From mal at europython.eu Fri Dec 7 12:04:40 2018 From: mal at europython.eu (M.-A. Lemburg) Date: Fri, 7 Dec 2018 18:04:40 +0100 Subject: EuroPython 2019: Venue and location selected Message-ID: <8fcf30ff-00f2-c898-e6ca-3427ca8edd07@europython.eu> After a very work intense RFP with more than 40 venues competing, 17 entries, and two rounds of refinements, we are now happy to announce the winner: EuroPython 2019 will be held in Basel, Switzerland, from July 8 - 14 2019 We will now start work on the contracts and get the organization going, so that we can all enjoy another edition of EuroPython next year. Help spread the word -------------------- Please help us spread this message by sharing it on your social networks as widely as possible. Thank you ! Link to the blog post: https://www.europython-society.org/post/180894308215/europython-2019-venue-and-location-selected Tweet: https://twitter.com/europythons/status/1071082681000185857 Thank you, -- EuroPython Society https://www.europython-society.org/ From erik.tollerud at gmail.com Tue Dec 11 19:16:08 2018 From: erik.tollerud at gmail.com (Erik Tollerud) Date: Tue, 11 Dec 2018 19:16:08 -0500 Subject: ANN: Astropy v3.1 released Message-ID: Dear colleagues, We are very happy to announce the v3.1 release of the Astropy package, a core Python package for Astronomy: http://www.astropy.org Astropy is a community-driven Python package intended to contain much of the core functionality and common tools needed for astronomy and astrophysics. It is part of the Astropy Project, which aims to foster an ecosystem of interoperable astronomy packages for Python. The focus of this release is on performance, but it also contains new and improved major functionality. Highlights include: * Performance Improvements across-the-board * A new sub-package for Uncertainties and Distributions * A new Box Least Squares Periodogram * J-style coordinates parser * Support for use of Time and TimeDelta columns within a Table * Array-valued Time and TimeDelta objects are now mutable * Better uncertainty support and bit planes in NDData * A new operator for Quantity performance * Thermodynamic temperature equivalency * Little-h equivalency * Change in default cosmology * Significant improvements in WCSAxes * A new convenience function for imshow with ImageNormalize * A common API for World Coordinate Systems In addition, hundreds of smaller improvements and fixes have been made. An overview of the changes is provided at: http://docs.astropy.org/en/stable/whatsnew/3.1.html Note that the Astropy 3.x series only supports Python 3. Python 2 users can continue to use the 2.x (LTS) series (but without new features). Instructions for installing Astropy are provided on our website, and extensive documentation can be found at: http://docs.astropy.org If you make use of the Anaconda Python Distribution, you can update to Astropy v3.1 with: conda update astropy Whereas if you usually use pip, you can do: pip install astropy --upgrade Please report any issues, or request new features via our GitHub repository: https://github.com/astropy/astropy/issues Over 300 developers have contributed code to Astropy so far, and you can find out more about the team behind Astropy here: http://www.astropy.org/team.html As a reminder, Astropy v2.0 (our long term support release) will continue to be supported with bug fixes (but no new features) until the end of 2019, so if you need to use Astropy in a very stable environment, you may want to consider staying on the v2.0.x set of releases (for which we have recently released v2.0.10). If you use Astropy directly for your work, or as a dependency to another package, please remember to acknowledgment it by citing the appropriate Astropy paper. For the most up-to-date suggestions, see the acknowledgement page (http://www.astropy.org/acknowledging.html), but as of this release the recommendation is: This research made use of Astropy, a community-developed core Python package for Astronomy (Astropy Collaboration, 2018). where (Astropy Collaboration, 2018) is a reference to https://doi.org/10.3847/1538-3881/aabc4f Special thanks to the coordinator for this release: Brigitta Sipocz. We hope that you enjoy using Astropy as much as we enjoyed developing it! Erik Tollerud, Tom Robitaille, Kelle Cruz, and Tom Aldcroft on behalf of The Astropy Collaboration From nad at python.org Tue Dec 11 22:14:04 2018 From: nad at python.org (Ned Deily) Date: Tue, 11 Dec 2018 22:14:04 -0500 Subject: [RELEASE] Python 3.7.2rc1 and 3.6.8rc1 now available for testing Message-ID: <091E715F-EC84-4796-B193-D96414F4D62E@python.org> https://blog.python.org/2018/12/python-372rc1-and-368rc1-now-available.html Python 3.7.2rc1 and 3.6.8rc1 are now available. 3.7.2rc1 is the release preview of the next maintenance release of Python 3.7, the latest feature release of Python. 3.6.8rc1 is the release preview of the next and last maintenance release of Python 3.6, the previous feature release of Python. Assuming no critical problems are found prior to 2018-12-20, no code changes are planned between these release candidates and the final releases. These release candidates are intended to give you the opportunity to test the new security and bug fixes in 3.7.2 and 3.6.8. We strongly encourage you to test your projects and report issues found to bugs.python.org as soon as possible. Please keep in mind that these are preview releases and, thus, their use is not recommended for production environments. You can find these releases and more information here: https://www.python.org/downloads/release/python-372rc1/ https://www.python.org/downloads/release/python-368rc1/ -- Ned Deily nad at python.org -- [] From nicoddemus at gmail.com Fri Dec 14 05:29:26 2018 From: nicoddemus at gmail.com (Bruno Oliveira) Date: Fri, 14 Dec 2018 08:29:26 -0200 Subject: pytest 4.0.2 Message-ID: Hi everyone, pytest 4.0.2 has just been released to PyPI. This is a bug-fix release, being a drop-in replacement. To upgrade:: pip install --upgrade pytest The full changelog is available at https://docs.pytest.org/en/latest/changelog.html. Thanks to all who contributed to this release, among them: * Anthony Sottile * Bruno Oliveira * Daniel Hahler * Pedro Algarvio * Ronny Pfannschmidt * Tomer Keren * Yash Todi Happy testing, The pytest Development Team From renesd at gmail.com Wed Dec 5 05:32:28 2018 From: renesd at gmail.com (=?UTF-8?Q?Ren=C3=A9_Dudfield?=) Date: Wed, 5 Dec 2018 11:32:28 +0100 Subject: =?UTF-8?Q?=5BANN=5D_Josh_Bartlett_=E2=80=94_pygame_Artist_in_Residence_e?= =?UTF-8?Q?xhibit=2E?= Message-ID: Hello, Josh Bartlett has made a video for his pygame Artist in Residence exhibit. It's a timelapse of Trosnoth development in October. There is also a blog post about it: timelapse trosnoth development video . See the trosnoth tag on his blog to see his earlier blog posts made during October about Trosnoth. https://www.youtube.com/watch?v=k1tS0Fbukic Thanks Josh! ps. if you want to see the text more clearly you'll need to watch it fullscreen in 1080p. - Trosnoth is a networked multi player game that was originally developed as part of a technology camp. More info here: https://trosnoth.org/ and here: https://www.pygame .org/artist-in-residence/1 and here: https://sqizit.bartletts.id.au/tag/trosnoth/ - pygame (the library) is for making multimedia apps like games, video and audio creation. Software made with pygame has been used by billions of people around the world. pygame (the community) is a small volunteer group of creative humans who ? making things. pygame (the website) https://www.pygame.org/news is where people can share, learn, and collaborate on their creative endeavors. From dev at anteru.net Sun Dec 16 11:34:19 2018 From: dev at anteru.net (=?UTF-8?Q?Matth=c3=a4us_G=2e_Chajdas?=) Date: Sun, 16 Dec 2018 17:34:19 +0100 Subject: Pygments 2.3.1 released Message-ID: <4430cac2-b36d-28d2-0412-ec99cddd0eff@anteru.net> I'm happy to announce the release of Pygments 2.3.1. Pygments is a generic syntax highlighter written in Python. This is a maintenance release with over a dozen improvements to various lexers, as well as Python 3.7 compatibility fixes. Please have a look at the changelog . Report bugs and feature requests in the issue tracker: . Thanks go to all the contributors of these lexers, and to all those who reported bugs and waited very patiently for this release. Download it from , or look at the demonstration at . Enjoy, Matth?us From tyler.je.reddy at gmail.com Tue Dec 18 11:57:02 2018 From: tyler.je.reddy at gmail.com (Tyler Reddy) Date: Tue, 18 Dec 2018 08:57:02 -0800 Subject: ANN: SciPy 1.2.0 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 1.2.0. This is an LTS release and the last to support Python 2.7. Sources and binary wheels can be found at: https://pypi.org/project/scipy/ and at: https://github.com/scipy/scipy/releases/tag/v1.2.0 One of a few ways to install this release with pip: pip install scipy==1.2.0 ========================== SciPy 1.2.0 Release Notes ========================== 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 ? 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 V?zquez Baeza * Bence Bagi + * Christoph Baumgarten * Lucas Bellomo + * BH4 + * Aditya Bharti * Max Bolingbroke * Fran?ois Boulogne * Ward Bradt + * Matthew Brett * Evgeni Burovski * Rafa? Byczek + * Alfredo Canziani + * CJ Carey * Luc?a Cheung + * Poom Chiarawongse + * Jeanne Choo + * Robert Cimrman * Graham Clenaghan + * cynthia-rempel + * Johannes Damp + * Jaime Fernandez del Rio * Dowon + * emmi474 + * Stefan Endres + * Thomas Etherington + * Piotr Figiel * 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 Schl?ter * jeanpauphilet + * josephmernst + * Kai + * Kai-Striega + * kalash04 + * Toshiki Kataoka + * Konrad0 + * Tom Krauss + * Johannes Kulick * Lars Gr?ter + * 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 Vi?as + * 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 Luki? + * 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 ------------------------ * `#9520 `__: signal.correlate with method='fft' doesn't benefit from long... * `#9547 `__: signature of dual_annealing doesn't match other optimizers * `#9540 `__: SciPy v1.2.0rc1 cannot be imported on Python 2.7.15 * `#1240 `__: Allowing multithreaded use of minpack through scipy.optimize... * `#1432 `__: scipy.stats.mode extremely slow (Trac #905) * `#3372 `__: Please add Sphinx search field to online scipy html docs * `#3678 `__: _clough_tocher_2d_single direction between centroids * `#4174 `__: lobpcg "largest" option invalid? * `#5493 `__: anderson_ksamp p-values>1 * `#5743 `__: slsqp fails to detect infeasible problem * `#6139 `__: scipy.optimize.linprog failed to find a feasible starting point... * `#6358 `__: stats: docstring for `vonmises_line` points to `vonmises_line`... * `#6498 `__: runtests.py is missing in pypi distfile * `#7426 `__: scipy.stats.ksone(n).pdf(x) returns nan for positive values of... * `#7455 `__: scipy.stats.ksone.pdf(2,x) return incorrect values for x near... * `#7456 `__: scipy.special.smirnov and scipy.special.smirnovi have accuracy... * `#7492 `__: scipy.special.kolmogorov(x)/kolmogi(p) inefficient, inaccurate... * `#7914 `__: TravisCI not failing when it should for -OO run * `#8064 `__: linalg.solve test crashes on Windows * `#8212 `__: LAPACK Rectangular Full Packed routines * `#8256 `__: differential_evolution bug converges to wrong results in complex... * `#8443 `__: Deprecate `hyp2f0`, `hyp1f2`, and `hyp3f0`? * `#8452 `__: DOC: ARPACK tutorial has two conflicting equations * `#8680 `__: scipy fails compilation when building from source * `#8686 `__: Division by zero in _trustregion.py when x0 is exactly equal... * `#8700 `__: _MINPACK_LOCK not held when calling into minpack from least_squares * `#8786 `__: erroneous moment values for t-distribution * `#8791 `__: Checking COLA condition in istft should be optional (or omitted) * `#8843 `__: imresize cannot be deprecated just yet * `#8844 `__: Inverse Wishart Log PDF Incorrect for Non-diagonal Scale Matrix? * `#8878 `__: vonmises and vonmises_line in stats: vonmises wrong and superfluous? * `#8895 `__: v1.1.0 `ndi.rotate` documentation ? reused parameters not filled... * `#8900 `__: Missing complex conjugation in scipy.sparse.linalg.LinearOperator * `#8904 `__: BUG: if zero derivative at root, then Newton fails with RuntimeWarning * `#8911 `__: make_interp_spline bc_type incorrect input interpretation * `#8942 `__: MAINT: Refactor `_linprog.py` and `_linprog_ip.py` to remove... * `#8947 `__: np.int64 in scipy.fftpack.next_fast_len * `#9020 `__: BUG: linalg.subspace_angles gives wrong results * `#9033 `__: scipy.stats.normaltest sometimes gives incorrect returns b/c... * `#9036 `__: Bizarre times for `scipy.sparse.rand` function with 'low' density... * `#9044 `__: optimize.minimize(method=`trust-constr`) result dict does not... * `#9071 `__: doc/linalg: add cho_solve_banded to see also of cholesky_banded * `#9082 `__: eigenvalue sorting in scipy.sparse.linalg.eigsh * `#9086 `__: signaltools.py:491: FutureWarning: Using a non-tuple sequence... * `#9091 `__: test_spline_filter failure on 32-bit * `#9122 `__: Typo on scipy minimization tutorial * `#9135 `__: doc error at https://docs.scipy.org/doc/scipy/reference/tutorial/stats/discrete_poisson.html * `#9167 `__: DOC: BUG: typo in ndimage LowLevelCallable tutorial example * `#9169 `__: truncnorm does not work if b < a in scipy.stats * `#9250 `__: scipy.special.tests.test_mpmath::TestSystematic::test_pcfw fails... * `#9259 `__: rv.expect() == rv.mean() is false for rv.mean() == nan (and inf) * `#9286 `__: DOC: Rosenbrock expression in optimize.minimize tutorial * `#9316 `__: SLSQP fails in nested optimization * `#9337 `__: scipy.signal.find_peaks key typo in documentation * `#9345 `__: Example from documentation of scipy.sparse.linalg.eigs raises... * `#9383 `__: Default value for "mode" in "ndimage.shift" * `#9419 `__: dual_annealing off by one in the number of iterations * `#9442 `__: Error in Defintion of Rosenbrock Function * `#9453 `__: TST: test_eigs_consistency() doesn't have consistent results Pull requests for 1.2.0 ------------------------ * `#9526 `__: TST: relax precision requirements in signal.correlate tests * `#9507 `__: CI: MAINT: Skip a ckdtree test on pypy * `#9512 `__: TST: test_random_sampling 32-bit handling * `#9494 `__: TST: test_kolmogorov xfail 32-bit * `#9486 `__: BUG: fix sparse random int handling * `#9550 `__: BUG: scipy/_lib/_numpy_compat: get_randint * `#9549 `__: MAINT: make dual_annealing signature match other optimizers * `#9541 `__: BUG: fix SyntaxError due to non-ascii character on Python 2.7 * `#7352 `__: ENH: add Brunner Munzel test to scipy.stats. * `#7373 `__: BUG: Jaccard distance for all-zero arrays would return np.nan * `#7374 `__: ENH: Add PDF, CDF and parameter estimation for Stable Distributions * `#8098 `__: ENH: Add shgo for global optimization of NLPs. * `#8203 `__: ENH: adding simulated dual annealing to optimize * `#8259 `__: Option to follow original Storn and Price algorithm and its parallelisation * `#8293 `__: ENH add ratio-of-uniforms method for rv generation to scipy.stats * `#8294 `__: BUG: Fix slowness in stats.mode * `#8295 `__: ENH: add Jensen Shannon distance to `scipy.spatial.distance` * `#8357 `__: ENH: vectorize scalar zero-search-functions * `#8397 `__: Add `fs=` parameter to filter design functions * `#8537 `__: ENH: Implement mode parameter for spline filtering. * `#8558 `__: ENH: small speedup for stats.gaussian_kde * `#8560 `__: BUG: fix p-value calc of anderson_ksamp in scipy.stats * `#8614 `__: ENH: correct p-values for stats.kendalltau and stats.mstats.kendalltau * `#8670 `__: ENH: Require Lapack 3.4.0 * `#8683 `__: Correcting kmeans documentation * `#8725 `__: MAINT: Cleanup scipy.optimize.leastsq * `#8726 `__: BUG: Fix _get_output in scipy.ndimage to support string * `#8733 `__: MAINT: stats: A bit of clean up. * `#8737 `__: BUG: Improve numerical precision/convergence failures of smirnov/kolmogorov * `#8738 `__: MAINT: stats: A bit of clean up in test_distributions.py. * `#8740 `__: BF/ENH: make minpack thread safe * `#8742 `__: BUG: Fix division by zero in trust-region optimization methods * `#8746 `__: MAINT: signal: Fix a docstring of a private function, and fix... * `#8750 `__: DOC clarified description of norminvgauss in scipy.stats * `#8753 `__: DOC: signal: Fix a plot title in the chirp docstring. * `#8755 `__: DOC: MAINT: Fix link to the wheel documentation in developer... * `#8760 `__: BUG: stats: boltzmann wasn't setting the upper bound. * `#8763 `__: [DOC] Improved scipy.cluster.hierarchy documentation * `#8765 `__: DOC: added example for scipy.stat.mstats.tmin * `#8788 `__: DOC: fix definition of optional `disp` parameter * `#8802 `__: MAINT: Suppress dd_real unused function compiler warnings. * `#8803 `__: ENH: Add full_output support to optimize.newton() * `#8804 `__: MAINT: stats cleanup * `#8808 `__: DOC: add note about isinstance for frozen rvs * `#8812 `__: Updated numpydoc submodule * `#8813 `__: MAINT: stats: Fix multinomial docstrings, and do some clean up. * `#8816 `__: BUG: fixed _stats of t-distribution in scipy.stats * `#8817 `__: BUG: ndimage: Fix validation of the origin argument in correlate... * `#8822 `__: BUG: integrate: Fix crash with repeated t values in odeint. * `#8832 `__: Hyperlink DOIs against preferred resolver * `#8837 `__: BUG: sparse: Ensure correct dtype for sparse comparison operations. * `#8839 `__: DOC: stats: A few tweaks to the linregress docstring. * `#8846 `__: BUG: stats: Fix logpdf method of invwishart. * `#8849 `__: DOC: signal: Fixed mistake in the firwin docstring. * `#8854 `__: DOC: fix type descriptors in ltisys documentation * `#8865 `__: Fix tiny typo in docs for chi2 pdf * `#8870 `__: Fixes related to invertibility of STFT * `#8872 `__: ENH: special: Add the softmax function * `#8874 `__: DOC correct gamma function in docstrings in scipy.stats * `#8876 `__: ENH: Added TOMS Algorithm 748 as 1-d root finder; 17 test function... * `#8882 `__: ENH: Only use Halley's adjustment to Newton if close enough. * `#8883 `__: FIX: optimize: make jac and hess truly optional for 'trust-constr' * `#8885 `__: TST: Do not error on warnings raised about non-tuple indexing. * `#8887 `__: MAINT: filter out np.matrix PendingDeprecationWarning's in numpy... * `#8889 `__: DOC: optimize: separate legacy interfaces from new ones * `#8890 `__: ENH: Add optimize.root_scalar() as a universal dispatcher for... * `#8899 `__: DCT-IV, DST-IV and DCT-I, DST-I orthonormalization support in... * `#8901 `__: MAINT: Reorganize flapack.pyf.src file * `#8907 `__: BUG: ENH: Check if guess for newton is already zero before checking... * `#8908 `__: ENH: Make sorting optional for cKDTree.query_ball_point() * `#8910 `__: DOC: sparse.csgraph simple examples. * `#8914 `__: DOC: interpolate: fix equivalences of string aliases * `#8918 `__: add float_control(precise, on) to _fpumode.c * `#8919 `__: MAINT: interpolate: improve error messages for common `bc_type`... * `#8920 `__: DOC: update Contributing to SciPy to say "prefer no PEP8 only... * `#8924 `__: MAINT: special: deprecate `hyp2f0`, `hyp1f2`, and `hyp3f0` * `#8927 `__: MAINT: special: remove `errprint` * `#8932 `__: Fix broadcasting scale arg of entropy * `#8936 `__: Fix (some) non-tuple index warnings * `#8937 `__: ENH: implement sparse matrix BSR to CSR conversion directly. * `#8938 `__: DOC: add @_ni_docstrings.docfiller in ndimage.rotate * `#8940 `__: Update _discrete_distns.py * `#8943 `__: DOC: Finish dangling sentence in `convolve` docstring * `#8944 `__: MAINT: Address tuple indexing and warnings * `#8945 `__: ENH: spatial.transform.Rotation [GSOC2018] * `#8950 `__: csgraph Dijkstra function description rewording * `#8953 `__: DOC, MAINT: HTTP -> HTTPS, and other linkrot fixes * `#8955 `__: BUG: np.int64 in scipy.fftpack.next_fast_len * `#8958 `__: MAINT: Add more descriptive error message for phase one simplex. * `#8962 `__: BUG: sparse.linalg: add missing conjugate to _ScaledLinearOperator.adjoint * `#8963 `__: BUG: sparse.linalg: downgrade LinearOperator TypeError to warning * `#8965 `__: ENH: Wrapped RFP format and RZ decomposition routines * `#8969 `__: MAINT: doc and code fixes for optimize.newton * `#8970 `__: Added 'average' keyword for welch/csd to enable median averaging * `#8971 `__: Better imresize deprecation warning * `#8972 `__: MAINT: Switch np.where(c) for np.nonzero(c) * `#8975 `__: MAINT: Fix warning-based failures * `#8979 `__: DOC: fix description of count_sort keyword of dendrogram * `#8982 `__: MAINT: optimize: Fixed minor mistakes in test_linprog.py (#8978) * `#8984 `__: BUG: sparse.linalg: ensure expm casts integer inputs to float * `#8986 `__: BUG: optimize/slsqp: do not exit with convergence on steps where... * `#8989 `__: MAINT: use collections.abc in basinhopping * `#8990 `__: ENH extend p-values of anderson_ksamp in scipy.stats * `#8991 `__: ENH: Weighted kde * `#8993 `__: ENH: spatial.transform.Rotation.random [GSOC 2018] * `#8994 `__: ENH: spatial.transform.Slerp [GSOC 2018] * `#8995 `__: TST: time.time in test * `#9007 `__: Fix typo in fftpack.rst * `#9013 `__: Added correct plotting code for two sided output from spectrogram * `#9014 `__: BUG: differential_evolution with inf objective functions * `#9017 `__: BUG: fixed #8446 corner case for asformat(array|dense) * `#9018 `__: MAINT: _lib/ccallback: remove unused code * `#9021 `__: BUG: Issue with subspace_angles * `#9022 `__: DOC: Added "See Also" section to lombscargle docstring * `#9034 `__: BUG: Fix tolerance printing behavior, remove meaningless tol... * `#9035 `__: TST: improve signal.bsplines test coverage * `#9037 `__: ENH: add a new init method for k-means * `#9039 `__: DOC: Add examples to fftpack.irfft docstrings * `#9048 `__: ENH: scipy.sparse.random * `#9050 `__: BUG: scipy.io.hb_write: fails for matrices not in csc format * `#9051 `__: MAINT: Fix slow sparse.rand for k < mn/3 (#9036). * `#9054 `__: MAINT: spatial: Explicitly initialize LAPACK output parameters. * `#9055 `__: DOC: Add examples to scipy.special docstrings * `#9056 `__: ENH: Use one thread in OpenBLAS * `#9059 `__: DOC: Update README with link to Code of Conduct * `#9060 `__: BLD: remove support for the Bento build system. * `#9062 `__: DOC add sections to overview in scipy.stats * `#9066 `__: BUG: Correct "remez" error message * `#9069 `__: DOC: update linalg section of roadmap for LAPACK versions. * `#9079 `__: MAINT: add spatial.transform to refguide check; complete some... * `#9081 `__: MAINT: Add warnings if pivot value is close to tolerance in linprog(method='simplex') * `#9084 `__: BUG fix incorrect p-values of kurtosistest in scipy.stats * `#9095 `__: DOC: add sections to mstats overview in scipy.stats * `#9096 `__: BUG: Add test for Stackoverflow example from issue 8174. * `#9101 `__: ENH: add Siegel slopes (robust regression) to scipy.stats * `#9105 `__: allow resample_poly() to output float32 for float32 inputs. * `#9112 `__: MAINT: optimize: make trust-constr accept constraint dict (#9043) * `#9118 `__: Add doc entry to cholesky_banded * `#9120 `__: eigsh documentation parameters * `#9125 `__: interpolative: correctly reconstruct full rank matrices * `#9126 `__: MAINT: Use warnings for unexpected peak properties * `#9129 `__: BUG: Do not catch and silence KeyboardInterrupt * `#9131 `__: DOC: Correct the typo in scipy.optimize tutorial page * `#9133 `__: FIX: Avoid use of bare except * `#9134 `__: DOC: Update of 'return_eigenvectors' description * `#9137 `__: DOC: typo fixes for discrete Poisson tutorial * `#9139 `__: FIX: Doctest failure in optimize tutorial * `#9143 `__: DOC: missing sigma in Pearson r formula * `#9145 `__: MAINT: Refactor linear programming solvers * `#9149 `__: FIX: Make scipy.odr.ODR ifixx equal to its data.fix if given * `#9156 `__: DOC: special: Mention the sigmoid function in the expit docstring. * `#9160 `__: Fixed a latex delimiter error in levy() * `#9170 `__: DOC: correction / update of docstrings of distributions in scipy.stats * `#9171 `__: better description of the hierarchical clustering parameter * `#9174 `__: domain check for a < b in stats.truncnorm * `#9175 `__: DOC: Minor grammar fix * `#9176 `__: BUG: CloughTocher2DInterpolator: fix miscalculation at neighborless... * `#9177 `__: BUILD: Document the "clean" target in the doc/Makefile. * `#9178 `__: MAINT: make refguide-check more robust for printed numpy arrays * `#9186 `__: MAINT: Remove np.ediff1d occurence * `#9188 `__: DOC: correct typo in extending ndimage with C * `#9190 `__: ENH: Support specifying axes for fftconvolve * `#9192 `__: MAINT: optimize: fixed @pv style suggestions from #9112 * `#9200 `__: Fix make_interp_spline(..., k=0 or 1, axis<0) * `#9201 `__: BUG: sparse.linalg/gmres: use machine eps in breakdown check * `#9204 `__: MAINT: fix up stats.spearmanr and match mstats.spearmanr with... * `#9206 `__: MAINT: include benchmarks and dev files in sdist. * `#9208 `__: TST: signal: bump bsplines test tolerance for complex data * `#9210 `__: TST: mark tests as slow, fix missing random seed * `#9211 `__: ENH: add capability to specify orders in pade func * `#9217 `__: MAINT: Include ``success`` and ``nit`` in OptimizeResult returned... * `#9222 `__: ENH: interpolate: Use scipy.spatial.distance to speed-up Rbf * `#9229 `__: MNT: Fix Fourier filter double case * `#9233 `__: BUG: spatial/distance: fix pdist/cdist performance regression... * `#9234 `__: FIX: Proper suppression * `#9235 `__: BENCH: rationalize slow benchmarks + miscellaneous fixes * `#9238 `__: BENCH: limit number of parameter combinations in spatial.*KDTree... * `#9239 `__: DOC: stats: Fix LaTeX markup of a couple distribution PDFs. * `#9241 `__: ENH: Evaluate plateau size during peak finding * `#9242 `__: ENH: stats: Implement _ppf and _logpdf for crystalball, and do... * `#9246 `__: DOC: Properly render versionadded directive in HTML documentation * `#9255 `__: DOC: mention RootResults in optimization reference guide * `#9260 `__: TST: relax some tolerances so tests pass with x87 math * `#9264 `__: TST Use assert_raises "match" parameter instead of the "message"... * `#9267 `__: DOC: clarify expect() return val when moment is inf/nan * `#9272 `__: DOC: Add description of default bounds to linprog * `#9277 `__: MAINT: sparse/linalg: make test deterministic * `#9278 `__: MAINT: interpolate: pep8 cleanup in test_polyint * `#9279 `__: Fixed docstring for resample * `#9280 `__: removed first check for float in get_sum_dtype * `#9281 `__: BUG: only accept 1d input for bartlett / levene in scipy.stats * `#9282 `__: MAINT: dense_output and t_eval are mutually exclusive inputs * `#9283 `__: MAINT: add docs and do some cleanups in interpolate.Rbf * `#9288 `__: Run distance_transform_edt tests on all types * `#9294 `__: DOC: fix the formula typo * `#9298 `__: MAINT: optimize/trust-constr: restore .niter attribute for backward-compat * `#9299 `__: DOC: clarification of default rvs method in scipy.stats * `#9301 `__: MAINT: removed unused import sys * `#9302 `__: MAINT: removed unused imports * `#9303 `__: DOC: signal: Refer to fs instead of nyq in the firwin docstring. * `#9305 `__: ENH: Added Yeo-Johnson power transformation * `#9306 `__: ENH - add dual annealing * `#9309 `__: ENH add the yulesimon distribution to scipy.stats * `#9317 `__: Nested SLSQP bug fix. * `#9320 `__: MAINT: stats: avoid underflow in stats.geom.ppf * `#9326 `__: Add example for Rosenbrock function * `#9332 `__: Sort file lists * `#9340 `__: Fix typo in find_peaks documentation * `#9343 `__: MAINT Use np.full when possible * `#9344 `__: DOC: added examples to docstring of dirichlet class * `#9346 `__: DOC: Fix import of scipy.sparse.linalg in example (#9345) * `#9350 `__: Fix interpolate read only * `#9351 `__: MAINT: special.erf: use the x->-x symmetry * `#9356 `__: Fix documentation typo * `#9358 `__: DOC: improve doc for ksone and kstwobign in scipy.stats * `#9362 `__: DOC: Change datatypes of A matrices in linprog * `#9364 `__: MAINT: Adds implicit none to fftpack fortran sources * `#9369 `__: DOC: minor tweak to CoC (updated NumFOCUS contact address). * `#9373 `__: Fix exception if python is called with -OO option * `#9374 `__: FIX: AIX compilation issue with NAN and INFINITY * `#9376 `__: COBLYA -> COBYLA in docs * `#9377 `__: DOC: Add examples integrate: fixed_quad and quadrature * `#9379 `__: MAINT: TST: Make tests NumPy 1.8 compatible * `#9385 `__: CI: On Travis matrix "OPTIMIZE=-OO" flag ignored * `#9387 `__: Fix defaut value for 'mode' in 'ndimage.shift' in the doc * `#9392 `__: BUG: rank has to be integer in rank_filter: fixed issue 9388 * `#9399 `__: DOC: Misc. typos * `#9400 `__: TST: stats: Fix the expected r-value of a linregress test. * `#9405 `__: BUG: np.hstack does not accept generator expressions * `#9408 `__: ENH: linalg: Shorter ill-conditioned warning message * `#9418 `__: DOC: Fix ndimage docstrings and reduce doc build warnings * `#9421 `__: DOC: Add missing docstring examples in scipy.spatial * `#9422 `__: DOC: Add an example to integrate.newton_cotes * `#9427 `__: BUG: Fixed defect with maxiter #9419 in dual annealing * `#9431 `__: BENCH: Add dual annealing to scipy benchmark (see #9415) * `#9435 `__: DOC: Add docstring examples for stats.binom_test * `#9443 `__: DOC: Fix the order of indices in optimize tutorial * `#9444 `__: MAINT: interpolate: use operator.index for checking/coercing... * `#9445 `__: DOC: Added missing example to stats.mstats.kruskal * `#9446 `__: DOC: Add note about version changed for jaccard distance * `#9447 `__: BLD: version-script handling in setup.py * `#9448 `__: TST: skip a problematic linalg test * `#9449 `__: TST: fix missing seed in lobpcg test. * `#9456 `__: TST: test_eigs_consistency() now sorts output Checksums ========= MD5 ~~~ 0bb53a49e77bca11fb26698744c60f97 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charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 18 Dec 2018 15:08:43 -0700 Subject: [SciPy-Dev] ANN: SciPy 1.2.0 In-Reply-To: References: Message-ID: Congratulations. May there be many more :) Chuck On Tue, Dec 18, 2018 at 9:57 AM 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 1.2.0. This is an LTS release and the > last to support Python 2.7. > > Sources and binary wheels can be found at: > https://pypi.org/project/scipy/ > and at: > https://github.com/scipy/scipy/releases/tag/v1.2.0 > > One of a few ways to install this release with pip: > > pip install scipy==1.2.0 > > ========================== > SciPy 1.2.0 Release Notes > ========================== > > 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 ? 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 V?zquez Baeza > * Bence Bagi + > * Christoph Baumgarten > * Lucas Bellomo + > * BH4 + > * Aditya Bharti > * Max Bolingbroke > * Fran?ois Boulogne > * Ward Bradt + > * Matthew Brett > * Evgeni Burovski > * Rafa? Byczek + > * Alfredo Canziani + > * CJ Carey > * Luc?a Cheung + > * Poom Chiarawongse + > * Jeanne Choo + > * Robert Cimrman > * Graham Clenaghan + > * cynthia-rempel + > * Johannes Damp + > * Jaime Fernandez del Rio > * Dowon + > * emmi474 + > * Stefan Endres + > * Thomas Etherington + > * Piotr Figiel > * 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 Schl?ter > * jeanpauphilet + > * josephmernst + > * Kai + > * Kai-Striega + > * kalash04 + > * Toshiki Kataoka + > * Konrad0 + > * Tom Krauss + > * Johannes Kulick > * Lars Gr?ter + > * 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 Vi?as + > * 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 Luki? + > * 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 > ------------------------ > > * `#9520 `__: > signal.correlate with method='fft' doesn't benefit from long... > * `#9547 `__: signature of > dual_annealing doesn't match other optimizers > * `#9540 `__: SciPy v1.2.0rc1 > cannot be imported on Python 2.7.15 > * `#1240 `__: Allowing > multithreaded use of minpack through scipy.optimize... > * `#1432 `__: > scipy.stats.mode extremely slow (Trac #905) > * `#3372 `__: Please add > Sphinx search field to online scipy html docs > * `#3678 `__: > _clough_tocher_2d_single direction between centroids > * `#4174 `__: lobpcg > "largest" option invalid? > * `#5493 `__: anderson_ksamp > p-values>1 > * `#5743 `__: slsqp fails to > detect infeasible problem > * `#6139 `__: > scipy.optimize.linprog failed to find a feasible starting point... > * `#6358 `__: stats: > docstring for `vonmises_line` points to `vonmises_line`... > * `#6498 `__: runtests.py is > missing in pypi distfile > * `#7426 `__: > scipy.stats.ksone(n).pdf(x) returns nan for positive values of... > * `#7455 `__: > scipy.stats.ksone.pdf(2,x) return incorrect values for x near... > * `#7456 `__: > scipy.special.smirnov and scipy.special.smirnovi have accuracy... > * `#7492 `__: > scipy.special.kolmogorov(x)/kolmogi(p) inefficient, inaccurate... > * `#7914 `__: TravisCI not > failing when it should for -OO run > * `#8064 `__: linalg.solve > test crashes on Windows > * `#8212 `__: LAPACK > Rectangular Full Packed routines > * `#8256 `__: > differential_evolution bug converges to wrong results in complex... > * `#8443 `__: Deprecate > `hyp2f0`, `hyp1f2`, and `hyp3f0`? > * `#8452 `__: DOC: ARPACK > tutorial has two conflicting equations > * `#8680 `__: scipy fails > compilation when building from source > * `#8686 `__: Division by > zero in _trustregion.py when x0 is exactly equal... > * `#8700 `__: _MINPACK_LOCK > not held when calling into minpack from least_squares > * `#8786 `__: erroneous > moment values for t-distribution > * `#8791 `__: Checking COLA > condition in istft should be optional (or omitted) > * `#8843 `__: imresize cannot > be deprecated just yet > * `#8844 `__: Inverse Wishart > Log PDF Incorrect for Non-diagonal Scale Matrix? > * `#8878 `__: vonmises and > vonmises_line in stats: vonmises wrong and superfluous? > * `#8895 `__: v1.1.0 > `ndi.rotate` documentation ? reused parameters not filled... > * `#8900 `__: Missing complex > conjugation in scipy.sparse.linalg.LinearOperator > * `#8904 `__: BUG: if zero > derivative at root, then Newton fails with RuntimeWarning > * `#8911 `__: > make_interp_spline bc_type incorrect input interpretation > * `#8942 `__: MAINT: Refactor > `_linprog.py` and `_linprog_ip.py` to remove... > * `#8947 `__: np.int64 in > scipy.fftpack.next_fast_len > * `#9020 `__: BUG: > linalg.subspace_angles gives wrong results > * `#9033 `__: > scipy.stats.normaltest sometimes gives incorrect returns b/c... > * `#9036 `__: Bizarre times > for `scipy.sparse.rand` function with 'low' density... > * `#9044 `__: > optimize.minimize(method=`trust-constr`) result dict does not... > * `#9071 `__: doc/linalg: add > cho_solve_banded to see also of cholesky_banded > * `#9082 `__: eigenvalue > sorting in scipy.sparse.linalg.eigsh > * `#9086 `__: > signaltools.py:491: FutureWarning: Using a non-tuple sequence... > * `#9091 `__: > test_spline_filter failure on 32-bit > * `#9122 `__: Typo on scipy > minimization tutorial > * `#9135 `__: doc error at > https://docs.scipy.org/doc/scipy/reference/tutorial/stats/discrete_poisson.html > * `#9167 `__: DOC: BUG: typo > in ndimage LowLevelCallable tutorial example > * `#9169 `__: truncnorm does > not work if b < a in scipy.stats > * `#9250 `__: > scipy.special.tests.test_mpmath::TestSystematic::test_pcfw fails... > * `#9259 `__: rv.expect() == > rv.mean() is false for rv.mean() == nan (and inf) > * `#9286 `__: DOC: Rosenbrock > expression in optimize.minimize tutorial > * `#9316 `__: SLSQP fails in > nested optimization > * `#9337 `__: > scipy.signal.find_peaks key typo in documentation > * `#9345 `__: Example from > documentation of scipy.sparse.linalg.eigs raises... > * `#9383 `__: Default value > for "mode" in "ndimage.shift" > * `#9419 `__: dual_annealing > off by one in the number of iterations > * `#9442 `__: Error in > Defintion of Rosenbrock Function > * `#9453 `__: TST: > test_eigs_consistency() doesn't have consistent results > > > Pull requests for 1.2.0 > ------------------------ > > * `#9526 `__: TST: relax > precision requirements in signal.correlate tests > * `#9507 `__: CI: MAINT: Skip a > ckdtree test on pypy > * `#9512 `__: TST: > test_random_sampling 32-bit handling > * `#9494 `__: TST: > test_kolmogorov xfail 32-bit > * `#9486 `__: BUG: fix sparse > random int handling > * `#9550 `__: BUG: > scipy/_lib/_numpy_compat: get_randint > * `#9549 `__: MAINT: make > dual_annealing signature match other optimizers > * `#9541 `__: BUG: fix > SyntaxError due to non-ascii character on Python 2.7 > * `#7352 `__: ENH: add Brunner > Munzel test to scipy.stats. > * `#7373 `__: BUG: Jaccard > distance for all-zero arrays would return np.nan > * `#7374 `__: ENH: Add PDF, CDF > and parameter estimation for Stable Distributions > * `#8098 `__: ENH: Add shgo for > global optimization of NLPs. > * `#8203 `__: ENH: adding > simulated dual annealing to optimize > * `#8259 `__: Option to follow > original Storn and Price algorithm and its parallelisation > * `#8293 `__: ENH add > ratio-of-uniforms method for rv generation to scipy.stats > * `#8294 `__: BUG: Fix slowness > in stats.mode > * `#8295 `__: ENH: add Jensen > Shannon distance to `scipy.spatial.distance` > * `#8357 `__: ENH: vectorize > scalar zero-search-functions > * `#8397 `__: Add `fs=` > parameter to filter design functions > * `#8537 `__: ENH: Implement > mode parameter for spline filtering. > * `#8558 `__: ENH: small > speedup for stats.gaussian_kde > * `#8560 `__: BUG: fix p-value > calc of anderson_ksamp in scipy.stats > * `#8614 `__: ENH: correct > p-values for stats.kendalltau and stats.mstats.kendalltau > * `#8670 `__: ENH: Require > Lapack 3.4.0 > * `#8683 `__: Correcting kmeans > documentation > * `#8725 `__: MAINT: Cleanup > scipy.optimize.leastsq > * `#8726 `__: BUG: Fix > _get_output in scipy.ndimage to support string > * `#8733 `__: MAINT: stats: A > bit of clean up. > * `#8737 `__: BUG: Improve > numerical precision/convergence failures of smirnov/kolmogorov > * `#8738 `__: MAINT: stats: A > bit of clean up in test_distributions.py. > * `#8740 `__: BF/ENH: make > minpack thread safe > * `#8742 `__: BUG: Fix division > by zero in trust-region optimization methods > * `#8746 `__: MAINT: signal: > Fix a docstring of a private function, and fix... > * `#8750 `__: DOC clarified > description of norminvgauss in scipy.stats > * `#8753 `__: DOC: signal: Fix > a plot title in the chirp docstring. > * `#8755 `__: DOC: MAINT: Fix > link to the wheel documentation in developer... > * `#8760 `__: BUG: stats: > boltzmann wasn't setting the upper bound. > * `#8763 `__: [DOC] Improved > scipy.cluster.hierarchy documentation > * `#8765 `__: DOC: added > example for scipy.stat.mstats.tmin > * `#8788 `__: DOC: fix > definition of optional `disp` parameter > * `#8802 `__: MAINT: Suppress > dd_real unused function compiler warnings. > * `#8803 `__: ENH: Add > full_output support to optimize.newton() > * `#8804 `__: MAINT: stats > cleanup > * `#8808 `__: DOC: add note > about isinstance for frozen rvs > * `#8812 `__: Updated numpydoc > submodule > * `#8813 `__: MAINT: stats: Fix > multinomial docstrings, and do some clean up. > * `#8816 `__: BUG: fixed _stats > of t-distribution in scipy.stats > * `#8817 `__: BUG: ndimage: Fix > validation of the origin argument in correlate... > * `#8822 `__: BUG: integrate: > Fix crash with repeated t values in odeint. > * `#8832 `__: Hyperlink DOIs > against preferred resolver > * `#8837 `__: BUG: sparse: > Ensure correct dtype for sparse comparison operations. > * `#8839 `__: DOC: stats: A few > tweaks to the linregress docstring. > * `#8846 `__: BUG: stats: Fix > logpdf method of invwishart. > * `#8849 `__: DOC: signal: > Fixed mistake in the firwin docstring. > * `#8854 `__: DOC: fix type > descriptors in ltisys documentation > * `#8865 `__: Fix tiny typo in > docs for chi2 pdf > * `#8870 `__: Fixes related to > invertibility of STFT > * `#8872 `__: ENH: special: Add > the softmax function > * `#8874 `__: DOC correct gamma > function in docstrings in scipy.stats > * `#8876 `__: ENH: Added TOMS > Algorithm 748 as 1-d root finder; 17 test function... > * `#8882 `__: ENH: Only use > Halley's adjustment to Newton if close enough. > * `#8883 `__: FIX: optimize: > make jac and hess truly optional for 'trust-constr' > * `#8885 `__: TST: Do not error > on warnings raised about non-tuple indexing. > * `#8887 `__: MAINT: filter out > np.matrix PendingDeprecationWarning's in numpy... > * `#8889 `__: DOC: optimize: > separate legacy interfaces from new ones > * `#8890 `__: ENH: Add > optimize.root_scalar() as a universal dispatcher for... > * `#8899 `__: DCT-IV, DST-IV > and DCT-I, DST-I orthonormalization support in... > * `#8901 `__: MAINT: Reorganize > flapack.pyf.src file > * `#8907 `__: BUG: ENH: Check > if guess for newton is already zero before checking... > * `#8908 `__: ENH: Make sorting > optional for cKDTree.query_ball_point() > * `#8910 `__: DOC: > sparse.csgraph simple examples. > * `#8914 `__: DOC: interpolate: > fix equivalences of string aliases > * `#8918 `__: add > float_control(precise, on) to _fpumode.c > * `#8919 `__: MAINT: > interpolate: improve error messages for common `bc_type`... > * `#8920 `__: DOC: update > Contributing to SciPy to say "prefer no PEP8 only... > * `#8924 `__: MAINT: special: > deprecate `hyp2f0`, `hyp1f2`, and `hyp3f0` > * `#8927 `__: MAINT: special: > remove `errprint` > * `#8932 `__: Fix broadcasting > scale arg of entropy > * `#8936 `__: Fix (some) > non-tuple index warnings > * `#8937 `__: ENH: implement > sparse matrix BSR to CSR conversion directly. > * `#8938 `__: DOC: add > @_ni_docstrings.docfiller in ndimage.rotate > * `#8940 `__: Update > _discrete_distns.py > * `#8943 `__: DOC: Finish > dangling sentence in `convolve` docstring > * `#8944 `__: MAINT: Address > tuple indexing and warnings > * `#8945 `__: ENH: > spatial.transform.Rotation [GSOC2018] > * `#8950 `__: csgraph Dijkstra > function description rewording > * `#8953 `__: DOC, MAINT: HTTP > -> HTTPS, and other linkrot fixes > * `#8955 `__: BUG: np.int64 in > scipy.fftpack.next_fast_len > * `#8958 `__: MAINT: Add more > descriptive error message for phase one simplex. > * `#8962 `__: BUG: > sparse.linalg: add missing conjugate to _ScaledLinearOperator.adjoint > * `#8963 `__: BUG: > sparse.linalg: downgrade LinearOperator TypeError to warning > * `#8965 `__: ENH: Wrapped RFP > format and RZ decomposition routines > * `#8969 `__: MAINT: doc and > code fixes for optimize.newton > * `#8970 `__: Added 'average' > keyword for welch/csd to enable median averaging > * `#8971 `__: Better imresize > deprecation warning > * `#8972 `__: MAINT: Switch > np.where(c) for np.nonzero(c) > * `#8975 `__: MAINT: Fix > warning-based failures > * `#8979 `__: DOC: fix > description of count_sort keyword of dendrogram > * `#8982 `__: MAINT: optimize: > Fixed minor mistakes in test_linprog.py (#8978) > * `#8984 `__: BUG: > sparse.linalg: ensure expm casts integer inputs to float > * `#8986 `__: BUG: > optimize/slsqp: do not exit with convergence on steps where... > * `#8989 `__: MAINT: use > collections.abc in basinhopping > * `#8990 `__: ENH extend > p-values of anderson_ksamp in scipy.stats > * `#8991 `__: ENH: Weighted kde > * `#8993 `__: ENH: > spatial.transform.Rotation.random [GSOC 2018] > * `#8994 `__: ENH: > spatial.transform.Slerp [GSOC 2018] > * `#8995 `__: TST: time.time in > test > * `#9007 `__: Fix typo in > fftpack.rst > * `#9013 `__: Added correct > plotting code for two sided output from spectrogram > * `#9014 `__: BUG: > differential_evolution with inf objective functions > * `#9017 `__: BUG: fixed #8446 > corner case for asformat(array|dense) > * `#9018 `__: MAINT: > _lib/ccallback: remove unused code > * `#9021 `__: BUG: Issue with > subspace_angles > * `#9022 `__: DOC: Added "See > Also" section to lombscargle docstring > * `#9034 `__: BUG: Fix > tolerance printing behavior, remove meaningless tol... > * `#9035 `__: TST: improve > signal.bsplines test coverage > * `#9037 `__: ENH: add a new > init method for k-means > * `#9039 `__: DOC: Add examples > to fftpack.irfft docstrings > * `#9048 `__: ENH: > scipy.sparse.random > * `#9050 `__: BUG: > scipy.io.hb_write: fails for matrices not in csc format > * `#9051 `__: MAINT: Fix slow > sparse.rand for k < mn/3 (#9036). > * `#9054 `__: MAINT: spatial: > Explicitly initialize LAPACK output parameters. > * `#9055 `__: DOC: Add examples > to scipy.special docstrings > * `#9056 `__: ENH: Use one > thread in OpenBLAS > * `#9059 `__: DOC: Update > README with link to Code of Conduct > * `#9060 `__: BLD: remove > support for the Bento build system. > * `#9062 `__: DOC add sections > to overview in scipy.stats > * `#9066 `__: BUG: Correct > "remez" error message > * `#9069 `__: DOC: update > linalg section of roadmap for LAPACK versions. > * `#9079 `__: MAINT: add > spatial.transform to refguide check; complete some... > * `#9081 `__: MAINT: Add > warnings if pivot value is close to tolerance in linprog(method='simplex') > * `#9084 `__: BUG fix incorrect > p-values of kurtosistest in scipy.stats > * `#9095 `__: DOC: add sections > to mstats overview in scipy.stats > * `#9096 `__: BUG: Add test for > Stackoverflow example from issue 8174. > * `#9101 `__: ENH: add Siegel > slopes (robust regression) to scipy.stats > * `#9105 `__: allow > resample_poly() to output float32 for float32 inputs. > * `#9112 `__: MAINT: optimize: > make trust-constr accept constraint dict (#9043) > * `#9118 `__: Add doc entry to > cholesky_banded > * `#9120 `__: eigsh > documentation parameters > * `#9125 `__: interpolative: > correctly reconstruct full rank matrices > * `#9126 `__: MAINT: Use > warnings for unexpected peak properties > * `#9129 `__: BUG: Do not catch > and silence KeyboardInterrupt > * `#9131 `__: DOC: Correct the > typo in scipy.optimize tutorial page > * `#9133 `__: FIX: Avoid use of > bare except > * `#9134 `__: DOC: Update of > 'return_eigenvectors' description > * `#9137 `__: DOC: typo fixes > for discrete Poisson tutorial > * `#9139 `__: FIX: Doctest > failure in optimize tutorial > * `#9143 `__: DOC: missing > sigma in Pearson r formula > * `#9145 `__: MAINT: Refactor > linear programming solvers > * `#9149 `__: FIX: Make > scipy.odr.ODR ifixx equal to its data.fix if given > * `#9156 `__: DOC: special: > Mention the sigmoid function in the expit docstring. > * `#9160 `__: Fixed a latex > delimiter error in levy() > * `#9170 `__: DOC: correction / > update of docstrings of distributions in scipy.stats > * `#9171 `__: better > description of the hierarchical clustering parameter > * `#9174 `__: domain check for > a < b in stats.truncnorm > * `#9175 `__: DOC: Minor > grammar fix > * `#9176 `__: BUG: > CloughTocher2DInterpolator: fix miscalculation at neighborless... > * `#9177 `__: BUILD: Document > the "clean" target in the doc/Makefile. > * `#9178 `__: MAINT: make > refguide-check more robust for printed numpy arrays > * `#9186 `__: MAINT: Remove > np.ediff1d occurence > * `#9188 `__: DOC: correct typo > in extending ndimage with C > * `#9190 `__: ENH: Support > specifying axes for fftconvolve > * `#9192 `__: MAINT: optimize: > fixed @pv style suggestions from #9112 > * `#9200 `__: Fix > make_interp_spline(..., k=0 or 1, axis<0) > * `#9201 `__: BUG: > sparse.linalg/gmres: use machine eps in breakdown check > * `#9204 `__: MAINT: fix up > stats.spearmanr and match mstats.spearmanr with... > * `#9206 `__: MAINT: include > benchmarks and dev files in sdist. > * `#9208 `__: TST: signal: bump > bsplines test tolerance for complex data > * `#9210 `__: TST: mark tests > as slow, fix missing random seed > * `#9211 `__: ENH: add > capability to specify orders in pade func > * `#9217 `__: MAINT: Include > ``success`` and ``nit`` in OptimizeResult returned... > * `#9222 `__: ENH: interpolate: > Use scipy.spatial.distance to speed-up Rbf > * `#9229 `__: MNT: Fix Fourier > filter double case > * `#9233 `__: BUG: > spatial/distance: fix pdist/cdist performance regression... > * `#9234 `__: FIX: Proper > suppression > * `#9235 `__: BENCH: > rationalize slow benchmarks + miscellaneous fixes > * `#9238 `__: BENCH: limit > number of parameter combinations in spatial.*KDTree... > * `#9239 `__: DOC: stats: Fix > LaTeX markup of a couple distribution PDFs. > * `#9241 `__: ENH: Evaluate > plateau size during peak finding > * `#9242 `__: ENH: stats: > Implement _ppf and _logpdf for crystalball, and do... > * `#9246 `__: DOC: Properly > render versionadded directive in HTML documentation > * `#9255 `__: DOC: mention > RootResults in optimization reference guide > * `#9260 `__: TST: relax some > tolerances so tests pass with x87 math > * `#9264 `__: TST Use > assert_raises "match" parameter instead of the "message"... > * `#9267 `__: DOC: clarify > expect() return val when moment is inf/nan > * `#9272 `__: DOC: Add > description of default bounds to linprog > * `#9277 `__: MAINT: > sparse/linalg: make test deterministic > * `#9278 `__: MAINT: > interpolate: pep8 cleanup in test_polyint > * `#9279 `__: Fixed docstring > for resample > * `#9280 `__: removed first > check for float in get_sum_dtype > * `#9281 `__: BUG: only accept > 1d input for bartlett / levene in scipy.stats > * `#9282 `__: MAINT: > dense_output and t_eval are mutually exclusive inputs > * `#9283 `__: MAINT: add docs > and do some cleanups in interpolate.Rbf > * `#9288 `__: Run > distance_transform_edt tests on all types > * `#9294 `__: DOC: fix the > formula typo > * `#9298 `__: MAINT: > optimize/trust-constr: restore .niter attribute for backward-compat > * `#9299 `__: DOC: > clarification of default rvs method in scipy.stats > * `#9301 `__: MAINT: removed > unused import sys > * `#9302 `__: MAINT: removed > unused imports > * `#9303 `__: DOC: signal: > Refer to fs instead of nyq in the firwin docstring. > * `#9305 `__: ENH: Added > Yeo-Johnson power transformation > * `#9306 `__: ENH - add dual > annealing > * `#9309 `__: ENH add the > yulesimon distribution to scipy.stats > * `#9317 `__: Nested SLSQP bug > fix. > * `#9320 `__: MAINT: stats: > avoid underflow in stats.geom.ppf > * `#9326 `__: Add example for > Rosenbrock function > * `#9332 `__: Sort file lists > * `#9340 `__: Fix typo in > find_peaks documentation > * `#9343 `__: MAINT Use np.full > when possible > * `#9344 `__: DOC: added > examples to docstring of dirichlet class > * `#9346 `__: DOC: Fix import > of scipy.sparse.linalg in example (#9345) > * `#9350 `__: Fix interpolate > read only > * `#9351 `__: MAINT: > special.erf: use the x->-x symmetry > * `#9356 `__: Fix documentation > typo > * `#9358 `__: DOC: improve doc > for ksone and kstwobign in scipy.stats > * `#9362 `__: DOC: Change > datatypes of A matrices in linprog > * `#9364 `__: MAINT: Adds > implicit none to fftpack fortran sources > * `#9369 `__: DOC: minor tweak > to CoC (updated NumFOCUS contact address). > * `#9373 `__: Fix exception if > python is called with -OO option > * `#9374 `__: FIX: AIX > compilation issue with NAN and INFINITY > * `#9376 `__: COBLYA -> COBYLA > in docs > * `#9377 `__: DOC: Add examples > integrate: fixed_quad and quadrature > * `#9379 `__: MAINT: TST: Make > tests NumPy 1.8 compatible > * `#9385 `__: CI: On Travis > matrix "OPTIMIZE=-OO" flag ignored > * `#9387 `__: Fix defaut value > for 'mode' in 'ndimage.shift' in the doc > * `#9392 `__: BUG: rank has to > be integer in rank_filter: fixed issue 9388 > * `#9399 `__: DOC: Misc. typos > * `#9400 `__: TST: stats: Fix > the expected r-value of a linregress test. > * `#9405 `__: BUG: np.hstack > does not accept generator expressions > * `#9408 `__: ENH: linalg: > Shorter ill-conditioned warning message > * `#9418 `__: DOC: Fix ndimage > docstrings and reduce doc build warnings > * `#9421 `__: DOC: Add missing > docstring examples in scipy.spatial > * `#9422 `__: DOC: Add an > example to integrate.newton_cotes > * `#9427 `__: BUG: Fixed defect > with maxiter #9419 in dual annealing > * `#9431 `__: BENCH: Add dual > annealing to scipy benchmark (see #9415) > * `#9435 `__: DOC: Add > docstring examples for stats.binom_test > * `#9443 `__: DOC: Fix the > order of indices in optimize tutorial > * `#9444 `__: MAINT: > interpolate: use operator.index for checking/coercing... > * `#9445 `__: DOC: Added > missing example to stats.mstats.kruskal > * `#9446 `__: DOC: Add note > about version changed for jaccard distance > * `#9447 `__: BLD: > version-script handling in setup.py > * `#9448 `__: TST: skip a > problematic linalg test > * `#9449 `__: TST: fix missing > seed in lobpcg test. > * `#9456 `__: TST: > test_eigs_consistency() now sorts output > > Checksums > ========= > > MD5 > ~~~ > > 0bb53a49e77bca11fb26698744c60f97 > scipy-1.2.0-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 > 39e215ac7e8d6de33d939486987dcba4 > scipy-1.2.0-cp27-cp27m-manylinux1_i686.whl > d6e33b2c05ffbcf9790628d656c8e61f > scipy-1.2.0-cp27-cp27m-manylinux1_x86_64.whl > a463a12d77b87df0a2d202323771a908 scipy-1.2.0-cp27-cp27m-win32.whl > 3dc17a11c7dd211ce51a338cfe30eb48 scipy-1.2.0-cp27-cp27m-win_amd64.whl > 82b1ecbecadfeddd2be1c6d616491029 > 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gmail.com (Charles R Harris) Date: Thu, 20 Dec 2018 09:16:50 -0700 Subject: NumPy 1.16.0rc1 released Message-ID: Hi All, On behalf of the NumPy team I'm pleased to announce the release of NumPy 1.16.0rc1. This is the last NumPy release to support Python 2.7 and will be maintained as a long term release with bug fixes until 2020. This release has seen a lot of refactoring and features many bug fixes, improved code organization, and better cross platform compatibility. Not all of these improvements will be visible to users, but they should help make maintenance easier going forward. Highlights are - Experimental support for overriding numpy functions in downstream projects. - The matmul function is now a ufunc and can be overridden using __array_ufunc__. - Improved support for the ARM and POWER architectures. - Improved support for AIX and PyPy. - Improved interoperation with ctypes. - Improved support for PEP 3118. The supported Python versions are 2.7 and 3.5-3.7, support for 3.4 has been dropped. The wheels on PyPI are linked with OpenBLAS v0.3.4+, which should fix the known threading issues found in previous OpenBLAS versions. Downstream developers building this release should use Cython >= 0.29 and, if linking OpenBLAS, OpenBLAS > v0.3.4. Wheels for this release can be downloaded from PyPI , source archives are available from Github . *Contributors* A total of 111 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Alan Fontenot + - Allan Haldane - Alon Hershenhorn + - Alyssa Quek + - Andreas Nussbaumer + - Anner + - Anthony Sottile + - Antony Lee - Ayappan P + - Bas van Schaik + - C.A.M. Gerlach + - Charles Harris - Chris Billington - Christian Clauss - Christoph Gohlke - Christopher Pezley + - Daniel B Allan + - Daniel Smith - Dawid Zych + - Derek Kim + - Dima Pasechnik + - Edgar Giovanni Lepe + - Elena Mokeeva + - Elliott Sales de Andrade + - Emil Hessman + - Eric Schles + - Eric Wieser - Giulio Benetti + - Guillaume Gautier + - Guo Ci - Heath Henley + - Isuru Fernando + - J. Lewis Muir + - Jack Vreeken + - Jaime Fernandez - James Bourbeau - Jeff VanOss - Jeffrey Yancey + - Jeremy Chen + - Jeremy Manning + - Jeroen Demeyer - John Darbyshire + - John Zwinck - Jonas Jensen + - Joscha Reimer + - Juan Azcarreta + - Julian Taylor - Kevin Sheppard - Krzysztof Chomski + - Kyle Sunden - Lars Gr?ter - Lilian Besson + - MSeifert04 - Mark Harfouche - Marten van Kerkwijk - Martin Thoma - Matt Harrigan + - Matthew Bowden + - Matthew Brett - Matthias Bussonnier - Matti Picus - Max Aifer + - Michael Hirsch, Ph.D + - Michael James Jamie Schnaitter + - MichaelSaah + - Mike Toews - Minkyu Lee + - Mircea Akos Bruma + - Mircea-Akos Brum? + - Moshe Looks + - Muhammad Kasim + - Nathaniel J. Smith - Nikita Titov + - Paul M?ller + - Paul van Mulbregt - Pauli Virtanen - Pierre Glaser + - Pim de Haan - Ralf Gommers - Robert Kern - Robin Aggleton + - Rohit Pandey + - Roman Yurchak + - Ryan Soklaski - Sebastian Berg - Sho Nakamura + - Simon Gibbons - Stan Seibert + - Stefan Otte - Stefan van der Walt - Stephan Hoyer - Stuart Archibald - Taylor Smith + - Tim Felgentreff + - Tim Swast + - Tim Teichmann + - Toshiki Kataoka - Travis Oliphant - Tyler Reddy - Uddeshya Singh + - Warren Weckesser - Weitang Li + - Wenjamin Petrenko + - William D. Irons - Yannick Jadoul + - Yaroslav Halchenko - Yug Khanna + - Yuji Kanagawa + - Yukun Guo + - lerbuke + - @ankokumoyashi + Cheers, Charles Harris From robbmcleod at gmail.com Fri Dec 21 13:44:53 2018 From: robbmcleod at gmail.com (Robert McLeod) Date: Fri, 21 Dec 2018 10:44:53 -0800 Subject: ANN: NumExpr 2.6.9 Message-ID: Hi everyone, This is a version-bump release to provide wheels for Python 3.7.1 on Windows platforms. Also Mike Toews made the handling of our environment variables more robust. Project documentation is available at: http://numexpr.readthedocs.io/ Changes from 2.6.8 to 2.6.9 --------------------------- - Thanks to Mike Toews for more robust handling of the thread-setting environment variables. - With Appveyor updating to Python 3.7.1, wheels for Python 3.7 are now available in addition to those for other OSes. What's Numexpr? --------------- Numexpr is a fast numerical expression evaluator for NumPy. With it, expressions that operate on arrays (like "3*a+4*b") are accelerated and use less memory than doing the same calculation in Python. It has multi-threaded capabilities, as well as support for Intel's MKL (Math Kernel Library), which allows an extremely fast evaluation of transcendental functions (sin, cos, tan, exp, log...) while squeezing the last drop of performance out of your multi-core processors. Look here for a some benchmarks of numexpr using MKL: https://github.com/pydata/numexpr/wiki/NumexprMKL Its only dependency is NumPy (MKL is optional), so it works well as an easy-to-deploy, easy-to-use, computational engine for projects that don't want to adopt other solutions requiring more heavy dependencies. Where I can find Numexpr? ------------------------- The project is hosted at GitHub in: https://github.com/pydata/numexpr You can get the packages from PyPI as well (but not for RC releases): http://pypi.python.org/pypi/numexpr Documentation is hosted at: http://numexpr.readthedocs.io/en/latest/ Share your experience --------------------- Let us know of any bugs, suggestions, gripes, kudos, etc. you may have. Enjoy data! -- Robert McLeod, Ph.D. robbmcleod at gmail.com robbmcleod at protonmail.com robert.mcleod at hitachi-hhtc.ca www.entropyreduction.al From nad at python.org Mon Dec 24 06:57:53 2018 From: nad at python.org (Ned Deily) Date: Mon, 24 Dec 2018 06:57:53 -0500 Subject: [RELEASE] Python 3.7.2 and 3.6.8 are now available Message-ID: <3041C039-C5F6-4A01-BEB8-783238B07970@python.org> https://blog.python.org/2018/12/python-372-and-368-are-now-available.html Python 3.7.2 and 3.6.8 are now available. Python 3.7.2 is the next maintenance release of Python 3.7, the latest feature release of Python. You can find Python 3.7.2 here: https://www.python.org/downloads/release/python-372/ See the What?s New In Python 3.7 document for more information about the many new features and optimizations included in the 3.7 series. Detailed information about the changes made in 3.7.2 can be found in its change log. We are also happy to announce the availability of Python 3.6.8: https://www.python.org/downloads/release/python-368/ Python 3.6.8 is planned to be the last bugfix release of Python 3.6. Per our support policy, we plan to provide security fixes for Python 3.6 as needed through 2021, five years following its initial release. Thanks to all of the many volunteers who help make Python Development and these releases possible! Please consider supporting our efforts by volunteering yourself or through organization contributions to the Python Software Foundation. https://docs.python.org/3.7/whatsnew/3.7.html https://docs.python.org/3.7/whatsnew/changelog.html#python-3-7-2-final https://docs.python.org/3.6/whatsnew/changelog.html#python-3-6-8-final https://www.python.org/psf/ -- Ned Deily nad at python.org -- [] From cimrman3 at ntc.zcu.cz Wed Dec 26 19:31:25 2018 From: cimrman3 at ntc.zcu.cz (Robert Cimrman) Date: Thu, 27 Dec 2018 01:31:25 +0100 Subject: ANN: SfePy 2018.4 Message-ID: I am pleased to announce release 2018.4 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 -------------------------- - better support for eigenvalue problems - improved MUMPS solver interface - support for logging and plotting of complex values 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 Jan Heczko Lubos Kejzlar From valentin at haenel.co Thu Dec 27 10:01:06 2018 From: valentin at haenel.co (Valentin Haenel) Date: Thu, 27 Dec 2018 16:01:06 +0100 Subject: [ANN] python-blosc 1.7.0 Message-ID: <20181227150106.GA21592@kudu.in-berlin.de> ============================= Announcing python-blosc 1.7.0 ============================= What is new? ============ This is a maintenance release which takes care of several housekeepting tasks. Support for older versions of Python (2.6 and 3.3) has been removed from the codebase. A new version of C-Blosc (1.5.1) that now passes all unit and integration tests across all supported platforms has been included. Finally, a the vendored cpuinfo.py has been upgraded and the automatic tests on Windows via Appveyor have been upgraded to include a larger variety of Windows/Python combinations. A big thank you goes out to Daniel Stender from the Debian project for his continued efforts to package the Blosc stack -- including python-blosc -- for Debian. This also means it is likely that a recent version of python-blosc will be included in Buster. For more info, you can have a look at the release notes in: https://github.com/Blosc/python-blosc/blob/master/RELEASE_NOTES.rst More docs and examples are available in the documentation site: http://python-blosc.blosc.org What is it? =========== Blosc (http://www.blosc.org) is a high performance compressor optimized for binary data. It has been designed to transmit data to the processor cache faster than the traditional, non-compressed, direct memory fetch approach via a memcpy() OS call. Blosc works well for compressing numerical arrays that contains data with relatively low entropy, like sparse data, time series, grids with regular-spaced values, etc. python-blosc (http://python-blosc.blosc.org/) is the Python wrapper for the Blosc compression library, with added functions (`compress_ptr()` and `pack_array()`) for efficiently compressing NumPy arrays, minimizing the number of memory copies during the process. python-blosc can be used to compress in-memory data buffers for transmission to other machines, persistence or just as a compressed cache. There is also a handy tool built on top of python-blosc called Bloscpack (https://github.com/Blosc/bloscpack). It features a commmand line interface that allows you to compress large binary datafiles on-disk. It also comes with a Python API that has built-in support for serializing and deserializing Numpy arrays both on-disk and in-memory at speeds that are competitive with regular Pickle/cPickle machinery. Sources repository ================== The sources and documentation are managed through github services at: http://github.com/Blosc/python-blosc ---- **Enjoy data!** From juanlu001 at gmail.com Fri Dec 28 16:17:27 2018 From: juanlu001 at gmail.com (Juan Luis Cano) Date: Fri, 28 Dec 2018 22:17:27 +0100 Subject: ANN: poliastro 0.11.1 released =?UTF-8?B?8J+agA==?= Message-ID: <1546031847.9555.0@smtp.gmail.com> Hi all, It fills us with astronomical joy to announce the release of poliastro 0.11.1! ? poliastro is a pure Python library that allows you to simulate and analyze interplanetary orbits in a Jupyter notebook in an interactive and easy way, used in academia and the industry by people from all around the world. You can install it using pip or conda: pip install poliastro conda install poliastro --channel conda-forge This release brought some bug fixes that we accumulated while preparing the next major version. You can read the full release notes in the documentation: http://docs.poliastro.space/en/v0.11.1/changelog.html#poliastro-0-11-1-2018-12-27 If you want to know more, don't miss my talk on the Open Source Cubesat Worshop held at the European Space Operations Centre last year: https://youtu.be/KnoYzqAw_vM?t=1h36m14s Please join our chat on Matrix/Riot and feel free to ask any questions you might have: https://riot.im/app/#/room/#poliastro:matrix.org Per Python ad astra! -- Juan Luis Cano From garabik-news-2005-05 at kassiopeia.juls.savba.sk Sat Dec 29 14:38:37 2018 From: garabik-news-2005-05 at kassiopeia.juls.savba.sk (garabik-news-2005-05 at kassiopeia.juls.savba.sk) Date: Sat, 29 Dec 2018 19:38:37 +0000 (UTC) Subject: ANN: unicode 2.7 Message-ID: unicode is a simple python command line utility that displays properties for a given unicode character, or searches unicode database for a given name. It was written with Linux in mind, but should work almost everywhere (including MS Windows and MacOSX), UTF-8 console is recommended. ?p??pu??s ?po???u? ??? ?o ?sn p??u??p? pu? s?ld???u???d ??? ?u??????suo??p loo? ??????p??p ?u?ll??x? u? s?? ?I ?s?u??od?po? ?u???????p ?l???ld?o? ?u??sn ?l???? 's?d?l? ?o ?????s ??l?????s ?ll?ns??? o?u?? ?x?? ??? ????uo? o? p??pu??s ?po???u? ??? ?o ???od lln? ??? s???oldx? ???? '????l???n ,?po????d, osl? su????uo? ??????d ??? Changes since previous versions: * add East Asian width * hack to consider regular expressions ending with '$' * do not flush stdout (prevents exception if stdout pipe breaks) URL: http://kassiopeia.juls.savba.sk/~garabik/software/unicode.html License: GPL v3 Installation: pip install unicode -- ----------------------------------------------------------- | Radovan Garab?k http://kassiopeia.juls.savba.sk/~garabik/ | | __..--^^^--..__ garabik @ kassiopeia.juls.savba.sk | ----------------------------------------------------------- Antivirus alert: file .signature infected by signature virus. Hi! I'm a signature virus! Copy me into your signature file to help me spread! From keith.dart at gmail.com Sat Dec 29 14:54:53 2018 From: keith.dart at gmail.com (kdart) Date: Sat, 29 Dec 2018 11:54:53 -0800 (PST) Subject: ANN: elicit CLI framework with enhanced debugger 1.7 Message-ID: <5587f269-3ab6-4481-882b-40c1482eff17@googlegroups.com> I really like the exception chaining feature of Python 3. I also like the fact that an exception instance now has access to the traceback, making it the only object you need to start a debugging session from an exception. However, the stock pdb module still does not make it easy to inspect the chained exceptions. So I've recently added that feature to my debugger module. It's contained in the Elicit package. https://pypi.org/project/elicit/ The new commands "switch", and "cause" will switch tracebacks to the "context", or "cause" exceptions, respectively. The elicit framework is a CLI framework that the debugger uses (replaces cmd). It has no other dependencies itself. To get this feature you should enter the debugger from the function "from_exception(exc)". The "post_mortem" function only takes a traceback, so you lose the active exception in some cases.