Congratulations. May there be many more :)
Chuck
On Tue, Dec 18, 2018 at 9:57 AM Tyler Reddy
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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 π for ``freqz``), leading to errors and confusion. With the ``fs`` parameter, ordinary frequencies can now be entered directly into functions, with the normalization handled internally.
``find_peaks`` and related functions no longer raise an exception if the properties of a peak have unexpected values (e.g. a prominence of 0). A ``PeakPropertyWarning`` is given instead.
The new keyword argument ``plateau_size`` was added to ``find_peaks``. ``plateau_size`` may be used to select peaks based on the length of the flat top of a peak.
``welch()`` and ``csd()`` methods in `scipy.signal` now support calculation of a median average PSD, using ``average='mean'`` keyword
`scipy.sparse` improvements ----------------------------
The `scipy.sparse.bsr_matrix.tocsr` method is now implemented directly instead of converting via COO format, and the `scipy.sparse.bsr_matrix.tocsc` method is now also routed via CSR conversion instead of COO. The efficiency of both conversions is now improved.
The issue where SuperLU or UMFPACK solvers crashed on matrices with non-canonical format in `scipy.sparse.linalg` was fixed. The solver wrapper canonicalizes the matrix if necessary before calling the SuperLU or UMFPACK solver.
The ``largest`` option of `scipy.sparse.linalg.lobpcg()` was fixed to have a correct (and expected) behavior. The order of the eigenvalues was made consistent with the ARPACK solver (``eigs()``), i.e. ascending for the smallest eigenvalues, and descending for the largest eigenvalues.
The `scipy.sparse.random` function is now faster and also supports integer and complex values by passing the appropriate value to the ``dtype`` argument.
`scipy.spatial` improvements -----------------------------
The function `scipy.spatial.distance.jaccard` was modified to return 0 instead of ``np.nan`` when two all-zero vectors are compared.
Support for the Jensen Shannon distance, the square-root of the divergence, has been added under `scipy.spatial.distance.jensenshannon`
An optional keyword was added to the function `scipy.spatial.cKDTree.query_ball_point()` to sort or not sort the returned indices. Not sorting the indices can speed up calls.
A new category of quaternion-based transformations are available in `scipy.spatial.transform`, including spherical linear interpolation of rotations (``Slerp``), conversions to and from quaternions, Euler angles, and general rotation and inversion capabilities (`spatial.transform.Rotation`), and uniform random sampling of 3D rotations (`spatial.transform.Rotation.random`).
`scipy.stats` improvements ---------------------------
The Yeo-Johnson power transformation is now supported (``yeojohnson``, ``yeojohnson_llf``, ``yeojohnson_normmax``, ``yeojohnson_normplot``). Unlike the Box-Cox transformation, the Yeo-Johnson transformation can accept negative values.
Added a general method to sample random variates based on the density only, in the new function ``rvs_ratio_uniforms``.
The Yule-Simon distribution (``yulesimon``) was added -- this is a new discrete probability distribution.
``stats`` and ``mstats`` now have access to a new regression method, ``siegelslopes``, a robust linear regression algorithm
`scipy.stats.gaussian_kde` now has the ability to deal with weighted samples, and should have a modest improvement in performance
Levy Stable Parameter Estimation, PDF, and CDF calculations are now supported for `scipy.stats.levy_stable`.
The Brunner-Munzel test is now available as ``brunnermunzel`` in ``stats`` and ``mstats``
`scipy.linalg` improvements ---------------------------
`scipy.linalg.lapack` now exposes the LAPACK routines using the Rectangular Full Packed storage (RFP) for upper triangular, lower triangular, symmetric, or Hermitian matrices; the upper trapezoidal fat matrix RZ decomposition routines are now available as well.
Deprecated features =================== The functions ``hyp2f0``, ``hyp1f2`` and ``hyp3f0`` in ``scipy.special`` have been deprecated.
Backwards incompatible changes ==============================
LAPACK version 3.4.0 or later is now required. Building with Apple Accelerate is no longer supported.
The function ``scipy.linalg.subspace_angles(A, B)`` now gives correct results for all angles. Before this, the function only returned correct values for those angles which were greater than pi/4.
Support for the Bento build system has been removed. Bento has not been maintained for several years, and did not have good Python 3 or wheel support, hence it was time to remove it.
The required signature of `scipy.optimize.lingprog` ``method=simplex`` callback function has changed. Before iteration begins, the simplex solver first converts the problem into a standard form that does not, in general, have the same variables or constraints as the problem defined by the user. Previously, the simplex solver would pass a user-specified callback function several separate arguments, such as the current solution vector ``xk``, corresponding to this standard form problem. Unfortunately, the relationship between the standard form problem and the user-defined problem was not documented, limiting the utility of the information passed to the callback function.
In addition to numerous bug fix changes, the simplex solver now passes a user-specified callback function a single ``OptimizeResult`` object containing information that corresponds directly to the user-defined problem. In future releases, this ``OptimizeResult`` object may be expanded to include additional information, such as variables corresponding to the standard-form problem and information concerning the relationship between the standard-form and user-defined problems.
The implementation of `scipy.sparse.random` has changed, and this affects the numerical values returned for both ``sparse.random`` and ``sparse.rand`` for some matrix shapes and a given seed.
`scipy.optimize.newton` will no longer use Halley's method in cases where it negatively impacts convergence
Other changes =============
Authors =======
* @endolith * @luzpaz * Hameer Abbasi + * akahard2dj + * Anton Akhmerov * Joseph Albert * alexthomas93 + * ashish + * atpage + * Blair Azzopardi + * Yoshiki Vázquez Baeza * Bence Bagi + * Christoph Baumgarten * Lucas Bellomo + * BH4 + * Aditya Bharti * Max Bolingbroke * François Boulogne * Ward Bradt + * Matthew Brett * Evgeni Burovski * Rafał Byczek + * Alfredo Canziani + * CJ Carey * Lucía Cheung + * Poom Chiarawongse + * Jeanne Choo + * Robert Cimrman * Graham Clenaghan + * cynthia-rempel + * Johannes Damp + * Jaime Fernandez del Rio * Dowon + * emmi474 + * Stefan Endres + * Thomas Etherington + * 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 Schlüter * jeanpauphilet + * josephmernst + * Kai + * Kai-Striega + * kalash04 + * Toshiki Kataoka + * Konrad0 + * Tom Krauss + * Johannes Kulick * Lars Grüter + * Eric Larson * Denis Laxalde * Will Lee + * Katrin Leinweber + * Yin Li + * P. L. Lim + * Jesse Livezey + * Duncan Macleod + * MatthewFlamm + * Nikolay Mayorov * Mike McClurg + * Christian Meyer + * Mark Mikofski * Naoto Mizuno + * mohmmadd + * Nathan Musoke * Anju Geetha Nair + * Andrew Nelson * Ayappan P + * Nick Papior * Haesun Park + * Ronny Pfannschmidt + * pijyoi + * Ilhan Polat * Anthony Polloreno + * Ted Pudlik * puenka * Eric Quintero * Pradeep Reddy Raamana + * Vyas Ramasubramani + * Ramon Viñas + * Tyler Reddy * Joscha Reimer * Antonio H Ribeiro * richardjgowers + * Rob + * robbystk + * Lucas Roberts + * rohan + * Joaquin Derrac Rus + * Josua Sassen + * Bruce Sharpe + * Max Shinn + * Scott Sievert * Sourav Singh * Strahinja Lukić + * Kai Striega + * Shinya SUZUKI + * Mike Toews + * Piotr Uchwat * Miguel de Val-Borro + * Nicky van Foreest * Paul van Mulbregt * Gael Varoquaux * Pauli Virtanen * Stefan van der Walt * Warren Weckesser * Joshua Wharton + * Bernhard M. Wiedemann + * Eric Wieser * Josh Wilson * Tony Xiang + * Roman Yurchak + * Roy Zywina +
A total of 137 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.
Issues closed for 1.2.0 ------------------------
* `#9520 https://github.com/scipy/scipy/issues/9520`__: signal.correlate with method='fft' doesn't benefit from long... * `#9547 https://github.com/scipy/scipy/issues/9547`__: signature of dual_annealing doesn't match other optimizers * `#9540 https://github.com/scipy/scipy/issues/9540`__: SciPy v1.2.0rc1 cannot be imported on Python 2.7.15 * `#1240 https://github.com/scipy/scipy/issues/1240`__: Allowing multithreaded use of minpack through scipy.optimize... * `#1432 https://github.com/scipy/scipy/issues/1432`__: scipy.stats.mode extremely slow (Trac #905) * `#3372 https://github.com/scipy/scipy/issues/3372`__: Please add Sphinx search field to online scipy html docs * `#3678 https://github.com/scipy/scipy/issues/3678`__: _clough_tocher_2d_single direction between centroids * `#4174 https://github.com/scipy/scipy/issues/4174`__: lobpcg "largest" option invalid? * `#5493 https://github.com/scipy/scipy/issues/5493`__: anderson_ksamp p-values>1 * `#5743 https://github.com/scipy/scipy/issues/5743`__: slsqp fails to detect infeasible problem * `#6139 https://github.com/scipy/scipy/issues/6139`__: scipy.optimize.linprog failed to find a feasible starting point... * `#6358 https://github.com/scipy/scipy/issues/6358`__: stats: docstring for `vonmises_line` points to `vonmises_line`... * `#6498 https://github.com/scipy/scipy/issues/6498`__: runtests.py is missing in pypi distfile * `#7426 https://github.com/scipy/scipy/issues/7426`__: scipy.stats.ksone(n).pdf(x) returns nan for positive values of... * `#7455 https://github.com/scipy/scipy/issues/7455`__: scipy.stats.ksone.pdf(2,x) return incorrect values for x near... * `#7456 https://github.com/scipy/scipy/issues/7456`__: scipy.special.smirnov and scipy.special.smirnovi have accuracy... * `#7492 https://github.com/scipy/scipy/issues/7492`__: scipy.special.kolmogorov(x)/kolmogi(p) inefficient, inaccurate... * `#7914 https://github.com/scipy/scipy/issues/7914`__: TravisCI not failing when it should for -OO run * `#8064 https://github.com/scipy/scipy/issues/8064`__: linalg.solve test crashes on Windows * `#8212 https://github.com/scipy/scipy/issues/8212`__: LAPACK Rectangular Full Packed routines * `#8256 https://github.com/scipy/scipy/issues/8256`__: differential_evolution bug converges to wrong results in complex... * `#8443 https://github.com/scipy/scipy/issues/8443`__: Deprecate `hyp2f0`, `hyp1f2`, and `hyp3f0`? * `#8452 https://github.com/scipy/scipy/issues/8452`__: DOC: ARPACK tutorial has two conflicting equations * `#8680 https://github.com/scipy/scipy/issues/8680`__: scipy fails compilation when building from source * `#8686 https://github.com/scipy/scipy/issues/8686`__: Division by zero in _trustregion.py when x0 is exactly equal... * `#8700 https://github.com/scipy/scipy/issues/8700`__: _MINPACK_LOCK not held when calling into minpack from least_squares * `#8786 https://github.com/scipy/scipy/issues/8786`__: erroneous moment values for t-distribution * `#8791 https://github.com/scipy/scipy/issues/8791`__: Checking COLA condition in istft should be optional (or omitted) * `#8843 https://github.com/scipy/scipy/issues/8843`__: imresize cannot be deprecated just yet * `#8844 https://github.com/scipy/scipy/issues/8844`__: Inverse Wishart Log PDF Incorrect for Non-diagonal Scale Matrix? * `#8878 https://github.com/scipy/scipy/issues/8878`__: vonmises and vonmises_line in stats: vonmises wrong and superfluous? * `#8895 https://github.com/scipy/scipy/issues/8895`__: v1.1.0 `ndi.rotate` documentation – reused parameters not filled... * `#8900 https://github.com/scipy/scipy/issues/8900`__: Missing complex conjugation in scipy.sparse.linalg.LinearOperator * `#8904 https://github.com/scipy/scipy/issues/8904`__: BUG: if zero derivative at root, then Newton fails with RuntimeWarning * `#8911 https://github.com/scipy/scipy/issues/8911`__: make_interp_spline bc_type incorrect input interpretation * `#8942 https://github.com/scipy/scipy/issues/8942`__: MAINT: Refactor `_linprog.py` and `_linprog_ip.py` to remove... * `#8947 https://github.com/scipy/scipy/issues/8947`__: np.int64 in scipy.fftpack.next_fast_len * `#9020 https://github.com/scipy/scipy/issues/9020`__: BUG: linalg.subspace_angles gives wrong results * `#9033 https://github.com/scipy/scipy/issues/9033`__: scipy.stats.normaltest sometimes gives incorrect returns b/c... * `#9036 https://github.com/scipy/scipy/issues/9036`__: Bizarre times for `scipy.sparse.rand` function with 'low' density... * `#9044 https://github.com/scipy/scipy/issues/9044`__: optimize.minimize(method=`trust-constr`) result dict does not... * `#9071 https://github.com/scipy/scipy/issues/9071`__: doc/linalg: add cho_solve_banded to see also of cholesky_banded * `#9082 https://github.com/scipy/scipy/issues/9082`__: eigenvalue sorting in scipy.sparse.linalg.eigsh * `#9086 https://github.com/scipy/scipy/issues/9086`__: signaltools.py:491: FutureWarning: Using a non-tuple sequence... * `#9091 https://github.com/scipy/scipy/issues/9091`__: test_spline_filter failure on 32-bit * `#9122 https://github.com/scipy/scipy/issues/9122`__: Typo on scipy minimization tutorial * `#9135 https://github.com/scipy/scipy/issues/9135`__: doc error at https://docs.scipy.org/doc/scipy/reference/tutorial/stats/discrete_poisson.h... * `#9167 https://github.com/scipy/scipy/issues/9167`__: DOC: BUG: typo in ndimage LowLevelCallable tutorial example * `#9169 https://github.com/scipy/scipy/issues/9169`__: truncnorm does not work if b < a in scipy.stats * `#9250 https://github.com/scipy/scipy/issues/9250`__: scipy.special.tests.test_mpmath::TestSystematic::test_pcfw fails... * `#9259 https://github.com/scipy/scipy/issues/9259`__: rv.expect() == rv.mean() is false for rv.mean() == nan (and inf) * `#9286 https://github.com/scipy/scipy/issues/9286`__: DOC: Rosenbrock expression in optimize.minimize tutorial * `#9316 https://github.com/scipy/scipy/issues/9316`__: SLSQP fails in nested optimization * `#9337 https://github.com/scipy/scipy/issues/9337`__: scipy.signal.find_peaks key typo in documentation * `#9345 https://github.com/scipy/scipy/issues/9345`__: Example from documentation of scipy.sparse.linalg.eigs raises... * `#9383 https://github.com/scipy/scipy/issues/9383`__: Default value for "mode" in "ndimage.shift" * `#9419 https://github.com/scipy/scipy/issues/9419`__: dual_annealing off by one in the number of iterations * `#9442 https://github.com/scipy/scipy/issues/9442`__: Error in Defintion of Rosenbrock Function * `#9453 https://github.com/scipy/scipy/issues/9453`__: TST: test_eigs_consistency() doesn't have consistent results
Pull requests for 1.2.0 ------------------------
* `#9526 https://github.com/scipy/scipy/pull/9526`__: TST: relax precision requirements in signal.correlate tests * `#9507 https://github.com/scipy/scipy/pull/9507`__: CI: MAINT: Skip a ckdtree test on pypy * `#9512 https://github.com/scipy/scipy/pull/9512`__: TST: test_random_sampling 32-bit handling * `#9494 https://github.com/scipy/scipy/pull/9494`__: TST: test_kolmogorov xfail 32-bit * `#9486 https://github.com/scipy/scipy/pull/9486`__: BUG: fix sparse random int handling * `#9550 https://github.com/scipy/scipy/pull/9550`__: BUG: scipy/_lib/_numpy_compat: get_randint * `#9549 https://github.com/scipy/scipy/pull/9549`__: MAINT: make dual_annealing signature match other optimizers * `#9541 https://github.com/scipy/scipy/pull/9541`__: BUG: fix SyntaxError due to non-ascii character on Python 2.7 * `#7352 https://github.com/scipy/scipy/pull/7352`__: ENH: add Brunner Munzel test to scipy.stats. * `#7373 https://github.com/scipy/scipy/pull/7373`__: BUG: Jaccard distance for all-zero arrays would return np.nan * `#7374 https://github.com/scipy/scipy/pull/7374`__: ENH: Add PDF, CDF and parameter estimation for Stable Distributions * `#8098 https://github.com/scipy/scipy/pull/8098`__: ENH: Add shgo for global optimization of NLPs. * `#8203 https://github.com/scipy/scipy/pull/8203`__: ENH: adding simulated dual annealing to optimize * `#8259 https://github.com/scipy/scipy/pull/8259`__: Option to follow original Storn and Price algorithm and its parallelisation * `#8293 https://github.com/scipy/scipy/pull/8293`__: ENH add ratio-of-uniforms method for rv generation to scipy.stats * `#8294 https://github.com/scipy/scipy/pull/8294`__: BUG: Fix slowness in stats.mode * `#8295 https://github.com/scipy/scipy/pull/8295`__: ENH: add Jensen Shannon distance to `scipy.spatial.distance` * `#8357 https://github.com/scipy/scipy/pull/8357`__: ENH: vectorize scalar zero-search-functions * `#8397 https://github.com/scipy/scipy/pull/8397`__: Add `fs=` parameter to filter design functions * `#8537 https://github.com/scipy/scipy/pull/8537`__: ENH: Implement mode parameter for spline filtering. * `#8558 https://github.com/scipy/scipy/pull/8558`__: ENH: small speedup for stats.gaussian_kde * `#8560 https://github.com/scipy/scipy/pull/8560`__: BUG: fix p-value calc of anderson_ksamp in scipy.stats * `#8614 https://github.com/scipy/scipy/pull/8614`__: ENH: correct p-values for stats.kendalltau and stats.mstats.kendalltau * `#8670 https://github.com/scipy/scipy/pull/8670`__: ENH: Require Lapack 3.4.0 * `#8683 https://github.com/scipy/scipy/pull/8683`__: Correcting kmeans documentation * `#8725 https://github.com/scipy/scipy/pull/8725`__: MAINT: Cleanup scipy.optimize.leastsq * `#8726 https://github.com/scipy/scipy/pull/8726`__: BUG: Fix _get_output in scipy.ndimage to support string * `#8733 https://github.com/scipy/scipy/pull/8733`__: MAINT: stats: A bit of clean up. * `#8737 https://github.com/scipy/scipy/pull/8737`__: BUG: Improve numerical precision/convergence failures of smirnov/kolmogorov * `#8738 https://github.com/scipy/scipy/pull/8738`__: MAINT: stats: A bit of clean up in test_distributions.py. * `#8740 https://github.com/scipy/scipy/pull/8740`__: BF/ENH: make minpack thread safe * `#8742 https://github.com/scipy/scipy/pull/8742`__: BUG: Fix division by zero in trust-region optimization methods * `#8746 https://github.com/scipy/scipy/pull/8746`__: MAINT: signal: Fix a docstring of a private function, and fix... * `#8750 https://github.com/scipy/scipy/pull/8750`__: DOC clarified description of norminvgauss in scipy.stats * `#8753 https://github.com/scipy/scipy/pull/8753`__: DOC: signal: Fix a plot title in the chirp docstring. * `#8755 https://github.com/scipy/scipy/pull/8755`__: DOC: MAINT: Fix link to the wheel documentation in developer... * `#8760 https://github.com/scipy/scipy/pull/8760`__: BUG: stats: boltzmann wasn't setting the upper bound. * `#8763 https://github.com/scipy/scipy/pull/8763`__: [DOC] Improved scipy.cluster.hierarchy documentation * `#8765 https://github.com/scipy/scipy/pull/8765`__: DOC: added example for scipy.stat.mstats.tmin * `#8788 https://github.com/scipy/scipy/pull/8788`__: DOC: fix definition of optional `disp` parameter * `#8802 https://github.com/scipy/scipy/pull/8802`__: MAINT: Suppress dd_real unused function compiler warnings. * `#8803 https://github.com/scipy/scipy/pull/8803`__: ENH: Add full_output support to optimize.newton() * `#8804 https://github.com/scipy/scipy/pull/8804`__: MAINT: stats cleanup * `#8808 https://github.com/scipy/scipy/pull/8808`__: DOC: add note about isinstance for frozen rvs * `#8812 https://github.com/scipy/scipy/pull/8812`__: Updated numpydoc submodule * `#8813 https://github.com/scipy/scipy/pull/8813`__: MAINT: stats: Fix multinomial docstrings, and do some clean up. * `#8816 https://github.com/scipy/scipy/pull/8816`__: BUG: fixed _stats of t-distribution in scipy.stats * `#8817 https://github.com/scipy/scipy/pull/8817`__: BUG: ndimage: Fix validation of the origin argument in correlate... * `#8822 https://github.com/scipy/scipy/pull/8822`__: BUG: integrate: Fix crash with repeated t values in odeint. * `#8832 https://github.com/scipy/scipy/pull/8832`__: Hyperlink DOIs against preferred resolver * `#8837 https://github.com/scipy/scipy/pull/8837`__: BUG: sparse: Ensure correct dtype for sparse comparison operations. * `#8839 https://github.com/scipy/scipy/pull/8839`__: DOC: stats: A few tweaks to the linregress docstring. * `#8846 https://github.com/scipy/scipy/pull/8846`__: BUG: stats: Fix logpdf method of invwishart. * `#8849 https://github.com/scipy/scipy/pull/8849`__: DOC: signal: Fixed mistake in the firwin docstring. * `#8854 https://github.com/scipy/scipy/pull/8854`__: DOC: fix type descriptors in ltisys documentation * `#8865 https://github.com/scipy/scipy/pull/8865`__: Fix tiny typo in docs for chi2 pdf * `#8870 https://github.com/scipy/scipy/pull/8870`__: Fixes related to invertibility of STFT * `#8872 https://github.com/scipy/scipy/pull/8872`__: ENH: special: Add the softmax function * `#8874 https://github.com/scipy/scipy/pull/8874`__: DOC correct gamma function in docstrings in scipy.stats * `#8876 https://github.com/scipy/scipy/pull/8876`__: ENH: Added TOMS Algorithm 748 as 1-d root finder; 17 test function... * `#8882 https://github.com/scipy/scipy/pull/8882`__: ENH: Only use Halley's adjustment to Newton if close enough. * `#8883 https://github.com/scipy/scipy/pull/8883`__: FIX: optimize: make jac and hess truly optional for 'trust-constr' * `#8885 https://github.com/scipy/scipy/pull/8885`__: TST: Do not error on warnings raised about non-tuple indexing. * `#8887 https://github.com/scipy/scipy/pull/8887`__: MAINT: filter out np.matrix PendingDeprecationWarning's in numpy... * `#8889 https://github.com/scipy/scipy/pull/8889`__: DOC: optimize: separate legacy interfaces from new ones * `#8890 https://github.com/scipy/scipy/pull/8890`__: ENH: Add optimize.root_scalar() as a universal dispatcher for... * `#8899 https://github.com/scipy/scipy/pull/8899`__: DCT-IV, DST-IV and DCT-I, DST-I orthonormalization support in... * `#8901 https://github.com/scipy/scipy/pull/8901`__: MAINT: Reorganize flapack.pyf.src file * `#8907 https://github.com/scipy/scipy/pull/8907`__: BUG: ENH: Check if guess for newton is already zero before checking... * `#8908 https://github.com/scipy/scipy/pull/8908`__: ENH: Make sorting optional for cKDTree.query_ball_point() * `#8910 https://github.com/scipy/scipy/pull/8910`__: DOC: sparse.csgraph simple examples. * `#8914 https://github.com/scipy/scipy/pull/8914`__: DOC: interpolate: fix equivalences of string aliases * `#8918 https://github.com/scipy/scipy/pull/8918`__: add float_control(precise, on) to _fpumode.c * `#8919 https://github.com/scipy/scipy/pull/8919`__: MAINT: interpolate: improve error messages for common `bc_type`... * `#8920 https://github.com/scipy/scipy/pull/8920`__: DOC: update Contributing to SciPy to say "prefer no PEP8 only... * `#8924 https://github.com/scipy/scipy/pull/8924`__: MAINT: special: deprecate `hyp2f0`, `hyp1f2`, and `hyp3f0` * `#8927 https://github.com/scipy/scipy/pull/8927`__: MAINT: special: remove `errprint` * `#8932 https://github.com/scipy/scipy/pull/8932`__: Fix broadcasting scale arg of entropy * `#8936 https://github.com/scipy/scipy/pull/8936`__: Fix (some) non-tuple index warnings * `#8937 https://github.com/scipy/scipy/pull/8937`__: ENH: implement sparse matrix BSR to CSR conversion directly. * `#8938 https://github.com/scipy/scipy/pull/8938`__: DOC: add @_ni_docstrings.docfiller in ndimage.rotate * `#8940 https://github.com/scipy/scipy/pull/8940`__: Update _discrete_distns.py * `#8943 https://github.com/scipy/scipy/pull/8943`__: DOC: Finish dangling sentence in `convolve` docstring * `#8944 https://github.com/scipy/scipy/pull/8944`__: MAINT: Address tuple indexing and warnings * `#8945 https://github.com/scipy/scipy/pull/8945`__: ENH: spatial.transform.Rotation [GSOC2018] * `#8950 https://github.com/scipy/scipy/pull/8950`__: csgraph Dijkstra function description rewording * `#8953 https://github.com/scipy/scipy/pull/8953`__: DOC, MAINT: HTTP -> HTTPS, and other linkrot fixes * `#8955 https://github.com/scipy/scipy/pull/8955`__: BUG: np.int64 in scipy.fftpack.next_fast_len * `#8958 https://github.com/scipy/scipy/pull/8958`__: MAINT: Add more descriptive error message for phase one simplex. * `#8962 https://github.com/scipy/scipy/pull/8962`__: BUG: sparse.linalg: add missing conjugate to _ScaledLinearOperator.adjoint * `#8963 https://github.com/scipy/scipy/pull/8963`__: BUG: sparse.linalg: downgrade LinearOperator TypeError to warning * `#8965 https://github.com/scipy/scipy/pull/8965`__: ENH: Wrapped RFP format and RZ decomposition routines * `#8969 https://github.com/scipy/scipy/pull/8969`__: MAINT: doc and code fixes for optimize.newton * `#8970 https://github.com/scipy/scipy/pull/8970`__: Added 'average' keyword for welch/csd to enable median averaging * `#8971 https://github.com/scipy/scipy/pull/8971`__: Better imresize deprecation warning * `#8972 https://github.com/scipy/scipy/pull/8972`__: MAINT: Switch np.where(c) for np.nonzero(c) * `#8975 https://github.com/scipy/scipy/pull/8975`__: MAINT: Fix warning-based failures * `#8979 https://github.com/scipy/scipy/pull/8979`__: DOC: fix description of count_sort keyword of dendrogram * `#8982 https://github.com/scipy/scipy/pull/8982`__: MAINT: optimize: Fixed minor mistakes in test_linprog.py (#8978) * `#8984 https://github.com/scipy/scipy/pull/8984`__: BUG: sparse.linalg: ensure expm casts integer inputs to float * `#8986 https://github.com/scipy/scipy/pull/8986`__: BUG: optimize/slsqp: do not exit with convergence on steps where... * `#8989 https://github.com/scipy/scipy/pull/8989`__: MAINT: use collections.abc in basinhopping * `#8990 https://github.com/scipy/scipy/pull/8990`__: ENH extend p-values of anderson_ksamp in scipy.stats * `#8991 https://github.com/scipy/scipy/pull/8991`__: ENH: Weighted kde * `#8993 https://github.com/scipy/scipy/pull/8993`__: ENH: spatial.transform.Rotation.random [GSOC 2018] * `#8994 https://github.com/scipy/scipy/pull/8994`__: ENH: spatial.transform.Slerp [GSOC 2018] * `#8995 https://github.com/scipy/scipy/pull/8995`__: TST: time.time in test * `#9007 https://github.com/scipy/scipy/pull/9007`__: Fix typo in fftpack.rst * `#9013 https://github.com/scipy/scipy/pull/9013`__: Added correct plotting code for two sided output from spectrogram * `#9014 https://github.com/scipy/scipy/pull/9014`__: BUG: differential_evolution with inf objective functions * `#9017 https://github.com/scipy/scipy/pull/9017`__: BUG: fixed #8446 corner case for asformat(array|dense) * `#9018 https://github.com/scipy/scipy/pull/9018`__: MAINT: _lib/ccallback: remove unused code * `#9021 https://github.com/scipy/scipy/pull/9021`__: BUG: Issue with subspace_angles * `#9022 https://github.com/scipy/scipy/pull/9022`__: DOC: Added "See Also" section to lombscargle docstring * `#9034 https://github.com/scipy/scipy/pull/9034`__: BUG: Fix tolerance printing behavior, remove meaningless tol... * `#9035 https://github.com/scipy/scipy/pull/9035`__: TST: improve signal.bsplines test coverage * `#9037 https://github.com/scipy/scipy/pull/9037`__: ENH: add a new init method for k-means * `#9039 https://github.com/scipy/scipy/pull/9039`__: DOC: Add examples to fftpack.irfft docstrings * `#9048 https://github.com/scipy/scipy/pull/9048`__: ENH: scipy.sparse.random * `#9050 https://github.com/scipy/scipy/pull/9050`__: BUG: scipy.io.hb_write: fails for matrices not in csc format * `#9051 https://github.com/scipy/scipy/pull/9051`__: MAINT: Fix slow sparse.rand for k < mn/3 (#9036). * `#9054 https://github.com/scipy/scipy/pull/9054`__: MAINT: spatial: Explicitly initialize LAPACK output parameters. * `#9055 https://github.com/scipy/scipy/pull/9055`__: DOC: Add examples to scipy.special docstrings * `#9056 https://github.com/scipy/scipy/pull/9056`__: ENH: Use one thread in OpenBLAS * `#9059 https://github.com/scipy/scipy/pull/9059`__: DOC: Update README with link to Code of Conduct * `#9060 https://github.com/scipy/scipy/pull/9060`__: BLD: remove support for the Bento build system. * `#9062 https://github.com/scipy/scipy/pull/9062`__: DOC add sections to overview in scipy.stats * `#9066 https://github.com/scipy/scipy/pull/9066`__: BUG: Correct "remez" error message * `#9069 https://github.com/scipy/scipy/pull/9069`__: DOC: update linalg section of roadmap for LAPACK versions. * `#9079 https://github.com/scipy/scipy/pull/9079`__: MAINT: add spatial.transform to refguide check; complete some... * `#9081 https://github.com/scipy/scipy/pull/9081`__: MAINT: Add warnings if pivot value is close to tolerance in linprog(method='simplex') * `#9084 https://github.com/scipy/scipy/pull/9084`__: BUG fix incorrect p-values of kurtosistest in scipy.stats * `#9095 https://github.com/scipy/scipy/pull/9095`__: DOC: add sections to mstats overview in scipy.stats * `#9096 https://github.com/scipy/scipy/pull/9096`__: BUG: Add test for Stackoverflow example from issue 8174. * `#9101 https://github.com/scipy/scipy/pull/9101`__: ENH: add Siegel slopes (robust regression) to scipy.stats * `#9105 https://github.com/scipy/scipy/pull/9105`__: allow resample_poly() to output float32 for float32 inputs. * `#9112 https://github.com/scipy/scipy/pull/9112`__: MAINT: optimize: make trust-constr accept constraint dict (#9043) * `#9118 https://github.com/scipy/scipy/pull/9118`__: Add doc entry to cholesky_banded * `#9120 https://github.com/scipy/scipy/pull/9120`__: eigsh documentation parameters * `#9125 https://github.com/scipy/scipy/pull/9125`__: interpolative: correctly reconstruct full rank matrices * `#9126 https://github.com/scipy/scipy/pull/9126`__: MAINT: Use warnings for unexpected peak properties * `#9129 https://github.com/scipy/scipy/pull/9129`__: BUG: Do not catch and silence KeyboardInterrupt * `#9131 https://github.com/scipy/scipy/pull/9131`__: DOC: Correct the typo in scipy.optimize tutorial page * `#9133 https://github.com/scipy/scipy/pull/9133`__: FIX: Avoid use of bare except * `#9134 https://github.com/scipy/scipy/pull/9134`__: DOC: Update of 'return_eigenvectors' description * `#9137 https://github.com/scipy/scipy/pull/9137`__: DOC: typo fixes for discrete Poisson tutorial * `#9139 https://github.com/scipy/scipy/pull/9139`__: FIX: Doctest failure in optimize tutorial * `#9143 https://github.com/scipy/scipy/pull/9143`__: DOC: missing sigma in Pearson r formula * `#9145 https://github.com/scipy/scipy/pull/9145`__: MAINT: Refactor linear programming solvers * `#9149 https://github.com/scipy/scipy/pull/9149`__: FIX: Make scipy.odr.ODR ifixx equal to its data.fix if given * `#9156 https://github.com/scipy/scipy/pull/9156`__: DOC: special: Mention the sigmoid function in the expit docstring. * `#9160 https://github.com/scipy/scipy/pull/9160`__: Fixed a latex delimiter error in levy() * `#9170 https://github.com/scipy/scipy/pull/9170`__: DOC: correction / update of docstrings of distributions in scipy.stats * `#9171 https://github.com/scipy/scipy/pull/9171`__: better description of the hierarchical clustering parameter * `#9174 https://github.com/scipy/scipy/pull/9174`__: domain check for a < b in stats.truncnorm * `#9175 https://github.com/scipy/scipy/pull/9175`__: DOC: Minor grammar fix * `#9176 https://github.com/scipy/scipy/pull/9176`__: BUG: CloughTocher2DInterpolator: fix miscalculation at neighborless... * `#9177 https://github.com/scipy/scipy/pull/9177`__: BUILD: Document the "clean" target in the doc/Makefile. * `#9178 https://github.com/scipy/scipy/pull/9178`__: MAINT: make refguide-check more robust for printed numpy arrays * `#9186 https://github.com/scipy/scipy/pull/9186`__: MAINT: Remove np.ediff1d occurence * `#9188 https://github.com/scipy/scipy/pull/9188`__: DOC: correct typo in extending ndimage with C * `#9190 https://github.com/scipy/scipy/pull/9190`__: ENH: Support specifying axes for fftconvolve * `#9192 https://github.com/scipy/scipy/pull/9192`__: MAINT: optimize: fixed @pv style suggestions from #9112 * `#9200 https://github.com/scipy/scipy/pull/9200`__: Fix make_interp_spline(..., k=0 or 1, axis<0) * `#9201 https://github.com/scipy/scipy/pull/9201`__: BUG: sparse.linalg/gmres: use machine eps in breakdown check * `#9204 https://github.com/scipy/scipy/pull/9204`__: MAINT: fix up stats.spearmanr and match mstats.spearmanr with... * `#9206 https://github.com/scipy/scipy/pull/9206`__: MAINT: include benchmarks and dev files in sdist. * `#9208 https://github.com/scipy/scipy/pull/9208`__: TST: signal: bump bsplines test tolerance for complex data * `#9210 https://github.com/scipy/scipy/pull/9210`__: TST: mark tests as slow, fix missing random seed * `#9211 https://github.com/scipy/scipy/pull/9211`__: ENH: add capability to specify orders in pade func * `#9217 https://github.com/scipy/scipy/pull/9217`__: MAINT: Include ``success`` and ``nit`` in OptimizeResult returned... * `#9222 https://github.com/scipy/scipy/pull/9222`__: ENH: interpolate: Use scipy.spatial.distance to speed-up Rbf * `#9229 https://github.com/scipy/scipy/pull/9229`__: MNT: Fix Fourier filter double case * `#9233 https://github.com/scipy/scipy/pull/9233`__: BUG: spatial/distance: fix pdist/cdist performance regression... * `#9234 https://github.com/scipy/scipy/pull/9234`__: FIX: Proper suppression * `#9235 https://github.com/scipy/scipy/pull/9235`__: BENCH: rationalize slow benchmarks + miscellaneous fixes * `#9238 https://github.com/scipy/scipy/pull/9238`__: BENCH: limit number of parameter combinations in spatial.*KDTree... * `#9239 https://github.com/scipy/scipy/pull/9239`__: DOC: stats: Fix LaTeX markup of a couple distribution PDFs. * `#9241 https://github.com/scipy/scipy/pull/9241`__: ENH: Evaluate plateau size during peak finding * `#9242 https://github.com/scipy/scipy/pull/9242`__: ENH: stats: Implement _ppf and _logpdf for crystalball, and do... * `#9246 https://github.com/scipy/scipy/pull/9246`__: DOC: Properly render versionadded directive in HTML documentation * `#9255 https://github.com/scipy/scipy/pull/9255`__: DOC: mention RootResults in optimization reference guide * `#9260 https://github.com/scipy/scipy/pull/9260`__: TST: relax some tolerances so tests pass with x87 math * `#9264 https://github.com/scipy/scipy/pull/9264`__: TST Use assert_raises "match" parameter instead of the "message"... * `#9267 https://github.com/scipy/scipy/pull/9267`__: DOC: clarify expect() return val when moment is inf/nan * `#9272 https://github.com/scipy/scipy/pull/9272`__: DOC: Add description of default bounds to linprog * `#9277 https://github.com/scipy/scipy/pull/9277`__: MAINT: sparse/linalg: make test deterministic * `#9278 https://github.com/scipy/scipy/pull/9278`__: MAINT: interpolate: pep8 cleanup in test_polyint * `#9279 https://github.com/scipy/scipy/pull/9279`__: Fixed docstring for resample * `#9280 https://github.com/scipy/scipy/pull/9280`__: removed first check for float in get_sum_dtype * `#9281 https://github.com/scipy/scipy/pull/9281`__: BUG: only accept 1d input for bartlett / levene in scipy.stats * `#9282 https://github.com/scipy/scipy/pull/9282`__: MAINT: dense_output and t_eval are mutually exclusive inputs * `#9283 https://github.com/scipy/scipy/pull/9283`__: MAINT: add docs and do some cleanups in interpolate.Rbf * `#9288 https://github.com/scipy/scipy/pull/9288`__: Run distance_transform_edt tests on all types * `#9294 https://github.com/scipy/scipy/pull/9294`__: DOC: fix the formula typo * `#9298 https://github.com/scipy/scipy/pull/9298`__: MAINT: optimize/trust-constr: restore .niter attribute for backward-compat * `#9299 https://github.com/scipy/scipy/pull/9299`__: DOC: clarification of default rvs method in scipy.stats * `#9301 https://github.com/scipy/scipy/pull/9301`__: MAINT: removed unused import sys * `#9302 https://github.com/scipy/scipy/pull/9302`__: MAINT: removed unused imports * `#9303 https://github.com/scipy/scipy/pull/9303`__: DOC: signal: Refer to fs instead of nyq in the firwin docstring. * `#9305 https://github.com/scipy/scipy/pull/9305`__: ENH: Added Yeo-Johnson power transformation * `#9306 https://github.com/scipy/scipy/pull/9306`__: ENH - add dual annealing * `#9309 https://github.com/scipy/scipy/pull/9309`__: ENH add the yulesimon distribution to scipy.stats * `#9317 https://github.com/scipy/scipy/pull/9317`__: Nested SLSQP bug fix. * `#9320 https://github.com/scipy/scipy/pull/9320`__: MAINT: stats: avoid underflow in stats.geom.ppf * `#9326 https://github.com/scipy/scipy/pull/9326`__: Add example for Rosenbrock function * `#9332 https://github.com/scipy/scipy/pull/9332`__: Sort file lists * `#9340 https://github.com/scipy/scipy/pull/9340`__: Fix typo in find_peaks documentation * `#9343 https://github.com/scipy/scipy/pull/9343`__: MAINT Use np.full when possible * `#9344 https://github.com/scipy/scipy/pull/9344`__: DOC: added examples to docstring of dirichlet class * `#9346 https://github.com/scipy/scipy/pull/9346`__: DOC: Fix import of scipy.sparse.linalg in example (#9345) * `#9350 https://github.com/scipy/scipy/pull/9350`__: Fix interpolate read only * `#9351 https://github.com/scipy/scipy/pull/9351`__: MAINT: special.erf: use the x->-x symmetry * `#9356 https://github.com/scipy/scipy/pull/9356`__: Fix documentation typo * `#9358 https://github.com/scipy/scipy/pull/9358`__: DOC: improve doc for ksone and kstwobign in scipy.stats * `#9362 https://github.com/scipy/scipy/pull/9362`__: DOC: Change datatypes of A matrices in linprog * `#9364 https://github.com/scipy/scipy/pull/9364`__: MAINT: Adds implicit none to fftpack fortran sources * `#9369 https://github.com/scipy/scipy/pull/9369`__: DOC: minor tweak to CoC (updated NumFOCUS contact address). * `#9373 https://github.com/scipy/scipy/pull/9373`__: Fix exception if python is called with -OO option * `#9374 https://github.com/scipy/scipy/pull/9374`__: FIX: AIX compilation issue with NAN and INFINITY * `#9376 https://github.com/scipy/scipy/pull/9376`__: COBLYA -> COBYLA in docs * `#9377 https://github.com/scipy/scipy/pull/9377`__: DOC: Add examples integrate: fixed_quad and quadrature * `#9379 https://github.com/scipy/scipy/pull/9379`__: MAINT: TST: Make tests NumPy 1.8 compatible * `#9385 https://github.com/scipy/scipy/pull/9385`__: CI: On Travis matrix "OPTIMIZE=-OO" flag ignored * `#9387 https://github.com/scipy/scipy/pull/9387`__: Fix defaut value for 'mode' in 'ndimage.shift' in the doc * `#9392 https://github.com/scipy/scipy/pull/9392`__: BUG: rank has to be integer in rank_filter: fixed issue 9388 * `#9399 https://github.com/scipy/scipy/pull/9399`__: DOC: Misc. typos * `#9400 https://github.com/scipy/scipy/pull/9400`__: TST: stats: Fix the expected r-value of a linregress test. * `#9405 https://github.com/scipy/scipy/pull/9405`__: BUG: np.hstack does not accept generator expressions * `#9408 https://github.com/scipy/scipy/pull/9408`__: ENH: linalg: Shorter ill-conditioned warning message * `#9418 https://github.com/scipy/scipy/pull/9418`__: DOC: Fix ndimage docstrings and reduce doc build warnings * `#9421 https://github.com/scipy/scipy/pull/9421`__: DOC: Add missing docstring examples in scipy.spatial * `#9422 https://github.com/scipy/scipy/pull/9422`__: DOC: Add an example to integrate.newton_cotes * `#9427 https://github.com/scipy/scipy/pull/9427`__: BUG: Fixed defect with maxiter #9419 in dual annealing * `#9431 https://github.com/scipy/scipy/pull/9431`__: BENCH: Add dual annealing to scipy benchmark (see #9415) * `#9435 https://github.com/scipy/scipy/pull/9435`__: DOC: Add docstring examples for stats.binom_test * `#9443 https://github.com/scipy/scipy/pull/9443`__: DOC: Fix the order of indices in optimize tutorial * `#9444 https://github.com/scipy/scipy/pull/9444`__: MAINT: interpolate: use operator.index for checking/coercing... * `#9445 https://github.com/scipy/scipy/pull/9445`__: DOC: Added missing example to stats.mstats.kruskal * `#9446 https://github.com/scipy/scipy/pull/9446`__: DOC: Add note about version changed for jaccard distance * `#9447 https://github.com/scipy/scipy/pull/9447`__: BLD: version-script handling in setup.py * `#9448 https://github.com/scipy/scipy/pull/9448`__: TST: skip a problematic linalg test * `#9449 https://github.com/scipy/scipy/pull/9449`__: TST: fix missing seed in lobpcg test. * `#9456 https://github.com/scipy/scipy/pull/9456`__: TST: test_eigs_consistency() now sorts output
Checksums =========
MD5 ~~~
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