Mailman 3 November 2018 - SciPy-Dev

SciPy 1.2.0 release schedule
by Tyler Reddy Feb. 7, 2019

Feb. 7, 2019

Hi all, It is almost 6 months after the 1.1.0 release on May 5, so probably time to plan the 1.2.0 release. It would be a good idea to look over the PRs with a 1.2.0 milestone <https://github.com/scipy/scipy/pulls?q=is%3Aopen+is%3Apr+milestone%3A1.2.0>, and tag anything else that should have this milestone appropriately. I'd like to propose the following schedule: Nov. 5: branch 1.2.x Nov. 8: rc1 Nov. 21: rc2 (if needed) Nov. 30: final release Thoughts? Best wishes, Tyler

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SciPy 1.0 paper writing proposal
by Ralf Gommers Jan. 29, 2019

Jan. 29, 2019

Hi all, TL;DR, let's write the long journal paper on SciPy that we've wanted for a while, let's form a small committee to coordinate, and get it out the door in 2-3 months. Motivation --------------- (credits for most of this text: Evgeni) Many scipy contributors' day jobs are in academia. Bibliometry -- papers in refereed journals and citations of papers by other papers -- is one of the main performance indicators in most academic establishments. Since we do not generate papers, scipy contributions are all but invisible for the purposes of a contributor's annual report. Of course, details vary wildly; in many cases a contributor manages to balance their time, or to argue common sense with their superiors, or get an approval for scipy work, or just ignores the issue altogether -- but sooner or later there is a form to be filled or boxes to be checked, and scipy contributions simply do not fit in. A peer-reviewed journal paper on scipy will help contributors get the academic credit they deserve. We can write *the* paper for SciPy 1.0, with overall project structure, goals, etc., and for specific features/modules a focus on say the last 3 years. History ---------- For SciPy 1.0 we had three targets on the publicity/credits front: an interesting release announcement, interesting blogs/stories (NumFOCUS blog, Hacker News, etc.) and a paper. We didn't have the bandwidth for a paper in the end, the rest was successful. [1] is a previous announcement on this list about writing (a) paper(s) on SciPy. We wanted both "short papers" to cover one or two releases (target journal JOSS) and a full paper as the authoritative reference for SciPy. We had an earlier attempt for a "short paper", it's mostly written but has stalled (see [2]). We ran out of steam on that one. To avoid that this time around, it would be good to have a clear public plan, target dates, and a small committee rather than one person to drive things forward. Proposal ------------ Here's a proposal for all aspects of this exercise that I can think about now. Some parts stolen from the AstroPy paper [3] (because their process worked quite well). Form a small coordination committee of 3-5 people that set up the paper structure, move things along when parts stall, propose/take decisions as needed, invite co-authors, and organise paper submission/rework. Paper writing to be done by whoever volunteers for a section, not just the coordination committee. First outline/structure to be done by committee, which then asks for review of structure and volunteers for section writing. Scope: a 6-10 page paper, covering history, package scope and structure, community/organisational aspects, key features and recent enhancements per module, and roadmap. Authorship: anyone who made a substantial contribution in the history of the project. Here "substantial" is interpreted as anything beyond a one-line doc fix. Rationale: better to be too inclusive than exclusive. Sign-up via a web form, we send the link to that form to all email addresses in the commit history till v1.0. Author order (details tbd by committee): 1. The SciPy Developers 2. Maintainers, paper writers, other key contributors - in order of contribution level 3. All other authors - alphabetically ordered Submission target: mid-April, to either PeerJ Computer Science or Journal of Open Research Software (tbd by committee). Comments? Volunteers for committee? References ---------------- [1] https://mail.python.org/pipermail/scipy-dev/2016-August/021474.html [2] https://github.com/scipy/scipy-articles/pull/4 [3] https://github.com/astropy/astropy-v2.0-paper Cheers, Ralf

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Preparing project proposal for GSoC 2019
by Sourav Singh Dec. 7, 2018

Dec. 7, 2018

Hello, I am writing the mail regarding project proposal for GSoC 2019. I am interested in working with SciPy for the upcoming Google Summer of Code and I am interested in either working on enhancing the randomized numerical linear algebra functionality or fixing the scipy.fftpack module. I understand that it is quite early to talk, since the organization proposals haven't started yet, but I would like to know if a project proposal can be started right now so that the proposals can be better fleshed out by the time the application period starts? Regards, Sourav

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PR 9556: Using convex hull centroids instead of tetrahedron circumcenters as Spherical Voronoi vertices
by Oliver Arend Nov. 30, 2018

Nov. 30, 2018

Hello everybody, I started a pull request https://github.com/scipy/scipy/pull/9556 that gives the user the ability to select a method to determine the vertices of a Voronoi tesselation of a spherical surface. I also expanded the tests accordingly. Someone more experienced should please do a code review on it. To see what that kind of difference (or not) it can make, look at e.g. https://www.redblobgames.com/x/1842-delaunay-voronoi-sphere/#voronoi I needed this functionality and found it easiest to just extend the existing scipy.spatial.SphericalVoronoi class. Others might find it useful as well. Oliver

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ANN: SciPy 1.2.0rc1 -- please test
by Tyler Reddy Nov. 26, 2018

Nov. 26, 2018

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Hi all, On behalf of the SciPy development team I'm pleased to announce the release candidate SciPy 1.2.0rc1. Please help us test out this release candidate -- the 1.2.x series will be an LTS release and the last to support Python 2.7. Sources and binary wheels can be found at: https://pypi.python.org/pypi/scipy and at: https://github.com/scipy/scipy/releases/tag/v1.2.0rc1 To install the release candidate with pip: pip install scipy==1.2.0rc1 ========================== SciPy 1.2.0 Release Notes ========================== Note: Scipy 1.2.0 is not released yet! SciPy 1.2.0 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 1.2.x branch, and on adding new features on the master branch. This release requires Python 2.7 or 3.4+ and NumPy 1.8.2 or greater. Note: This will be the last SciPy release to support Python 2.7. Consequently, the 1.2.x series will be a long term support (LTS) release; we will backport bug fixes until 1 Jan 2020. For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. Highlights of this release ---------------------------- - - 1-D root finding improvements with a new solver, ``toms748``, and a new unified interface, ``root_scalar`` - - New ``dual_annealing`` optimization method that combines stochastic and local deterministic searching - - A new optimization algorithm, ``shgo`` (simplicial homology global optimization) for derivative free optimization problems - - A new category of quaternion-based transformations are available in `scipy.spatial.transform` New features ============ `scipy.ndimage` improvements - -------------------------------- Proper spline coefficient calculations have been added for the ``mirror``, ``wrap``, and ``reflect`` modes of `scipy.ndimage.rotate` `scipy.fftpack` improvements - -------------------------------- DCT-IV, DST-IV, DCT-I, and DST-I orthonormalization are now supported in `scipy.fftpack`. `scipy.interpolate` improvements - -------------------------------- `scipy.interpolate.pade` now accepts a new argument for the order of the numerator `scipy.cluster` improvements - ---------------------------- `scipy.cluster.vq.kmeans2` gained a new initialization method, kmeans++. `scipy.special` improvements - ---------------------------- The function ``softmax`` was added to `scipy.special`. `scipy.optimize` improvements - ----------------------------- The one-dimensional nonlinear solvers have been given a unified interface `scipy.optimize.root_scalar`, similar to the `scipy.optimize.root` interface for multi-dimensional solvers. ``scipy.optimize.root_scalar(f, bracket=[a ,b], method="brenth")`` is equivalent to ``scipy.optimize.brenth(f, a ,b)``. If no ``method`` is specified, an appropriate one will be selected based upon the bracket and the number of derivatives available. The so-called Algorithm 748 of Alefeld, Potra and Shi for root-finding within an enclosing interval has been added as `scipy.optimize.toms748`. This provides guaranteed convergence to a root with convergence rate per function evaluation of approximately 1.65 (for sufficiently well-behaved functions.) ``differential_evolution`` now has the ``updating`` and ``workers`` keywords. The first chooses between continuous updating of the best solution vector (the default), or once per generation. Continuous updating can lead to faster convergence. The ``workers`` keyword accepts an ``int`` or map-like callable, and parallelises the solver (having the side effect of updating once per generation). Supplying an ``int`` evaluates the trial solutions in N parallel parts. Supplying a map-like callable allows other parallelisation approaches (such as ``mpi4py``, or ``joblib``) to be used. ``dual_annealing`` (and ``shgo`` below) is a powerful new general purpose global optizimation (GO) algorithm. ``dual_annealing`` uses two annealing processes to accelerate the convergence towards the global minimum of an objective mathematical function. The first annealing process controls the stochastic Markov chain searching and the second annealing process controls the deterministic minimization. So, dual annealing is a hybrid method that takes advantage of stochastic and local deterministic searching in an efficient way. ``shgo`` (simplicial homology global optimization) is a similar algorithm appropriate for solving black box and derivative free optimization (DFO) problems. The algorithm generally converges to the global solution in finite time. The convergence holds for non-linear inequality and equality constraints. In addition to returning a global minimum, the algorithm also returns any other global and local minima found after every iteration. This makes it useful for exploring the solutions in a domain. `scipy.optimize.newton` can now accept a scalar or an array ``MINPACK`` usage is now thread-safe, such that ``MINPACK`` + callbacks may be used on multiple threads. `scipy.signal` improvements - --------------------------- Digital filter design functions now include a parameter to specify the sampling rate. Previously, digital filters could only be specified using normalized frequency, but different functions used different scales (e.g. 0 to 1 for ``butter`` vs 0 to π for ``freqz``), leading to errors and confusion. With the ``fs`` parameter, ordinary frequencies can now be entered directly into functions, with the normalization handled internally. ``find_peaks`` and related functions no longer raise an exception if the properties of a peak have unexpected values (e.g. a prominence of 0). A ``PeakPropertyWarning`` is given instead. The new keyword argument ``plateau_size`` was added to ``find_peaks``. ``plateau_size`` may be used to select peaks based on the length of the flat top of a peak. ``welch()`` and ``csd()`` methods in `scipy.signal` now support calculation of a median average PSD, using ``average='mean'`` keyword `scipy.sparse` improvements - --------------------------- The `scipy.sparse.bsr_matrix.tocsr` method is now implemented directly instead of converting via COO format, and the `scipy.sparse.bsr_matrix.tocsc` method is now also routed via CSR conversion instead of COO. The efficiency of both conversions is now improved. The issue where SuperLU or UMFPACK solvers crashed on matrices with non-canonical format in `scipy.sparse.linalg` was fixed. The solver wrapper canonicalizes the matrix if necessary before calling the SuperLU or UMFPACK solver. The ``largest`` option of `scipy.sparse.linalg.lobpcg()` was fixed to have a correct (and expected) behavior. The order of the eigenvalues was made consistent with the ARPACK solver (``eigs()``), i.e. ascending for the smallest eigenvalues, and descending for the largest eigenvalues. The `scipy.sparse.random` function is now faster and also supports integer and complex values by passing the appropriate value to the ``dtype`` argument. `scipy.spatial` improvements - ---------------------------- The function `scipy.spatial.distance.jaccard` was modified to return 0 instead of ``np.nan`` when two all-zero vectors are compared. Support for the Jensen Shannon distance, the square-root of the divergence, has been added under `scipy.spatial.distance.jensenshannon` An optional keyword was added to the function `scipy.spatial.cKDTree.query_ball_point()` to sort or not sort the returned indices. Not sorting the indices can speed up calls. A new category of quaternion-based transformations are available in `scipy.spatial.transform`, including spherical linear interpolation of rotations (``Slerp``), conversions to and from quaternions, Euler angles, and general rotation and inversion capabilities (`spatial.transform.Rotation`), and uniform random sampling of 3D rotations (`spatial.transform.Rotation.random`). `scipy.stats` improvements - -------------------------- The Yeo-Johnson power transformation is now supported (``yeojohnson``, ``yeojohnson_llf``, ``yeojohnson_normmax``, ``yeojohnson_normplot``). Unlike the Box-Cox transformation, the Yeo-Johnson transformation can accept negative values. Added a general method to sample random variates based on the density only, in the new function ``rvs_ratio_uniforms``. The Yule-Simon distribution (``yulesimon``) was added -- this is a new discrete probability distribution. ``stats`` and ``mstats`` now have access to a new regression method, ``siegelslopes``, a robust linear regression algorithm `scipy.stats.gaussian_kde` now has the ability to deal with weighted samples, and should have a modest improvement in performance Levy Stable Parameter Estimation, PDF, and CDF calculations are now supported for `scipy.stats.levy_stable`. The Brunner-Munzel test is now available as ``brunnermunzel`` in ``stats`` and ``mstats`` `scipy.linalg` improvements - -------------------------- `scipy.linalg.lapack` now exposes the LAPACK routines using the Rectangular Full Packed storage (RFP) for upper triangular, lower triangular, symmetric, or Hermitian matrices; the upper trapezoidal fat matrix RZ decomposition routines are now available as well. Deprecated features =================== The functions ``hyp2f0``, ``hyp1f2`` and ``hyp3f0`` in ``scipy.special`` have been deprecated. Backwards incompatible changes ============================== LAPACK version 3.4.0 or later is now required. Building with Apple Accelerate is no longer supported. The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct results for all angles. Before this, the function only returned correct values for those angles which were greater than pi/4. Support for the Bento build system has been removed. Bento has not been maintained for several years, and did not have good Python 3 or wheel support, hence it was time to remove it. The required signature of `scipy.optimize.lingprog` ``method=simplex`` callback function has changed. Before iteration begins, the simplex solver first converts the problem into a standard form that does not, in general, have the same variables or constraints as the problem defined by the user. Previously, the simplex solver would pass a user-specified callback function several separate arguments, such as the current solution vector ``xk``, corresponding to this standard form problem. Unfortunately, the relationship between the standard form problem and the user-defined problem was not documented, limiting the utility of the information passed to the callback function. In addition to numerous bug fix changes, the simplex solver now passes a user-specified callback function a single ``OptimizeResult`` object containing information that corresponds directly to the user-defined problem. In future releases, this ``OptimizeResult`` object may be expanded to include additional information, such as variables corresponding to the standard-form problem and information concerning the relationship between the standard-form and user-defined problems. The implementation of `scipy.sparse.random` has changed, and this affects the numerical values returned for both ``sparse.random`` and ``sparse.rand`` for some matrix shapes and a given seed. `scipy.optimize.newton` will no longer use Halley's method in cases where it negatively impacts convergence Other changes ============= Authors ======= * @endolith * @luzpaz * Hameer Abbasi + * akahard2dj + * Anton Akhmerov * Joseph Albert * alexthomas93 + * ashish + * atpage + * Blair Azzopardi + * Yoshiki Vázquez Baeza * Bence Bagi + * Christoph Baumgarten * Lucas Bellomo + * BH4 + * Aditya Bharti * Max Bolingbroke * François Boulogne * Ward Bradt + * Matthew Brett * Evgeni Burovski * Rafał Byczek + * Alfredo Canziani + * CJ Carey * Lucía Cheung + * Poom Chiarawongse + * Jeanne Choo + * Robert Cimrman * Graham Clenaghan + * cynthia-rempel + * Johannes Damp + * Jaime Fernandez del Rio * Dowon + * emmi474 + * Stefan Endres + * Thomas Etherington + * Alex Fikl + * fo40225 + * Joseph Fox-Rabinovitz * Lars G * Abhinav Gautam + * Stiaan Gerber + * C.A.M. Gerlach + * Ralf Gommers * Todd Goodall * Lars Grueter + * Sylvain Gubian + * Matt Haberland * David Hagen * Will Handley + * Charles Harris * Ian Henriksen * Thomas Hisch + * Theodore Hu * Michael Hudson-Doyle + * Nicolas Hug + * jakirkham + * Jakob Jakobson + * James + * Jan Schlüter * jeanpauphilet + * josephmernst + * Kai + * Kai-Striega + * kalash04 + * Toshiki Kataoka + * Konrad0 + * Tom Krauss + * Johannes Kulick * Lars Grüter + * Eric Larson * Denis Laxalde * Will Lee + * Katrin Leinweber + * Yin Li + * P. L. Lim + * Jesse Livezey + * Duncan Macleod + * MatthewFlamm + * Nikolay Mayorov * Mike McClurg + * Christian Meyer + * Mark Mikofski * Naoto Mizuno + * mohmmadd + * Nathan Musoke * Anju Geetha Nair + * Andrew Nelson * Ayappan P + * Nick Papior * Haesun Park + * Ronny Pfannschmidt + * pijyoi + * Ilhan Polat * Anthony Polloreno + * Ted Pudlik * puenka * Eric Quintero * Pradeep Reddy Raamana + * Vyas Ramasubramani + * Ramon Viñas + * Tyler Reddy * Joscha Reimer * Antonio H Ribeiro * richardjgowers + * Rob + * robbystk + * Lucas Roberts + * rohan + * Joaquin Derrac Rus + * Josua Sassen + * Bruce Sharpe + * Max Shinn + * Scott Sievert * Sourav Singh * Strahinja Lukić + * Kai Striega + * Shinya SUZUKI + * Mike Toews + * Piotr Uchwat * Miguel de Val-Borro + * Nicky van Foreest * Paul van Mulbregt * Gael Varoquaux * Pauli Virtanen * Stefan van der Walt * Warren Weckesser * Joshua Wharton + * Bernhard M. Wiedemann + * Eric Wieser * Josh Wilson * Tony Xiang + * Roman Yurchak + * Roy Zywina + A total of 137 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 1.2.0 - ----------------------- * `#1240 <https://github.com/scipy/scipy/issues/1240>`__: Allowing multithreaded use of minpack through scipy.optimize... * `#1432 <https://github.com/scipy/scipy/issues/1432>`__: scipy.stats.mode extremely slow (Trac #905) * `#3372 <https://github.com/scipy/scipy/issues/3372>`__: Please add Sphinx search field to online scipy html docs * `#3678 <https://github.com/scipy/scipy/issues/3678>`__: _clough_tocher_2d_single direction between centroids * `#4174 <https://github.com/scipy/scipy/issues/4174>`__: lobpcg "largest" option invalid? * `#5493 <https://github.com/scipy/scipy/issues/5493>`__: anderson_ksamp p-values>1 * `#5743 <https://github.com/scipy/scipy/issues/5743>`__: slsqp fails to detect infeasible problem * `#6139 <https://github.com/scipy/scipy/issues/6139>`__: scipy.optimize.linprog failed to find a feasible starting point... * `#6358 <https://github.com/scipy/scipy/issues/6358>`__: stats: docstring for `vonmises_line` points to `vonmises_line`... * `#6498 <https://github.com/scipy/scipy/issues/6498>`__: runtests.py is missing in pypi distfile * `#7426 <https://github.com/scipy/scipy/issues/7426>`__: scipy.stats.ksone(n).pdf(x) returns nan for positive values of... * `#7455 <https://github.com/scipy/scipy/issues/7455>`__: scipy.stats.ksone.pdf(2,x) return incorrect values for x near... * `#7456 <https://github.com/scipy/scipy/issues/7456>`__: scipy.special.smirnov and scipy.special.smirnovi have accuracy... * `#7492 <https://github.com/scipy/scipy/issues/7492>`__: scipy.special.kolmogorov(x)/kolmogi(p) inefficient, inaccurate... * `#7914 <https://github.com/scipy/scipy/issues/7914>`__: TravisCI not failing when it should for -OO run * `#8064 <https://github.com/scipy/scipy/issues/8064>`__: linalg.solve test crashes on Windows * `#8212 <https://github.com/scipy/scipy/issues/8212>`__: LAPACK Rectangular Full Packed routines * `#8256 <https://github.com/scipy/scipy/issues/8256>`__: differential_evolution bug converges to wrong results in complex... * `#8443 <https://github.com/scipy/scipy/issues/8443>`__: Deprecate `hyp2f0`, `hyp1f2`, and `hyp3f0`? * `#8452 <https://github.com/scipy/scipy/issues/8452>`__: DOC: ARPACK tutorial has two conflicting equations * `#8680 <https://github.com/scipy/scipy/issues/8680>`__: scipy fails compilation when building from source * `#8686 <https://github.com/scipy/scipy/issues/8686>`__: Division by zero in _trustregion.py when x0 is exactly equal... * `#8700 <https://github.com/scipy/scipy/issues/8700>`__: _MINPACK_LOCK not held when calling into minpack from least_squares * `#8786 <https://github.com/scipy/scipy/issues/8786>`__: erroneous moment values for t-distribution * `#8791 <https://github.com/scipy/scipy/issues/8791>`__: Checking COLA condition in istft should be optional (or omitted) * `#8843 <https://github.com/scipy/scipy/issues/8843>`__: imresize cannot be deprecated just yet * `#8844 <https://github.com/scipy/scipy/issues/8844>`__: Inverse Wishart Log PDF Incorrect for Non-diagonal Scale Matrix? * `#8878 <https://github.com/scipy/scipy/issues/8878>`__: vonmises and vonmises_line in stats: vonmises wrong and superfluous? * `#8895 <https://github.com/scipy/scipy/issues/8895>`__: v1.1.0 `ndi.rotate` documentation – reused parameters not filled... * `#8900 <https://github.com/scipy/scipy/issues/8900>`__: Missing complex conjugation in scipy.sparse.linalg.LinearOperator * `#8904 <https://github.com/scipy/scipy/issues/8904>`__: BUG: if zero derivative at root, then Newton fails with RuntimeWarning * `#8911 <https://github.com/scipy/scipy/issues/8911>`__: make_interp_spline bc_type incorrect input interpretation * `#8942 <https://github.com/scipy/scipy/issues/8942>`__: MAINT: Refactor `_linprog.py` and `_linprog_ip.py` to remove... * `#8947 <https://github.com/scipy/scipy/issues/8947>`__: np.int64 in scipy.fftpack.next_fast_len * `#9020 <https://github.com/scipy/scipy/issues/9020>`__: BUG: linalg.subspace_angles gives wrong results * `#9033 <https://github.com/scipy/scipy/issues/9033>`__: scipy.stats.normaltest sometimes gives incorrect returns b/c... * `#9036 <https://github.com/scipy/scipy/issues/9036>`__: Bizarre times for `scipy.sparse.rand` function with 'low' density... * `#9044 <https://github.com/scipy/scipy/issues/9044>`__: optimize.minimize(method=`trust-constr`) result dict does not... * `#9071 <https://github.com/scipy/scipy/issues/9071>`__: doc/linalg: add cho_solve_banded to see also of cholesky_banded * `#9082 <https://github.com/scipy/scipy/issues/9082>`__: eigenvalue sorting in scipy.sparse.linalg.eigsh * `#9086 <https://github.com/scipy/scipy/issues/9086>`__: signaltools.py:491: FutureWarning: Using a non-tuple sequence... * `#9091 <https://github.com/scipy/scipy/issues/9091>`__: test_spline_filter failure on 32-bit * `#9122 <https://github.com/scipy/scipy/issues/9122>`__: Typo on scipy minimization tutorial * `#9135 <https://github.com/scipy/scipy/issues/9135>`__: doc error at https://docs.scipy.org/doc/scipy/reference/tutorial/stats/discrete_poisson.… * `#9167 <https://github.com/scipy/scipy/issues/9167>`__: DOC: BUG: typo in ndimage LowLevelCallable tutorial example * `#9169 <https://github.com/scipy/scipy/issues/9169>`__: truncnorm does not work if b < a in scipy.stats * `#9250 <https://github.com/scipy/scipy/issues/9250>`__: scipy.special.tests.test_mpmath::TestSystematic::test_pcfw fails... * `#9259 <https://github.com/scipy/scipy/issues/9259>`__: rv.expect() == rv.mean() is false for rv.mean() == nan (and inf) * `#9286 <https://github.com/scipy/scipy/issues/9286>`__: DOC: Rosenbrock expression in optimize.minimize tutorial * `#9316 <https://github.com/scipy/scipy/issues/9316>`__: SLSQP fails in nested optimization * `#9337 <https://github.com/scipy/scipy/issues/9337>`__: scipy.signal.find_peaks key typo in documentation * `#9345 <https://github.com/scipy/scipy/issues/9345>`__: Example from documentation of scipy.sparse.linalg.eigs raises... * `#9383 <https://github.com/scipy/scipy/issues/9383>`__: Default value for "mode" in "ndimage.shift" * `#9419 <https://github.com/scipy/scipy/issues/9419>`__: dual_annealing off by one in the number of iterations * `#9442 <https://github.com/scipy/scipy/issues/9442>`__: Error in Defintion of Rosenbrock Function * `#9453 <https://github.com/scipy/scipy/issues/9453>`__: TST: test_eigs_consistency() doesn't have consistent results Pull requests for 1.2.0 - ----------------------- * `#7352 <https://github.com/scipy/scipy/pull/7352>`__: ENH: add Brunner Munzel test to scipy.stats. * `#7373 <https://github.com/scipy/scipy/pull/7373>`__: BUG: Jaccard distance for all-zero arrays would return np.nan * `#7374 <https://github.com/scipy/scipy/pull/7374>`__: ENH: Add PDF, CDF and parameter estimation for Stable Distributions * `#8098 <https://github.com/scipy/scipy/pull/8098>`__: ENH: Add shgo for global optimization of NLPs. * `#8203 <https://github.com/scipy/scipy/pull/8203>`__: ENH: adding simulated dual annealing to optimize * `#8259 <https://github.com/scipy/scipy/pull/8259>`__: Option to follow original Storn and Price algorithm and its parallelisation * `#8293 <https://github.com/scipy/scipy/pull/8293>`__: ENH add ratio-of-uniforms method for rv generation to scipy.stats * `#8294 <https://github.com/scipy/scipy/pull/8294>`__: BUG: Fix slowness in stats.mode * `#8295 <https://github.com/scipy/scipy/pull/8295>`__: ENH: add Jensen Shannon distance to `scipy.spatial.distance` * `#8357 <https://github.com/scipy/scipy/pull/8357>`__: ENH: vectorize scalar zero-search-functions * `#8397 <https://github.com/scipy/scipy/pull/8397>`__: Add `fs=` parameter to filter design functions * `#8537 <https://github.com/scipy/scipy/pull/8537>`__: ENH: Implement mode parameter for spline filtering. * `#8558 <https://github.com/scipy/scipy/pull/8558>`__: ENH: small speedup for stats.gaussian_kde * `#8560 <https://github.com/scipy/scipy/pull/8560>`__: BUG: fix p-value calc of anderson_ksamp in scipy.stats * `#8614 <https://github.com/scipy/scipy/pull/8614>`__: ENH: correct p-values for stats.kendalltau and stats.mstats.kendalltau * `#8670 <https://github.com/scipy/scipy/pull/8670>`__: ENH: Require Lapack 3.4.0 * `#8683 <https://github.com/scipy/scipy/pull/8683>`__: Correcting kmeans documentation * `#8725 <https://github.com/scipy/scipy/pull/8725>`__: MAINT: Cleanup scipy.optimize.leastsq * `#8726 <https://github.com/scipy/scipy/pull/8726>`__: BUG: Fix _get_output in scipy.ndimage to support string * `#8733 <https://github.com/scipy/scipy/pull/8733>`__: MAINT: stats: A bit of clean up. * `#8737 <https://github.com/scipy/scipy/pull/8737>`__: BUG: Improve numerical precision/convergence failures of smirnov/kolmogorov * `#8738 <https://github.com/scipy/scipy/pull/8738>`__: MAINT: stats: A bit of clean up in test_distributions.py. * `#8740 <https://github.com/scipy/scipy/pull/8740>`__: BF/ENH: make minpack thread safe * `#8742 <https://github.com/scipy/scipy/pull/8742>`__: BUG: Fix division by zero in trust-region optimization methods * `#8746 <https://github.com/scipy/scipy/pull/8746>`__: MAINT: signal: Fix a docstring of a private function, and fix... * `#8750 <https://github.com/scipy/scipy/pull/8750>`__: DOC clarified description of norminvgauss in scipy.stats * `#8753 <https://github.com/scipy/scipy/pull/8753>`__: DOC: signal: Fix a plot title in the chirp docstring. * `#8755 <https://github.com/scipy/scipy/pull/8755>`__: DOC: MAINT: Fix link to the wheel documentation in developer... * `#8760 <https://github.com/scipy/scipy/pull/8760>`__: BUG: stats: boltzmann wasn't setting the upper bound. * `#8763 <https://github.com/scipy/scipy/pull/8763>`__: [DOC] Improved scipy.cluster.hierarchy documentation * `#8765 <https://github.com/scipy/scipy/pull/8765>`__: DOC: added example for scipy.stat.mstats.tmin * `#8788 <https://github.com/scipy/scipy/pull/8788>`__: DOC: fix definition of optional `disp` parameter * `#8802 <https://github.com/scipy/scipy/pull/8802>`__: MAINT: Suppress dd_real unused function compiler warnings. * `#8803 <https://github.com/scipy/scipy/pull/8803>`__: ENH: Add full_output support to optimize.newton() * `#8804 <https://github.com/scipy/scipy/pull/8804>`__: MAINT: stats cleanup * `#8808 <https://github.com/scipy/scipy/pull/8808>`__: DOC: add note about isinstance for frozen rvs * `#8812 <https://github.com/scipy/scipy/pull/8812>`__: Updated numpydoc submodule * `#8813 <https://github.com/scipy/scipy/pull/8813>`__: MAINT: stats: Fix multinomial docstrings, and do some clean up. * `#8816 <https://github.com/scipy/scipy/pull/8816>`__: BUG: fixed _stats of t-distribution in scipy.stats * `#8817 <https://github.com/scipy/scipy/pull/8817>`__: BUG: ndimage: Fix validation of the origin argument in correlate... * `#8822 <https://github.com/scipy/scipy/pull/8822>`__: BUG: integrate: Fix crash with repeated t values in odeint. * `#8832 <https://github.com/scipy/scipy/pull/8832>`__: Hyperlink DOIs against preferred resolver * `#8837 <https://github.com/scipy/scipy/pull/8837>`__: BUG: sparse: Ensure correct dtype for sparse comparison operations. * `#8839 <https://github.com/scipy/scipy/pull/8839>`__: DOC: stats: A few tweaks to the linregress docstring. * `#8846 <https://github.com/scipy/scipy/pull/8846>`__: BUG: stats: Fix logpdf method of invwishart. * `#8849 <https://github.com/scipy/scipy/pull/8849>`__: DOC: signal: Fixed mistake in the firwin docstring. * `#8854 <https://github.com/scipy/scipy/pull/8854>`__: DOC: fix type descriptors in ltisys documentation * `#8865 <https://github.com/scipy/scipy/pull/8865>`__: Fix tiny typo in docs for chi2 pdf * `#8870 <https://github.com/scipy/scipy/pull/8870>`__: Fixes related to invertibility of STFT * `#8872 <https://github.com/scipy/scipy/pull/8872>`__: ENH: special: Add the softmax function * `#8874 <https://github.com/scipy/scipy/pull/8874>`__: DOC correct gamma function in docstrings in scipy.stats * `#8876 <https://github.com/scipy/scipy/pull/8876>`__: ENH: Added TOMS Algorithm 748 as 1-d root finder; 17 test function... * `#8882 <https://github.com/scipy/scipy/pull/8882>`__: ENH: Only use Halley's adjustment to Newton if close enough. * `#8883 <https://github.com/scipy/scipy/pull/8883>`__: FIX: optimize: make jac and hess truly optional for 'trust-constr' * `#8885 <https://github.com/scipy/scipy/pull/8885>`__: TST: Do not error on warnings raised about non-tuple indexing. * `#8887 <https://github.com/scipy/scipy/pull/8887>`__: MAINT: filter out np.matrix PendingDeprecationWarning's in numpy... * `#8889 <https://github.com/scipy/scipy/pull/8889>`__: DOC: optimize: separate legacy interfaces from new ones * `#8890 <https://github.com/scipy/scipy/pull/8890>`__: ENH: Add optimize.root_scalar() as a universal dispatcher for... * `#8899 <https://github.com/scipy/scipy/pull/8899>`__: DCT-IV, DST-IV and DCT-I, DST-I orthonormalization support in... * `#8901 <https://github.com/scipy/scipy/pull/8901>`__: MAINT: Reorganize flapack.pyf.src file * `#8907 <https://github.com/scipy/scipy/pull/8907>`__: BUG: ENH: Check if guess for newton is already zero before checking... * `#8908 <https://github.com/scipy/scipy/pull/8908>`__: ENH: Make sorting optional for cKDTree.query_ball_point() * `#8910 <https://github.com/scipy/scipy/pull/8910>`__: DOC: sparse.csgraph simple examples. * `#8914 <https://github.com/scipy/scipy/pull/8914>`__: DOC: interpolate: fix equivalences of string aliases * `#8918 <https://github.com/scipy/scipy/pull/8918>`__: add float_control(precise, on) to _fpumode.c * `#8919 <https://github.com/scipy/scipy/pull/8919>`__: MAINT: interpolate: improve error messages for common `bc_type`... * `#8920 <https://github.com/scipy/scipy/pull/8920>`__: DOC: update Contributing to SciPy to say "prefer no PEP8 only... * `#8924 <https://github.com/scipy/scipy/pull/8924>`__: MAINT: special: deprecate `hyp2f0`, `hyp1f2`, and `hyp3f0` * `#8927 <https://github.com/scipy/scipy/pull/8927>`__: MAINT: special: remove `errprint` * `#8932 <https://github.com/scipy/scipy/pull/8932>`__: Fix broadcasting scale arg of entropy * `#8936 <https://github.com/scipy/scipy/pull/8936>`__: Fix (some) non-tuple index warnings * `#8937 <https://github.com/scipy/scipy/pull/8937>`__: ENH: implement sparse matrix BSR to CSR conversion directly. * `#8938 <https://github.com/scipy/scipy/pull/8938>`__: DOC: add @_ni_docstrings.docfiller in ndimage.rotate * `#8940 <https://github.com/scipy/scipy/pull/8940>`__: Update _discrete_distns.py * `#8943 <https://github.com/scipy/scipy/pull/8943>`__: DOC: Finish dangling sentence in `convolve` docstring * `#8944 <https://github.com/scipy/scipy/pull/8944>`__: MAINT: Address tuple indexing and warnings * `#8945 <https://github.com/scipy/scipy/pull/8945>`__: ENH: spatial.transform.Rotation [GSOC2018] * `#8950 <https://github.com/scipy/scipy/pull/8950>`__: csgraph Dijkstra function description rewording * `#8953 <https://github.com/scipy/scipy/pull/8953>`__: DOC, MAINT: HTTP -> HTTPS, and other linkrot fixes * `#8955 <https://github.com/scipy/scipy/pull/8955>`__: BUG: np.int64 in scipy.fftpack.next_fast_len * `#8958 <https://github.com/scipy/scipy/pull/8958>`__: MAINT: Add more descriptive error message for phase one simplex. * `#8962 <https://github.com/scipy/scipy/pull/8962>`__: BUG: sparse.linalg: add missing conjugate to _ScaledLinearOperator.adjoint * `#8963 <https://github.com/scipy/scipy/pull/8963>`__: BUG: sparse.linalg: downgrade LinearOperator TypeError to warning * `#8965 <https://github.com/scipy/scipy/pull/8965>`__: ENH: Wrapped RFP format and RZ decomposition routines * `#8969 <https://github.com/scipy/scipy/pull/8969>`__: MAINT: doc and code fixes for optimize.newton * `#8970 <https://github.com/scipy/scipy/pull/8970>`__: Added 'average' keyword for welch/csd to enable median averaging * `#8971 <https://github.com/scipy/scipy/pull/8971>`__: Better imresize deprecation warning * `#8972 <https://github.com/scipy/scipy/pull/8972>`__: MAINT: Switch np.where(c) for np.nonzero(c) * `#8975 <https://github.com/scipy/scipy/pull/8975>`__: MAINT: Fix warning-based failures * `#8979 <https://github.com/scipy/scipy/pull/8979>`__: DOC: fix description of count_sort keyword of dendrogram * `#8982 <https://github.com/scipy/scipy/pull/8982>`__: MAINT: optimize: Fixed minor mistakes in test_linprog.py (#8978) * `#8984 <https://github.com/scipy/scipy/pull/8984>`__: BUG: sparse.linalg: ensure expm casts integer inputs to float * `#8986 <https://github.com/scipy/scipy/pull/8986>`__: BUG: optimize/slsqp: do not exit with convergence on steps where... * `#8989 <https://github.com/scipy/scipy/pull/8989>`__: MAINT: use collections.abc in basinhopping * `#8990 <https://github.com/scipy/scipy/pull/8990>`__: ENH extend p-values of anderson_ksamp in scipy.stats * `#8991 <https://github.com/scipy/scipy/pull/8991>`__: ENH: Weighted kde * `#8993 <https://github.com/scipy/scipy/pull/8993>`__: ENH: spatial.transform.Rotation.random [GSOC 2018] * `#8994 <https://github.com/scipy/scipy/pull/8994>`__: ENH: spatial.transform.Slerp [GSOC 2018] * `#8995 <https://github.com/scipy/scipy/pull/8995>`__: TST: time.time in test * `#9007 <https://github.com/scipy/scipy/pull/9007>`__: Fix typo in fftpack.rst * `#9013 <https://github.com/scipy/scipy/pull/9013>`__: Added correct plotting code for two sided output from spectrogram * `#9014 <https://github.com/scipy/scipy/pull/9014>`__: BUG: differential_evolution with inf objective functions * `#9017 <https://github.com/scipy/scipy/pull/9017>`__: BUG: fixed #8446 corner case for asformat(array|dense) * `#9018 <https://github.com/scipy/scipy/pull/9018>`__: MAINT: _lib/ccallback: remove unused code * `#9021 <https://github.com/scipy/scipy/pull/9021>`__: BUG: Issue with subspace_angles * `#9022 <https://github.com/scipy/scipy/pull/9022>`__: DOC: Added "See Also" section to lombscargle docstring * `#9034 <https://github.com/scipy/scipy/pull/9034>`__: BUG: Fix tolerance printing behavior, remove meaningless tol... * `#9035 <https://github.com/scipy/scipy/pull/9035>`__: TST: improve signal.bsplines test coverage * `#9037 <https://github.com/scipy/scipy/pull/9037>`__: ENH: add a new init method for k-means * `#9039 <https://github.com/scipy/scipy/pull/9039>`__: DOC: Add examples to fftpack.irfft docstrings * `#9048 <https://github.com/scipy/scipy/pull/9048>`__: ENH: scipy.sparse.random * `#9050 <https://github.com/scipy/scipy/pull/9050>`__: BUG: scipy.io.hb_write: fails for matrices not in csc format * `#9051 <https://github.com/scipy/scipy/pull/9051>`__: MAINT: Fix slow sparse.rand for k < mn/3 (#9036). * `#9054 <https://github.com/scipy/scipy/pull/9054>`__: MAINT: spatial: Explicitly initialize LAPACK output parameters. * `#9055 <https://github.com/scipy/scipy/pull/9055>`__: DOC: Add examples to scipy.special docstrings * `#9056 <https://github.com/scipy/scipy/pull/9056>`__: ENH: Use one thread in OpenBLAS * `#9059 <https://github.com/scipy/scipy/pull/9059>`__: DOC: Update README with link to Code of Conduct * `#9060 <https://github.com/scipy/scipy/pull/9060>`__: BLD: remove support for the Bento build system. * `#9062 <https://github.com/scipy/scipy/pull/9062>`__: DOC add sections to overview in scipy.stats * `#9066 <https://github.com/scipy/scipy/pull/9066>`__: BUG: Correct "remez" error message * `#9069 <https://github.com/scipy/scipy/pull/9069>`__: DOC: update linalg section of roadmap for LAPACK versions. * `#9079 <https://github.com/scipy/scipy/pull/9079>`__: MAINT: add spatial.transform to refguide check; complete some... * `#9081 <https://github.com/scipy/scipy/pull/9081>`__: MAINT: Add warnings if pivot value is close to tolerance in linprog(method='simplex') * `#9084 <https://github.com/scipy/scipy/pull/9084>`__: BUG fix incorrect p-values of kurtosistest in scipy.stats * `#9095 <https://github.com/scipy/scipy/pull/9095>`__: DOC: add sections to mstats overview in scipy.stats * `#9096 <https://github.com/scipy/scipy/pull/9096>`__: BUG: Add test for Stackoverflow example from issue 8174. * `#9101 <https://github.com/scipy/scipy/pull/9101>`__: ENH: add Siegel slopes (robust regression) to scipy.stats * `#9105 <https://github.com/scipy/scipy/pull/9105>`__: allow resample_poly() to output float32 for float32 inputs. * `#9112 <https://github.com/scipy/scipy/pull/9112>`__: MAINT: optimize: make trust-constr accept constraint dict (#9043) * `#9118 <https://github.com/scipy/scipy/pull/9118>`__: Add doc entry to cholesky_banded * `#9120 <https://github.com/scipy/scipy/pull/9120>`__: eigsh documentation parameters * `#9125 <https://github.com/scipy/scipy/pull/9125>`__: interpolative: correctly reconstruct full rank matrices * `#9126 <https://github.com/scipy/scipy/pull/9126>`__: MAINT: Use warnings for unexpected peak properties * `#9129 <https://github.com/scipy/scipy/pull/9129>`__: BUG: Do not catch and silence KeyboardInterrupt * `#9131 <https://github.com/scipy/scipy/pull/9131>`__: DOC: Correct the typo in scipy.optimize tutorial page * `#9133 <https://github.com/scipy/scipy/pull/9133>`__: FIX: Avoid use of bare except * `#9134 <https://github.com/scipy/scipy/pull/9134>`__: DOC: Update of 'return_eigenvectors' description * `#9137 <https://github.com/scipy/scipy/pull/9137>`__: DOC: typo fixes for discrete Poisson tutorial * `#9139 <https://github.com/scipy/scipy/pull/9139>`__: FIX: Doctest failure in optimize tutorial * `#9143 <https://github.com/scipy/scipy/pull/9143>`__: DOC: missing sigma in Pearson r formula * `#9145 <https://github.com/scipy/scipy/pull/9145>`__: MAINT: Refactor linear programming solvers * `#9149 <https://github.com/scipy/scipy/pull/9149>`__: FIX: Make scipy.odr.ODR ifixx equal to its data.fix if given * `#9156 <https://github.com/scipy/scipy/pull/9156>`__: DOC: special: Mention the sigmoid function in the expit docstring. * `#9160 <https://github.com/scipy/scipy/pull/9160>`__: Fixed a latex delimiter error in levy() * `#9170 <https://github.com/scipy/scipy/pull/9170>`__: DOC: correction / update of docstrings of distributions in scipy.stats * `#9171 <https://github.com/scipy/scipy/pull/9171>`__: better description of the hierarchical clustering parameter * `#9174 <https://github.com/scipy/scipy/pull/9174>`__: domain check for a < b in stats.truncnorm * `#9175 <https://github.com/scipy/scipy/pull/9175>`__: DOC: Minor grammar fix * `#9176 <https://github.com/scipy/scipy/pull/9176>`__: BUG: CloughTocher2DInterpolator: fix miscalculation at neighborless... * `#9177 <https://github.com/scipy/scipy/pull/9177>`__: BUILD: Document the "clean" target in the doc/Makefile. * `#9178 <https://github.com/scipy/scipy/pull/9178>`__: MAINT: make refguide-check more robust for printed numpy arrays * `#9186 <https://github.com/scipy/scipy/pull/9186>`__: MAINT: Remove np.ediff1d occurence * `#9188 <https://github.com/scipy/scipy/pull/9188>`__: DOC: correct typo in extending ndimage with C * `#9190 <https://github.com/scipy/scipy/pull/9190>`__: ENH: Support specifying axes for fftconvolve * `#9192 <https://github.com/scipy/scipy/pull/9192>`__: MAINT: optimize: fixed @pv style suggestions from #9112 * `#9200 <https://github.com/scipy/scipy/pull/9200>`__: Fix make_interp_spline(..., k=0 or 1, axis<0) * `#9201 <https://github.com/scipy/scipy/pull/9201>`__: BUG: sparse.linalg/gmres: use machine eps in breakdown check * `#9204 <https://github.com/scipy/scipy/pull/9204>`__: MAINT: fix up stats.spearmanr and match mstats.spearmanr with... * `#9206 <https://github.com/scipy/scipy/pull/9206>`__: MAINT: include benchmarks and dev files in sdist. * `#9208 <https://github.com/scipy/scipy/pull/9208>`__: TST: signal: bump bsplines test tolerance for complex data * `#9210 <https://github.com/scipy/scipy/pull/9210>`__: TST: mark tests as slow, fix missing random seed * `#9211 <https://github.com/scipy/scipy/pull/9211>`__: ENH: add capability to specify orders in pade func * `#9217 <https://github.com/scipy/scipy/pull/9217>`__: MAINT: Include ``success`` and ``nit`` in OptimizeResult returned... * `#9222 <https://github.com/scipy/scipy/pull/9222>`__: ENH: interpolate: Use scipy.spatial.distance to speed-up Rbf * `#9229 <https://github.com/scipy/scipy/pull/9229>`__: MNT: Fix Fourier filter double case * `#9233 <https://github.com/scipy/scipy/pull/9233>`__: BUG: spatial/distance: fix pdist/cdist performance regression... * `#9234 <https://github.com/scipy/scipy/pull/9234>`__: FIX: Proper suppression * `#9235 <https://github.com/scipy/scipy/pull/9235>`__: BENCH: rationalize slow benchmarks + miscellaneous fixes * `#9238 <https://github.com/scipy/scipy/pull/9238>`__: BENCH: limit number of parameter combinations in spatial.*KDTree... * `#9239 <https://github.com/scipy/scipy/pull/9239>`__: DOC: stats: Fix LaTeX markup of a couple distribution PDFs. * `#9241 <https://github.com/scipy/scipy/pull/9241>`__: ENH: Evaluate plateau size during peak finding * `#9242 <https://github.com/scipy/scipy/pull/9242>`__: ENH: stats: Implement _ppf and _logpdf for crystalball, and do... * `#9246 <https://github.com/scipy/scipy/pull/9246>`__: DOC: Properly render versionadded directive in HTML documentation * `#9255 <https://github.com/scipy/scipy/pull/9255>`__: DOC: mention RootResults in optimization reference guide * `#9260 <https://github.com/scipy/scipy/pull/9260>`__: TST: relax some tolerances so tests pass with x87 math * `#9264 <https://github.com/scipy/scipy/pull/9264>`__: TST Use assert_raises "match" parameter instead of the "message"... * `#9267 <https://github.com/scipy/scipy/pull/9267>`__: DOC: clarify expect() return val when moment is inf/nan * `#9272 <https://github.com/scipy/scipy/pull/9272>`__: DOC: Add description of default bounds to linprog * `#9277 <https://github.com/scipy/scipy/pull/9277>`__: MAINT: sparse/linalg: make test deterministic * `#9278 <https://github.com/scipy/scipy/pull/9278>`__: MAINT: interpolate: pep8 cleanup in test_polyint * `#9279 <https://github.com/scipy/scipy/pull/9279>`__: Fixed docstring for resample * `#9280 <https://github.com/scipy/scipy/pull/9280>`__: removed first check for float in get_sum_dtype * `#9281 <https://github.com/scipy/scipy/pull/9281>`__: BUG: only accept 1d input for bartlett / levene in scipy.stats * `#9282 <https://github.com/scipy/scipy/pull/9282>`__: MAINT: dense_output and t_eval are mutually exclusive inputs * `#9283 <https://github.com/scipy/scipy/pull/9283>`__: MAINT: add docs and do some cleanups in interpolate.Rbf * `#9288 <https://github.com/scipy/scipy/pull/9288>`__: Run distance_transform_edt tests on all types * `#9294 <https://github.com/scipy/scipy/pull/9294>`__: DOC: fix the formula typo * `#9298 <https://github.com/scipy/scipy/pull/9298>`__: MAINT: optimize/trust-constr: restore .niter attribute for backward-compat * `#9299 <https://github.com/scipy/scipy/pull/9299>`__: DOC: clarification of default rvs method in scipy.stats * `#9301 <https://github.com/scipy/scipy/pull/9301>`__: MAINT: removed unused import sys * `#9302 <https://github.com/scipy/scipy/pull/9302>`__: MAINT: removed unused imports * `#9303 <https://github.com/scipy/scipy/pull/9303>`__: DOC: signal: Refer to fs instead of nyq in the firwin docstring. * `#9305 <https://github.com/scipy/scipy/pull/9305>`__: ENH: Added Yeo-Johnson power transformation * `#9306 <https://github.com/scipy/scipy/pull/9306>`__: ENH - add dual annealing * `#9309 <https://github.com/scipy/scipy/pull/9309>`__: ENH add the yulesimon distribution to scipy.stats * `#9317 <https://github.com/scipy/scipy/pull/9317>`__: Nested SLSQP bug fix. * `#9320 <https://github.com/scipy/scipy/pull/9320>`__: MAINT: stats: avoid underflow in stats.geom.ppf * `#9326 <https://github.com/scipy/scipy/pull/9326>`__: Add example for Rosenbrock function * `#9332 <https://github.com/scipy/scipy/pull/9332>`__: Sort file lists * `#9340 <https://github.com/scipy/scipy/pull/9340>`__: Fix typo in find_peaks 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NumFOCUS contact address). * `#9373 <https://github.com/scipy/scipy/pull/9373>`__: Fix exception if python is called with -OO option * `#9374 <https://github.com/scipy/scipy/pull/9374>`__: FIX: AIX compilation issue with NAN and INFINITY * `#9376 <https://github.com/scipy/scipy/pull/9376>`__: COBLYA -> COBYLA in docs * `#9377 <https://github.com/scipy/scipy/pull/9377>`__: DOC: Add examples integrate: fixed_quad and quadrature * `#9379 <https://github.com/scipy/scipy/pull/9379>`__: MAINT: TST: Make tests NumPy 1.8 compatible * `#9385 <https://github.com/scipy/scipy/pull/9385>`__: CI: On Travis matrix "OPTIMIZE=-OO" flag ignored * `#9387 <https://github.com/scipy/scipy/pull/9387>`__: Fix defaut value for 'mode' in 'ndimage.shift' in the doc * `#9392 <https://github.com/scipy/scipy/pull/9392>`__: BUG: rank has to be integer in rank_filter: fixed issue 9388 * `#9399 <https://github.com/scipy/scipy/pull/9399>`__: DOC: Misc. typos * `#9400 <https://github.com/scipy/scipy/pull/9400>`__: TST: stats: Fix the expected r-value of a linregress test. * `#9405 <https://github.com/scipy/scipy/pull/9405>`__: BUG: np.hstack does not accept generator expressions * `#9408 <https://github.com/scipy/scipy/pull/9408>`__: ENH: linalg: Shorter ill-conditioned warning message * `#9418 <https://github.com/scipy/scipy/pull/9418>`__: DOC: Fix ndimage docstrings and reduce doc build warnings * `#9421 <https://github.com/scipy/scipy/pull/9421>`__: DOC: Add missing docstring examples in scipy.spatial * `#9422 <https://github.com/scipy/scipy/pull/9422>`__: DOC: Add an example to integrate.newton_cotes * `#9427 <https://github.com/scipy/scipy/pull/9427>`__: BUG: Fixed defect with maxiter #9419 in dual annealing * `#9431 <https://github.com/scipy/scipy/pull/9431>`__: BENCH: Add dual annealing to scipy benchmark (see #9415) * `#9435 <https://github.com/scipy/scipy/pull/9435>`__: DOC: Add docstring examples for stats.binom_test * `#9443 <https://github.com/scipy/scipy/pull/9443>`__: DOC: Fix the order of indices in optimize tutorial * `#9444 <https://github.com/scipy/scipy/pull/9444>`__: MAINT: interpolate: use operator.index for checking/coercing... * `#9445 <https://github.com/scipy/scipy/pull/9445>`__: DOC: Added missing example to stats.mstats.kruskal * `#9446 <https://github.com/scipy/scipy/pull/9446>`__: DOC: Add note about version changed for jaccard distance * `#9447 <https://github.com/scipy/scipy/pull/9447>`__: BLD: version-script handling in setup.py * `#9448 <https://github.com/scipy/scipy/pull/9448>`__: TST: skip a problematic linalg test * `#9449 <https://github.com/scipy/scipy/pull/9449>`__: TST: fix missing seed in lobpcg test. * `#9456 <https://github.com/scipy/scipy/pull/9456>`__: TST: test_eigs_consistency() now sorts output Checksums ========= MD5 ~~~ 47d309402d2e5574be8fa261fadfaf58 scipy-1.2.0rc1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl 911dfde5be66403c07c60e19aa631dc2 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3 2

memory leak in LinearNDInterpolator?
by Aronne Merrelli Nov. 25, 2018

Nov. 25, 2018

Hello, I am having a problem with the LinearNDInterpolator in SciPy, where it looks like there is a memory leak. I have a simple example here, all I do is setup a very small LinearNDInterpolator object and call the interpolator many times in a loop: https://gist.github.com/aronnem/707dfeec07b74888fb7390d828684184 Note that if the "pts_list" and "vals" are swapped with the integer versions, there is no leak. Using the floats seems to produce the leak. I have tried both conda and Canopy installed environments, they all seem to have the same behavior. For example, here is the output I get with a scipy 1.1.0 compiled with Cython 0.28.5, numpy 1.13.3 on Mac OS X: rss_used= 4 KB vms_used= 0 KB rss_used= 2516 KB vms_used= 2560 KB rss_used= 4836 KB vms_used= 5188 KB rss_used= 6880 KB vms_used= 6664 KB rss_used= 9408 KB vms_used= 10248 KB rss_used= 11680 KB vms_used= 12076 KB rss_used= 14356 KB vms_used= 15872 KB rss_used= 16736 KB vms_used= 17792 KB rss_used= 19416 KB vms_used= 20496 KB rss_used= 22100 KB vms_used= 23472 KB The only workaround I have found so far is to downgrade my numpy version to 1.11.3. So that seems to suggest it is a numpy problem; however this function is implemented in cython, so I am not sure how to tell whether this is a numpy, scipy, or cython problem. Regards, Aronne

4 5

Added functionality to find_peaks tool
by Luca Nov. 23, 2018

Nov. 23, 2018

Hi everybody First of all, this is my first post here, so excuse me if I do anything wrong. I'm mostly a user of SciPy, but recently I needed few functionalities from find_peaks that I discovered weren't implemented. I therefore decided to implement them myself. I'm now wondering if they could be useful for everybody and not just for me. Unfortunately I almost never worked on big projects on Git, so I'm a bit struggling understanding how should I proceed. First of all. The changes I'm talking of are: - Allow to work with unevenly spaced samples specifying a abscissas array x. More specifically: - Filter peaks depending on their distance with not-uniformly spaced points - Evaluate width and width's intersection points correctly with not-uniformly spaced points - Allow the above-mentioned abscissas to be a np.datetime64 array. In this case the minimum distance between two objects can (must) be specified as a np.timedelta64 value and the width of the peaks is also returned as an array of np.timedelta64 values. - Allow the output peaks to be sorted, either ascending or descending, depending either on their height or their prominence. - Allow to specify a maximum number of peaks to be returned. The output would then depend on the sorting method one has chosen. I would therefore ask you: - do you think these changes could be considered useful for the community? - could someone help me in my first-time submission process? Thank you very much and please tell me if I'm doing anything wrong Best regards Luca Amerio Luca

3 2

dropping python 2.7 and numpy <1.13.3
by Ralf Gommers Nov. 20, 2018

Nov. 20, 2018

Hi all, I've always had in mind that SciPy would follow NumPy in its timeline for dropping Python 2.7. However, as far as I can tell we've never had the discussion on this list. So here's the proposal: Let's follow NumPy's timeline [1], which says that from 1 Jan 2019 onwards new releases will be Python 3 only, and the last release before that date will be an LTS release. That means SciPy 1.2.0 will be the LTS release, and 1.3.0 will be >= py3.5. Also, we haven't changed the minimum numpy version we support in quite a while, we're still at 1.8.2. And that will have to change anyway after dropping Python 2.7. The current minimum numpy versions we require are: - py27: 1.8.2 - py35: 1.9.3 - py36: 1.12.1 - py37: 1.13.1 We have always aimed to support at least 4 numpy versions (i.e. 2 year old versions). The differences per Python version in minimum numpy version are annoying (we don't consistently check that in our main __init__.py or in setup.py even), so I propose that for SciPy 1.3.0 we raise the minimum required NumPy version to 1.13.3. That'll still be 4 supported releases, 1.13.3-1.16.x. Cheers, Ralf [1] http://www.numpy.org/neps/nep-0014-dropping-python2.7-proposal.html [2] NumPy thread on dropping py27: https://mail.python.org/pipermail/numpy-discussion/2017-November/077341.html

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heads up - removed deprecated functions for 1.3.0
by Ralf Gommers Nov. 20, 2018

Nov. 20, 2018

Hi all, Just a heads up that in master we removed many deprecated functions just now (in https://github.com/scipy/scipy/pull/9325). The ones from scipy.interpolate not many people are going to care about, however the image-related functions from scipy.misc used to be popular (they've been deprecated for a while though). In particular misc.imread. The misc namespace is getting empty. If the new datasets package that Warren is working on lands, only 6 functions left.... Cheers, Ralf

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Building From Source on Windows
by Christoph Baumgarten Nov. 15, 2018

Nov. 15, 2018

Hi, I tried to follow the instructions on https://github.com/scipy/scipy/blob/master/doc/source/building/windows.rst to build scipy on Windows. When trying to clone the repo https://github.com/matthew-brett/build-openblas.git, I noted that this repo has been moved: "This repository retired in favor of https://github.com/matthew-brett/openblas-libs" However, that link is broken. Should it be https://github.com/matthew-brett/OpenBLAS instead? If that is the case, I still don't know how to continue: The scipy guide says to start the build with ./build_openblas.sh whereas the readme in https://github.com/matthew-brett/OpenBLAS mentions the command "make" Am I looking at the right place? Maybe someone can help. Thanks Christoph

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