``unit_diagonal`` > argument to improve call signature similarity with its dense counterpart, > `scipy.linalg.solve_triangular` > > ``assertAlmostEqual`` may now be used with sparse matrices, which have > added > support for ``__round__`` > > `scipy.spatial` improvements > --------------------------------------- > The bundled Qhull library was upgraded to version 2019.1, fixing several > issues. Scipy-specific patches are no longer applied to it. > > `scipy.spatial.SphericalVoronoi` now has linear memory complexity, improved > performance, and supports single-hemisphere generators. Support has also > been > added for handling generators that lie on a great circle arc (geodesic > input) > and for generators in n-dimensions. > > `scipy.spatial.transform.Rotation` now includes functions for calculation > of a > mean rotation, generation of the 3D rotation groups, and reduction of > rotations > with rotational symmetries. > > `scipy.spatial.transform.Slerp` is now callable with a scalar argument > > `scipy.spatial.voronoi_plot_2d` now supports furthest site Voronoi diagrams > > `scipy.spatial.Delaunay` and `scipy.spatial.Voronoi` now have attributes > for tracking whether they are furthest site diagrams > > `scipy.special` improvements > ----------------------------------------- > The Voigt profile has been added as `scipy.special.voigt_profile`. > > A real dispatch has been added for the Wright Omega function > (`scipy.special.wrightomega`). > > The analytic continuation of the Riemann zeta function has been added. (The > Riemann zeta function is the one-argument variant of `scipy.special.zeta`.) > > The complete elliptic integral of the first kind (`scipy.special.ellipk`) > is > now available in `scipy.special.cython_special`. > > The accuracy of `scipy.special.hyp1f1` for real arguments has been > improved. > > The documentation of many functions has been improved. > > `scipy.stats` improvements > ------------------------------------- > `scipy.stats.multiscale_graphcorr` added as an independence test that > operates on high dimensional and nonlinear data sets. It has higher > statistical > power than other `scipy.stats` tests while being the only one that operates > on > multivariate data. > > The generalized inverse Gaussian distribution (`scipy.stats.geninvgauss`) > has > been added. > > It is now possible to efficiently reuse `scipy.stats.binned_statistic_dd` > with new values by providing the result of a previous call to the function. > > `scipy.stats.hmean` now handles input with zeros more gracefully. > > The beta-binomial distribution is now available in `scipy.stats.betabinom`. > > `scipy.stats.zscore`, `scipy.stats.circmean`, `scipy.stats.circstd`, and > `scipy.stats.circvar` now support the ``nan_policy`` argument for enhanced > handling of ``NaN`` values > > `scipy.stats.entropy` now accepts an ``axis`` argument > > `scipy.stats.gaussian_kde.resample` now accepts a ``seed`` argument to > empower > reproducibility > > `scipy.stats.kendalltau` performance has improved, especially for large > inputs, > due to improved cache usage > > `scipy.stats.truncnorm` distribution has been rewritten to support much > wider > tails > > > Deprecated features > =================== > > `scipy` deprecations > ----------------------------- > Support for NumPy functions exposed via the root SciPy namespace is > deprecated > and will be removed in 2.0.0. For example, if you use ``scipy.rand`` or > ``scipy.diag``, you should change your code to directly use > ``numpy.random.default_rng`` or ``numpy.diag``, respectively. > They remain available in the currently continuing Scipy 1.x release series. > > The exception to this rule is using ``scipy.fft`` as a function -- > :mod:`scipy.fft` is now meant to be used only as a module, so the ability > to > call ``scipy.fft(...)`` will be removed in SciPy 1.5.0. > > In `scipy.spatial.Rotation` methods ``from_dcm``, ``as_dcm`` were renamed > to > ``from_matrix``, ``as_matrix`` respectively. The old names will be removed > in > SciPy 1.6.0. > > Method ``Rotation.match_vectors`` was deprecated in favor of > ``Rotation.align_vectors``, which provides a more logical and > general API to the same functionality. The old method > will be removed in SciPy 1.6.0. > > Backwards incompatible changes > ========================== > > `scipy.special` changes > --------------------------------- > The deprecated functions ``hyp2f0``, ``hyp1f2``, and ``hyp3f0`` have been > removed. > > The deprecated function ``bessel_diff_formula`` has been removed. > > The function ``i0`` is no longer registered with ``numpy.dual``, so that > ``numpy.dual.i0`` will unconditionally refer to the NumPy version > regardless > of whether `scipy.special` is imported. > > The function ``expn`` has been changed to return ``nan`` outside of its > domain of definition (``x, n < 0``) instead of ``inf``. > > `scipy.sparse` changes > -------------------------------- > Sparse matrix reshape now raises an error if shape is not two-dimensional, > rather than guessing what was meant. The behavior is now the same as before > SciPy 1.1.0. > > ``CSR`` and ``CSC`` sparse matrix classes should now return empty matrices > of the same type when indexed out of bounds. Previously, for some versions > of SciPy, this would raise an ``IndexError``. The change is largely > motivated > by greater consistency with ``ndarray`` and ``numpy.matrix`` semantics. > > `scipy.signal` changes > ------------------------------- > `scipy.signal.resample` behavior for length-1 signal inputs has been > fixed to output a constant (DC) value rather than an impulse, consistent > with > the assumption of signal periodicity in the FFT method. > > `scipy.signal.cwt` now performs complex conjugation and time-reversal of > wavelet data, which is a backwards-incompatible bugfix for > time-asymmetric wavelets. > > `scipy.stats` changes > ------------------------------ > `scipy.stats.loguniform` added with better documentation as (an alias for > ``scipy.stats.reciprocal``). ``loguniform`` generates random variables > that are equally likely in the log space; e.g., ``1``, ``10`` and ``100`` > are all equally likely if ``loguniform(10 ** 0, 10 ** 2).rvs()`` is used. > > > Other changes > ============= > The ``LSODA`` method of `scipy.integrate.solve_ivp` now correctly detects > stiff > problems. > > `scipy.spatial.cKDTree` now accepts and correctly handles empty input data > > `scipy.stats.binned_statistic_dd` now calculates the standard deviation > statistic in a numerically stable way. > > `scipy.stats.binned_statistic_dd` now throws an error if the input data > contains either ``np.nan`` or ``np.inf``. Similarly, in `scipy.stats` now > all > continuous distributions' ``.fit()`` methods throw an error if the input > data > contain any instance of either ``np.nan`` or ``np.inf``. > > > Authors > ======= > > * @endolith > * @wenhui-prudencemed + > * Abhinav + > * Anne Archibald > * ashwinpathak20nov1996 + > * Danilo Augusto + > * Nelson Auner + > * aypiggott + > * Christoph Baumgarten > * Peter Bell > * Sebastian Berg > * Arman Bilge + > * Benedikt Boecking + > * Christoph Boeddeker + > * Daniel Bunting > * Evgeni Burovski > * Angeline Burrell + > * Angeline G. Burrell + > * CJ Carey > * Carlos Ramos Carre?o + > * Mak Sze Chun + > * Malayaja Chutani + > * Christian Clauss + > * Jonathan Conroy + > * Stephen P Cook + > * Dylan Cutler + > * Anirudh Dagar + > * Aidan Dang + > * dankleeman + > * Brandon David + > * Tyler Dawson + > * Dieter Werthm?ller > * Joe Driscoll + > * Jakub Dyczek + > * D?vid Bodn?r > * Fletcher Easton + > * Stefan Endres > * etienne + > * Johann Faouzi > * Yu Feng > * Isuru Fernando + > * Matthew H Flamm > * Martin Gauch + > * Gabriel Gerlero + > * Ralf Gommers > * Chris Gorgolewski + > * Domen Gorjup + > * Edouard Goudenhoofdt + > * Jan Gwinner + > * Maja Gwozdz + > * Matt Haberland > * hadshirt + > * Pierre Haessig + > * David Hagen > * Charles Harris > * Gina Helfrich + > * Alex Henrie + > * Francisco J. Hernandez Heras + > * Andreas Hilboll > * Lindsey Hiltner > * Thomas Hisch > * Min ho Kim + > * Gert-Ludwig Ingold > * jakobjakobson13 + > * Todd Jennings > * He Jia > * Muhammad Firmansyah Kasim + > * Andrew Knyazev + > * Holger Kohr + > * Mateusz Konieczny + > * Krzysztof Pi?ro + > * Philipp Lang + > * Peter Mahler Larsen + > * Eric Larson > * Antony Lee > * Gregory R. Lee > * Chelsea Liu + > * Jesse Livezey > * Peter Lysakovski + > * Jason Manley + > * Michael Marien + > * Nikolay Mayorov > * G. D. McBain + > * Sam McCormack + > * Melissa Weber Mendon?a + > * Kevin Michel + > * mikeWShef + > * Sturla Molden > * Eric Moore > * Peyton Murray + > * Andrew Nelson > * Clement Ng + > * Juan Nunez-Iglesias > * Renee Otten + > * Kellie Ottoboni + > * Ayappan P > * Sambit Panda + > * Tapasweni Pathak + > * Oleksandr Pavlyk > * Fabian Pedregosa > * Petar Mlinari? > * Matti Picus > * Marcel Plch + > * Christoph Pohl + > * Ilhan Polat > * Siddhesh Poyarekar + > * Ioannis Prapas + > * James Alan Preiss + > * Yisheng Qiu + > * Eric Quintero > * Bharat Raghunathan + > * Tyler Reddy > * Joscha Reimer > * Antonio Horta Ribeiro > * Lucas Roberts > * rtshort + > * Josua Sassen > * Kevin Sheppard > * Scott Sievert > * Leo Singer > * Kai Striega > * S?ren Fuglede J?rgensen > * tborisow + > * ?tienne Tremblay + > * tuxcell + > * Miguel de Val-Borro > * Andrew Valentine + > * Hugo van Kemenade > * Paul van Mulbregt > * Sebastiano Vigna > * Pauli Virtanen > * Dany Vohl + > * Ben Walsh + > * Huize Wang + > * Warren Weckesser > * Anreas Weh + > * Joseph Weston + > * Adrian Wijaya + > * Timothy Willard + > * Josh Wilson > * Kentaro Yamamoto + > * Dave Zbarsky + > > A total of 142 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 1.4.0 > -------------------------------- > > * `#1255 `__: maxiter broken > for Scipy.sparse.linalg gmres, in addition to... > * `#1301 `__: consolidate > multipack.h from interpolate and integrate packages... > * `#1739 `__: Single precision > FFT insufficiently accurate. (Trac #1212) > * `#1795 `__: stats > test_distributions.py: replace old fuzz tests (Trac #1269) > * `#2233 `__: fftpack segfault > with big arrays (Trac #1714) > * `#2434 `__: rmatmat and the > sophistication of linear operator objects > * `#2477 `__: > stats.truncnorm.rvs() does not give symmetric results for negative... > * `#2629 `__: FFTpack is > unacceptably slow on non power of 2 > * `#2883 `__: UnboundLocalError > in scipy.interpolate.splrep > * `#2956 `__: Feature Request: > axis argument for stats.entropy function > * `#3528 `__: Segfault on > test_djbfft (possibly MKL-related?) > * `#3793 `__: cwt should also > return complex array > * `#4464 `__: TST: > residue/residuez/invres/invresz don't have any tests > * `#4561 `__: BUG: tf filter > trailing and leading zeros in residuez > * `#4669 `__: Rewrite sosfilt > to make a single loop over the input? > * `#5040 `__: BUG: Empty data > handling of (c)KDTrees > * `#5112 `__: boxcox transform > edge cases could use more care > * `#5441 `__: scipy.stats.ncx2 > fails for nc=0 > * `#5502 `__: args keyword not > handled in optimize.curve_fit > * `#6484 `__: Qhull > segmentation fault > * `#6900 `__: > linear_sum_assignment with infinite weights > * `#6966 `__: Hypergeometric > Functions documentation is lacking > * `#6999 `__: possible false > positive corruption check in compressed loadmat() > * `#7018 `__: ydata that needs > broadcasting renders curve_fit unable to compute... > * `#7140 `__: trouble with > documentation for windows > * `#7327 `__: > interpolate.ndgriddata.griddata causes Python to crash rather... > * `#7396 `__: > MatrixLinearOperator implements _adjoint(), but not _transpose() > * `#7400 `__: BUG(?): special: > factorial and factorial2 return a 0-dimensional... > * `#7434 `__: Testing of > scipy.stats continuous distributions misses 25 distributions > * `#7491 `__: Several > scipy.stats distributions (fisk, burr, burr12, f) return... > * `#7759 `__: Overflow in > stats.kruskal for large samples > * `#7906 `__: Wrong result from > scipy.interpolate.UnivariateSpline.integral... > * `#8165 `__: ENH: match > functionality of R for hmean > * `#8417 `__: > optimimze.minimize(method='L-BFGS-B', options={'disp': True})... > * `#8535 `__: Strictly > increasing requirement in UnivariateSpline > * `#8815 `__: [BUG] GMRES: > number of iteration is only increased if callback... > * `#9207 `__: > scipy.linalg.solve_triangular speed after scipy.linalg.lu_factor > * `#9275 `__: new feature: > adding LOBPCG solver in svds in addition to ARPACK > * `#9403 `__: range of > truncnorm.logpdf could be extended > * `#9429 `__: gaussian_kde not > working with numpy matrix > * `#9515 `__: ndimage > implementation relies on undefined behavior > * `#9643 `__: arpack returns > singular values in ascending order > * `#9669 `__: DOC: > matthew-brett/build-openblas has been retired > * `#9852 `__: > scipy.spatial.ConvexHull exit with code 134, free(): invalid... > * `#9902 `__: > scipy.stats.truncnorm second moment may be wrong > * `#9943 `__: Custom sampling > methods in shgo do not work > * `#9947 `__: DOC: Incorrect > documentation for \`nan_policy='propagate\` in... > * `#9994 `__: BUG: sparse: > reshape method allows a shape containing an arbitrary... > * `#10036 `__: Official Nelder > mead tutorial uses xtol instead of xatol, which... > * `#10078 `__: possible to get > a better error message when objective function... > * `#10092 `__: overflow in > truncnorm.rvs > * `#10121 `__: A little > spelling mistake > * `#10126 `__: inaccurate std > implementation in binned_statistic > * `#10161 `__: Error in > documentation scipy.special.modstruve > * `#10195 `__: Derivative of > spline with 'const' extrapolation is also extrapolted... > * `#10206 `__: sparse matrices > indexing with scipy 1.3 > * `#10236 `__: Non-descriptive > error on type mismatch for functions of scipy.optimize... > * `#10258 `__: LOBPCG > convergence failure if guess provided > * `#10262 `__: distance matrix > lacks dtype checks / warnings > * `#10271 `__: BUG: optimize > failure on wheels > * `#10277 `__: > scipy.special.zeta(0) = NAN > * `#10292 `__: DOC/REL: Some > sections of the release notes are not nested correctly. > * `#10300 `__: > scipy.stats.rv_continuous.fit throws empty RuntimeError when... > * `#10319 `__: events in > scipy.integrate.solve_ivp: How do I setup an events... > * `#10323 `__: Adding more > low-level LAPACK wrappers > * `#10360 `__: firwin2 > inadvertently modifies input and may result in undefined... > * `#10388 `__: BLD: > TestHerd::test_hetrd core dumps with Python-dbg > * `#10395 `__: Remove warning > about output shape of zoom > * `#10403 `__: DOC: > scipy.signal.resample ignores t parameter > * `#10421 `__: Yeo-Johnson > power transformation fails with integer input data > * `#10422 `__: BUG: scipy.fft > does not support multiprocessing > * `#10427 `__: ENH: convolve > numbers should be updated > * `#10444 `__: BUG: > scipy.spatial.transform.Rotation.match_vectors returns improper... > * `#10488 `__: ENH: DCTs/DSTs > for scipy.fft > * `#10501 `__: BUG: > scipy.spatial.HalfspaceIntersection works incorrectly > * `#10514 `__: BUG: cKDTree > GIL handling is incorrect > * `#10535 `__: TST: master > branch CI failures > * `#10588 `__: scipy.fft and > numpy.fft inconsistency when axes=None and shape... > * `#10628 `__: Scipy > python>3.6 Windows wheels don't ship msvcp\*.dll > * `#10733 `__: DOC/BUG: > min_only result does not match documentation > * `#10774 `__: min_only=true > djisktra infinite loop with duplicate indices > * `#10775 `__: > UnboundLocalError in Radau when given a NaN > * `#10835 `__: io.wavfile.read > unnecessarily raises an error for a bad wav header > * `#10838 `__: Error in > documentation for scipy.linalg.lu_factor > * `#10875 `__: DOC: Graphical > guides (using TikZ) > * `#10880 `__: setting verbose >> 2 in minimize with trust-constr method leads... > * `#10887 `__: > scipy.signal.signaltools._fftconv_faster has incorrect estimates > * `#10948 `__: gammainc(0,x) = > nan but should be 1, gammaincc(0,x) = nan but... > * `#10952 `__: > TestQRdelete_F.test_delete_last_p_col test failure > * `#10968 `__: API: Change > normalized=False to normalize=True in Rotation > * `#10987 `__: Memory leak in > shgo triangulation > * `#10991 `__: Error running > openBlas probably missing a step > * `#11033 `__: deadlock on osx > for python 3.8 > * `#11041 `__: Test failure in > wheel builds for TestTf2zpk.test_simple > * `#11089 `__: Regression in > scipy.stats where distribution will not accept loc and scale parameters > * `#11100 `__: BUG: > multiscale_graphcorr random state seeding and parallel use > * `#11121 `__: Calls to > `scipy.interpolate.splprep` increase RAM usage. > * `#11125 `__: BUG: segfault > when slicing a CSR or CSC sparse matrix with slice start index > stop index > * `#11198 `__: BUG: sparse > eigs (arpack) shift-invert drops the smallest eigenvalue for some k > > Pull requests for 1.4.0 > ------------------------------- > > * `#4591 `__: BUG, TST: Several > issues with scipy.signal.residue > * `#6629 `__: ENH: sparse: > canonicalize on initialization > * `#7076 `__: ENH: add complex > wavelet support to scipy.signal.cwt. > * `#8681 `__: ENH add generalized > inverse Gaussian distribution to scipy.stats > * `#9064 `__: BUG/ENH: Added > default _transpose into LinearOperator. Fixes... > * `#9215 `__: ENH: Rbf > interpolation of large multi-dimensional data > * `#9311 `__: ENH: Added voigt in > scipy.special. > * `#9642 `__: ENH: integrate: > quad() for vector-valued functions > * `#9679 `__: DOC: expand > docstring of exponweib distribution > * `#9684 `__: TST: add ppc64le ci > testing > * `#9800 `__: WIP : ENH: > Refactored _hungarian.py for speed and added a minimize/maximize? > * `#9847 `__: DOC: Change > integrate tutorial to use solve_ivp instead of odeint > * `#9876 `__: ENH: Use rfft when > possible in resampling > * `#9998 `__: BUG: Do not remove > 1s when calling sparse: reshape method #9994 > * `#10002 `__: ENH: adds > constraints for differential evolution > * `#10098 `__: ENH: integrate: > add args argument to solve_ivp. > * `#10099 `__: DOC: Add missing > docs for linprog unknown_options > * `#10104 `__: BUG: Rewrite of > stats.truncnorm distribution. > * `#10105 `__: MAINT improve > efficiency of rvs_ratio_uniforms in scipy.stats > * `#10107 `__: TST: > dual_annealing set seed > * `#10108 `__: ENH: stats: > improve kendall_tau cache usage > * `#10110 `__: MAINT: _lib: Fix > a build warning. > * `#10114 `__: FIX: only print > bounds when supported by minimizer (shgo) > * `#10115 `__: TST: Add a test > with an almost singular design matrix for lsq_linear > * `#10118 `__: MAINT: fix rdist > methods in scipy.stats > * `#10119 `__: MAINT: improve > rvs of randint in scipy.stats > * `#10127 `__: Fix typo in > record array field name (spatial-ckdtree-sparse_distance? > * `#10130 `__: MAINT: ndimage: > Fix some compiler warnings. > * `#10131 `__: DOC: Note the > solve_ivp args enhancement in the 1.4.0 release... > * `#10133 `__: MAINT: add rvs > for semicircular in scipy.stats > * `#10138 `__: BUG: special: > Invalid arguments to ellip_harm can crash Python. > * `#10139 `__: MAINT: spatial: > Fix some compiler warnings in the file distance_wrap.c. > * `#10140 `__: ENH: add handling > of NaN in RuntimeWarning except clause > * `#10142 `__: DOC: return value > of scipy.special.comb > * `#10143 `__: MAINT: Loosen > linprog tol > * `#10152 `__: BUG: Fix custom > sampling input for shgo, add unittest > * `#10154 `__: MAINT: add > moments and improve doc of mielke in scipy.stats > * `#10158 `__: Issue #6999: read > zlib checksum before checking bytes read. > * `#10166 `__: BUG: Correctly > handle broadcasted ydata in curve_fit pcov computation. > * `#10167 `__: DOC: special: Add > missing factor of \`i\` to \`modstruve\` docstring > * `#10168 `__: MAINT: stats: Fix > an incorrect comment. > * `#10169 `__: ENH: optimize: > Clarify error when objective function returns... > * `#10172 `__: DEV: Run tests in > parallel when --parallel flag is passed to... > * `#10173 `__: ENH: Implement > DOP853 ODE integrator > * `#10176 `__: Fixed typo > * `#10182 `__: TST: fix test > issue for stats.pearsonr > * `#10184 `__: MAINT: stats: > Simplify zmap and zscore (we can use keepdims now). > * `#10191 `__: DOC: fix a > formatting issue in the scipy.spatial module docstring. > * `#10193 `__: DOC: Updated > docstring for optimize.nnls > * `#10198 `__: DOC, ENH: > special: Make \`hyp2f1\` references more specific > * `#10202 `__: DOC: Format DST > and DCT definitions as latex equations > * `#10207 `__: BUG: Compressed > matrix indexing should return a scalar > * `#10210 `__: DOC: Update docs > for connection='weak' in connected_components > * `#10225 `__: DOC: Clarify new > interfaces for legacy functions in 'optimize' > * `#10231 `__: DOC, MAINT: gpg2 > updates to release docs / pavement > * `#10235 `__: LICENSE: split > license file in standard BSD 3-clause and bundled. > * `#10238 `__: ENH: Add new > scipy.fft module using pocketfft > * `#10243 `__: BUG: fix ARFF > reader regression with quoted values. > * `#10248 `__: DOC: update > README file > * `#10255 `__: CI: bump OpenBLAS > to match wheels > * `#10264 `__: TST: add tests > for stats.tvar with unflattened arrays > * `#10280 `__: MAINT: stats: Use > a constant value for sqrt(2/PI). > * `#10286 `__: Development > Documentation Overhaul > * `#10290 `__: MAINT: Deprecate > NumPy functions in SciPy root > * `#10291 `__: FIX: Avoid > importing xdist when checking for availability > * `#10295 `__: Disable > deprecated Numpy API in __odrpack.c > * `#10296 `__: ENH: C++ > extension for linear assignment problem > * `#10298 `__: ENH: Made pade > function work with complex inputs > * `#10301 `__: DOC: Fix critical > value significance levels in stats.anderson_ksamp > * `#10307 `__: Minkowski > Distance Type Fix (issue #10262) > * `#10309 `__: BUG: Pass > jac=None directly to lsoda > * `#10310 `__: BUG: interpolate: > UnivariateSpline.derivative.ext is 'zeros'... > * `#10312 `__: FIX: Fixing a > typo in a comment > * `#10314 `__: scipy.spatial > enhancement request > * `#10315 `__: DOC: Update > integration tutorial to solve_ivp > * `#10318 `__: DOC: update the > example for PPoly.solve > * `#10333 `__: TST: add tests > for stats.tvar with unflattened arrays > * `#10334 `__: MAINT: special: > Remove deprecated \`hyp2f0\`, \`hyp1f2\`, and... > * `#10336 `__: BUG: > linalg/interpolative: fix interp_decomp modifying input > * `#10341 `__: BUG: > sparse.linalg/gmres: deprecate effect of callback on semantics... > * `#10344 `__: DOC: improve > wording of mathematical formulation > * `#10345 `__: ENH: Tiled QR > wrappers for scipy.linalg.lapack > * `#10350 `__: MAINT: linalg: > Use the new fft subpackage in linalg.dft test... > * `#10351 `__: BUG: Fix unstable > standard deviation calculation in histogram > * `#10353 `__: Bug: > interpolate.NearestNDInterpolator (issue #10352) > * `#10357 `__: DOC: linalg: > Refer to scipy.fft.fft (not fftpack) in the dft... > * `#10359 `__: DOC: Update > roadmap now scipy.fft has been merged > * `#10361 `__: ENH: Prefer > scipy.fft to scipy.fftpack in scipy.signal > * `#10371 `__: DOC: Tweaks to > fft documentation > * `#10372 `__: DOC: Fix typos > * `#10377 `__: TST, MAINT: > adjustments for pytest 5.0 > * `#10378 `__: ENH: _lib: allow > new np.random.Generator in check_random_state > * `#10379 `__: BUG: sparse: set > writeability to be forward-compatible with numpy>=1.17 > * `#10381 `__: BUG: Fixes > gh-7491, pdf at x=0 of fisk/burr/burr12/f distributions. > * `#10387 `__: ENH: > optimize/bfgs: don't evaluate twice at initial point for... > * `#10392 `__: [DOC] Add an > example for _binned_statistic_dd > * `#10396 `__: Remove warning > about output shape of zoom > * `#10397 `__: ENH: Add > check_finite to sp.linalg.norm > * `#10399 `__: ENH: Add > __round__ method to sparse matrix > * `#10407 `__: MAINT: drop > pybind11 from install_requires, it's only build-time... > * `#10408 `__: TST: use > pytest.raises, not numpy assert_raises > * `#10409 `__: CI: uninstall > nose on Travis > * `#10410 `__: [ENH] ncx2 > dispatch to chi2 when nc=0 > * `#10411 `__: TST: optimize: > test should use assert_allclose for fp comparisons > * `#10414 `__: DOC: add pybind11 > to the other part of quickstart guides > * `#10417 `__: DOC: special: > don't mark non-ufuncs with a \`[+]\` > * `#10423 `__: FIX: Use > pybind11::isinstace to check array dtypes > * `#10424 `__: DOC: add doctest > example for binary data for ttest_ind_from_stats > * `#10425 `__: ENH: Add missing > Hermitian transforms to scipy.fft > * `#10426 `__: MAINT: Fix doc > build bugs > * `#10431 `__: Update numpy > version for AIX > * `#10433 `__: MAINT: Minor > fixes for the stats > * `#10434 `__: BUG: special: > make \`ndtri\` return NaN outside domain of definition > * `#10435 `__: BUG: Allow > integer input data in scipy.stats.yeojohnson > * `#10438 `__: [DOC] Add example > for kurtosis > * `#10440 `__: ENH: special: > make \`ellipk\` a ufunc > * `#10443 `__: MAINT: ndimage: > malloc fail check > * `#10447 `__: BLD: Divert > output from test compiles into a temporary directory > * `#10451 `__: MAINT: signal: > malloc fail check > * `#10455 `__: BUG: special: fix > values of \`hyperu\` for negative \`x\` > * `#10456 `__: DOC: Added > comment clarifying the call for dcsrch.f in lbfgsb.f > * `#10457 `__: BUG: Allow > ckdtree to accept empty data input > * `#10459 `__: BUG:TST: Compute > lwork safely > * `#10460 `__: [DOC] Add example > to entropy > * `#10461 `__: DOC: Quickstart > Guide updates > * `#10462 `__: TST: special: > only show max atol/rtol for test points that failed > * `#10465 `__: BUG: Correctly > align fft inputs > * `#10467 `__: ENH: lower-memory > duplicate generator checking in spatial.SphericalVoronoi > * `#10470 `__: ENH: Normalise > the inverse DCT/DST in scipy.fft > * `#10472 `__: BENCH: adjust > timeout for slow setup_cache > * `#10475 `__: CI: include > python debug for Travis-ci > * `#10476 `__: TST: special: use > \`__tracebackhide__\` to get better error messages > * `#10477 `__: ENH: faster > region building in spatial.SphericalVoronoi > * `#10479 `__: BUG: stats: Fix a > few issues with the distributions' fit method. > * `#10480 `__: Add RuntimeError > in _distn_infrastructure.py in fit() method > * `#10481 `__: BENCH, MAINT: > wheel_cache_size has been renamed build_cache_size > * `#10494 `__: ENH: faster > circumcenter calculation in spatial.SphericalVoronoi > * `#10500 `__: Splrep > _curfit_cache global variable bugfix > * `#10503 `__: BUG: > spatial/qhull: get HalfspaceIntersection.dual_points from... > * `#10506 `__: DOC: interp2d, > note nearest neighbor extrapolation > * `#10507 `__: MAINT: Remove > fortran fftpack library in favour of pypocketfft > * `#10508 `__: TST: fix a bug in > the circular import test. > * `#10509 `__: MAINT: Set up > _build_utils as subpackage > * `#10516 `__: BUG: Use nogil > contexts in cKDTree > * `#10517 `__: ENH: fftconvolve > should not FFT broadcastable axes > * `#10518 `__: ENH: Speedup > fftconvolve > * `#10520 `__: DOC: Proper .rst > formatting for deprecated features and Backwards... > * `#10523 `__: DOC: Improve > scipy.signal.resample documentation > * `#10524 `__: ENH: Add MGC to > scipy.stats > * `#10525 `__: [ENH] ncx2.ppf > dispatch to chi2 when nc=0 > * `#10526 `__: DOC: clarify > laplacian normalization > * `#10528 `__: API: Rename > scipy.fft DCT/DST shape argument to s > * `#10531 `__: BUG: fixed > improper rotations in spatial.transform.rotation.match_vectors > * `#10533 `__: [DOC] Add example > for winsorize function > * `#10539 `__: MAINT: special: > don't register \`i0\` with \`numpy.dual\` > * `#10540 `__: MAINT: Fix Travis > and Circle > * `#10542 `__: MAINT: > interpolate: use cython_lapack > * `#10547 `__: Feature request. > Add furthest site Voronoi diagrams to scipy.spatial.plotutils. > * `#10549 `__: [BUG] Fix bug in > trimr when inclusive=False > * `#10552 `__: add > scipy.signal.upfirdn signal extension modes > * `#10555 `__: MAINT: special: > move \`c_misc\` into Cephes > * `#10556 `__: [DOC] Add example > for trima > * `#10562 `__: [DOC] Fix triple > string fo trimmed so that __doc__ can show... > * `#10563 `__: improve > least_squares error msg for mismatched shape > * `#10564 `__: ENH: linalg: > memoize get_lapack/blas_funcs to speed it up > * `#10566 `__: ENH: add > implementation of solver for the maximum flow problem > * `#10567 `__: BUG: spatial: use > c++11 construct for getting start of vector... > * `#10568 `__: DOC: special: > small tweaks to the \`zetac\` docstring > * `#10571 `__: [ENH] > Gaussian_kde can accept matrix dataset > * `#10574 `__: ENH: linalg: > speed up _compute_lwork by avoiding numpy constructs > * `#10582 `__: Fix typos with > typos in bundled libraries reverted > * `#10583 `__: ENH: special: add > the analytic continuation of Riemann zeta > * `#10584 `__: MAINT: special: > clean up \`special.__all__\` > * `#10586 `__: BUG: > multidimensional scipy.fft functions should accept 's' rather... > * `#10587 `__: BUG: > integrate/lsoda: never abort run, set error istate instead > * `#10594 `__: API: Replicate > numpy's fftn behaviour when s is given but not... > * `#10599 `__: DOC: dev: update > documentation vs. github pull request workflow... > * `#10603 `__: MAINT: installer > scripts removed > * `#10604 `__: MAINT: Change > c\*np.ones(...) to np.full(..., c, ...) in many... > * `#10608 `__: Univariate > splines should require x to be strictly increasing... > * `#10613 `__: ENH: Add seed > option for gaussian_kde.resample > * `#10614 `__: ENH: Add parallel > computation to scipy.fft > * `#10615 `__: MAINT: > interpolate: remove unused header file > * `#10616 `__: MAINT: Clean up > 32-bit platform xfail markers > * `#10618 `__: BENCH: Added > 'trust-constr' to minimize benchmarks > * `#10621 `__: [MRG] multiple > stability updates in lobpcg > * `#10622 `__: MAINT: forward > port 1.3.1 release notes > * `#10624 `__: DOC: stats: Fix > spelling of 'support'. > * `#10627 `__: DOC: stats: Add > references for the alpha distribution. > * `#10629 `__: MAINT: special: > avoid overflow longer in \`zeta\` for negative... > * `#10630 `__: TST: GH10271, > relax test assertion, fixes #10271 > * `#10631 `__: DOC: nelder-mean > uses xatol fixes #10036 > * `#10633 `__: BUG: interpolate: > integral(a, b) should be zero when both limits... > * `#10635 `__: DOC: special: > complete hypergeometric functions documentation > * `#10636 `__: BUG: special: use > series for \`hyp1f1\` when it converges rapidly > * `#10641 `__: ENH: allow > matching of general bipartite graphs > * `#10643 `__: ENH: > scipy.sparse.linalg.spsolve triangular unit diagonal > * `#10650 `__: ENH: Cythonize > sosfilt > * `#10654 `__: DOC: Vertical > alignment of table entries > * `#10655 `__: ENH: Dockerfile > for scipy development > * `#10660 `__: TST: clean up > tests for rvs in scipy.stats > * `#10664 `__: Throw error on > non-finite input for binned_statistic_dd() > * `#10665 `__: DOC: special: > improve the docstrings for \`gamma\` and \`gammasgn\` > * `#10669 `__: TST: Update > scipy.fft real transform tests > * `#10670 `__: DOC: Clarify docs > and error messages for scipy.signal.butter > * `#10672 `__: ENH: return > solution attribute when using events in solve_ivp > * `#10675 `__: MAINT: special: > add an explicit NaN check for \`iv\` arguments > * `#10679 `__: DOC: special: Add > documentation for \`beta\` function > * `#10681 `__: TST: > sparse.linalg: fix arnoldi test seed > * `#10682 `__: DOC: special: Add > documentation for \`betainc\` function > * `#10684 `__: TST: special: > require Mpmath 1.1.0 for \`test_hyperu_around_0\` > * `#10686 `__: FIX: sphinx > isattributedescriptor is not available in sphinx... > * `#10687 `__: DOC: added Docker > quickstart guide by @andyfaff > * `#10689 `__: DOC: special: > clarify format of parameters/returns sections for... > * `#10690 `__: DOC: special: > improve docstrings of incomplete gamma functions > * `#10692 `__: ENH: > higher-dimensional input in \`spatial.SphericalVoronoi\` > * `#10694 `__: ENH: > ScalarFunction.fun_and_grad > * `#10698 `__: DOC: special: Add > documentation for \`betaincinv\` > * `#10699 `__: MAINT: remove > time print lbfgsb fixes #8417 > * `#10701 `__: TST, MAINT: bump > OpenBLAS to 0.3.7 stable > * `#10702 `__: DOC: clarify > iterations consume multiple function calls > * `#10703 `__: DOC: iprint doc > lbfgsb closes #5482 > * `#10708 `__: TST: test > suggested in gh1758 > * `#10710 `__: ENH: Added > nan_policy to circ functions in \`stats\` > * `#10712 `__: ENH: add axis > parameter to stats.entropy > * `#10714 `__: DOC: Formatting > fix rv_continuous.expect docs > * `#10715 `__: DOC: BLD: update > doc Makefile for python version; add scipy version... > * `#10717 `__: MAINT: modernize > doc/Makefile > * `#10719 `__: Enable setting > minres initial vector > * `#10720 `__: DOC: silence > random warning in doc build for \`stats.binned_statistic_dd\` > * `#10724 `__: DEV: Add doc > option to runtests.py > * `#10728 `__: MAINT: get rid of > gramA, gramB text files that lobpcg tests leave... > * `#10732 `__: DOC: add min_only > to docstring for Dijkstra's algorithm > * `#10734 `__: DOC: spell out > difference between source and target in shortest... > * `#10735 `__: Fix for Python 4 > * `#10739 `__: BUG: > optimize/slsqp: deal with singular BFGS update > * `#10741 `__: ENH: LAPACK > wrappers for ?geequ, ?geequb, ?syequb, ?heequb > * `#10742 `__: DOC: special: add > to the docstring of \`gammaln\` > * `#10743 `__: ENH: special: add > a real dispatch for \`wrightomega\` > * `#10746 `__: MAINT: Fix typos > in comments, docs and test name > * `#10747 `__: Remove spurious > quotes > * `#10750 `__: MAINT: make > cython code more precise > * `#10751 `__: MAINT: Check that > scipy.linalg.lapack functions are documented > * `#10752 `__: MAINT: special: > use \`sf_error\` in Cephes > * `#10755 `__: DOC: cluster: Add > 'See Also' and 'Examples' for kmeans2. > * `#10763 `__: MAINT: list of > minimize methods > * `#10768 `__: BUG: Fix corner > case for sos2zpk > * `#10773 `__: Fix error type > for complex input to scipy.fftpack.rfft and irfft > * `#10776 `__: ENH: handle > geodesic input in \`spatial.SphericalVoronoi\` > * `#10777 `__: MAINT: > minimizer-->custom should handle the kinds of bounds/constrain?... > * `#10781 `__: ENH: > solve_triangular C order improvement > * `#10787 `__: Fix behavior of > \`exp1\` on branch cut and add docstring > * `#10789 `__: DOC: special: add > parameters/returns doc sections for erfc/erfcx/erfi > * `#10790 `__: Travis CI: sudo > is deprecated and Xenial is default distro > * `#10792 `__: DOC: special: add > full docstring for \`expi\` > * `#10799 `__: DOC: special: add > a complete docstring for \`expn\` > * `#10800 `__: Docs edits (GSoD) > * `#10802 `__: BUG: fix > UnboundLocalError in Radau (scipy#10775) > * `#10804 `__: ENH: Speed up > next_fast_len with LRU cache > * `#10805 `__: DOC: Fix > unbalanced quotes in signal.place_poles > * `#10809 `__: ENH: Speed up > next_fast_len > * `#10810 `__: ENH: Raise > catchable exceptions for bad Fortran files > * `#10811 `__: MAINT: optimize: > Remove extra variable from _remove_redundancy_dense > * `#10813 `__: MAINT: special: > Remove unused variables from _kolmogi and _smirnovi > * `#10815 `__: DOC, API: > scipy.stats.reciprocal is "log-uniform" > * `#10816 `__: MAINT: special: > remove deprecated \`bessel_diff_formula\` > * `#10817 `__: DOC: special: > complete the docstring for \`fresnel\` > * `#10820 `__: Fixed > compiler_helper.py to allow compilation with ICC on Linux > * `#10823 `__: DOC: updated > reference guide text for consistency in writing... > * `#10825 `__: MAINT: special: > change some features of the Voigt function > * `#10828 `__: MAINT: integrate: > Remove unused variable from init_callback > * `#10830 `__: Adding LOBPCG > solver in svds in addition to ARPACK > * `#10837 `__: WIP: ENH: > reduction function for \`spatial.tranform.Rotation\`... > * `#10843 `__: ENH: Adding > optional parameter to stats.zscores to allow for... > * `#10845 `__: Rebase kruskal > fix > * `#10847 `__: remove redundant > __getitem__ from scipy.sparse.lil > * `#10848 `__: Better handling > of empty (not missing) docstrings > * `#10849 `__: ENH: implement > rmatmat for LinearOperator > * `#10850 `__: MAINT : > Refactoring lil List of Lists > * `#10851 `__: DOC: add a > generative art example to the scipy.spatial tutorial. > * `#10852 `__: DOC: linalg: > fixed gh-10838 unused imports in example deleted > * `#10854 `__: DOC: special: add > a full docstring for \`pdtr\` > * `#10861 `__: ENH: option to > reuse binnumbers in stats.binned_statistic_dd > * `#10863 `__: DOC: partial > standardization and validation of scipy.stats reference... > * `#10865 `__: BUG: special: fix > incomplete gamma functions for infinite \`a\` > * `#10866 `__: ENH: calculation > of mean in spatial.transform.Rotation > * `#10867 `__: MAINT: Also store > latex directory > * `#10869 `__: ENH: Implement > overlap-add convolution > * `#10870 `__: ENH: Do not raise > EOF error if wavfile data read > * `#10876 `__: ENH: Add > beta-binomial distribution to scipy.stats > * `#10878 `__: MAINT: Update R > project URL > * `#10883 `__: MAINT: (ndimage) > More robust check for output being a numpy dtype > * `#10884 `__: DOC: Added > instructions on adding a new distribution to scipy.stats. > * `#10885 `__: [BUG] fix lobpcg > with maxiter=None results in Exception > * `#10899 `__: ENH: Match R > functionality for hmean > * `#10900 `__: MAINT: stats: Use > keepdims to simplify a few lines in power_divergence. > * `#10901 `__: ENH: > sparse/linalg: support pydata/sparse matrices > * `#10907 `__: Check whether > \`maxiter\` is integer > * `#10912 `__: ENH: warn user > that quad() ignores \`points=...\` when \`weight=...\`... > * `#10918 `__: CI: fix Travis CI > py3.8 build > * `#10920 `__: MAINT: Update > constants to codata 2018 values (second try) > * `#10921 `__: ENH: > scipy.sparse.lil: tocsr accelerated > * `#10924 `__: BUG: Forbid > passing 'args' as kwarg in scipy.optimize.curve_fit > * `#10928 `__: DOC: Add examples > to io.wavfile docstrings > * `#10934 `__: typo fix > * `#10935 `__: BUG: Avoid > undefined behaviour on float to unsigned conversion > * `#10936 `__: DOC: Added > missing example to stats.mstats.variation > * `#10939 `__: ENH: > scipy.sparse.lil: tocsr accelerated depending on density > * `#10946 `__: BUG: setting > verbose > 2 in minimize with trust-constr method... > * `#10947 `__: DOC: special: > small improvements to the \`poch\` docstring > * `#10949 `__: BUG: fix return > type of erlang_gen._argcheck > * `#10951 `__: DOC: fixed Ricker > wavelet formula > * `#10954 `__: BUG: special: fix > \`factorial\` return type for 0-d inputs > * `#10955 `__: MAINT: Relax the > assert_unitary atol value > * `#10956 `__: WIP: make > pdtr(int, double) be pdtr(double, double) > * `#10957 `__: BUG: Ensure full > binary compatibility of long double test data > * `#10964 `__: ENH: Make Slerp > callable with a scalar argument > * `#10972 `__: BUG: Handle > complex gains in zpk2sos > * `#10975 `__: TST: skip > test_kendalltau ppc64le > * `#10978 `__: BUG: boxcox data > dimension and constancy check #5112 > * `#10979 `__: API: Rename dcm > to (rotation) matrix in Rotation class > * `#10981 `__: MAINT: add > support for a==0 and x>0 edge case to igam and igamc > * `#10986 `__: MAINT: Remove > direct imports from numpy in signaltools.py > * `#10988 `__: BUG: signal: > fixed issue #10360 > * `#10989 `__: FIX > binned_statistic_dd Mac wheel test fails > * `#10990 `__: BUG: Fix memory > leak in shgo triangulation > * `#10992 `__: TST: Relax > tolerance in upfirdn test_modes > * `#10993 `__: TST: bump > tolerance in optimize tests > * `#10997 `__: MAINT: Rework > residue and residuez > * `#11001 `__: DOC: Updated > Windows build tutorial > * `#11004 `__: BUG: > integrate/quad_vec: fix several bugs in quad_vec > * `#11005 `__: TST: add Python > 3.8 Win CI > * `#11006 `__: DOC: special: add > a reference for \`kl_div\` > * `#11012 `__: MAINT: Rework > invres and invresz > * `#11015 `__: DOC: special: add > references for \`rel_entr\` > * `#11017 `__: DOC: numpydoc > validation of morestats.py > * `#11018 `__: MAINT: Filter > unrelated warning > * `#11031 `__: MAINT: update > choose_conv_method for pocketfft implementation > * `#11034 `__: MAINT: TST: Skip > tests with multiprocessing that use "spawn"... > * `#11036 `__: DOC: update > doc/README with some more useful content. > * `#11037 `__: DOC: special: add > a complete docstring for \`rgamma\` > * `#11038 `__: DOC: special: add > a reference for the polygamma function > * `#11042 `__: TST: fix tf2zpk > test failure due to incorrect complex sorting. > * `#11044 `__: MAINT: > choose_conv_method can choose fftconvolution for longcomplex > * `#11046 `__: TST: Reduce > tolerance for ppc64le with reference lapack > * `#11048 `__: DOC: special: add > reference for orthogonal polynomial functions > * `#11049 `__: MAINT: proper > random number initialization and readability fix > * `#11051 `__: MAINT: pep8 > cleanup > * `#11054 `__: TST: bump test > precision for dual_annealing SLSQP test > * `#11055 `__: DOC: special: add > a reference for \`zeta\` > * `#11056 `__: API: Deprecated > normalized keyword in Rotation > * `#11065 `__: DOC: Ubuntu > Development Environment Quickstart should not modify... > * `#11066 `__: BUG: skip > deprecation for numpy top-level types > * `#11067 `__: DOC: updated > documentation for consistency in writing style > * `#11070 `__: DOC: Amendment to > Ubuntu Development Environment Quickstart should... > * `#11073 `__: DOC: fix 1.4.0 > release notes > * `#11081 `__: API: Replace > Rotation.match_vectors with align_vectors > * `#11083 `__: DOC: more 1.4.0 > release note fixes > * `#11092 `__: BUG: stats: fix > freezing of some distributions > * `#11096 `__: BUG: > scipy.sparse.csgraph: fixed issue #10774 > * `#11124 `__: fix Cython > warnings related to _stats.pyx > * `#11126 `__: BUG: > interpolate/fitpack: fix memory leak in splprep > * `#11127 `__: Avoid potential > segfault in CSR and CSC matrix indexing > * `#11152 `__: BUG: Fix random > state bug multiscale_graphcorr > * `#11166 `__: BUG: empty sparse > slice shapes > * `#11167 `__: BUG: redundant > fft in signal.resample > * `#11181 `__: TST: Fix > tolerance of tests for aarch64 > * `#11182 `__: TST: Bump up > tolerance for test_maxiter_worsening > * `#11199 `__: BUG: > sparse.linalg: mistake in unsymm. real shift-invert ARPACK eigenvalue > selection > > Checksums > ========= > > MD5 > ~~~ > > aa98f881f11681a35e18eadbf2c403fd > scipy-1.4.0-cp35-cp35m-macosx_10_6_intel.whl > d99b88d888f8a78a67896b2f895c3aba > scipy-1.4.0-cp35-cp35m-manylinux1_i686.whl > 13d1ab63e2ca8d2c2ac9f0b01f37b374 > scipy-1.4.0-cp35-cp35m-manylinux1_x86_64.whl > b9908d9dddf3fa5bd9b2458ea42c2813 scipy-1.4.0-cp35-cp35m-win32.whl > e6a6bb14d377ef8b893a710b9fcd05a8 scipy-1.4.0-cp35-cp35m-win_amd64.whl > 203b3f7e9bee44d3ccb3d3e0ffd62a81 > scipy-1.4.0-cp36-cp36m-macosx_10_6_intel.whl > 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scipy-1.4.0-cp38-cp38-macosx_10_9_x86_64.whl > bbb21e998e136e1fdfd77e808abf16c72e75c6ffbb87f4b5a41f19c9a4b3e2de > scipy-1.4.0-cp38-cp38-manylinux1_i686.whl > fa39935d7db5066a1b88575fdb196bb576474a17987637430df6bede311906be > scipy-1.4.0-cp38-cp38-manylinux1_x86_64.whl > 461ca398ac6cb46bc89bdbc9f6a81c0302ee370cebe8be682c84a51977e21ded > scipy-1.4.0-cp38-cp38-win32.whl > e588454fd6899d93b73d648d4d90d3d1285c91d08530a6ab94826676c862cabc > scipy-1.4.0-cp38-cp38-win_amd64.whl > 31f7cfa93b01507c935c12b535e24812594002a02a56803d7cd063e9920d25e8 > scipy-1.4.0.tar.gz > 6d174683254ed39d4659f63ce512b843bc45479ce06a05dc089a48c17f1d68e7 > scipy-1.4.0.tar.xz > 704af03ecd4e2191daa12106449c5921f155d210812cce0d9c5f47194f312cda > scipy-1.4.0.zip > -----BEGIN PGP SIGNATURE----- > > iQGzBAEBCAAdFiEEuinQzfUTSK0iykiguEZ+VI8xggYFAl34CSgACgkQuEZ+VI8x > ggY+FQv/TiG+T2eNdpy7t9gwe5aH+sGT5Fi0sli73C3I76fU/WCAx8N9MGnufIMK > hM1gF6feVWDiZRmEjXXHiVQM3ae4TAhq7V0ucxBQ+nonQf98EEWg0M1AHwEKx7HK > mRUT+50hCzqqRnv9axHHUxs93SPjv+xWkGvhZX9UfhrjPUCbglOd1yM60GZZkvxZ > Gj0thpz/eob8w8BM/NNo0TUyCG2e3nREobUdaGxPTaWJR53mYM4caC9dk7+ZvvCl > MsPEtFVuPpWUawSbqILQHo/Nqv8NYvIP0/90y6w9A+7oRCgh1U+BeI4JEQYpQAxT > EDUTw0bG3aG9SRqqZWPj86gMmvioFpxyLh2+zv5pN34ivaFR3hcsxrUsku/1B8u5 > VkUaZwf7QXM+LhrbpxlhFLxad8wXEZjdYeD/l4TXGKSadMER5tRSSL/kUgEgC+KC > CpP+Jy1BIU2ypahyTr5siQrLP/kzYvKjeZsGS/RlGRoiZ6qUGA4I0/HFpUoQIZfE > Bfzgh2Kx > =QU1D > -----END PGP SIGNATURE----- > From ralf.gommers at gmail.com Tue Dec 17 01:40:30 2019 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Mon, 16 Dec 2019 22:40:30 -0800 Subject: [Numpy-discussion] [SciPy-Dev] ANN: SciPy 1.4.0 In-Reply-To: References: Message-ID: On Mon, Dec 16, 2019 at 5:13 PM Warren Weckesser wrote: > On 12/16/19, Tyler Reddy wrote: > > -----BEGIN PGP SIGNED MESSAGE----- > > Hash: SHA256 > > > > Hi all, > > > > On behalf of the SciPy development team I'm pleased to announce > > the release of SciPy 1.4.0. > > > Fantastic, thanks Tyler! > > +1 thanks for taking care of this release Tyler! Ralf > Warren > > > > > > Sources and binary wheels can be found at: > > https://pypi.org/project/scipy/ > > and at: > > https://github.com/scipy/scipy/releases/tag/v1.4.0 > > > > One of a few ways to install this release with pip: > > > > pip install scipy==1.4.0 > > > > ========================== > > SciPy 1.4.0 Release Notes > > ========================== > > > > SciPy 1.4.0 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 > > 1.4.x branch, and on adding new features on the master branch. > > > > This release requires Python 3.5+ and NumPy >=1.13.3 (for Python 3.5, > 3.6), > >>=1.14.5 (for Python 3.7), >= 1.17.3 (for Python 3.8) > > > > For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. > > > > Highlights of this release > > ---------------------------------- > > > > - a new submodule, `scipy.fft`, now supersedes `scipy.fftpack`; this > > means support for ``long double`` transforms, faster multi-dimensional > > transforms, improved algorithm time complexity, release of the global > > intepreter lock, and control over threading behavior > > - support for ``pydata/sparse`` arrays in `scipy.sparse.linalg` > > - substantial improvement to the documentation and functionality of > > several `scipy.special` functions, and some new additions > > - the generalized inverse Gaussian distribution has been added to > > `scipy.stats` > > - an implementation of the Edmonds-Karp algorithm in > > `scipy.sparse.csgraph.maximum_flow` > > - `scipy.spatial.SphericalVoronoi` now supports n-dimensional input, > > has linear memory complexity, improved performance, and > > supports single-hemisphere generators > > > > > > New features > > ============ > > > > Infrastructure > > -------------------- > > Documentation can now be built with ``runtests.py --doc`` > > > > A ``Dockerfile`` is now available in the ``scipy/scipy-dev`` repository > to > > facilitate getting started with SciPy development. > > > > `scipy.constants` improvements > > --------------------------------------------- > > `scipy.constants` has been updated with the CODATA 2018 constants. > > > > > > `scipy.fft` added > > ------------------------ > > `scipy.fft` is a new submodule that supersedes the `scipy.fftpack` > > submodule. > > For the most part, this is a drop-in replacement for ``numpy.fft`` and > > `scipy.fftpack` alike. With some important differences, `scipy.fft`: > > - uses NumPy's conventions for real transforms (``rfft``). This means the > > return value is a complex array, half the size of the full ``fft`` > output. > > This is different from the output of ``fftpack`` which returned a real > > array > > representing complex components packed together. > > - the inverse real to real transforms (``idct`` and ``idst``) are > > normalized > > for ``norm=None`` in thesame way as ``ifft``. This means the identity > > ``idct(dct(x)) == x`` is now ``True`` for all norm modes. > > - does not include the convolutions or pseudo-differential operators > > from ``fftpack``. > > > > This submodule is based on the ``pypocketfft`` library, developed by the > > author of ``pocketfft`` which was recently adopted by NumPy as well. > > ``pypocketfft`` offers a number of advantages over fortran ``FFTPACK``: > > - support for long double (``np.longfloat``) precision transforms. > > - faster multi-dimensional transforms using vectorisation > > - Bluestein?s algorithm removes the worst-case ``O(n^2)`` complexity of > > ``FFTPACK`` > > - the global interpreter lock (``GIL``) is released during transforms > > - optional multithreading of multi-dimensional transforms via the > > ``workers`` > > argument > > > > Note that `scipy.fftpack` has not been deprecated and will continue to be > > maintained but is now considered legacy. New code is recommended to use > > `scipy.fft` instead, where possible. > > > > `scipy.fftpack` improvements > > ---------------------------------------- > > `scipy.fftpack` now uses pypocketfft to perform its FFTs, offering the > same > > speed and accuracy benefits listed for scipy.fft above but without the > > improved API. > > > > `scipy.integrate` improvements > > ------------------------------------------- > > > > The function `scipy.integrate.solve_ivp` now has an ``args`` argument. > > This allows the user-defined functions passed to the function to have > > additional parameters without having to create wrapper functions or > > lambda expressions for them. > > > > `scipy.integrate.solve_ivp` can now return a ``y_events`` attribute > > representing the solution of the ODE at event times > > > > New ``OdeSolver`` is implemented --- ``DOP853``. This is a high-order > > explicit > > Runge-Kutta method originally implemented in Fortran. Now we provide a > pure > > Python implementation usable through ``solve_ivp`` with all its features. > > > > `scipy.integrate.quad` provides better user feedback when break points > are > > specified with a weighted integrand. > > > > `scipy.integrate.quad_vec` is now available for general purpose > integration > > of vector-valued functions > > > > > > `scipy.interpolate` improvements > > --------------------------------------------- > > `scipy.interpolate.pade` now handles complex input data gracefully > > > > `scipy.interpolate.Rbf` can now interpolate multi-dimensional functions > > > > `scipy.io` improvements > > --------------------------------- > > > > `scipy.io.wavfile.read` can now read data from a `WAV` file that has a > > malformed header, similar to other modern `WAV` file parsers > > > > `scipy.io.FortranFile` now has an expanded set of available ``Exception`` > > classes for handling poorly-formatted files > > > > > > `scipy.linalg` improvements > > ------------------------------------- > > The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct > > results for complex-valued matrices. Before this, the function only > > returned > > correct values for real-valued matrices. > > > > New boolean keyword argument ``check_finite`` for `scipy.linalg.norm`; > > whether > > to check that the input matrix contains only finite numbers. Disabling > may > > give a performance gain, but may result in problems (crashes, > > non-termination) > > if the inputs do contain infinities or NaNs. > > > > `scipy.linalg.solve_triangular` has improved performance for a C-ordered > > triangular matrix > > > > ``LAPACK`` wrappers have been added for ``?geequ``, ``?geequb``, > > ``?syequb``, > > and ``?heequb`` > > > > Some performance improvements may be observed due to an internal > > optimization > > in operations involving LAPACK routines via ``_compute_lwork``. This is > > particularly true for operations on small arrays. > > > > Block ``QR`` wrappers are now available in `scipy.linalg.lapack` > > > > > > `scipy.ndimage` improvements > > ------------------------------------------ > > > > > > `scipy.optimize` improvements > > ------------------------------------------ > > It is now possible to use linear and non-linear constraints with > > `scipy.optimize.differential_evolution`. > > > > `scipy.optimize.linear_sum_assignment` has been re-written in C++ to > > improve > > performance, and now allows input costs to be infinite. > > > > A ``ScalarFunction.fun_and_grad`` method was added for convenient > > simultaneous > > retrieval of a function and gradient evaluation > > > > `scipy.optimize.minimize` ``BFGS`` method has improved performance by > > avoiding > > duplicate evaluations in some cases > > > > Better user feedback is provided when an objective function returns an > > array > > instead of a scalar. > > > > > > `scipy.signal` improvements > > -------------------------------------- > > > > Added a new function to calculate convolution using the overlap-add > method, > > named `scipy.signal.oaconvolve`. Like `scipy.signal.fftconvolve`, this > > function supports specifying dimensions along which to do the > convolution. > > > > `scipy.signal.cwt` now supports complex wavelets. > > > > The implementation of ``choose_conv_method`` has been updated to reflect > > the > > new FFT implementation. In addition, the performance has been > significantly > > improved (with rather drastic improvements in edge cases). > > > > The function ``upfirdn`` now has a ``mode`` keyword argument that can be > > used > > to select the signal extension mode used at the signal boundaries. These > > modes > > are also available for use in ``resample_poly`` via a newly added > > ``padtype`` > > argument. > > > > `scipy.signal.sosfilt` now benefits from Cython code for improved > > performance > > > > `scipy.signal.resample` should be more efficient by leveraging ``rfft`` > > when > > possible > > > > `scipy.sparse` improvements > > --------------------------------------- > > It is now possible to use the LOBPCG method in > `scipy.sparse.linalg.svds`. > > > > `scipy.sparse.linalg.LinearOperator` now supports the operation > ``rmatmat`` > > for adjoint matrix-matrix multiplication, in addition to ``rmatvec``. > > > > Multiple stability updates enable float32 support in the LOBPCG > eigenvalue > > solver for symmetric and Hermitian eigenvalues problems in > > ``scipy.sparse.linalg.lobpcg``. > > > > A solver for the maximum flow problem has been added as > > `scipy.sparse.csgraph.maximum_flow`. > > > > `scipy.sparse.csgraph.maximum_bipartite_matching` now allows non-square > > inputs, > > no longer requires a perfect matching to exist, and has improved > > performance. > > > > `scipy.sparse.lil_matrix` conversions now perform better in some > scenarios > > > > Basic support is available for ``pydata/sparse`` arrays in > > `scipy.sparse.linalg` > > > > `scipy.sparse.linalg.spsolve_triangular` now supports the > ``unit_diagonal`` > > argument to improve call signature similarity with its dense counterpart, > > `scipy.linalg.solve_triangular` > > > > ``assertAlmostEqual`` may now be used with sparse matrices, which have > > added > > support for ``__round__`` > > > > `scipy.spatial` improvements > > --------------------------------------- > > The bundled Qhull library was upgraded to version 2019.1, fixing several > > issues. Scipy-specific patches are no longer applied to it. > > > > `scipy.spatial.SphericalVoronoi` now has linear memory complexity, > improved > > performance, and supports single-hemisphere generators. Support has also > > been > > added for handling generators that lie on a great circle arc (geodesic > > input) > > and for generators in n-dimensions. > > > > `scipy.spatial.transform.Rotation` now includes functions for calculation > > of a > > mean rotation, generation of the 3D rotation groups, and reduction of > > rotations > > with rotational symmetries. > > > > `scipy.spatial.transform.Slerp` is now callable with a scalar argument > > > > `scipy.spatial.voronoi_plot_2d` now supports furthest site Voronoi > diagrams > > > > `scipy.spatial.Delaunay` and `scipy.spatial.Voronoi` now have attributes > > for tracking whether they are furthest site diagrams > > > > `scipy.special` improvements > > ----------------------------------------- > > The Voigt profile has been added as `scipy.special.voigt_profile`. > > > > A real dispatch has been added for the Wright Omega function > > (`scipy.special.wrightomega`). > > > > The analytic continuation of the Riemann zeta function has been added. > (The > > Riemann zeta function is the one-argument variant of > `scipy.special.zeta`.) > > > > The complete elliptic integral of the first kind (`scipy.special.ellipk`) > > is > > now available in `scipy.special.cython_special`. > > > > The accuracy of `scipy.special.hyp1f1` for real arguments has been > > improved. > > > > The documentation of many functions has been improved. > > > > `scipy.stats` improvements > > ------------------------------------- > > `scipy.stats.multiscale_graphcorr` added as an independence test that > > operates on high dimensional and nonlinear data sets. It has higher > > statistical > > power than other `scipy.stats` tests while being the only one that > operates > > on > > multivariate data. > > > > The generalized inverse Gaussian distribution (`scipy.stats.geninvgauss`) > > has > > been added. > > > > It is now possible to efficiently reuse `scipy.stats.binned_statistic_dd` > > with new values by providing the result of a previous call to the > function. > > > > `scipy.stats.hmean` now handles input with zeros more gracefully. > > > > The beta-binomial distribution is now available in > `scipy.stats.betabinom`. > > > > `scipy.stats.zscore`, `scipy.stats.circmean`, `scipy.stats.circstd`, and > > `scipy.stats.circvar` now support the ``nan_policy`` argument for > enhanced > > handling of ``NaN`` values > > > > `scipy.stats.entropy` now accepts an ``axis`` argument > > > > `scipy.stats.gaussian_kde.resample` now accepts a ``seed`` argument to > > empower > > reproducibility > > > > `scipy.stats.kendalltau` performance has improved, especially for large > > inputs, > > due to improved cache usage > > > > `scipy.stats.truncnorm` distribution has been rewritten to support much > > wider > > tails > > > > > > Deprecated features > > =================== > > > > `scipy` deprecations > > ----------------------------- > > Support for NumPy functions exposed via the root SciPy namespace is > > deprecated > > and will be removed in 2.0.0. For example, if you use ``scipy.rand`` or > > ``scipy.diag``, you should change your code to directly use > > ``numpy.random.default_rng`` or ``numpy.diag``, respectively. > > They remain available in the currently continuing Scipy 1.x release > series. > > > > The exception to this rule is using ``scipy.fft`` as a function -- > > :mod:`scipy.fft` is now meant to be used only as a module, so the ability > > to > > call ``scipy.fft(...)`` will be removed in SciPy 1.5.0. > > > > In `scipy.spatial.Rotation` methods ``from_dcm``, ``as_dcm`` were renamed > > to > > ``from_matrix``, ``as_matrix`` respectively. The old names will be > removed > > in > > SciPy 1.6.0. > > > > Method ``Rotation.match_vectors`` was deprecated in favor of > > ``Rotation.align_vectors``, which provides a more logical and > > general API to the same functionality. The old method > > will be removed in SciPy 1.6.0. > > > > Backwards incompatible changes > > ========================== > > > > `scipy.special` changes > > --------------------------------- > > The deprecated functions ``hyp2f0``, ``hyp1f2``, and ``hyp3f0`` have been > > removed. > > > > The deprecated function ``bessel_diff_formula`` has been removed. > > > > The function ``i0`` is no longer registered with ``numpy.dual``, so that > > ``numpy.dual.i0`` will unconditionally refer to the NumPy version > > regardless > > of whether `scipy.special` is imported. > > > > The function ``expn`` has been changed to return ``nan`` outside of its > > domain of definition (``x, n < 0``) instead of ``inf``. > > > > `scipy.sparse` changes > > -------------------------------- > > Sparse matrix reshape now raises an error if shape is not > two-dimensional, > > rather than guessing what was meant. The behavior is now the same as > before > > SciPy 1.1.0. > > > > ``CSR`` and ``CSC`` sparse matrix classes should now return empty > matrices > > of the same type when indexed out of bounds. Previously, for some > versions > > of SciPy, this would raise an ``IndexError``. The change is largely > > motivated > > by greater consistency with ``ndarray`` and ``numpy.matrix`` semantics. > > > > `scipy.signal` changes > > ------------------------------- > > `scipy.signal.resample` behavior for length-1 signal inputs has been > > fixed to output a constant (DC) value rather than an impulse, consistent > > with > > the assumption of signal periodicity in the FFT method. > > > > `scipy.signal.cwt` now performs complex conjugation and time-reversal of > > wavelet data, which is a backwards-incompatible bugfix for > > time-asymmetric wavelets. > > > > `scipy.stats` changes > > ------------------------------ > > `scipy.stats.loguniform` added with better documentation as (an alias for > > ``scipy.stats.reciprocal``). ``loguniform`` generates random variables > > that are equally likely in the log space; e.g., ``1``, ``10`` and ``100`` > > are all equally likely if ``loguniform(10 ** 0, 10 ** 2).rvs()`` is used. > > > > > > Other changes > > ============= > > The ``LSODA`` method of `scipy.integrate.solve_ivp` now correctly detects > > stiff > > problems. > > > > `scipy.spatial.cKDTree` now accepts and correctly handles empty input > data > > > > `scipy.stats.binned_statistic_dd` now calculates the standard deviation > > statistic in a numerically stable way. > > > > `scipy.stats.binned_statistic_dd` now throws an error if the input data > > contains either ``np.nan`` or ``np.inf``. Similarly, in `scipy.stats` now > > all > > continuous distributions' ``.fit()`` methods throw an error if the input > > data > > contain any instance of either ``np.nan`` or ``np.inf``. > > > > > > Authors > > ======= > > > > * @endolith > > * @wenhui-prudencemed + > > * Abhinav + > > * Anne Archibald > > * ashwinpathak20nov1996 + > > * Danilo Augusto + > > * Nelson Auner + > > * aypiggott + > > * Christoph Baumgarten > > * Peter Bell > > * Sebastian Berg > > * Arman Bilge + > > * Benedikt Boecking + > > * Christoph Boeddeker + > > * Daniel Bunting > > * Evgeni Burovski > > * Angeline Burrell + > > * Angeline G. Burrell + > > * CJ Carey > > * Carlos Ramos Carre?o + > > * Mak Sze Chun + > > * Malayaja Chutani + > > * Christian Clauss + > > * Jonathan Conroy + > > * Stephen P Cook + > > * Dylan Cutler + > > * Anirudh Dagar + > > * Aidan Dang + > > * dankleeman + > > * Brandon David + > > * Tyler Dawson + > > * Dieter Werthm?ller > > * Joe Driscoll + > > * Jakub Dyczek + > > * D?vid Bodn?r > > * Fletcher Easton + > > * Stefan Endres > > * etienne + > > * Johann Faouzi > > * Yu Feng > > * Isuru Fernando + > > * Matthew H Flamm > > * Martin Gauch + > > * Gabriel Gerlero + > > * Ralf Gommers > > * Chris Gorgolewski + > > * Domen Gorjup + > > * Edouard Goudenhoofdt + > > * Jan Gwinner + > > * Maja Gwozdz + > > * Matt Haberland > > * hadshirt + > > * Pierre Haessig + > > * David Hagen > > * Charles Harris > > * Gina Helfrich + > > * Alex Henrie + > > * Francisco J. Hernandez Heras + > > * Andreas Hilboll > > * Lindsey Hiltner > > * Thomas Hisch > > * Min ho Kim + > > * Gert-Ludwig Ingold > > * jakobjakobson13 + > > * Todd Jennings > > * He Jia > > * Muhammad Firmansyah Kasim + > > * Andrew Knyazev + > > * Holger Kohr + > > * Mateusz Konieczny + > > * Krzysztof Pi?ro + > > * Philipp Lang + > > * Peter Mahler Larsen + > > * Eric Larson > > * Antony Lee > > * Gregory R. Lee > > * Chelsea Liu + > > * Jesse Livezey > > * Peter Lysakovski + > > * Jason Manley + > > * Michael Marien + > > * Nikolay Mayorov > > * G. D. McBain + > > * Sam McCormack + > > * Melissa Weber Mendon?a + > > * Kevin Michel + > > * mikeWShef + > > * Sturla Molden > > * Eric Moore > > * Peyton Murray + > > * Andrew Nelson > > * Clement Ng + > > * Juan Nunez-Iglesias > > * Renee Otten + > > * Kellie Ottoboni + > > * Ayappan P > > * Sambit Panda + > > * Tapasweni Pathak + > > * Oleksandr Pavlyk > > * Fabian Pedregosa > > * Petar Mlinari? > > * Matti Picus > > * Marcel Plch + > > * Christoph Pohl + > > * Ilhan Polat > > * Siddhesh Poyarekar + > > * Ioannis Prapas + > > * James Alan Preiss + > > * Yisheng Qiu + > > * Eric Quintero > > * Bharat Raghunathan + > > * Tyler Reddy > > * Joscha Reimer > > * Antonio Horta Ribeiro > > * Lucas Roberts > > * rtshort + > > * Josua Sassen > > * Kevin Sheppard > > * Scott Sievert > > * Leo Singer > > * Kai Striega > > * S?ren Fuglede J?rgensen > > * tborisow + > > * ?tienne Tremblay + > > * tuxcell + > > * Miguel de Val-Borro > > * Andrew Valentine + > > * Hugo van Kemenade > > * Paul van Mulbregt > > * Sebastiano Vigna > > * Pauli Virtanen > > * Dany Vohl + > > * Ben Walsh + > > * Huize Wang + > > * Warren Weckesser > > * Anreas Weh + > > * Joseph Weston + > > * Adrian Wijaya + > > * Timothy Willard + > > * Josh Wilson > > * Kentaro Yamamoto + > > * Dave Zbarsky + > > > > A total of 142 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 1.4.0 > > -------------------------------- > > > > * `#1255 `__: maxiter broken > > for Scipy.sparse.linalg gmres, in addition to... > > * `#1301 `__: consolidate > > multipack.h from interpolate and integrate packages... > > * `#1739 `__: Single > precision > > FFT insufficiently accurate. (Trac #1212) > > * `#1795 `__: stats > > test_distributions.py: replace old fuzz tests (Trac #1269) > > * `#2233 `__: fftpack > segfault > > with big arrays (Trac #1714) > > * `#2434 `__: rmatmat and > the > > sophistication of linear operator objects > > * `#2477 `__: > > stats.truncnorm.rvs() does not give symmetric results for negative... > > * `#2629 `__: FFTpack is > > unacceptably slow on non power of 2 > > * `#2883 `__: > UnboundLocalError > > in scipy.interpolate.splrep > > * `#2956 `__: Feature > Request: > > axis argument for stats.entropy function > > * `#3528 `__: Segfault on > > test_djbfft (possibly MKL-related?) > > * `#3793 `__: cwt should > also > > return complex array > > * `#4464 `__: TST: > > residue/residuez/invres/invresz don't have any tests > > * `#4561 `__: BUG: tf filter > > trailing and leading zeros in residuez > > * `#4669 `__: Rewrite > sosfilt > > to make a single loop over the input? > > * `#5040 `__: BUG: Empty > data > > handling of (c)KDTrees > > * `#5112 `__: boxcox > transform > > edge cases could use more care > > * `#5441 `__: > scipy.stats.ncx2 > > fails for nc=0 > > * `#5502 `__: args keyword > not > > handled in optimize.curve_fit > > * `#6484 `__: Qhull > > segmentation fault > > * `#6900 `__: > > linear_sum_assignment with infinite weights > > * `#6966 `__: Hypergeometric > > Functions documentation is lacking > > * `#6999 `__: possible false > > positive corruption check in compressed loadmat() > > * `#7018 `__: ydata that > needs > > broadcasting renders curve_fit unable to compute... > > * `#7140 `__: trouble with > > documentation for windows > > * `#7327 `__: > > interpolate.ndgriddata.griddata causes Python to crash rather... > > * `#7396 `__: > > MatrixLinearOperator implements _adjoint(), but not _transpose() > > * `#7400 `__: BUG(?): > special: > > factorial and factorial2 return a 0-dimensional... > > * `#7434 `__: Testing of > > scipy.stats continuous distributions misses 25 distributions > > * `#7491 `__: Several > > scipy.stats distributions (fisk, burr, burr12, f) return... > > * `#7759 `__: Overflow in > > stats.kruskal for large samples > > * `#7906 `__: Wrong result > from > > scipy.interpolate.UnivariateSpline.integral... > > * `#8165 `__: ENH: match > > functionality of R for hmean > > * `#8417 `__: > > optimimze.minimize(method='L-BFGS-B', options={'disp': True})... > > * `#8535 `__: Strictly > > increasing requirement in UnivariateSpline > > * `#8815 `__: [BUG] GMRES: > > number of iteration is only increased if callback... > > * `#9207 `__: > > scipy.linalg.solve_triangular speed after scipy.linalg.lu_factor > > * `#9275 `__: new feature: > > adding LOBPCG solver in svds in addition to ARPACK > > * `#9403 `__: range of > > truncnorm.logpdf could be extended > > * `#9429 `__: gaussian_kde > not > > working with numpy matrix > > * `#9515 `__: ndimage > > implementation relies on undefined behavior > > * `#9643 `__: arpack returns > > singular values in ascending order > > * `#9669 `__: DOC: > > matthew-brett/build-openblas has been retired > > * `#9852 `__: > > scipy.spatial.ConvexHull exit with code 134, free(): invalid... > > * `#9902 `__: > > scipy.stats.truncnorm second moment may be wrong > > * `#9943 `__: Custom > sampling > > methods in shgo do not work > > * `#9947 `__: DOC: Incorrect > > documentation for \`nan_policy='propagate\` in... > > * `#9994 `__: BUG: sparse: > > reshape method allows a shape containing an arbitrary... > > * `#10036 `__: Official > Nelder > > mead tutorial uses xtol instead of xatol, which... > > * `#10078 `__: possible to > get > > a better error message when objective function... > > * `#10092 `__: overflow in > > truncnorm.rvs > > * `#10121 `__: A little > > spelling mistake > > * `#10126 `__: inaccurate > std > > implementation in binned_statistic > > * `#10161 `__: Error in > > documentation scipy.special.modstruve > > * `#10195 `__: Derivative > of > > spline with 'const' extrapolation is also extrapolted... > > * `#10206 `__: sparse > matrices > > indexing with scipy 1.3 > > * `#10236 `__: > Non-descriptive > > error on type mismatch for functions of scipy.optimize... > > * `#10258 `__: LOBPCG > > convergence failure if guess provided > > * `#10262 `__: distance > matrix > > lacks dtype checks / warnings > > * `#10271 `__: BUG: > optimize > > failure on wheels > > * `#10277 `__: > > scipy.special.zeta(0) = NAN > > * `#10292 `__: DOC/REL: > Some > > sections of the release notes are not nested correctly. > > * `#10300 `__: > > scipy.stats.rv_continuous.fit throws empty RuntimeError when... > > * `#10319 `__: events in > > scipy.integrate.solve_ivp: How do I setup an events... > > * `#10323 `__: Adding more > > low-level LAPACK wrappers > > * `#10360 `__: firwin2 > > inadvertently modifies input and may result in undefined... > > * `#10388 `__: BLD: > > TestHerd::test_hetrd core dumps with Python-dbg > > * `#10395 `__: Remove > warning > > about output shape of zoom > > * `#10403 `__: DOC: > > scipy.signal.resample ignores t parameter > > * `#10421 `__: Yeo-Johnson > > power transformation fails with integer input data > > * `#10422 `__: BUG: > scipy.fft > > does not support multiprocessing > > * `#10427 `__: ENH: > convolve > > numbers should be updated > > * `#10444 `__: BUG: > > scipy.spatial.transform.Rotation.match_vectors returns improper... > > * `#10488 `__: ENH: > DCTs/DSTs > > for scipy.fft > > * `#10501 `__: BUG: > > scipy.spatial.HalfspaceIntersection works incorrectly > > * `#10514 `__: BUG: cKDTree > > GIL handling is incorrect > > * `#10535 `__: TST: master > > branch CI failures > > * `#10588 `__: scipy.fft > and > > numpy.fft inconsistency when axes=None and shape... > > * `#10628 `__: Scipy > > python>3.6 Windows wheels don't ship msvcp\*.dll > > * `#10733 `__: DOC/BUG: > > min_only result does not match documentation > > * `#10774 `__: > min_only=true > > djisktra infinite loop with duplicate indices > > * `#10775 `__: > > UnboundLocalError in Radau when given a NaN > > * `#10835 `__: > io.wavfile.read > > unnecessarily raises an error for a bad wav header > > * `#10838 `__: Error in > > documentation for scipy.linalg.lu_factor > > * `#10875 `__: DOC: > Graphical > > guides (using TikZ) > > * `#10880 `__: setting > verbose > >> 2 in minimize with trust-constr method leads... > > * `#10887 `__: > > scipy.signal.signaltools._fftconv_faster has incorrect estimates > > * `#10948 `__: > gammainc(0,x) = > > nan but should be 1, gammaincc(0,x) = nan but... > > * `#10952 `__: > > TestQRdelete_F.test_delete_last_p_col test failure > > * `#10968 `__: API: Change > > normalized=False to normalize=True in Rotation > > * `#10987 `__: Memory leak > in > > shgo triangulation > > * `#10991 `__: Error > running > > openBlas probably missing a step > > * `#11033 `__: deadlock on > osx > > for python 3.8 > > * `#11041 `__: Test > failure in > > wheel builds for TestTf2zpk.test_simple > > * `#11089 `__: Regression > in > > scipy.stats where distribution will not accept loc and scale parameters > > * `#11100 `__: BUG: > > multiscale_graphcorr random state seeding and parallel use > > * `#11121 `__: Calls to > > `scipy.interpolate.splprep` increase RAM usage. > > * `#11125 `__: BUG: > segfault > > when slicing a CSR or CSC sparse matrix with slice start index > stop > index > > * `#11198 `__: BUG: sparse > > eigs (arpack) shift-invert drops the smallest eigenvalue for some k > > > > Pull requests for 1.4.0 > > ------------------------------- > > > > * `#4591 `__: BUG, TST: > Several > > issues with scipy.signal.residue > > * `#6629 `__: ENH: sparse: > > canonicalize on initialization > > * `#7076 `__: ENH: add complex > > wavelet support to scipy.signal.cwt. > > * `#8681 `__: ENH add > generalized > > inverse Gaussian distribution to scipy.stats > > * `#9064 `__: BUG/ENH: Added > > default _transpose into LinearOperator. Fixes... > > * `#9215 `__: ENH: Rbf > > interpolation of large multi-dimensional data > > * `#9311 `__: ENH: Added > voigt in > > scipy.special. > > * `#9642 `__: ENH: integrate: > > quad() for vector-valued functions > > * `#9679 `__: DOC: expand > > docstring of exponweib distribution > > * `#9684 `__: TST: add > ppc64le ci > > testing > > * `#9800 `__: WIP : ENH: > > Refactored _hungarian.py for speed and added a minimize/maximize? > > * `#9847 `__: DOC: Change > > integrate tutorial to use solve_ivp instead of odeint > > * `#9876 `__: ENH: Use rfft > when > > possible in resampling > > * `#9998 `__: BUG: Do not > remove > > 1s when calling sparse: reshape method #9994 > > * `#10002 `__: ENH: adds > > constraints for differential evolution > > * `#10098 `__: ENH: > integrate: > > add args argument to solve_ivp. > > * `#10099 `__: DOC: Add > missing > > docs for linprog unknown_options > > * `#10104 `__: BUG: Rewrite > of > > stats.truncnorm distribution. > > * `#10105 `__: MAINT improve > > efficiency of rvs_ratio_uniforms in scipy.stats > > * `#10107 `__: TST: > > dual_annealing set seed > > * `#10108 `__: ENH: stats: > > improve kendall_tau cache usage > > * `#10110 `__: MAINT: _lib: > Fix > > a build warning. > > * `#10114 `__: FIX: only > print > > bounds when supported by minimizer (shgo) > > * `#10115 `__: TST: Add a > test > > with an almost singular design matrix for lsq_linear > > * `#10118 `__: MAINT: fix > rdist > > methods in scipy.stats > > * `#10119 `__: MAINT: improve > > rvs of randint in scipy.stats > > * `#10127 `__: Fix typo in > > record array field name (spatial-ckdtree-sparse_distance? > > * `#10130 `__: MAINT: > ndimage: > > Fix some compiler warnings. > > * `#10131 `__: DOC: Note the > > solve_ivp args enhancement in the 1.4.0 release... > > * `#10133 `__: MAINT: add rvs > > for semicircular in scipy.stats > > * `#10138 `__: BUG: special: > > Invalid arguments to ellip_harm can crash Python. > > * `#10139 `__: MAINT: > spatial: > > Fix some compiler warnings in the file distance_wrap.c. > > * `#10140 `__: ENH: add > handling > > of NaN in RuntimeWarning except clause > > * `#10142 `__: DOC: return > value > > of scipy.special.comb > > * `#10143 `__: MAINT: Loosen > > linprog tol > > * `#10152 `__: BUG: Fix > custom > > sampling input for shgo, add unittest > > * `#10154 `__: MAINT: add > > moments and improve doc of mielke in scipy.stats > > * `#10158 `__: Issue #6999: > read > > zlib checksum before checking bytes read. > > * `#10166 `__: BUG: Correctly > > handle broadcasted ydata in curve_fit pcov computation. > > * `#10167 `__: DOC: special: > Add > > missing factor of \`i\` to \`modstruve\` docstring > > * `#10168 `__: MAINT: stats: > Fix > > an incorrect comment. > > * `#10169 `__: ENH: optimize: > > Clarify error when objective function returns... > > * `#10172 `__: DEV: Run > tests in > > parallel when --parallel flag is passed to... > > * `#10173 `__: ENH: Implement > > DOP853 ODE integrator > > * `#10176 `__: Fixed typo > > * `#10182 `__: TST: fix test > > issue for stats.pearsonr > > * `#10184 `__: MAINT: stats: > > Simplify zmap and zscore (we can use keepdims now). > > * `#10191 `__: DOC: fix a > > formatting issue in the scipy.spatial module docstring. > > * `#10193 `__: DOC: Updated > > docstring for optimize.nnls > > * `#10198 `__: DOC, ENH: > > special: Make \`hyp2f1\` references more specific > > * `#10202 `__: DOC: Format > DST > > and DCT definitions as latex equations > > * `#10207 `__: BUG: > Compressed > > matrix indexing should return a scalar > > * `#10210 `__: DOC: Update > docs > > for connection='weak' in connected_components > > * `#10225 `__: DOC: Clarify > new > > interfaces for legacy functions in 'optimize' > > * `#10231 `__: DOC, MAINT: > gpg2 > > updates to release docs / pavement > > * `#10235 `__: LICENSE: split > > license file in standard BSD 3-clause and bundled. > > * `#10238 `__: ENH: Add new > > scipy.fft module using pocketfft > > * `#10243 `__: BUG: fix ARFF > > reader regression with quoted values. > > * `#10248 `__: DOC: update > > README file > > * `#10255 `__: CI: bump > OpenBLAS > > to match wheels > > * `#10264 `__: TST: add tests > > for stats.tvar with unflattened arrays > > * `#10280 `__: MAINT: stats: > Use > > a constant value for sqrt(2/PI). > > * `#10286 `__: Development > > Documentation Overhaul > > * `#10290 `__: MAINT: > Deprecate > > NumPy functions in SciPy root > > * `#10291 `__: FIX: Avoid > > importing xdist when checking for availability > > * `#10295 `__: Disable > > deprecated Numpy API in __odrpack.c > > * `#10296 `__: ENH: C++ > > extension for linear assignment problem > > * `#10298 `__: ENH: Made pade > > function work with complex inputs > > * `#10301 `__: DOC: Fix > critical > > value significance levels in stats.anderson_ksamp > > * `#10307 `__: Minkowski > > Distance Type Fix (issue #10262) > > * `#10309 `__: BUG: Pass > > jac=None directly to lsoda > > * `#10310 `__: BUG: > interpolate: > > UnivariateSpline.derivative.ext is 'zeros'... > > * `#10312 `__: FIX: Fixing a > > typo in a comment > > * `#10314 `__: scipy.spatial > > enhancement request > > * `#10315 `__: DOC: Update > > integration tutorial to solve_ivp > > * `#10318 `__: DOC: update > the > > example for PPoly.solve > > * `#10333 `__: TST: add tests > > for stats.tvar with unflattened arrays > > * `#10334 `__: MAINT: > special: > > Remove deprecated \`hyp2f0\`, \`hyp1f2\`, and... > > * `#10336 `__: BUG: > > linalg/interpolative: fix interp_decomp modifying input > > * `#10341 `__: BUG: > > sparse.linalg/gmres: deprecate effect of callback on semantics... > > * `#10344 `__: DOC: improve > > wording of mathematical formulation > > * `#10345 `__: ENH: Tiled QR > > wrappers for scipy.linalg.lapack > > * `#10350 `__: MAINT: linalg: > > Use the new fft subpackage in linalg.dft test... > > * `#10351 `__: BUG: Fix > unstable > > standard deviation calculation in histogram > > * `#10353 `__: Bug: > > interpolate.NearestNDInterpolator (issue #10352) > > * `#10357 `__: DOC: linalg: > > Refer to scipy.fft.fft (not fftpack) in the dft... > > * `#10359 `__: DOC: Update > > roadmap now scipy.fft has been merged > > * `#10361 `__: ENH: Prefer > > scipy.fft to scipy.fftpack in scipy.signal > > * `#10371 `__: DOC: Tweaks to > > fft documentation > > * `#10372 `__: DOC: Fix typos > > * `#10377 `__: TST, MAINT: > > adjustments for pytest 5.0 > > * `#10378 `__: ENH: _lib: > allow > > new np.random.Generator in check_random_state > > * `#10379 `__: BUG: sparse: > set > > writeability to be forward-compatible with numpy>=1.17 > > * `#10381 `__: BUG: Fixes > > gh-7491, pdf at x=0 of fisk/burr/burr12/f distributions. > > * `#10387 `__: ENH: > > optimize/bfgs: don't evaluate twice at initial point for... > > * `#10392 `__: [DOC] Add an > > example for _binned_statistic_dd > > * `#10396 `__: Remove warning > > about output shape of zoom > > * `#10397 `__: ENH: Add > > check_finite to sp.linalg.norm > > * `#10399 `__: ENH: Add > > __round__ method to sparse matrix > > * `#10407 `__: MAINT: drop > > pybind11 from install_requires, it's only build-time... > > * `#10408 `__: TST: use > > pytest.raises, not numpy assert_raises > > * `#10409 `__: CI: uninstall > > nose on Travis > > * `#10410 `__: [ENH] ncx2 > > dispatch to chi2 when nc=0 > > * `#10411 `__: TST: optimize: > > test should use assert_allclose for fp comparisons > > * `#10414 `__: DOC: add > pybind11 > > to the other part of quickstart guides > > * `#10417 `__: DOC: special: > > don't mark non-ufuncs with a \`[+]\` > > * `#10423 `__: FIX: Use > > pybind11::isinstace to check array dtypes > > * `#10424 `__: DOC: add > doctest > > example for binary data for ttest_ind_from_stats > > * `#10425 `__: ENH: Add > missing > > Hermitian transforms to scipy.fft > > * `#10426 `__: MAINT: Fix doc > > build bugs > > * `#10431 `__: Update numpy > > version for AIX > > * `#10433 `__: MAINT: Minor > > fixes for the stats > > * `#10434 `__: BUG: special: > > make \`ndtri\` return NaN outside domain of definition > > * `#10435 `__: BUG: Allow > > integer input data in scipy.stats.yeojohnson > > * `#10438 `__: [DOC] Add > example > > for kurtosis > > * `#10440 `__: ENH: special: > > make \`ellipk\` a ufunc > > * `#10443 `__: MAINT: > ndimage: > > malloc fail check > > * `#10447 `__: BLD: Divert > > output from test compiles into a temporary directory > > * `#10451 `__: MAINT: signal: > > malloc fail check > > * `#10455 `__: BUG: special: > fix > > values of \`hyperu\` for negative \`x\` > > * `#10456 `__: DOC: Added > > comment clarifying the call for dcsrch.f in lbfgsb.f > > * `#10457 `__: BUG: Allow > > ckdtree to accept empty data input > > * `#10459 `__: BUG:TST: > Compute > > lwork safely > > * `#10460 `__: [DOC] Add > example > > to entropy > > * `#10461 `__: DOC: > Quickstart > > Guide updates > > * `#10462 `__: TST: special: > > only show max atol/rtol for test points that failed > > * `#10465 `__: BUG: Correctly > > align fft inputs > > * `#10467 `__: ENH: > lower-memory > > duplicate generator checking in spatial.SphericalVoronoi > > * `#10470 `__: ENH: Normalise > > the inverse DCT/DST in scipy.fft > > * `#10472 `__: BENCH: adjust > > timeout for slow setup_cache > > * `#10475 `__: CI: include > > python debug for Travis-ci > > * `#10476 `__: TST: special: > use > > \`__tracebackhide__\` to get better error messages > > * `#10477 `__: ENH: faster > > region building in spatial.SphericalVoronoi > > * `#10479 `__: BUG: stats: > Fix a > > few issues with the distributions' fit method. > > * `#10480 `__: Add > RuntimeError > > in _distn_infrastructure.py in fit() method > > * `#10481 `__: BENCH, MAINT: > > wheel_cache_size has been renamed build_cache_size > > * `#10494 `__: ENH: faster > > circumcenter calculation in spatial.SphericalVoronoi > > * `#10500 `__: Splrep > > _curfit_cache global variable bugfix > > * `#10503 `__: BUG: > > spatial/qhull: get HalfspaceIntersection.dual_points from... > > * `#10506 `__: DOC: interp2d, > > note nearest neighbor extrapolation > > * `#10507 `__: MAINT: Remove > > fortran fftpack library in favour of pypocketfft > > * `#10508 `__: TST: fix a > bug in > > the circular import test. > > * `#10509 `__: MAINT: Set up > > _build_utils as subpackage > > * `#10516 `__: BUG: Use nogil > > contexts in cKDTree > > * `#10517 `__: ENH: > fftconvolve > > should not FFT broadcastable axes > > * `#10518 `__: ENH: Speedup > > fftconvolve > > * `#10520 `__: DOC: Proper > .rst > > formatting for deprecated features and Backwards... > > * `#10523 `__: DOC: Improve > > scipy.signal.resample documentation > > * `#10524 `__: ENH: Add MGC > to > > scipy.stats > > * `#10525 `__: [ENH] ncx2.ppf > > dispatch to chi2 when nc=0 > > * `#10526 `__: DOC: clarify > > laplacian normalization > > * `#10528 `__: API: Rename > > scipy.fft DCT/DST shape argument to s > > * `#10531 `__: BUG: fixed > > improper rotations in spatial.transform.rotation.match_vectors > > * `#10533 `__: [DOC] Add > example > > for winsorize function > > * `#10539 `__: MAINT: > special: > > don't register \`i0\` with \`numpy.dual\` > > * `#10540 `__: MAINT: Fix > Travis > > and Circle > > * `#10542 `__: MAINT: > > interpolate: use cython_lapack > > * `#10547 `__: Feature > request. > > Add furthest site Voronoi diagrams to scipy.spatial.plotutils. > > * `#10549 `__: [BUG] Fix bug > in > > trimr when inclusive=False > > * `#10552 `__: add > > scipy.signal.upfirdn signal extension modes > > * `#10555 `__: MAINT: > special: > > move \`c_misc\` into Cephes > > * `#10556 `__: [DOC] Add > example > > for trima > > * `#10562 `__: [DOC] Fix > triple > > string fo trimmed so that __doc__ can show... > > * `#10563 `__: improve > > least_squares error msg for mismatched shape > > * `#10564 `__: ENH: linalg: > > memoize get_lapack/blas_funcs to speed it up > > * `#10566 `__: ENH: add > > implementation of solver for the maximum flow problem > > * `#10567 `__: BUG: spatial: > use > > c++11 construct for getting start of vector... > > * `#10568 `__: DOC: special: > > small tweaks to the \`zetac\` docstring > > * `#10571 `__: [ENH] > > Gaussian_kde can accept matrix dataset > > * `#10574 `__: ENH: linalg: > > speed up _compute_lwork by avoiding numpy constructs > > * `#10582 `__: Fix typos with > > typos in bundled libraries reverted > > * `#10583 `__: ENH: special: > add > > the analytic continuation of Riemann zeta > > * `#10584 `__: MAINT: > special: > > clean up \`special.__all__\` > > * `#10586 `__: BUG: > > multidimensional scipy.fft functions should accept 's' rather... > > * `#10587 `__: BUG: > > integrate/lsoda: never abort run, set error istate instead > > * `#10594 `__: API: Replicate > > numpy's fftn behaviour when s is given but not... > > * `#10599 `__: DOC: dev: > update > > documentation vs. github pull request workflow... > > * `#10603 `__: MAINT: > installer > > scripts removed > > * `#10604 `__: MAINT: Change > > c\*np.ones(...) to np.full(..., c, ...) in many... > > * `#10608 `__: Univariate > > splines should require x to be strictly increasing... > > * `#10613 `__: ENH: Add seed > > option for gaussian_kde.resample > > * `#10614 `__: ENH: Add > parallel > > computation to scipy.fft > > * `#10615 `__: MAINT: > > interpolate: remove unused header file > > * `#10616 `__: MAINT: Clean > up > > 32-bit platform xfail markers > > * `#10618 `__: BENCH: Added > > 'trust-constr' to minimize benchmarks > > * `#10621 `__: [MRG] multiple > > stability updates in lobpcg > > * `#10622 `__: MAINT: forward > > port 1.3.1 release notes > > * `#10624 `__: DOC: stats: > Fix > > spelling of 'support'. > > * `#10627 `__: DOC: stats: > Add > > references for the alpha distribution. > > * `#10629 `__: MAINT: > special: > > avoid overflow longer in \`zeta\` for negative... > > * `#10630 `__: TST: GH10271, > > relax test assertion, fixes #10271 > > * `#10631 `__: DOC: > nelder-mean > > uses xatol fixes #10036 > > * `#10633 `__: BUG: > interpolate: > > integral(a, b) should be zero when both limits... > > * `#10635 `__: DOC: special: > > complete hypergeometric functions documentation > > * `#10636 `__: BUG: special: > use > > series for \`hyp1f1\` when it converges rapidly > > * `#10641 `__: ENH: allow > > matching of general bipartite graphs > > * `#10643 `__: ENH: > > scipy.sparse.linalg.spsolve triangular unit diagonal > > * `#10650 `__: ENH: Cythonize > > sosfilt > > * `#10654 `__: DOC: Vertical > > alignment of table entries > > * `#10655 `__: ENH: > Dockerfile > > for scipy development > > * `#10660 `__: TST: clean up > > tests for rvs in scipy.stats > > * `#10664 `__: Throw error on > > non-finite input for binned_statistic_dd() > > * `#10665 `__: DOC: special: > > improve the docstrings for \`gamma\` and \`gammasgn\` > > * `#10669 `__: TST: Update > > scipy.fft real transform tests > > * `#10670 `__: DOC: Clarify > docs > > and error messages for scipy.signal.butter > > * `#10672 `__: ENH: return > > solution attribute when using events in solve_ivp > > * `#10675 `__: MAINT: > special: > > add an explicit NaN check for \`iv\` arguments > > * `#10679 `__: DOC: special: > Add > > documentation for \`beta\` function > > * `#10681 `__: TST: > > sparse.linalg: fix arnoldi test seed > > * `#10682 `__: DOC: special: > Add > > documentation for \`betainc\` function > > * `#10684 `__: TST: special: > > require Mpmath 1.1.0 for \`test_hyperu_around_0\` > > * `#10686 `__: FIX: sphinx > > isattributedescriptor is not available in sphinx... > > * `#10687 `__: DOC: added > Docker > > quickstart guide by @andyfaff > > * `#10689 `__: DOC: special: > > clarify format of parameters/returns sections for... > > * `#10690 `__: DOC: special: > > improve docstrings of incomplete gamma functions > > * `#10692 `__: ENH: > > higher-dimensional input in \`spatial.SphericalVoronoi\` > > * `#10694 `__: ENH: > > ScalarFunction.fun_and_grad > > * `#10698 `__: DOC: special: > Add > > documentation for \`betaincinv\` > > * `#10699 `__: MAINT: remove > > time print lbfgsb fixes #8417 > > * `#10701 `__: TST, MAINT: > bump > > OpenBLAS to 0.3.7 stable > > * `#10702 `__: DOC: clarify > > iterations consume multiple function calls > > * `#10703 `__: DOC: iprint > doc > > lbfgsb closes #5482 > > * `#10708 `__: TST: test > > suggested in gh1758 > > * `#10710 `__: ENH: Added > > nan_policy to circ functions in \`stats\` > > * `#10712 `__: ENH: add axis > > parameter to stats.entropy > > * `#10714 `__: DOC: > Formatting > > fix rv_continuous.expect docs > > * `#10715 `__: DOC: BLD: > update > > doc Makefile for python version; add scipy version... > > * `#10717 `__: MAINT: > modernize > > doc/Makefile > > * `#10719 `__: Enable setting > > minres initial vector > > * `#10720 `__: DOC: silence > > random warning in doc build for \`stats.binned_statistic_dd\` > > * `#10724 `__: DEV: Add doc > > option to runtests.py > > * `#10728 `__: MAINT: get > rid of > > gramA, gramB text files that lobpcg tests leave... > > * `#10732 `__: DOC: add > min_only > > to docstring for Dijkstra's algorithm > > * `#10734 `__: DOC: spell out > > difference between source and target in shortest... > > * `#10735 `__: Fix for > Python 4 > > * `#10739 `__: BUG: > > optimize/slsqp: deal with singular BFGS update > > * `#10741 `__: ENH: LAPACK > > wrappers for ?geequ, ?geequb, ?syequb, ?heequb > > * `#10742 `__: DOC: special: > add > > to the docstring of \`gammaln\` > > * `#10743 `__: ENH: special: > add > > a real dispatch for \`wrightomega\` > > * `#10746 `__: MAINT: Fix > typos > > in comments, docs and test name > > * `#10747 `__: Remove > spurious > > quotes > > * `#10750 `__: MAINT: make > > cython code more precise > > * `#10751 `__: MAINT: Check > that > > scipy.linalg.lapack functions are documented > > * `#10752 `__: MAINT: > special: > > use \`sf_error\` in Cephes > > * `#10755 `__: DOC: cluster: > Add > > 'See Also' and 'Examples' for kmeans2. > > * `#10763 `__: MAINT: list of > > minimize methods > > * `#10768 `__: BUG: Fix > corner > > case for sos2zpk > > * `#10773 `__: Fix error type > > for complex input to scipy.fftpack.rfft and irfft > > * `#10776 `__: ENH: handle > > geodesic input in \`spatial.SphericalVoronoi\` > > * `#10777 `__: MAINT: > > minimizer-->custom should handle the kinds of bounds/constrain?... > > * `#10781 `__: ENH: > > solve_triangular C order improvement > > * `#10787 `__: Fix behavior > of > > \`exp1\` on branch cut and add docstring > > * `#10789 `__: DOC: special: > add > > parameters/returns doc sections for erfc/erfcx/erfi > > * `#10790 `__: Travis CI: > sudo > > is deprecated and Xenial is default distro > > * `#10792 `__: DOC: special: > add > > full docstring for \`expi\` > > * `#10799 `__: DOC: special: > add > > a complete docstring for \`expn\` > > * `#10800 `__: Docs edits > (GSoD) > > * `#10802 `__: BUG: fix > > UnboundLocalError in Radau (scipy#10775) > > * `#10804 `__: ENH: Speed up > > next_fast_len with LRU cache > > * `#10805 `__: DOC: Fix > > unbalanced quotes in signal.place_poles > > * `#10809 `__: ENH: Speed up > > next_fast_len > > * `#10810 `__: ENH: Raise > > catchable exceptions for bad Fortran files > > * `#10811 `__: MAINT: > optimize: > > Remove extra variable from _remove_redundancy_dense > > * `#10813 `__: MAINT: > special: > > Remove unused variables from _kolmogi and _smirnovi > > * `#10815 `__: DOC, API: > > scipy.stats.reciprocal is "log-uniform" > > * `#10816 `__: MAINT: > special: > > remove deprecated \`bessel_diff_formula\` > > * `#10817 `__: DOC: special: > > complete the docstring for \`fresnel\` > > * `#10820 `__: Fixed > > compiler_helper.py to allow compilation with ICC on Linux > > * `#10823 `__: DOC: updated > > reference guide text for consistency in writing... > > * `#10825 `__: MAINT: > special: > > change some features of the Voigt function > > * `#10828 `__: MAINT: > integrate: > > Remove unused variable from init_callback > > * `#10830 `__: Adding LOBPCG > > solver in svds in addition to ARPACK > > * `#10837 `__: WIP: ENH: > > reduction function for \`spatial.tranform.Rotation\`... > > * `#10843 `__: ENH: Adding > > optional parameter to stats.zscores to allow for... > > * `#10845 `__: Rebase kruskal > > fix > > * `#10847 `__: remove > redundant > > __getitem__ from scipy.sparse.lil > > * `#10848 `__: Better > handling > > of empty (not missing) docstrings > > * `#10849 `__: ENH: implement > > rmatmat for LinearOperator > > * `#10850 `__: MAINT : > > Refactoring lil List of Lists > > * `#10851 `__: DOC: add a > > generative art example to the scipy.spatial tutorial. > > * `#10852 `__: DOC: linalg: > > fixed gh-10838 unused imports in example deleted > > * `#10854 `__: DOC: special: > add > > a full docstring for \`pdtr\` > > * `#10861 `__: ENH: option to > > reuse binnumbers in stats.binned_statistic_dd > > * `#10863 `__: DOC: partial > > standardization and validation of scipy.stats reference... > > * `#10865 `__: BUG: special: > fix > > incomplete gamma functions for infinite \`a\` > > * `#10866 `__: ENH: > calculation > > of mean in spatial.transform.Rotation > > * `#10867 `__: MAINT: Also > store > > latex directory > > * `#10869 `__: ENH: Implement > > overlap-add convolution > > * `#10870 `__: ENH: Do not > raise > > EOF error if wavfile data read > > * `#10876 `__: ENH: Add > > beta-binomial distribution to scipy.stats > > * `#10878 `__: MAINT: Update > R > > project URL > > * `#10883 `__: MAINT: > (ndimage) > > More robust check for output being a numpy dtype > > * `#10884 `__: DOC: Added > > instructions on adding a new distribution to scipy.stats. > > * `#10885 `__: [BUG] fix > lobpcg > > with maxiter=None results in Exception > > * `#10899 `__: ENH: Match R > > functionality for hmean > > * `#10900 `__: MAINT: stats: > Use > > keepdims to simplify a few lines in power_divergence. > > * `#10901 `__: ENH: > > sparse/linalg: support pydata/sparse matrices > > * `#10907 `__: Check whether > > \`maxiter\` is integer > > * `#10912 `__: ENH: warn user > > that quad() ignores \`points=...\` when \`weight=...\`... > > * `#10918 `__: CI: fix > Travis CI > > py3.8 build > > * `#10920 `__: MAINT: Update > > constants to codata 2018 values (second try) > > * `#10921 `__: ENH: > > scipy.sparse.lil: tocsr accelerated > > * `#10924 `__: BUG: Forbid > > passing 'args' as kwarg in scipy.optimize.curve_fit > > * `#10928 `__: DOC: Add > examples > > to io.wavfile docstrings > > * `#10934 `__: typo fix > > * `#10935 `__: BUG: Avoid > > undefined behaviour on float to unsigned conversion > > * `#10936 `__: DOC: Added > > missing example to stats.mstats.variation > > * `#10939 `__: ENH: > > scipy.sparse.lil: tocsr accelerated depending on density > > * `#10946 `__: BUG: setting > > verbose > 2 in minimize with trust-constr method... > > * `#10947 `__: DOC: special: > > small improvements to the \`poch\` docstring > > * `#10949 `__: BUG: fix > return > > type of erlang_gen._argcheck > > * `#10951 `__: DOC: fixed > Ricker > > wavelet formula > > * `#10954 `__: BUG: special: > fix > > \`factorial\` return type for 0-d inputs > > * `#10955 `__: MAINT: Relax > the > > assert_unitary atol value > > * `#10956 `__: WIP: make > > pdtr(int, double) be pdtr(double, double) > > * `#10957 `__: BUG: Ensure > full > > binary compatibility of long double test data > > * `#10964 `__: ENH: Make > Slerp > > callable with a scalar argument > > * `#10972 `__: BUG: Handle > > complex gains in zpk2sos > > * `#10975 `__: TST: skip > > test_kendalltau ppc64le > > * `#10978 `__: BUG: boxcox > data > > dimension and constancy check #5112 > > * `#10979 `__: API: Rename > dcm > > to (rotation) matrix in Rotation class > > * `#10981 `__: MAINT: add > > support for a==0 and x>0 edge case to igam and igamc > > * `#10986 `__: MAINT: Remove > > direct imports from numpy in signaltools.py > > * `#10988 `__: BUG: signal: > > fixed issue #10360 > > * `#10989 `__: FIX > > binned_statistic_dd Mac wheel test fails > > * `#10990 `__: BUG: Fix > memory > > leak in shgo triangulation > > * `#10992 `__: TST: Relax > > tolerance in upfirdn test_modes > > * `#10993 `__: TST: bump > > tolerance in optimize tests > > * `#10997 `__: MAINT: Rework > > residue and residuez > > * `#11001 `__: DOC: Updated > > Windows build tutorial > > * `#11004 `__: BUG: > > integrate/quad_vec: fix several bugs in quad_vec > > * `#11005 `__: TST: add > Python > > 3.8 Win CI > > * `#11006 `__: DOC: special: > add > > a reference for \`kl_div\` > > * `#11012 `__: MAINT: Rework > > invres and invresz > > * `#11015 `__: DOC: special: > add > > references for \`rel_entr\` > > * `#11017 `__: DOC: numpydoc > > validation of morestats.py > > * `#11018 `__: MAINT: Filter > > unrelated warning > > * `#11031 `__: MAINT: update > > choose_conv_method for pocketfft implementation > > * `#11034 `__: MAINT: TST: > Skip > > tests with multiprocessing that use "spawn"... > > * `#11036 `__: DOC: update > > doc/README with some more useful content. > > * `#11037 `__: DOC: special: > add > > a complete docstring for \`rgamma\` > > * `#11038 `__: DOC: special: > add > > a reference for the polygamma function > > * `#11042 `__: TST: fix > tf2zpk > > test failure due to incorrect complex sorting. > > * `#11044 `__: MAINT: > > choose_conv_method can choose fftconvolution for longcomplex > > * `#11046 `__: TST: Reduce > > tolerance for ppc64le with reference lapack > > * `#11048 `__: DOC: special: > add > > reference for orthogonal polynomial functions > > * `#11049 `__: MAINT: proper > > random number initialization and readability fix > > * `#11051 `__: MAINT: pep8 > > cleanup > > * `#11054 `__: TST: bump test > > precision for dual_annealing SLSQP test > > * `#11055 `__: DOC: special: > add > > a reference for \`zeta\` > > * `#11056 `__: API: > Deprecated > > normalized keyword in Rotation > > * `#11065 `__: DOC: Ubuntu > > Development Environment Quickstart should not modify... > > * `#11066 `__: BUG: skip > > deprecation for numpy top-level types > > * `#11067 `__: DOC: updated > > documentation for consistency in writing style > > * `#11070 `__: DOC: > Amendment to > > Ubuntu Development Environment Quickstart should... > > * `#11073 `__: DOC: fix 1.4.0 > > release notes > > * `#11081 `__: API: Replace > > Rotation.match_vectors with align_vectors > > * `#11083 `__: DOC: more > 1.4.0 > > release note fixes > > * `#11092 `__: BUG: stats: > fix > > freezing of some distributions > > * `#11096 `__: BUG: > > scipy.sparse.csgraph: fixed issue #10774 > > * `#11124 `__: fix Cython > > warnings related to _stats.pyx > > * `#11126 `__: BUG: > > interpolate/fitpack: fix memory leak in splprep > > * `#11127 `__: Avoid > potential > > segfault in CSR and CSC matrix indexing > > * `#11152 `__: BUG: Fix > random > > state bug multiscale_graphcorr > > * `#11166 `__: BUG: empty > sparse > > slice shapes > > * `#11167 `__: BUG: redundant > > fft in signal.resample > > * `#11181 `__: TST: Fix > > tolerance of tests for 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URL: From cournape at gmail.com Tue Dec 17 09:16:53 2019 From: cournape at gmail.com (David Cournapeau) Date: Tue, 17 Dec 2019 23:16:53 +0900 Subject: [Numpy-discussion] [SciPy-Dev] ANN: SciPy 1.4.0 In-Reply-To: References: Message-ID: Wow, good work. It is nice to see significant improvements made to FFT ! On Tue, Dec 17, 2019 at 3:41 PM Ralf Gommers wrote: > > > On Mon, Dec 16, 2019 at 5:13 PM Warren Weckesser < > warren.weckesser at gmail.com> wrote: > >> On 12/16/19, Tyler Reddy wrote: >> > -----BEGIN PGP SIGNED MESSAGE----- >> > Hash: SHA256 >> > >> > Hi all, >> > >> > On behalf of the SciPy development team I'm pleased to announce >> > the release of SciPy 1.4.0. >> >> >> Fantastic, thanks Tyler! >> >> > +1 thanks for taking care of this release Tyler! > > Ralf > > > >> Warren >> >> >> > >> > Sources and binary wheels can be found at: >> > https://pypi.org/project/scipy/ >> > and at: >> > https://github.com/scipy/scipy/releases/tag/v1.4.0 >> > >> > One of a few ways to install this release with pip: >> > >> > pip install scipy==1.4.0 >> > >> > ========================== >> > SciPy 1.4.0 Release Notes >> > ========================== >> > >> > SciPy 1.4.0 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 >> > 1.4.x branch, and on adding new features on the master branch. >> > >> > This release requires Python 3.5+ and NumPy >=1.13.3 (for Python 3.5, >> 3.6), >> >>=1.14.5 (for Python 3.7), >= 1.17.3 (for Python 3.8) >> > >> > For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. >> > >> > Highlights of this release >> > ---------------------------------- >> > >> > - a new submodule, `scipy.fft`, now supersedes `scipy.fftpack`; this >> > means support for ``long double`` transforms, faster multi-dimensional >> > transforms, improved algorithm time complexity, release of the global >> > intepreter lock, and control over threading behavior >> > - support for ``pydata/sparse`` arrays in `scipy.sparse.linalg` >> > - substantial improvement to the documentation and functionality of >> > several `scipy.special` functions, and some new additions >> > - the generalized inverse Gaussian distribution has been added to >> > `scipy.stats` >> > - an implementation of the Edmonds-Karp algorithm in >> > `scipy.sparse.csgraph.maximum_flow` >> > - `scipy.spatial.SphericalVoronoi` now supports n-dimensional input, >> > has linear memory complexity, improved performance, and >> > supports single-hemisphere generators >> > >> > >> > New features >> > ============ >> > >> > Infrastructure >> > -------------------- >> > Documentation can now be built with ``runtests.py --doc`` >> > >> > A ``Dockerfile`` is now available in the ``scipy/scipy-dev`` repository >> to >> > facilitate getting started with SciPy development. >> > >> > `scipy.constants` improvements >> > --------------------------------------------- >> > `scipy.constants` has been updated with the CODATA 2018 constants. >> > >> > >> > `scipy.fft` added >> > ------------------------ >> > `scipy.fft` is a new submodule that supersedes the `scipy.fftpack` >> > submodule. >> > For the most part, this is a drop-in replacement for ``numpy.fft`` and >> > `scipy.fftpack` alike. With some important differences, `scipy.fft`: >> > - uses NumPy's conventions for real transforms (``rfft``). This means >> the >> > return value is a complex array, half the size of the full ``fft`` >> output. >> > This is different from the output of ``fftpack`` which returned a real >> > array >> > representing complex components packed together. >> > - the inverse real to real transforms (``idct`` and ``idst``) are >> > normalized >> > for ``norm=None`` in thesame way as ``ifft``. This means the identity >> > ``idct(dct(x)) == x`` is now ``True`` for all norm modes. >> > - does not include the convolutions or pseudo-differential operators >> > from ``fftpack``. >> > >> > This submodule is based on the ``pypocketfft`` library, developed by the >> > author of ``pocketfft`` which was recently adopted by NumPy as well. >> > ``pypocketfft`` offers a number of advantages over fortran ``FFTPACK``: >> > - support for long double (``np.longfloat``) precision transforms. >> > - faster multi-dimensional transforms using vectorisation >> > - Bluestein?s algorithm removes the worst-case ``O(n^2)`` complexity of >> > ``FFTPACK`` >> > - the global interpreter lock (``GIL``) is released during transforms >> > - optional multithreading of multi-dimensional transforms via the >> > ``workers`` >> > argument >> > >> > Note that `scipy.fftpack` has not been deprecated and will continue to >> be >> > maintained but is now considered legacy. New code is recommended to use >> > `scipy.fft` instead, where possible. >> > >> > `scipy.fftpack` improvements >> > ---------------------------------------- >> > `scipy.fftpack` now uses pypocketfft to perform its FFTs, offering the >> same >> > speed and accuracy benefits listed for scipy.fft above but without the >> > improved API. >> > >> > `scipy.integrate` improvements >> > ------------------------------------------- >> > >> > The function `scipy.integrate.solve_ivp` now has an ``args`` argument. >> > This allows the user-defined functions passed to the function to have >> > additional parameters without having to create wrapper functions or >> > lambda expressions for them. >> > >> > `scipy.integrate.solve_ivp` can now return a ``y_events`` attribute >> > representing the solution of the ODE at event times >> > >> > New ``OdeSolver`` is implemented --- ``DOP853``. This is a high-order >> > explicit >> > Runge-Kutta method originally implemented in Fortran. Now we provide a >> pure >> > Python implementation usable through ``solve_ivp`` with all its >> features. >> > >> > `scipy.integrate.quad` provides better user feedback when break points >> are >> > specified with a weighted integrand. >> > >> > `scipy.integrate.quad_vec` is now available for general purpose >> integration >> > of vector-valued functions >> > >> > >> > `scipy.interpolate` improvements >> > --------------------------------------------- >> > `scipy.interpolate.pade` now handles complex input data gracefully >> > >> > `scipy.interpolate.Rbf` can now interpolate multi-dimensional functions >> > >> > `scipy.io` improvements >> > --------------------------------- >> > >> > `scipy.io.wavfile.read` can now read data from a `WAV` file that has a >> > malformed header, similar to other modern `WAV` file parsers >> > >> > `scipy.io.FortranFile` now has an expanded set of available >> ``Exception`` >> > classes for handling poorly-formatted files >> > >> > >> > `scipy.linalg` improvements >> > ------------------------------------- >> > The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct >> > results for complex-valued matrices. Before this, the function only >> > returned >> > correct values for real-valued matrices. >> > >> > New boolean keyword argument ``check_finite`` for `scipy.linalg.norm`; >> > whether >> > to check that the input matrix contains only finite numbers. Disabling >> may >> > give a performance gain, but may result in problems (crashes, >> > non-termination) >> > if the inputs do contain infinities or NaNs. >> > >> > `scipy.linalg.solve_triangular` has improved performance for a C-ordered >> > triangular matrix >> > >> > ``LAPACK`` wrappers have been added for ``?geequ``, ``?geequb``, >> > ``?syequb``, >> > and ``?heequb`` >> > >> > Some performance improvements may be observed due to an internal >> > optimization >> > in operations involving LAPACK routines via ``_compute_lwork``. This is >> > particularly true for operations on small arrays. >> > >> > Block ``QR`` wrappers are now available in `scipy.linalg.lapack` >> > >> > >> > `scipy.ndimage` improvements >> > ------------------------------------------ >> > >> > >> > `scipy.optimize` improvements >> > ------------------------------------------ >> > It is now possible to use linear and non-linear constraints with >> > `scipy.optimize.differential_evolution`. >> > >> > `scipy.optimize.linear_sum_assignment` has been re-written in C++ to >> > improve >> > performance, and now allows input costs to be infinite. >> > >> > A ``ScalarFunction.fun_and_grad`` method was added for convenient >> > simultaneous >> > retrieval of a function and gradient evaluation >> > >> > `scipy.optimize.minimize` ``BFGS`` method has improved performance by >> > avoiding >> > duplicate evaluations in some cases >> > >> > Better user feedback is provided when an objective function returns an >> > array >> > instead of a scalar. >> > >> > >> > `scipy.signal` improvements >> > -------------------------------------- >> > >> > Added a new function to calculate convolution using the overlap-add >> method, >> > named `scipy.signal.oaconvolve`. Like `scipy.signal.fftconvolve`, this >> > function supports specifying dimensions along which to do the >> convolution. >> > >> > `scipy.signal.cwt` now supports complex wavelets. >> > >> > The implementation of ``choose_conv_method`` has been updated to reflect >> > the >> > new FFT implementation. In addition, the performance has been >> significantly >> > improved (with rather drastic improvements in edge cases). >> > >> > The function ``upfirdn`` now has a ``mode`` keyword argument that can be >> > used >> > to select the signal extension mode used at the signal boundaries. These >> > modes >> > are also available for use in ``resample_poly`` via a newly added >> > ``padtype`` >> > argument. >> > >> > `scipy.signal.sosfilt` now benefits from Cython code for improved >> > performance >> > >> > `scipy.signal.resample` should be more efficient by leveraging ``rfft`` >> > when >> > possible >> > >> > `scipy.sparse` improvements >> > --------------------------------------- >> > It is now possible to use the LOBPCG method in >> `scipy.sparse.linalg.svds`. >> > >> > `scipy.sparse.linalg.LinearOperator` now supports the operation >> ``rmatmat`` >> > for adjoint matrix-matrix multiplication, in addition to ``rmatvec``. >> > >> > Multiple stability updates enable float32 support in the LOBPCG >> eigenvalue >> > solver for symmetric and Hermitian eigenvalues problems in >> > ``scipy.sparse.linalg.lobpcg``. >> > >> > A solver for the maximum flow problem has been added as >> > `scipy.sparse.csgraph.maximum_flow`. >> > >> > `scipy.sparse.csgraph.maximum_bipartite_matching` now allows non-square >> > inputs, >> > no longer requires a perfect matching to exist, and has improved >> > performance. >> > >> > `scipy.sparse.lil_matrix` conversions now perform better in some >> scenarios >> > >> > Basic support is available for ``pydata/sparse`` arrays in >> > `scipy.sparse.linalg` >> > >> > `scipy.sparse.linalg.spsolve_triangular` now supports the >> ``unit_diagonal`` >> > argument to improve call signature similarity with its dense >> counterpart, >> > `scipy.linalg.solve_triangular` >> > >> > ``assertAlmostEqual`` may now be used with sparse matrices, which have >> > added >> > support for ``__round__`` >> > >> > `scipy.spatial` improvements >> > --------------------------------------- >> > The bundled Qhull library was upgraded to version 2019.1, fixing several >> > issues. Scipy-specific patches are no longer applied to it. >> > >> > `scipy.spatial.SphericalVoronoi` now has linear memory complexity, >> improved >> > performance, and supports single-hemisphere generators. Support has also >> > been >> > added for handling generators that lie on a great circle arc (geodesic >> > input) >> > and for generators in n-dimensions. >> > >> > `scipy.spatial.transform.Rotation` now includes functions for >> calculation >> > of a >> > mean rotation, generation of the 3D rotation groups, and reduction of >> > rotations >> > with rotational symmetries. >> > >> > `scipy.spatial.transform.Slerp` is now callable with a scalar argument >> > >> > `scipy.spatial.voronoi_plot_2d` now supports furthest site Voronoi >> diagrams >> > >> > `scipy.spatial.Delaunay` and `scipy.spatial.Voronoi` now have attributes >> > for tracking whether they are furthest site diagrams >> > >> > `scipy.special` improvements >> > ----------------------------------------- >> > The Voigt profile has been added as `scipy.special.voigt_profile`. >> > >> > A real dispatch has been added for the Wright Omega function >> > (`scipy.special.wrightomega`). >> > >> > The analytic continuation of the Riemann zeta function has been added. >> (The >> > Riemann zeta function is the one-argument variant of >> `scipy.special.zeta`.) >> > >> > The complete elliptic integral of the first kind >> (`scipy.special.ellipk`) >> > is >> > now available in `scipy.special.cython_special`. >> > >> > The accuracy of `scipy.special.hyp1f1` for real arguments has been >> > improved. >> > >> > The documentation of many functions has been improved. >> > >> > `scipy.stats` improvements >> > ------------------------------------- >> > `scipy.stats.multiscale_graphcorr` added as an independence test that >> > operates on high dimensional and nonlinear data sets. It has higher >> > statistical >> > power than other `scipy.stats` tests while being the only one that >> operates >> > on >> > multivariate data. >> > >> > The generalized inverse Gaussian distribution >> (`scipy.stats.geninvgauss`) >> > has >> > been added. >> > >> > It is now possible to efficiently reuse >> `scipy.stats.binned_statistic_dd` >> > with new values by providing the result of a previous call to the >> function. >> > >> > `scipy.stats.hmean` now handles input with zeros more gracefully. >> > >> > The beta-binomial distribution is now available in >> `scipy.stats.betabinom`. >> > >> > `scipy.stats.zscore`, `scipy.stats.circmean`, `scipy.stats.circstd`, and >> > `scipy.stats.circvar` now support the ``nan_policy`` argument for >> enhanced >> > handling of ``NaN`` values >> > >> > `scipy.stats.entropy` now accepts an ``axis`` argument >> > >> > `scipy.stats.gaussian_kde.resample` now accepts a ``seed`` argument to >> > empower >> > reproducibility >> > >> > `scipy.stats.kendalltau` performance has improved, especially for large >> > inputs, >> > due to improved cache usage >> > >> > `scipy.stats.truncnorm` distribution has been rewritten to support much >> > wider >> > tails >> > >> > >> > Deprecated features >> > =================== >> > >> > `scipy` deprecations >> > ----------------------------- >> > Support for NumPy functions exposed via the root SciPy namespace is >> > deprecated >> > and will be removed in 2.0.0. For example, if you use ``scipy.rand`` or >> > ``scipy.diag``, you should change your code to directly use >> > ``numpy.random.default_rng`` or ``numpy.diag``, respectively. >> > They remain available in the currently continuing Scipy 1.x release >> series. >> > >> > The exception to this rule is using ``scipy.fft`` as a function -- >> > :mod:`scipy.fft` is now meant to be used only as a module, so the >> ability >> > to >> > call ``scipy.fft(...)`` will be removed in SciPy 1.5.0. >> > >> > In `scipy.spatial.Rotation` methods ``from_dcm``, ``as_dcm`` were >> renamed >> > to >> > ``from_matrix``, ``as_matrix`` respectively. The old names will be >> removed >> > in >> > SciPy 1.6.0. >> > >> > Method ``Rotation.match_vectors`` was deprecated in favor of >> > ``Rotation.align_vectors``, which provides a more logical and >> > general API to the same functionality. The old method >> > will be removed in SciPy 1.6.0. >> > >> > Backwards incompatible changes >> > ========================== >> > >> > `scipy.special` changes >> > --------------------------------- >> > The deprecated functions ``hyp2f0``, ``hyp1f2``, and ``hyp3f0`` have >> been >> > removed. >> > >> > The deprecated function ``bessel_diff_formula`` has been removed. >> > >> > The function ``i0`` is no longer registered with ``numpy.dual``, so that >> > ``numpy.dual.i0`` will unconditionally refer to the NumPy version >> > regardless >> > of whether `scipy.special` is imported. >> > >> > The function ``expn`` has been changed to return ``nan`` outside of its >> > domain of definition (``x, n < 0``) instead of ``inf``. >> > >> > `scipy.sparse` changes >> > -------------------------------- >> > Sparse matrix reshape now raises an error if shape is not >> two-dimensional, >> > rather than guessing what was meant. The behavior is now the same as >> before >> > SciPy 1.1.0. >> > >> > ``CSR`` and ``CSC`` sparse matrix classes should now return empty >> matrices >> > of the same type when indexed out of bounds. Previously, for some >> versions >> > of SciPy, this would raise an ``IndexError``. The change is largely >> > motivated >> > by greater consistency with ``ndarray`` and ``numpy.matrix`` semantics. >> > >> > `scipy.signal` changes >> > ------------------------------- >> > `scipy.signal.resample` behavior for length-1 signal inputs has been >> > fixed to output a constant (DC) value rather than an impulse, consistent >> > with >> > the assumption of signal periodicity in the FFT method. >> > >> > `scipy.signal.cwt` now performs complex conjugation and time-reversal of >> > wavelet data, which is a backwards-incompatible bugfix for >> > time-asymmetric wavelets. >> > >> > `scipy.stats` changes >> > ------------------------------ >> > `scipy.stats.loguniform` added with better documentation as (an alias >> for >> > ``scipy.stats.reciprocal``). ``loguniform`` generates random variables >> > that are equally likely in the log space; e.g., ``1``, ``10`` and >> ``100`` >> > are all equally likely if ``loguniform(10 ** 0, 10 ** 2).rvs()`` is >> used. >> > >> > >> > Other changes >> > ============= >> > The ``LSODA`` method of `scipy.integrate.solve_ivp` now correctly >> detects >> > stiff >> > problems. >> > >> > `scipy.spatial.cKDTree` now accepts and correctly handles empty input >> data >> > >> > `scipy.stats.binned_statistic_dd` now calculates the standard deviation >> > statistic in a numerically stable way. >> > >> > `scipy.stats.binned_statistic_dd` now throws an error if the input data >> > contains either ``np.nan`` or ``np.inf``. Similarly, in `scipy.stats` >> now >> > all >> > continuous distributions' ``.fit()`` methods throw an error if the input >> > data >> > contain any instance of either ``np.nan`` or ``np.inf``. >> > >> > >> > Authors >> > ======= >> > >> > * @endolith >> > * @wenhui-prudencemed + >> > * Abhinav + >> > * Anne Archibald >> > * ashwinpathak20nov1996 + >> > * Danilo Augusto + >> > * Nelson Auner + >> > * aypiggott + >> > * Christoph Baumgarten >> > * Peter Bell >> > * Sebastian Berg >> > * Arman Bilge + >> > * Benedikt Boecking + >> > * Christoph Boeddeker + >> > * Daniel Bunting >> > * Evgeni Burovski >> > * Angeline Burrell + >> > * Angeline G. Burrell + >> > * CJ Carey >> > * Carlos Ramos Carre?o + >> > * Mak Sze Chun + >> > * Malayaja Chutani + >> > * Christian Clauss + >> > * Jonathan Conroy + >> > * Stephen P Cook + >> > * Dylan Cutler + >> > * Anirudh Dagar + >> > * Aidan Dang + >> > * dankleeman + >> > * Brandon David + >> > * Tyler Dawson + >> > * Dieter Werthm?ller >> > * Joe Driscoll + >> > * Jakub Dyczek + >> > * D?vid Bodn?r >> > * Fletcher Easton + >> > * Stefan Endres >> > * etienne + >> > * Johann Faouzi >> > * Yu Feng >> > * Isuru Fernando + >> > * Matthew H Flamm >> > * Martin Gauch + >> > * Gabriel Gerlero + >> > * Ralf Gommers >> > * Chris Gorgolewski + >> > * Domen Gorjup + >> > * Edouard Goudenhoofdt + >> > * Jan Gwinner + >> > * Maja Gwozdz + >> > * Matt Haberland >> > * hadshirt + >> > * Pierre Haessig + >> > * David Hagen >> > * Charles Harris >> > * Gina Helfrich + >> > * Alex Henrie + >> > * Francisco J. Hernandez Heras + >> > * Andreas Hilboll >> > * Lindsey Hiltner >> > * Thomas Hisch >> > * Min ho Kim + >> > * Gert-Ludwig Ingold >> > * jakobjakobson13 + >> > * Todd Jennings >> > * He Jia >> > * Muhammad Firmansyah Kasim + >> > * Andrew Knyazev + >> > * Holger Kohr + >> > * Mateusz Konieczny + >> > * Krzysztof Pi?ro + >> > * Philipp Lang + >> > * Peter Mahler Larsen + >> > * Eric Larson >> > * Antony Lee >> > * Gregory R. Lee >> > * Chelsea Liu + >> > * Jesse Livezey >> > * Peter Lysakovski + >> > * Jason Manley + >> > * Michael Marien + >> > * Nikolay Mayorov >> > * G. D. McBain + >> > * Sam McCormack + >> > * Melissa Weber Mendon?a + >> > * Kevin Michel + >> > * mikeWShef + >> > * Sturla Molden >> > * Eric Moore >> > * Peyton Murray + >> > * Andrew Nelson >> > * Clement Ng + >> > * Juan Nunez-Iglesias >> > * Renee Otten + >> > * Kellie Ottoboni + >> > * Ayappan P >> > * Sambit Panda + >> > * Tapasweni Pathak + >> > * Oleksandr Pavlyk >> > * Fabian Pedregosa >> > * Petar Mlinari? >> > * Matti Picus >> > * Marcel Plch + >> > * Christoph Pohl + >> > * Ilhan Polat >> > * Siddhesh Poyarekar + >> > * Ioannis Prapas + >> > * James Alan Preiss + >> > * Yisheng Qiu + >> > * Eric Quintero >> > * Bharat Raghunathan + >> > * Tyler Reddy >> > * Joscha Reimer >> > * Antonio Horta Ribeiro >> > * Lucas Roberts >> > * rtshort + >> > * Josua Sassen >> > * Kevin Sheppard >> > * Scott Sievert >> > * Leo Singer >> > * Kai Striega >> > * S?ren Fuglede J?rgensen >> > * tborisow + >> > * ?tienne Tremblay + >> > * tuxcell + >> > * Miguel de Val-Borro >> > * Andrew Valentine + >> > * Hugo van Kemenade >> > * Paul van Mulbregt >> > * Sebastiano Vigna >> > * Pauli Virtanen >> > * Dany Vohl + >> > * Ben Walsh + >> > * Huize Wang + >> > * Warren Weckesser >> > * Anreas Weh + >> > * Joseph Weston + >> > * Adrian Wijaya + >> > * Timothy Willard + >> > * Josh Wilson >> > * Kentaro Yamamoto + >> > * Dave Zbarsky + >> > >> > A total of 142 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 1.4.0 >> > -------------------------------- >> > >> > * `#1255 `__: maxiter >> broken >> > for Scipy.sparse.linalg gmres, in addition to... >> > * `#1301 `__: consolidate >> > multipack.h from interpolate and integrate packages... >> > * `#1739 `__: Single >> precision >> > FFT insufficiently accurate. (Trac #1212) >> > * `#1795 `__: stats >> > test_distributions.py: replace old fuzz tests (Trac #1269) >> > * `#2233 `__: fftpack >> segfault >> > with big arrays (Trac #1714) >> > * `#2434 `__: rmatmat and >> the >> > sophistication of linear operator objects >> > * `#2477 `__: >> > stats.truncnorm.rvs() does not give symmetric results for negative... >> > * `#2629 `__: FFTpack is >> > unacceptably slow on non power of 2 >> > * `#2883 `__: >> UnboundLocalError >> > in scipy.interpolate.splrep >> > * `#2956 `__: Feature >> Request: >> > axis argument for stats.entropy function >> > * `#3528 `__: Segfault on >> > test_djbfft (possibly MKL-related?) >> > * `#3793 `__: cwt should >> also >> > return complex array >> > * `#4464 `__: TST: >> > residue/residuez/invres/invresz don't have any tests >> > * `#4561 `__: BUG: tf >> filter >> > trailing and leading zeros in residuez >> > * `#4669 `__: Rewrite >> sosfilt >> > to make a single loop over the input? >> > * `#5040 `__: BUG: Empty >> data >> > handling of (c)KDTrees >> > * `#5112 `__: boxcox >> transform >> > edge cases could use more care >> > * `#5441 `__: >> scipy.stats.ncx2 >> > fails for nc=0 >> > * `#5502 `__: args keyword >> not >> > handled in optimize.curve_fit >> > * `#6484 `__: Qhull >> > segmentation fault >> > * `#6900 `__: >> > linear_sum_assignment with infinite weights >> > * `#6966 `__: >> Hypergeometric >> > Functions documentation is lacking >> > * `#6999 `__: possible >> false >> > positive corruption check in compressed loadmat() >> > * `#7018 `__: ydata that >> needs >> > broadcasting renders curve_fit unable to compute... >> > * `#7140 `__: trouble with >> > documentation for windows >> > * `#7327 `__: >> > interpolate.ndgriddata.griddata causes Python to crash rather... >> > * `#7396 `__: >> > MatrixLinearOperator implements _adjoint(), but not _transpose() >> > * `#7400 `__: BUG(?): >> special: >> > factorial and factorial2 return a 0-dimensional... >> > * `#7434 `__: Testing of >> > scipy.stats continuous distributions misses 25 distributions >> > * `#7491 `__: Several >> > scipy.stats distributions (fisk, burr, burr12, f) return... >> > * `#7759 `__: Overflow in >> > stats.kruskal for large samples >> > * `#7906 `__: Wrong result >> from >> > scipy.interpolate.UnivariateSpline.integral... >> > * `#8165 `__: ENH: match >> > functionality of R for hmean >> > * `#8417 `__: >> > optimimze.minimize(method='L-BFGS-B', options={'disp': True})... >> > * `#8535 `__: Strictly >> > increasing requirement in UnivariateSpline >> > * `#8815 `__: [BUG] GMRES: >> > number of iteration is only increased if callback... >> > * `#9207 `__: >> > scipy.linalg.solve_triangular speed after scipy.linalg.lu_factor >> > * `#9275 `__: new feature: >> > adding LOBPCG solver in svds in addition to ARPACK >> > * `#9403 `__: range of >> > truncnorm.logpdf could be extended >> > * `#9429 `__: gaussian_kde >> not >> > working with numpy matrix >> > * `#9515 `__: ndimage >> > implementation relies on undefined behavior >> > * `#9643 `__: arpack >> returns >> > singular values in ascending order >> > * `#9669 `__: DOC: >> > matthew-brett/build-openblas has been retired >> > * `#9852 `__: >> > scipy.spatial.ConvexHull exit with code 134, free(): invalid... >> > * `#9902 `__: >> > scipy.stats.truncnorm second moment may be wrong >> > * `#9943 `__: Custom >> sampling >> > methods in shgo do not work >> > * `#9947 `__: DOC: >> Incorrect >> > documentation for \`nan_policy='propagate\` in... >> > * `#9994 `__: BUG: sparse: >> > reshape method allows a shape containing an arbitrary... >> > * `#10036 `__: Official >> Nelder >> > mead tutorial uses xtol instead of xatol, which... >> > * `#10078 `__: possible >> to get >> > a better error message when objective function... >> > * `#10092 `__: overflow in >> > truncnorm.rvs >> > * `#10121 `__: A little >> > spelling mistake >> > * `#10126 `__: inaccurate >> std >> > implementation in binned_statistic >> > * `#10161 `__: Error in >> > documentation scipy.special.modstruve >> > * `#10195 `__: Derivative >> of >> > spline with 'const' extrapolation is also extrapolted... >> > * `#10206 `__: sparse >> matrices >> > indexing with scipy 1.3 >> > * `#10236 `__: >> Non-descriptive >> > error on type mismatch for functions of scipy.optimize... >> > * `#10258 `__: LOBPCG >> > convergence failure if guess provided >> > * `#10262 `__: distance >> matrix >> > lacks dtype checks / warnings >> > * `#10271 `__: BUG: >> optimize >> > failure on wheels >> > * `#10277 `__: >> > scipy.special.zeta(0) = NAN >> > * `#10292 `__: DOC/REL: >> Some >> > sections of the release notes are not nested correctly. >> > * `#10300 `__: >> > scipy.stats.rv_continuous.fit throws empty RuntimeError when... >> > * `#10319 `__: events in >> > scipy.integrate.solve_ivp: How do I setup an events... >> > * `#10323 `__: Adding more >> > low-level LAPACK wrappers >> > * `#10360 `__: firwin2 >> > inadvertently modifies input and may result in undefined... >> > * `#10388 `__: BLD: >> > TestHerd::test_hetrd core dumps with Python-dbg >> > * `#10395 `__: Remove >> warning >> > about output shape of zoom >> > * `#10403 `__: DOC: >> > scipy.signal.resample ignores t parameter >> > * `#10421 `__: Yeo-Johnson >> > power transformation fails with integer input data >> > * `#10422 `__: BUG: >> scipy.fft >> > does not support multiprocessing >> > * `#10427 `__: ENH: >> convolve >> > numbers should be updated >> > * `#10444 `__: BUG: >> > scipy.spatial.transform.Rotation.match_vectors returns improper... >> > * `#10488 `__: ENH: >> DCTs/DSTs >> > for scipy.fft >> > * `#10501 `__: BUG: >> > scipy.spatial.HalfspaceIntersection works incorrectly >> > * `#10514 `__: BUG: >> cKDTree >> > GIL handling is incorrect >> > * `#10535 `__: TST: master >> > branch CI failures >> > * `#10588 `__: scipy.fft >> and >> > numpy.fft inconsistency when axes=None and shape... >> > * `#10628 `__: Scipy >> > python>3.6 Windows wheels don't ship msvcp\*.dll >> > * `#10733 `__: DOC/BUG: >> > min_only result does not match documentation >> > * `#10774 `__: >> min_only=true >> > djisktra infinite loop with duplicate indices >> > * `#10775 `__: >> > UnboundLocalError in Radau when given a NaN >> > * `#10835 `__: >> io.wavfile.read >> > unnecessarily raises an error for a bad wav header >> > * `#10838 `__: Error in >> > documentation for scipy.linalg.lu_factor >> > * `#10875 `__: DOC: >> Graphical >> > guides (using TikZ) >> > * `#10880 `__: setting >> verbose >> >> 2 in minimize with trust-constr method leads... >> > * `#10887 `__: >> > scipy.signal.signaltools._fftconv_faster has incorrect estimates >> > * `#10948 `__: >> gammainc(0,x) = >> > nan but should be 1, gammaincc(0,x) = nan but... >> > * `#10952 `__: >> > TestQRdelete_F.test_delete_last_p_col test failure >> > * `#10968 `__: API: Change >> > normalized=False to normalize=True in Rotation >> > * `#10987 `__: Memory >> leak in >> > shgo triangulation >> > * `#10991 `__: Error >> running >> > openBlas probably missing a step >> > * `#11033 `__: deadlock >> on osx >> > for python 3.8 >> > * `#11041 `__: Test >> failure in >> > wheel builds for TestTf2zpk.test_simple >> > * `#11089 `__: Regression >> in >> > scipy.stats where distribution will not accept loc and scale parameters >> > * `#11100 `__: BUG: >> > multiscale_graphcorr random state seeding and parallel use >> > * `#11121 `__: Calls to >> > `scipy.interpolate.splprep` increase RAM usage. >> > * `#11125 `__: BUG: >> segfault >> > when slicing a CSR or CSC sparse matrix with slice start index > stop >> index >> > * `#11198 `__: BUG: sparse >> > eigs (arpack) shift-invert drops the smallest eigenvalue for some k >> > >> > Pull requests for 1.4.0 >> > ------------------------------- >> > >> > * `#4591 `__: BUG, TST: >> Several >> > issues with scipy.signal.residue >> > * `#6629 `__: ENH: sparse: >> > canonicalize on initialization >> > * `#7076 `__: ENH: add >> complex >> > wavelet support to scipy.signal.cwt. >> > * `#8681 `__: ENH add >> generalized >> > inverse Gaussian distribution to scipy.stats >> > * `#9064 `__: BUG/ENH: Added >> > default _transpose into LinearOperator. Fixes... >> > * `#9215 `__: ENH: Rbf >> > interpolation of large multi-dimensional data >> > * `#9311 `__: ENH: Added >> voigt in >> > scipy.special. >> > * `#9642 `__: ENH: integrate: >> > quad() for vector-valued functions >> > * `#9679 `__: DOC: expand >> > docstring of exponweib distribution >> > * `#9684 `__: TST: add >> ppc64le ci >> > testing >> > * `#9800 `__: WIP : ENH: >> > Refactored _hungarian.py for speed and added a minimize/maximize? >> > * `#9847 `__: DOC: Change >> > integrate tutorial to use solve_ivp instead of odeint >> > * `#9876 `__: ENH: Use rfft >> when >> > possible in resampling >> > * `#9998 `__: BUG: Do not >> remove >> > 1s when calling sparse: reshape method #9994 >> > * `#10002 `__: ENH: adds >> > constraints for differential evolution >> > * `#10098 `__: ENH: >> integrate: >> > add args argument to solve_ivp. >> > * `#10099 `__: DOC: Add >> missing >> > docs for linprog unknown_options >> > * `#10104 `__: BUG: Rewrite >> of >> > stats.truncnorm distribution. >> > * `#10105 `__: MAINT improve >> > efficiency of rvs_ratio_uniforms in scipy.stats >> > * `#10107 `__: TST: >> > dual_annealing set seed >> > * `#10108 `__: ENH: stats: >> > improve kendall_tau cache usage >> > * `#10110 `__: MAINT: _lib: >> Fix >> > a build warning. >> > * `#10114 `__: FIX: only >> print >> > bounds when supported by minimizer (shgo) >> > * `#10115 `__: TST: Add a >> test >> > with an almost singular design matrix for lsq_linear >> > * `#10118 `__: MAINT: fix >> rdist >> > methods in scipy.stats >> > * `#10119 `__: MAINT: >> improve >> > rvs of randint in scipy.stats >> > * `#10127 `__: Fix typo in >> > record array field name (spatial-ckdtree-sparse_distance? >> > * `#10130 `__: MAINT: >> ndimage: >> > Fix some compiler warnings. >> > * `#10131 `__: DOC: Note the >> > solve_ivp args enhancement in the 1.4.0 release... >> > * `#10133 `__: MAINT: add >> rvs >> > for semicircular in scipy.stats >> > * `#10138 `__: BUG: special: >> > Invalid arguments to ellip_harm can crash Python. >> > * `#10139 `__: MAINT: >> spatial: >> > Fix some compiler warnings in the file distance_wrap.c. >> > * `#10140 `__: ENH: add >> handling >> > of NaN in RuntimeWarning except clause >> > * `#10142 `__: DOC: return >> value >> > of scipy.special.comb >> > * `#10143 `__: MAINT: Loosen >> > linprog tol >> > * `#10152 `__: BUG: Fix >> custom >> > sampling input for shgo, add unittest >> > * `#10154 `__: MAINT: add >> > moments and improve doc of mielke in scipy.stats >> > * `#10158 `__: Issue #6999: >> read >> > zlib checksum before checking bytes read. >> > * `#10166 `__: BUG: >> Correctly >> > handle broadcasted ydata in curve_fit pcov computation. >> > * `#10167 `__: DOC: >> special: Add >> > missing factor of \`i\` to \`modstruve\` docstring >> > * `#10168 `__: MAINT: >> stats: Fix >> > an incorrect comment. >> > * `#10169 `__: ENH: >> optimize: >> > Clarify error when objective function returns... >> > * `#10172 `__: DEV: Run >> tests in >> > parallel when --parallel flag is passed to... >> > * `#10173 `__: ENH: >> Implement >> > DOP853 ODE integrator >> > * `#10176 `__: Fixed typo >> > * `#10182 `__: TST: fix test >> > issue for stats.pearsonr >> > * `#10184 `__: MAINT: stats: >> > Simplify zmap and zscore (we can use keepdims now). >> > * `#10191 `__: DOC: fix a >> > formatting issue in the scipy.spatial module docstring. >> > * `#10193 `__: DOC: Updated >> > docstring for optimize.nnls >> > * `#10198 `__: DOC, ENH: >> > special: Make \`hyp2f1\` references more specific >> > * `#10202 `__: DOC: Format >> DST >> > and DCT definitions as latex equations >> > * `#10207 `__: BUG: >> Compressed >> > matrix indexing should return a scalar >> > * `#10210 `__: DOC: Update >> docs >> > for connection='weak' in connected_components >> > * `#10225 `__: DOC: Clarify >> new >> > interfaces for legacy functions in 'optimize' >> > * `#10231 `__: DOC, MAINT: >> gpg2 >> > updates to release docs / pavement >> > * `#10235 `__: LICENSE: >> split >> > license file in standard BSD 3-clause and bundled. >> > * `#10238 `__: ENH: Add new >> > scipy.fft module using pocketfft >> > * `#10243 `__: BUG: fix ARFF >> > reader regression with quoted values. >> > * `#10248 `__: DOC: update >> > README file >> > * `#10255 `__: CI: bump >> OpenBLAS >> > to match wheels >> > * `#10264 `__: TST: add >> tests >> > for stats.tvar with unflattened arrays >> > * `#10280 `__: MAINT: >> stats: Use >> > a constant value for sqrt(2/PI). >> > * `#10286 `__: Development >> > Documentation Overhaul >> > * `#10290 `__: MAINT: >> Deprecate >> > NumPy functions in SciPy root >> > * `#10291 `__: FIX: Avoid >> > importing xdist when checking for availability >> > * `#10295 `__: Disable >> > deprecated Numpy API in __odrpack.c >> > * `#10296 `__: ENH: C++ >> > extension for linear assignment problem >> > * `#10298 `__: ENH: Made >> pade >> > function work with complex inputs >> > * `#10301 `__: DOC: Fix >> critical >> > value significance levels in stats.anderson_ksamp >> > * `#10307 `__: Minkowski >> > Distance Type Fix (issue #10262) >> > * `#10309 `__: BUG: Pass >> > jac=None directly to lsoda >> > * `#10310 `__: BUG: >> interpolate: >> > UnivariateSpline.derivative.ext is 'zeros'... >> > * `#10312 `__: FIX: Fixing a >> > typo in a comment >> > * `#10314 `__: scipy.spatial >> > enhancement request >> > * `#10315 `__: DOC: Update >> > integration tutorial to solve_ivp >> > * `#10318 `__: DOC: update >> the >> > example for PPoly.solve >> > * `#10333 `__: TST: add >> tests >> > for stats.tvar with unflattened arrays >> > * `#10334 `__: MAINT: >> special: >> > Remove deprecated \`hyp2f0\`, \`hyp1f2\`, and... >> > * `#10336 `__: BUG: >> > linalg/interpolative: fix interp_decomp modifying input >> > * `#10341 `__: BUG: >> > sparse.linalg/gmres: deprecate effect of callback on semantics... >> > * `#10344 `__: DOC: improve >> > wording of mathematical formulation >> > * `#10345 `__: ENH: Tiled QR >> > wrappers for scipy.linalg.lapack >> > * `#10350 `__: MAINT: >> linalg: >> > Use the new fft subpackage in linalg.dft test... >> > * `#10351 `__: BUG: Fix >> unstable >> > standard deviation calculation in histogram >> > * `#10353 `__: Bug: >> > interpolate.NearestNDInterpolator (issue #10352) >> > * `#10357 `__: DOC: linalg: >> > Refer to scipy.fft.fft (not fftpack) in the dft... >> > * `#10359 `__: DOC: Update >> > roadmap now scipy.fft has been merged >> > * `#10361 `__: ENH: Prefer >> > scipy.fft to scipy.fftpack in scipy.signal >> > * `#10371 `__: DOC: Tweaks >> to >> > fft documentation >> > * `#10372 `__: DOC: Fix >> typos >> > * `#10377 `__: TST, MAINT: >> > adjustments for pytest 5.0 >> > * `#10378 `__: ENH: _lib: >> allow >> > new np.random.Generator in check_random_state >> > * `#10379 `__: BUG: sparse: >> set >> > writeability to be forward-compatible with numpy>=1.17 >> > * `#10381 `__: BUG: Fixes >> > gh-7491, pdf at x=0 of fisk/burr/burr12/f distributions. >> > * `#10387 `__: ENH: >> > optimize/bfgs: don't evaluate twice at initial point for... >> > * `#10392 `__: [DOC] Add an >> > example for _binned_statistic_dd >> > * `#10396 `__: Remove >> warning >> > about output shape of zoom >> > * `#10397 `__: ENH: Add >> > check_finite to sp.linalg.norm >> > * `#10399 `__: ENH: Add >> > __round__ method to sparse matrix >> > * `#10407 `__: MAINT: drop >> > pybind11 from install_requires, it's only build-time... >> > * `#10408 `__: TST: use >> > pytest.raises, not numpy assert_raises >> > * `#10409 `__: CI: uninstall >> > nose on Travis >> > * `#10410 `__: [ENH] ncx2 >> > dispatch to chi2 when nc=0 >> > * `#10411 `__: TST: >> optimize: >> > test should use assert_allclose for fp comparisons >> > * `#10414 `__: DOC: add >> pybind11 >> > to the other part of quickstart guides >> > * `#10417 `__: DOC: special: >> > don't mark non-ufuncs with a \`[+]\` >> > * `#10423 `__: FIX: Use >> > pybind11::isinstace to check array dtypes >> > * `#10424 `__: DOC: add >> doctest >> > example for binary data for ttest_ind_from_stats >> > * `#10425 `__: ENH: Add >> missing >> > Hermitian transforms to scipy.fft >> > * `#10426 `__: MAINT: Fix >> doc >> > build bugs >> > * `#10431 `__: Update numpy >> > version for AIX >> > * `#10433 `__: MAINT: Minor >> > fixes for the stats >> > * `#10434 `__: BUG: special: >> > make \`ndtri\` return NaN outside domain of definition >> > * `#10435 `__: BUG: Allow >> > integer input data in scipy.stats.yeojohnson >> > * `#10438 `__: [DOC] Add >> example >> > for kurtosis >> > * `#10440 `__: ENH: special: >> > make \`ellipk\` a ufunc >> > * `#10443 `__: MAINT: >> ndimage: >> > malloc fail check >> > * `#10447 `__: BLD: Divert >> > output from test compiles into a temporary directory >> > * `#10451 `__: MAINT: >> signal: >> > malloc fail check >> > * `#10455 `__: BUG: >> special: fix >> > values of \`hyperu\` for negative \`x\` >> > * `#10456 `__: DOC: Added >> > comment clarifying the call for dcsrch.f in lbfgsb.f >> > * `#10457 `__: BUG: Allow >> > ckdtree to accept empty data input >> > * `#10459 `__: BUG:TST: >> Compute >> > lwork safely >> > * `#10460 `__: [DOC] Add >> example >> > to entropy >> > * `#10461 `__: DOC: >> Quickstart >> > Guide updates >> > * `#10462 `__: TST: special: >> > only show max atol/rtol for test points that failed >> > * `#10465 `__: BUG: >> Correctly >> > align fft inputs >> > * `#10467 `__: ENH: >> lower-memory >> > duplicate generator checking in spatial.SphericalVoronoi >> > * `#10470 `__: ENH: >> Normalise >> > the inverse DCT/DST in scipy.fft >> > * `#10472 `__: BENCH: adjust >> > timeout for slow setup_cache >> > * `#10475 `__: CI: include >> > python debug for Travis-ci >> > * `#10476 `__: TST: >> special: use >> > \`__tracebackhide__\` to get better error messages >> > * `#10477 `__: ENH: faster >> > region building in spatial.SphericalVoronoi >> > * `#10479 `__: BUG: stats: >> Fix a >> > few issues with the distributions' fit method. >> > * `#10480 `__: Add >> RuntimeError >> > in _distn_infrastructure.py in fit() method >> > * `#10481 `__: BENCH, MAINT: >> > wheel_cache_size has been renamed build_cache_size >> > * `#10494 `__: ENH: faster >> > circumcenter calculation in spatial.SphericalVoronoi >> > * `#10500 `__: Splrep >> > _curfit_cache global variable bugfix >> > * `#10503 `__: BUG: >> > spatial/qhull: get HalfspaceIntersection.dual_points from... >> > * `#10506 `__: DOC: >> interp2d, >> > note nearest neighbor extrapolation >> > * `#10507 `__: MAINT: Remove >> > fortran fftpack library in favour of pypocketfft >> > * `#10508 `__: TST: fix a >> bug in >> > the circular import test. >> > * `#10509 `__: MAINT: Set up >> > _build_utils as subpackage >> > * `#10516 `__: BUG: Use >> nogil >> > contexts in cKDTree >> > * `#10517 `__: ENH: >> fftconvolve >> > should not FFT broadcastable axes >> > * `#10518 `__: ENH: Speedup >> > fftconvolve >> > * `#10520 `__: DOC: Proper >> .rst >> > formatting for deprecated features and Backwards... >> > * `#10523 `__: DOC: Improve >> > scipy.signal.resample documentation >> > * `#10524 `__: ENH: Add MGC >> to >> > scipy.stats >> > * `#10525 `__: [ENH] >> ncx2.ppf >> > dispatch to chi2 when nc=0 >> > * `#10526 `__: DOC: clarify >> > laplacian normalization >> > * `#10528 `__: API: Rename >> > scipy.fft DCT/DST shape argument to s >> > * `#10531 `__: BUG: fixed >> > improper rotations in spatial.transform.rotation.match_vectors >> > * `#10533 `__: [DOC] Add >> example >> > for winsorize function >> > * `#10539 `__: MAINT: >> special: >> > don't register \`i0\` with \`numpy.dual\` >> > * `#10540 `__: MAINT: Fix >> Travis >> > and Circle >> > * `#10542 `__: MAINT: >> > interpolate: use cython_lapack >> > * `#10547 `__: Feature >> request. >> > Add furthest site Voronoi diagrams to scipy.spatial.plotutils. >> > * `#10549 `__: [BUG] Fix >> bug in >> > trimr when inclusive=False >> > * `#10552 `__: add >> > scipy.signal.upfirdn signal extension modes >> > * `#10555 `__: MAINT: >> special: >> > move \`c_misc\` into Cephes >> > * `#10556 `__: [DOC] Add >> example >> > for trima >> > * `#10562 `__: [DOC] Fix >> triple >> > string fo trimmed so that __doc__ can show... >> > * `#10563 `__: improve >> > least_squares error msg for mismatched shape >> > * `#10564 `__: ENH: linalg: >> > memoize get_lapack/blas_funcs to speed it up >> > * `#10566 `__: ENH: add >> > implementation of solver for the maximum flow problem >> > * `#10567 `__: BUG: >> spatial: use >> > c++11 construct for getting start of vector... >> > * `#10568 `__: DOC: special: >> > small tweaks to the \`zetac\` docstring >> > * `#10571 `__: [ENH] >> > Gaussian_kde can accept matrix dataset >> > * `#10574 `__: ENH: linalg: >> > speed up _compute_lwork by avoiding numpy constructs >> > * `#10582 `__: Fix typos >> with >> > typos in bundled libraries reverted >> > * `#10583 `__: ENH: >> special: add >> > the analytic continuation of Riemann zeta >> > * `#10584 `__: MAINT: >> special: >> > clean up \`special.__all__\` >> > * `#10586 `__: BUG: >> > multidimensional scipy.fft functions should accept 's' rather... >> > * `#10587 `__: BUG: >> > integrate/lsoda: never abort run, set error istate instead >> > * `#10594 `__: API: >> Replicate >> > numpy's fftn behaviour when s is given but not... >> > * `#10599 `__: DOC: dev: >> update >> > documentation vs. github pull request workflow... >> > * `#10603 `__: MAINT: >> installer >> > scripts removed >> > * `#10604 `__: MAINT: Change >> > c\*np.ones(...) to np.full(..., c, ...) in many... >> > * `#10608 `__: Univariate >> > splines should require x to be strictly increasing... >> > * `#10613 `__: ENH: Add seed >> > option for gaussian_kde.resample >> > * `#10614 `__: ENH: Add >> parallel >> > computation to scipy.fft >> > * `#10615 `__: MAINT: >> > interpolate: remove unused header file >> > * `#10616 `__: MAINT: Clean >> up >> > 32-bit platform xfail markers >> > * `#10618 `__: BENCH: Added >> > 'trust-constr' to minimize benchmarks >> > * `#10621 `__: [MRG] >> multiple >> > stability updates in lobpcg >> > * `#10622 `__: MAINT: >> forward >> > port 1.3.1 release notes >> > * `#10624 `__: DOC: stats: >> Fix >> > spelling of 'support'. >> > * `#10627 `__: DOC: stats: >> Add >> > references for the alpha distribution. >> > * `#10629 `__: MAINT: >> special: >> > avoid overflow longer in \`zeta\` for negative... >> > * `#10630 `__: TST: GH10271, >> > relax test assertion, fixes #10271 >> > * `#10631 `__: DOC: >> nelder-mean >> > uses xatol fixes #10036 >> > * `#10633 `__: BUG: >> interpolate: >> > integral(a, b) should be zero when both limits... >> > * `#10635 `__: DOC: special: >> > complete hypergeometric functions documentation >> > * `#10636 `__: BUG: >> special: use >> > series for \`hyp1f1\` when it converges rapidly >> > * `#10641 `__: ENH: allow >> > matching of general bipartite graphs >> > * `#10643 `__: ENH: >> > scipy.sparse.linalg.spsolve triangular unit diagonal >> > * `#10650 `__: ENH: >> Cythonize >> > sosfilt >> > * `#10654 `__: DOC: Vertical >> > alignment of table entries >> > * `#10655 `__: ENH: >> Dockerfile >> > for scipy development >> > * `#10660 `__: TST: clean up >> > tests for rvs in scipy.stats >> > * `#10664 `__: Throw error >> on >> > non-finite input for binned_statistic_dd() >> > * `#10665 `__: DOC: special: >> > improve the docstrings for \`gamma\` and \`gammasgn\` >> > * `#10669 `__: TST: Update >> > scipy.fft real transform tests >> > * `#10670 `__: DOC: Clarify >> docs >> > and error messages for scipy.signal.butter >> > * `#10672 `__: ENH: return >> > solution attribute when using events in solve_ivp >> > * `#10675 `__: MAINT: >> special: >> > add an explicit NaN check for \`iv\` arguments >> > * `#10679 `__: DOC: >> special: Add >> > documentation for \`beta\` function >> > * `#10681 `__: TST: >> > sparse.linalg: fix arnoldi test seed >> > * `#10682 `__: DOC: >> special: Add >> > documentation for \`betainc\` function >> > * `#10684 `__: TST: special: >> > require Mpmath 1.1.0 for \`test_hyperu_around_0\` >> > * `#10686 `__: FIX: sphinx >> > isattributedescriptor is not available in sphinx... >> > * `#10687 `__: DOC: added >> Docker >> > quickstart guide by @andyfaff >> > * `#10689 `__: DOC: special: >> > clarify format of parameters/returns sections for... >> > * `#10690 `__: DOC: special: >> > improve docstrings of incomplete gamma functions >> > * `#10692 `__: ENH: >> > higher-dimensional input in \`spatial.SphericalVoronoi\` >> > * `#10694 `__: ENH: >> > ScalarFunction.fun_and_grad >> > * `#10698 `__: DOC: >> special: Add >> > documentation for \`betaincinv\` >> > * `#10699 `__: MAINT: remove >> > time print lbfgsb fixes #8417 >> > * `#10701 `__: TST, MAINT: >> bump >> > OpenBLAS to 0.3.7 stable >> > * `#10702 `__: DOC: clarify >> > iterations consume multiple function calls >> > * `#10703 `__: DOC: iprint >> doc >> > lbfgsb closes #5482 >> > * `#10708 `__: TST: test >> > suggested in gh1758 >> > * `#10710 `__: ENH: Added >> > nan_policy to circ functions in \`stats\` >> > * `#10712 `__: ENH: add axis >> > parameter to stats.entropy >> > * `#10714 `__: DOC: >> Formatting >> > fix rv_continuous.expect docs >> > * `#10715 `__: DOC: BLD: >> update >> > doc Makefile for python version; add scipy version... >> > * `#10717 `__: MAINT: >> modernize >> > doc/Makefile >> > * `#10719 `__: Enable >> setting >> > minres initial vector >> > * `#10720 `__: DOC: silence >> > random warning in doc build for \`stats.binned_statistic_dd\` >> > * `#10724 `__: DEV: Add doc >> > option to runtests.py >> > * `#10728 `__: MAINT: get >> rid of >> > gramA, gramB text files that lobpcg tests leave... >> > * `#10732 `__: DOC: add >> min_only >> > to docstring for Dijkstra's algorithm >> > * `#10734 `__: DOC: spell >> out >> > difference between source and target in shortest... >> > * `#10735 `__: Fix for >> Python 4 >> > * `#10739 `__: BUG: >> > optimize/slsqp: deal with singular BFGS update >> > * `#10741 `__: ENH: LAPACK >> > wrappers for ?geequ, ?geequb, ?syequb, ?heequb >> > * `#10742 `__: DOC: >> special: add >> > to the docstring of \`gammaln\` >> > * `#10743 `__: ENH: >> special: add >> > a real dispatch for \`wrightomega\` >> > * `#10746 `__: MAINT: Fix >> typos >> > in comments, docs and test name >> > * `#10747 `__: Remove >> spurious >> > quotes >> > * `#10750 `__: MAINT: make >> > cython code more precise >> > * `#10751 `__: MAINT: Check >> that >> > scipy.linalg.lapack functions are documented >> > * `#10752 `__: MAINT: >> special: >> > use \`sf_error\` in Cephes >> > * `#10755 `__: DOC: >> cluster: Add >> > 'See Also' and 'Examples' for kmeans2. >> > * `#10763 `__: MAINT: list >> of >> > minimize methods >> > * `#10768 `__: BUG: Fix >> corner >> > case for sos2zpk >> > * `#10773 `__: Fix error >> type >> > for complex input to scipy.fftpack.rfft and irfft >> > * `#10776 `__: ENH: handle >> > geodesic input in \`spatial.SphericalVoronoi\` >> > * `#10777 `__: MAINT: >> > minimizer-->custom should handle the kinds of bounds/constrain?... >> > * `#10781 `__: ENH: >> > solve_triangular C order improvement >> > * `#10787 `__: Fix behavior >> of >> > \`exp1\` on branch cut and add docstring >> > * `#10789 `__: DOC: >> special: add >> > parameters/returns doc sections for erfc/erfcx/erfi >> > * `#10790 `__: Travis CI: >> sudo >> > is deprecated and Xenial is default distro >> > * `#10792 `__: DOC: >> special: add >> > full docstring for \`expi\` >> > * `#10799 `__: DOC: >> special: add >> > a complete docstring for \`expn\` >> > * `#10800 `__: Docs edits >> (GSoD) >> > * `#10802 `__: BUG: fix >> > UnboundLocalError in Radau (scipy#10775) >> > * `#10804 `__: ENH: Speed up >> > next_fast_len with LRU cache >> > * `#10805 `__: DOC: Fix >> > unbalanced quotes in signal.place_poles >> > * `#10809 `__: ENH: Speed up >> > next_fast_len >> > * `#10810 `__: ENH: Raise >> > catchable exceptions for bad Fortran files >> > * `#10811 `__: MAINT: >> optimize: >> > Remove extra variable from _remove_redundancy_dense >> > * `#10813 `__: MAINT: >> special: >> > Remove unused variables from _kolmogi and _smirnovi >> > * `#10815 `__: DOC, API: >> > scipy.stats.reciprocal is "log-uniform" >> > * `#10816 `__: MAINT: >> special: >> > remove deprecated \`bessel_diff_formula\` >> > * `#10817 `__: DOC: special: >> > complete the docstring for \`fresnel\` >> > * `#10820 `__: Fixed >> > compiler_helper.py to allow compilation with ICC on Linux >> > * `#10823 `__: DOC: updated >> > reference guide text for consistency in writing... >> > * `#10825 `__: MAINT: >> special: >> > change some features of the Voigt function >> > * `#10828 `__: MAINT: >> integrate: >> > Remove unused variable from init_callback >> > * `#10830 `__: Adding LOBPCG >> > solver in svds in addition to ARPACK >> > * `#10837 `__: WIP: ENH: >> > reduction function for \`spatial.tranform.Rotation\`... >> > * `#10843 `__: ENH: Adding >> > optional parameter to stats.zscores to allow for... >> > * `#10845 `__: Rebase >> kruskal >> > fix >> > * `#10847 `__: remove >> redundant >> > __getitem__ from scipy.sparse.lil >> > * `#10848 `__: Better >> handling >> > of empty (not missing) docstrings >> > * `#10849 `__: ENH: >> implement >> > rmatmat for LinearOperator >> > * `#10850 `__: MAINT : >> > Refactoring lil List of Lists >> > * `#10851 `__: DOC: add a >> > generative art example to the scipy.spatial tutorial. >> > * `#10852 `__: DOC: linalg: >> > fixed gh-10838 unused imports in example deleted >> > * `#10854 `__: DOC: >> special: add >> > a full docstring for \`pdtr\` >> > * `#10861 `__: ENH: option >> to >> > reuse binnumbers in stats.binned_statistic_dd >> > * `#10863 `__: DOC: partial >> > standardization and validation of scipy.stats reference... >> > * `#10865 `__: BUG: >> special: fix >> > incomplete gamma functions for infinite \`a\` >> > * `#10866 `__: ENH: >> calculation >> > of mean in spatial.transform.Rotation >> > * `#10867 `__: MAINT: Also >> store >> > latex directory >> > * `#10869 `__: ENH: >> Implement >> > overlap-add convolution >> > * `#10870 `__: ENH: Do not >> raise >> > EOF error if wavfile data read >> > * `#10876 `__: ENH: Add >> > beta-binomial distribution to scipy.stats >> > * `#10878 `__: MAINT: >> Update R >> > project URL >> > * `#10883 `__: MAINT: >> (ndimage) >> > More robust check for output being a numpy dtype >> > * `#10884 `__: DOC: Added >> > instructions on adding a new distribution to scipy.stats. >> > * `#10885 `__: [BUG] fix >> lobpcg >> > with maxiter=None results in Exception >> > * `#10899 `__: ENH: Match R >> > functionality for hmean >> > * `#10900 `__: MAINT: >> stats: Use >> > keepdims to simplify a few lines in power_divergence. >> > * `#10901 `__: ENH: >> > sparse/linalg: support pydata/sparse matrices >> > * `#10907 `__: Check whether >> > \`maxiter\` is integer >> > * `#10912 `__: ENH: warn >> user >> > that quad() ignores \`points=...\` when \`weight=...\`... >> > * `#10918 `__: CI: fix >> Travis CI >> > py3.8 build >> > * `#10920 `__: MAINT: Update >> > constants to codata 2018 values (second try) >> > * `#10921 `__: ENH: >> > scipy.sparse.lil: tocsr accelerated >> > * `#10924 `__: BUG: Forbid >> > passing 'args' as kwarg in scipy.optimize.curve_fit >> > * `#10928 `__: DOC: Add >> examples >> > to io.wavfile docstrings >> > * `#10934 `__: typo fix >> > * `#10935 `__: BUG: Avoid >> > undefined behaviour on float to unsigned conversion >> > * `#10936 `__: DOC: Added >> > missing example to stats.mstats.variation >> > * `#10939 `__: ENH: >> > scipy.sparse.lil: tocsr accelerated depending on density >> > * `#10946 `__: BUG: setting >> > verbose > 2 in minimize with trust-constr method... >> > * `#10947 `__: DOC: special: >> > small improvements to the \`poch\` docstring >> > * `#10949 `__: BUG: fix >> return >> > type of erlang_gen._argcheck >> > * `#10951 `__: DOC: fixed >> Ricker >> > wavelet formula >> > * `#10954 `__: BUG: >> special: fix >> > \`factorial\` return type for 0-d inputs >> > * `#10955 `__: MAINT: Relax >> the >> > assert_unitary atol value >> > * `#10956 `__: WIP: make >> > pdtr(int, double) be pdtr(double, double) >> > * `#10957 `__: BUG: Ensure >> full >> > binary compatibility of long double test data >> > * `#10964 `__: ENH: Make >> Slerp >> > callable with a scalar argument >> > * `#10972 `__: BUG: Handle >> > complex gains in zpk2sos >> > * `#10975 `__: TST: skip >> > test_kendalltau ppc64le >> > * `#10978 `__: BUG: boxcox >> data >> > dimension and constancy check #5112 >> > * `#10979 `__: API: Rename >> dcm >> > to (rotation) matrix in Rotation class >> > * `#10981 `__: MAINT: add >> > support for a==0 and x>0 edge case to igam and igamc >> > * `#10986 `__: MAINT: Remove >> > direct imports from numpy in signaltools.py >> > * `#10988 `__: BUG: signal: >> > fixed issue #10360 >> > * `#10989 `__: FIX >> > binned_statistic_dd Mac wheel test fails >> > * `#10990 `__: BUG: Fix >> memory >> > leak in shgo triangulation >> > * `#10992 `__: TST: Relax >> > tolerance in upfirdn test_modes >> > * `#10993 `__: TST: bump >> > tolerance in optimize tests >> > * `#10997 `__: MAINT: Rework >> > residue and residuez >> > * `#11001 `__: DOC: Updated >> > Windows build tutorial >> > * `#11004 `__: BUG: >> > integrate/quad_vec: fix several bugs in quad_vec >> > * `#11005 `__: TST: add >> Python >> > 3.8 Win CI >> > * `#11006 `__: DOC: >> special: add >> > a reference for \`kl_div\` >> > * `#11012 `__: MAINT: Rework >> > invres and invresz >> > * `#11015 `__: DOC: >> special: add >> > references for \`rel_entr\` >> > * `#11017 `__: DOC: numpydoc >> > validation of morestats.py >> > * `#11018 `__: MAINT: Filter >> > unrelated warning >> > * `#11031 `__: MAINT: update >> > choose_conv_method for pocketfft implementation >> > * `#11034 `__: MAINT: TST: >> Skip >> > tests with multiprocessing that use "spawn"... >> > * `#11036 `__: DOC: update >> > doc/README with some more useful content. >> > * `#11037 `__: DOC: >> special: add >> > a complete docstring for \`rgamma\` >> > * `#11038 `__: DOC: >> special: add >> > a reference for the polygamma function >> > * `#11042 `__: TST: fix >> tf2zpk >> > test failure due to incorrect complex sorting. >> > * `#11044 `__: MAINT: >> > choose_conv_method can choose fftconvolution for longcomplex >> > * `#11046 `__: TST: Reduce >> > tolerance for ppc64le with reference lapack >> > * `#11048 `__: DOC: >> special: add >> > reference for orthogonal polynomial functions >> > * `#11049 `__: MAINT: proper >> > random number initialization and readability fix >> > * `#11051 `__: MAINT: pep8 >> > cleanup >> > * `#11054 `__: TST: bump >> test >> > precision for dual_annealing SLSQP test >> > * `#11055 `__: DOC: >> special: add >> > a reference for \`zeta\` >> > * `#11056 `__: API: >> Deprecated >> > normalized keyword in Rotation >> > * `#11065 `__: DOC: Ubuntu >> > Development Environment Quickstart should not modify... >> > * `#11066 `__: BUG: skip >> > deprecation for numpy top-level types >> > * `#11067 `__: DOC: updated >> > documentation for consistency in writing style >> > * `#11070 `__: DOC: >> Amendment to >> > Ubuntu Development Environment Quickstart should... >> > * `#11073 `__: DOC: fix >> 1.4.0 >> > release notes >> > * `#11081 `__: API: Replace >> > Rotation.match_vectors with align_vectors >> > * `#11083 `__: DOC: more >> 1.4.0 >> > release note fixes >> > * `#11092 `__: BUG: stats: >> fix >> > freezing of some distributions >> > * `#11096 `__: BUG: >> > scipy.sparse.csgraph: fixed issue #10774 >> > * `#11124 `__: fix Cython >> > warnings related to _stats.pyx >> > * `#11126 `__: BUG: >> > interpolate/fitpack: fix memory leak in splprep >> > * `#11127 `__: Avoid >> potential >> > segfault in CSR and CSC matrix indexing >> > * `#11152 `__: BUG: Fix >> random >> > state bug multiscale_graphcorr >> > * `#11166 `__: BUG: empty >> sparse >> > slice shapes >> > * `#11167 `__: BUG: >> redundant >> > fft in signal.resample >> > * `#11181 `__: TST: Fix >> > tolerance of tests for aarch64 >> > * `#11182 `__: TST: Bump up >> > tolerance for test_maxiter_worsening >> > * `#11199 `__: BUG: >> > sparse.linalg: mistake in unsymm. real shift-invert ARPACK eigenvalue >> > selection >> > >> > Checksums >> > ========= >> > >> > MD5 >> > ~~~ >> > >> > aa98f881f11681a35e18eadbf2c403fd >> > scipy-1.4.0-cp35-cp35m-macosx_10_6_intel.whl >> > d99b88d888f8a78a67896b2f895c3aba >> > scipy-1.4.0-cp35-cp35m-manylinux1_i686.whl >> > 13d1ab63e2ca8d2c2ac9f0b01f37b374 >> > scipy-1.4.0-cp35-cp35m-manylinux1_x86_64.whl >> > b9908d9dddf3fa5bd9b2458ea42c2813 scipy-1.4.0-cp35-cp35m-win32.whl >> > e6a6bb14d377ef8b893a710b9fcd05a8 scipy-1.4.0-cp35-cp35m-win_amd64.whl >> > 203b3f7e9bee44d3ccb3d3e0ffd62a81 >> > scipy-1.4.0-cp36-cp36m-macosx_10_6_intel.whl >> > 3cb0fde221141e35dd7c759b727e86d1 >> > scipy-1.4.0-cp36-cp36m-manylinux1_i686.whl >> > 9ae6711749bb09f812e634fec628bd23 >> > scipy-1.4.0-cp36-cp36m-manylinux1_x86_64.whl >> > da06f24a28995b3495d7696727a3a113 scipy-1.4.0-cp36-cp36m-win32.whl >> > 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URL: From warren.weckesser at gmail.com Tue Dec 17 19:19:46 2019 From: warren.weckesser at gmail.com (Warren Weckesser) Date: Tue, 17 Dec 2019 19:19:46 -0500 Subject: [Numpy-discussion] NumPy Development Meeting - Triage Focus Message-ID: Hi all, Our bi-weekly triage-focused NumPy development meeting is tomorrow (Wednesday, December 18) at 11 am Pacific Time. Everyone is invited to join in and edit the work-in-progress meeting topics and notes: https://hackmd.io/68i_JvOYQfy9ERiHgXMPvg Best regards, Warren From sebastian at sipsolutions.net Wed Dec 18 15:08:41 2019 From: sebastian at sipsolutions.net (Sebastian Berg) Date: Wed, 18 Dec 2019 14:08:41 -0600 Subject: [Numpy-discussion] removing undocumented use of __array__(dtype, context) In-Reply-To: <490b70ed24d63c459ce5d774a50f01030f03a76e.camel@sipsolutions.net> References: <636b0506-6599-5e41-7283-91b906c5cc7c@gmail.com> <490b70ed24d63c459ce5d774a50f01030f03a76e.camel@sipsolutions.net> Message-ID: <51cec54b2eb8a93a10e52705275efdbcbb045a45.camel@sipsolutions.net> On Mon, 2019-12-16 at 13:41 -0600, Sebastian Berg wrote: > On Mon, 2019-12-16 at 21:01 +0200, Matti Picus wrote: > > A code path and test have been in the code since NumPy 0.4 for a > > two-argument variant of ``__array__(dtype=None, context=None)``. It > > was > > activated when calling ``ufunc(op)`` or ``ufunc.reduce(op)`` if > > ``op.__array__`` existed. However that variant is not documented, > > and > > it > > is not clear what the intention was for its use. > > Just to note, our plan is to merge this in a few days, since it seems like the only way to find out if someone might be using it is to put it in. We do not expect this at all. If anyone disagrees or finds a use-case, we can always stop or revert the change. But such changes will be nicer now that 1.18 is just branched rather than in a few months. Best, Sebastian > > > > The code was something like > > > > > > try: > > > > op.__array__(dtype, context) > > > > except TypeError: > > > > op.__array__(dtype) > > > > > > In PR 15118 https://github.com/numpy/numpy/pull/15118 I proposed > > to > > remove this, so the call is now simply > > > > > > op.__array__(dtype) > > > > > > or `op.__array__()` if there is no dtype > > > > > > Does anyone need the undocumented two-argument variant? > > > > I agree, if nobody knows any usecase, I am for trying to remove it. > It > seems like a Deprecation will not be super simple here. And since > there > are no known use-cases, and any new use-case is better covered by > `__array_ufunc__` (and probably also `__array_wrap__`), removing this > simplifies an already tricky enough corner of NumPy. > > Best, > > Sebastian > > > > Matti > > > > > > > > > > _______________________________________________ > > NumPy-Discussion mailing list > > NumPy-Discussion at python.org > > https://mail.python.org/mailman/listinfo/numpy-discussion > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 833 bytes Desc: This is a digitally signed message part URL: From tyler.je.reddy at gmail.com Thu Dec 19 11:05:43 2019 From: tyler.je.reddy at gmail.com (Tyler Reddy) Date: Thu, 19 Dec 2019 09:05:43 -0700 Subject: [Numpy-discussion] ANN: SciPy 1.4.1 Message-ID: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi all, On behalf of the SciPy development team I'm pleased to announce the release of SciPy 1.4.1, which is a bug fix release. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.4.1 One of a few ways to install this release with pip: pip install scipy==1.4.1 ========================== SciPy 1.4.1 Release Notes ========================== SciPy 1.4.1 is a bug-fix release with no new features compared to 1.4.0. Importantly, it aims to fix a problem where an older version of pybind11 may cause a segmentation fault when imported alongside incompatible libraries. Authors ====== * Ralf Gommers * Tyler Reddy Issues closed for 1.4.1 --------------------------------- * `#11237 `__: Seg fault when importing torch Pull requests for 1.4.1 -------------------------------- * `#11238 `__: BLD: update minimum pybind11 version to 2.4.0. 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URL: From warren.weckesser at gmail.com Thu Dec 19 13:52:06 2019 From: warren.weckesser at gmail.com (Warren Weckesser) Date: Thu, 19 Dec 2019 13:52:06 -0500 Subject: [Numpy-discussion] [SciPy-Dev] ANN: SciPy 1.4.1 In-Reply-To: References: Message-ID: On 12/19/19, Tyler Reddy wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA256 > > Hi all, > > On behalf of the SciPy development team I'm pleased to announce > the release of SciPy 1.4.1, which is a bug fix release. Thanks for the quick fix, Tyler! Warren > > Sources and binary wheels can be found at: > https://pypi.org/project/scipy/ > and at: https://github.com/scipy/scipy/releases/tag/v1.4.1 > > One of a few ways to install this release with pip: > > pip install scipy==1.4.1 > > ========================== > SciPy 1.4.1 Release Notes > ========================== > > SciPy 1.4.1 is a bug-fix release with no new features > compared to 1.4.0. Importantly, it aims to fix a problem > where an older version of pybind11 may cause a segmentation > fault when imported alongside incompatible libraries. > > Authors > ====== > > * Ralf Gommers > * Tyler Reddy > > Issues closed for 1.4.1 > --------------------------------- > > * `#11237 `__: Seg fault when > importing torch > > Pull requests for 1.4.1 > -------------------------------- > > * `#11238 `__: BLD: update > minimum pybind11 version to 2.4.0. > > Checksums > ========= > > MD5 > ~~~ > > 82a6df2d23315b9e7f7ab334ae4ed98d > scipy-1.4.1-cp35-cp35m-macosx_10_6_intel.whl > 68a72f96918911586cc3b01566c8719a > scipy-1.4.1-cp35-cp35m-manylinux1_i686.whl > 644e69ec76bc34276117aa377df6b56b > scipy-1.4.1-cp35-cp35m-manylinux1_x86_64.whl > 94a4cc9c9b0b9fdfd5159317a34ecf04 scipy-1.4.1-cp35-cp35m-win32.whl > 00a88c31baa15561b726182b46a90bbf scipy-1.4.1-cp35-cp35m-win_amd64.whl > f1ae0ec2394531c043dd66a4d87644ae > scipy-1.4.1-cp36-cp36m-macosx_10_6_intel.whl > 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KxYDEi6xHAtClWbYFf/v/eWAoX651o+m/SaR9DcsOAk5IEHIm9kK+HG3F0cCGnGo > snwVnRncSJWiYL3bayC0loQhZh44j4XdHsK1k82sF6BbMK0VWo2tdYRRoQ+7kYId > tomNJzhxtPGvgDRbakYFKekp6/5f1UF49jh5UBGx1YrD56+SfUUU91ro1XldziG2 > 29G8cfnFO0PT6PbLwM35Gw/s4QehGx9dQh3cuY7DoxglVE9q/TE/zLyo9SvhR7gn > Y7EBMR5yqECbWLBHCDMyJ3VbwzdCx79VRofr/DUwse7u+2ndT4eAd/cuO8e3xfBg > jKpgPVr9TZ1Cik+vWTjYsAdXTmPNMkNfv9ECUDULJP91Ct1nd9KE4BhvxxZgGYvi > M0CyeKbq > =eneK > -----END PGP SIGNATURE----- > From mikofski at berkeley.edu Thu Dec 19 16:39:52 2019 From: mikofski at berkeley.edu (Dr. Mark Alexander Mikofski PhD) Date: Thu, 19 Dec 2019 13:39:52 -0800 Subject: [Numpy-discussion] [ANN] pvlib-python v0.7.0: predicting power for solar energy Message-ID: pvlib has a new major release, v0.7.0 Release Notes: https://pvlib-python.readthedocs.io/en/v0.7.0/whatsnew.html PyPI: https://pypi.org/project/pvlib/ Read the Docs: https://pvlib-python.readthedocs.io/en/latest/ GitHub: https://github.com/pvlib/pvlib-python Here's a quick summary: - dropped support for Python-2.7 - new `ivtools` module for fitting solar panel parameters - new implementation of the cloud wavelet variability model (WVM) - new functions for temperature and incidence angle modifier (IAM) models - updated solar panel and inverter parameters databases from National Renewable Energy Lab (NREL) Also note this is a major release so there are a few breaking API changes. Users should probably read the release notes and check their code before updating: https://pvlib-python.readthedocs.io/en/v0.7.0/whatsnew.html#api-breaking-changes -- Mark Mikofski, PhD (2005) *Fiat Lux* -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefanv at berkeley.edu Thu Dec 19 20:12:41 2019 From: stefanv at berkeley.edu (Stefan van der Walt) Date: Thu, 19 Dec 2019 17:12:41 -0800 Subject: [Numpy-discussion] BIDS-NumPy progress reports, 2018/2019 Message-ID: <20191220011241.cklfa73zlgcd7ezr@aurelius.localdomain> Dear colleagues, I'd like to thank everyone who contributed to NumPy over the past year. NumPy is a complex undertaking that requires inputs from many spheres to progress. Your contribution, however big or small, is important, and we appreciate you taking the time to make it. As we look back over the past year, I would like to share with you the two grant reports we've written, reporting on our work done with the community: 2018: http://doi.org/10.5281/zenodo.3585761 2019: http://doi.org/10.5281/zenodo.3585767 I fully appreciate that none of this work could have happened in isolation, and that we depend on the community to help set a development agenda, review code, establish regular meetings, do outreach, and much more. Thank you. We look forward to seeing you on 8 January for the next community call. With Ralf's CZI award coming into play, 2020 promises to be an exciting year for NumPy! Happy holidays, St?fan From charlesr.harris at gmail.com Sun Dec 22 11:57:04 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Sun, 22 Dec 2019 09:57:04 -0700 Subject: [Numpy-discussion] NumPy 1.18.0 release Message-ID: Hi All, On behalf of the NumPy team I am pleased to announce that NumPy 1.18.0 has been released. In addition to the usual bug fixes, this NumPy release cleans up and documents the new random C-API, expires a large number of old deprecations, and improves the appearance and organization of the documentation. The Python versions supported are 3.5-3.8. This is the last NumPy release series that will support Python 3.5. The highlights of this release are: - the C-API for ``numpy.random`` has been defined and documented, - basic infrastructure for linking with 64 bit BLAS and LAPACK libraries, - many documentation improvements. Downstream developers should use Cython >= 0.29.14 for Python 3.8 support and OpenBLAS >= 3.7 to avoid wrong results on the Skylake architecture. The NumPy Wheels for this release can be downloaded from PyPI , source archives and release notes are available from Github . *Highlights* - The C-API for ``numpy.random`` has been defined and documented. - Basic infrastructure for linking with 64 bit BLAS and LAPACK libraries. - Many documentation improvements. *Contributors* A total of 114 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Abhinav Sagar - Alex Henrie + - Alexander Jung + - Allan Haldane - Andrea Pattori - Andrew Liu + - Anis Ladram + - Anne Bonner + - Antoine Dechaume + - Aryan Naraghi + - Bastian Eichenberger + - Brian Wignall + - Brigitta Sipocz - CakeWithSteak + - Charles Harris - Chris Barker - Chris Burr + - Chris Markiewicz + - Christoph Gohlke - Christopher Whelan - Colin Snyder - Dan Allan - Daniel Ching - David Stansby + - David Zwicker + - Dieter Werthm?ller - Disconnect3d + - Dmytro + - Doug Davis + - Eric Larson - Eric Wieser - Esben Haabendal + - Eugene Prilepin + - Felix Divo + - Gary Gurlaskie - Gina + - Giuseppe Cuccu + - Grzegorz Bokota + - Guanqun Lu + - Guilherme Leobas + - Guillaume Horel - G?raud Le Falher + - Hameer Abbasi - Harmon - Hiroyuki V. Yamazaki - Huang, Guangtai + - Hugo + - Hyeonguk Ryu + - Ilhan Polat + - Isaac Virshup - Jack J. Woehr + - Jack Woehr + - Jackie Leng - Jaime Fernandez - Jeff Hale + - Johann Faouzi + - Jon Dufresne + - Joseph Fox-Rabinovitz - Joseph R. Fox-Rabinovitz + - Jo?o Marcos Gris + - Justus Magin + - J?r?mie du Boisberranger - Kai Striega - Kevin Sheppard - Kexuan Sun - Kmol Yuan + - Kriti Singh - Larry Bradley + - Lars Grueter - Luis Pedro Coelho - MSeifert04 - Magdalena Proszewska + - Manny + - Mark Harfouche - Martin Reinecke - Martin Thoma - Matt Haberland + - Matt McCormick + - Matthias Bussonnier - Matti Picus - Max Bolingbroke + - Maxwell Aladago + - Michael Hudson-Doyle + - Oleksandr Pavlyk - Omar Merghany + - Pauli Virtanen - Peter Andreas Entschev - Peter Bell - Peter Cock + - Pradeep Reddy Raamana + - Qiming Sun + - Raghuveer Devulapalli - Ralf Gommers - Samesh + - Samesh Lakhotia + - Sebastian Berg - Sergei Lebedev - Seth Troisi + - Siddhesh Poyarekar + - Simon + - Simon Notley + - Stefan van der Walt - Stephan Hoyer - Steve Stagg - Thomas A Caswell - Thomas Kluyver - Tim Hoffmann + - Tirth Patel + - Tyler Reddy - Vladimir Pershin + - Warren Weckesser - Yadong Zhang + - Zieji Pohz + - Zolisa Bleki + Cheers, Charles Harris -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Mon Dec 23 13:24:55 2019 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Mon, 23 Dec 2019 19:24:55 +0100 Subject: [Numpy-discussion] BIDS-NumPy progress reports, 2018/2019 In-Reply-To: <20191220011241.cklfa73zlgcd7ezr@aurelius.localdomain> References: <20191220011241.cklfa73zlgcd7ezr@aurelius.localdomain> Message-ID: On Fri, Dec 20, 2019 at 2:12 AM Stefan van der Walt wrote: > Dear colleagues, > > I'd like to thank everyone who contributed to NumPy over the past year. > NumPy is a complex undertaking that requires inputs from many spheres to > progress. Your contribution, however big or small, is important, and we > appreciate you taking the time to make it. > I'll echo that sentiment - thanks to everyone who has contributed to any aspect of the project! > As we look back over the past year, I would like to share with you the > two grant reports we've written, reporting on our work done with the > community: > > 2018: http://doi.org/10.5281/zenodo.3585761 > 2019: http://doi.org/10.5281/zenodo.3585767 These reports are great, thanks for publishing them St?fan! Cheers, Ralf I fully appreciate that none of this work could have happened in > isolation, and that we depend on the community to help set a development > agenda, review code, establish regular meetings, do outreach, and much > more. Thank you. > > We look forward to seeing you on 8 January for the next community call. > With Ralf's CZI award coming into play, 2020 promises to be an exciting > year for NumPy! > > Happy holidays, > St?fan > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion at python.org > https://mail.python.org/mailman/listinfo/numpy-discussion > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cimrman3 at ntc.zcu.cz Mon Dec 23 16:34:32 2019 From: cimrman3 at ntc.zcu.cz (Robert Cimrman) Date: Mon, 23 Dec 2019 22:34:32 +0100 Subject: [Numpy-discussion] ANN: SfePy 2019.4 Message-ID: I am pleased to announce release 2019.4 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method or by the isogeometric analysis (limited support). It is distributed under the new BSD license. Home page: http://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - support surface terms in 1D problems - improved Gmsh mesh format support (write .msh files) - new updating procedure in nonlinear homogenization - improved/faster log plotter For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Vladimir Lukes Matyas Novak Tom?? Z?tka From magdalena.proszewska at gmail.com Tue Dec 24 08:42:41 2019 From: magdalena.proszewska at gmail.com (mpro) Date: Tue, 24 Dec 2019 06:42:41 -0700 (MST) Subject: [Numpy-discussion] Reverse parameter in ordering functions In-Reply-To: <34822fe03f6a637eb3155caec0a5198f0a3403c0.camel@sipsolutions.net> References: <1574874054151-0.post@n7.nabble.com> <34822fe03f6a637eb3155caec0a5198f0a3403c0.camel@sipsolutions.net> Message-ID: <1577194961726-0.post@n7.nabble.com> I added 'reverse' in all ordering functions. The question is whether it's better to add reverse to all C ordering methods or to make changes on Python level. -- Sent from: http://numpy-discussion.10968.n7.nabble.com/ From charlesr.harris at gmail.com Fri Dec 27 12:30:13 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Fri, 27 Dec 2019 10:30:13 -0700 Subject: [Numpy-discussion] Upcoming NumPy 1.16.6 release. Message-ID: Hi All, The NumPy 1.16.6 release is under preparation. The release notes and changelog may be found at #15191 . Because this is the last planned release that supports Python 2.7 it is important to make sure it has all the relevant fixes, so if this affects you, please review the notes and comment if you think a needed fix has been omitted. Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Sun Dec 29 19:27:25 2019 From: charlesr.harris at gmail.com (Charles R Harris) Date: Sun, 29 Dec 2019 17:27:25 -0700 Subject: [Numpy-discussion] NumPy 1.16.6 release. Message-ID: Hi All, On behalf of the NumPy team I am pleased to announce that NumPy 1.16.6 has been released. This release fixes bugs reported against the 1.16.5 release and backports several enhancements from master that seem appropriate for an LTS series. The supported Python versions are 2.7, 3.5-3.7. This is the last release planned that supports Python 2.7. Wheels for this release can be downloaded from PyPI , source archives and release notes are available from Github . Downstream developers building this release should use Cython >= 0.29.2 and, if using OpenBLAS, OpenBLAS >= v0.3.7. *Highlights* - The ``np.testing.utils`` functions have been updated from 1.19.0-dev0. This improves the function documentation and error messages as well extending the ``assert_array_compare`` function to additional types. *Contributors* A total of 10 people contributed to this release. - CakeWithSteak - Charles Harris - Chris Burr - Eric Wieser - Fernando Saravia - Lars Grueter - Matti Picus - Maxwell Aladago - Qiming Sun - Warren Weckesser *Pull requests merged* A total of 14 pull requests were merged for this release. - `#14211 `__: BUG: Fix uint-overflow if padding with linear_ramp and negative... - `#14275 `__: BUG: fixing to allow unpickling of PY3 pickles from PY2 - `#14340 `__: BUG: Fix misuse of .names and .fields in various places (backport... - `#14423 `__: BUG: test, fix regression in converting to ctypes. - `#14434 `__: BUG: Fixed maximum relative error reporting in assert_allclose - `#14509 `__: BUG: Fix regression in boolean matmul. - `#14686 `__: BUG: properly define PyArray_DescrCheck - `#14853 `__: BLD: add 'apt update' to shippable - `#14854 `__: BUG: Fix _ctypes class circular reference. (#13808) - `#14856 `__: BUG: Fix `np.einsum` errors on Power9 Linux and z/Linux - `#14863 `__: BLD: Prevent -flto from optimising long double representation... - `#14864 `__: BUG: lib: Fix histogram problem with signed integer arrays. - `#15172 `__: ENH: Backport improvements to testing functions. - `#15191 `__: REL: Prepare for 1.16.6 release. Cheers, Charles Harris -------------- next part -------------- An HTML attachment was scrubbed... URL: From warren.weckesser at gmail.com Mon Dec 30 06:10:35 2019 From: warren.weckesser at gmail.com (Warren Weckesser) Date: Mon, 30 Dec 2019 06:10:35 -0500 Subject: [Numpy-discussion] [SciPy-Dev] NumPy 1.16.6 release. In-Reply-To: References: Message-ID: Thanks Chuck! Warren On 12/29/19, Charles R Harris wrote: > Hi All, > > On behalf of the NumPy team I am pleased to announce that NumPy 1.16.6 has > been released. This release fixes bugs reported against the 1.16.5 release > and backports several enhancements from master that seem appropriate for an > LTS series. The supported Python versions are 2.7, 3.5-3.7. This is the > last release planned that supports Python 2.7. Wheels for this release can > be downloaded from PyPI , source > archives and release notes are available from Github > . Downstream > developers building this release should use Cython >= 0.29.2 and, if using > OpenBLAS, OpenBLAS >= v0.3.7. > > *Highlights* > > - The ``np.testing.utils`` functions have been updated from 1.19.0-dev0. > This improves the function documentation and error messages as well > extending the ``assert_array_compare`` function to additional types. > > *Contributors* > > A total of 10 people contributed to this release. > > > - CakeWithSteak > - Charles Harris > - Chris Burr > - Eric Wieser > - Fernando Saravia > - Lars Grueter > - Matti Picus > - Maxwell Aladago > - Qiming Sun > - Warren Weckesser > > > *Pull requests merged* > > A total of 14 pull requests were merged for this release. > > > - `#14211 `__: BUG: Fix > uint-overflow if padding with linear_ramp and negative... > - `#14275 `__: BUG: fixing to > allow unpickling of PY3 pickles from PY2 > - `#14340 `__: BUG: Fix > misuse of .names and .fields in various places (backport... > - `#14423 `__: BUG: test, fix > regression in converting to ctypes. > - `#14434 `__: BUG: Fixed > maximum relative error reporting in assert_allclose > - `#14509 `__: BUG: Fix > regression in boolean matmul. > - `#14686 `__: BUG: properly > define PyArray_DescrCheck > - `#14853 `__: BLD: add 'apt > update' to shippable > - `#14854 `__: BUG: Fix > _ctypes class circular reference. (#13808) > - `#14856 `__: BUG: Fix > `np.einsum` errors on Power9 Linux and z/Linux > - `#14863 `__: BLD: Prevent > -flto from optimising long double representation... > - `#14864 `__: BUG: lib: Fix > histogram problem with signed integer arrays. > - `#15172 `__: ENH: Backport > improvements to testing functions. > - `#15191 `__: REL: Prepare > for 1.16.6 release. > > Cheers, > > Charles Harris >