Hi Tyler, I just tested scipy.optimize.cython_optimize using the jupyter notebooks in this gist: https://gist.github.com/mikofski/ac30065073d0d32d6ea3569f6e24e5ec and it seems to be working fine.
procedure: 1. download the scipy-1.3.0rc1 asset for my platform (macosx py37) https://github.com/scipy/scipy/releases/tag/v1.3.0rc1 2. download a tarball and extract (or clone) the gist of the jupyter notebook 3. create virtualenv, activate, and install downloaded scipy-1.3.0rc1 wheel 4. also pip install cython, ipython, and jupyter into new venv 5. start jupyter notebook ($ juptyer notebook) navigate to gist, open and run all the benchmark times for 1e5 length array on my early 2011 pentium-i5 mac with 16gb were: cython loop: 39.2ms cython prange: 25.3ms python map: 122ms no-cython: 3120ms so best case in this scenario was 100X speedup thanks! On Sat, Apr 27, 2019 at 4:35 AM Tyler Reddy <tyler.je.re...@gmail.com> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi all, > > On behalf of the SciPy development team I'm pleased to announce > the release candidate SciPy 1.3.0rc1. Please help us test this pre-release. > > Sources and binary wheels can be found at:https://pypi.org/project/scipy/ > and at:https://github.com/scipy/scipy/releases/tag/v1.3.0rc1 > One of a few ways to install the release candidate with pip: > pip install scipy==1.3.0rc1 > > ========================== > SciPy 1.3.0 Release Notes > ========================== > > Note: Scipy 1.3.0 is not released yet! > > SciPy 1.3.0 is the culmination of 5 months of hard work. It contains > many new features, numerous bug-fixes, improved test coverage and better > documentation. There have been some 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 > 1.3.x branch, and on adding new features on the master branch. > > This release requires Python 3.5+ and NumPy 1.13.3 or greater. > > For running on PyPy, PyPy3 6.0+ and NumPy 1.15.0 are required. > > Highlights of this release > -------------------------- > > - Three new ``stats`` functions, a rewrite of ``pearsonr``, and an exact > computation of the Kolmogorov-Smirnov two-sample test > - A new Cython API for bounded scalar-function root-finders in > `scipy.optimize` > - Substantial ``CSR`` and ``CSC`` sparse matrix indexing performance > improvements > - Added support for interpolation of rotations with continuous angular > rate and acceleration in ``RotationSpline`` > > > New features > ============ > > `scipy.interpolate` improvements > -------------------------------- > > A new class ``CubicHermiteSpline`` is introduced. It is a piecewise-cubic > interpolator which matches observed values and first derivatives. Existing > cubic interpolators ``CubicSpline``, ``PchipInterpolator`` and > ``Akima1DInterpolator`` were made subclasses of ``CubicHermiteSpline``. > > `scipy.io` improvements > ----------------------- > > For the Attribute-Relation File Format (ARFF) `scipy.io.arff.loadarff` > now supports relational attributes. > > `scipy.io.mmread` can now parse Matrix Market format files with empty lines. > > `scipy.linalg` improvements > --------------------------- > > Added wrappers for ``?syconv`` routines, which convert a symmetric matrix > given by a triangular matrix factorization into two matrices and vice versa. > > `scipy.linalg.clarkson_woodruff_transform` now uses an algorithm that > leverages > sparsity. This may provide a 60-90 percent speedup for dense input matrices. > Truly sparse input matrices should also benefit from the improved sketch > algorithm, which now correctly runs in ``O(nnz(A))`` time. > > Added new functions to calculate symmetric Fiedler matrices and > Fiedler companion matrices, named `scipy.linalg.fiedler` and > `scipy.linalg.fiedler_companion`, respectively. These may be used > for root finding. > > `scipy.ndimage` improvements > ---------------------------- > > Gaussian filter performances may improve by an order of magnitude in > some cases, thanks to removal of a dependence on ``np.polynomial``. This > may impact `scipy.ndimage.gaussian_filter` for example. > > `scipy.optimize` improvements > ----------------------------- > > The `scipy.optimize.brute` minimizer obtained a new keyword ``workers``, which > can be used to parallelize computation. > > A Cython API for bounded scalar-function root-finders in `scipy.optimize` > is available in a new module `scipy.optimize.cython_optimize` via ``cimport``. > This API may be used with ``nogil`` and ``prange`` to loop > over an array of function arguments to solve for an array of roots more > quickly than with pure Python. > > ``'interior-point'`` is now the default method for ``linprog``, and > ``'interior-point'`` now uses SuiteSparse for sparse problems when the > required scikits (scikit-umfpack and scikit-sparse) are available. > On benchmark problems (gh-10026), execution time reductions by factors of 2-3 > were typical. Also, a new ``method='revised simplex'`` has been added. > It is not as fast or robust as ``method='interior-point'``, but it is a > faster, > more robust, and equally accurate substitute for the legacy > ``method='simplex'``. > > ``differential_evolution`` can now use a ``Bounds`` class to specify the > bounds for the optimizing argument of a function. > > `scipy.optimize.dual_annealing` performance improvements related to > vectorisation of some internal code. > > `scipy.signal` improvements > --------------------------- > > Two additional methods of discretization are now supported by > `scipy.signal.cont2discrete`: ``impulse`` and ``foh``. > > `scipy.signal.firls` now uses faster solvers > > `scipy.signal.detrend` now has a lower physical memory footprint in some > cases, which may be leveraged using the new ``overwrite_data`` keyword > argument > > `scipy.signal.firwin` ``pass_zero`` argument now accepts new string arguments > that allow specification of the desired filter type: ``'bandpass'``, > ``'lowpass'``, ``'highpass'``, and ``'bandstop'`` > > `scipy.signal.sosfilt` may have improved performance due to lower retention > of the global interpreter lock (GIL) in algorithm > > `scipy.sparse` improvements > --------------------------- > > A new keyword was added to ``csgraph.dijsktra`` that > allows users to query the shortest path to ANY of the passed in indices, > as opposed to the shortest path to EVERY passed index. > > `scipy.sparse.linalg.lsmr` performance has been improved by roughly 10 percent > on large problems > > Improved performance and reduced physical memory footprint of the algorithm > used by `scipy.sparse.linalg.lobpcg` > > ``CSR`` and ``CSC`` sparse matrix fancy indexing performance has been > improved substantially > > `scipy.spatial` improvements > ---------------------------- > > `scipy.spatial.ConvexHull` now has a ``good`` attribute that can be used > alongsize the ``QGn`` Qhull options to determine which external facets of a > convex hull are visible from an external query point. > > `scipy.spatial.cKDTree.query_ball_point` has been modernized to use some newer > Cython features, including GIL handling and exception translation. An issue > with ``return_sorted=True`` and scalar queries was fixed, and a new mode named > ``return_length`` was added. ``return_length`` only computes the length of the > returned indices list instead of allocating the array every time. > > `scipy.spatial.transform.RotationSpline` has been added to enable > interpolation > of rotations with continuous angular rates and acceleration > > `scipy.stats` improvements > -------------------------- > > Added a new function to compute the Epps-Singleton test statistic, > `scipy.stats.epps_singleton_2samp`, which can be applied to continuous and > discrete distributions. > > New functions `scipy.stats.median_absolute_deviation` and `scipy.stats.gstd` > (geometric standard deviation) were added. The `scipy.stats.combine_pvalues` > method now supports ``pearson``, ``tippett`` and ``mudholkar_george`` pvalue > combination methods. > > The `scipy.stats.ortho_group` and `scipy.stats.special_ortho_group` > ``rvs(dim)`` functions' algorithms were updated from a ``O(dim^4)`` > implementation to a ``O(dim^3)`` which gives large speed improvements > for ``dim>100``. > > A rewrite of `scipy.stats.pearsonr` to use a more robust algorithm, > provide meaningful exceptions and warnings on potentially pathological input, > and fix at least five separate reported issues in the original implementation. > > Improved the precision of ``hypergeom.logcdf`` and ``hypergeom.logsf``. > > Added exact computation for Kolmogorov-Smirnov (KS) two-sample test, replacing > the previously approximate computation for the two-sided test > `stats.ks_2samp`. > Also added a one-sided, two-sample KS test, and a keyword ``alternative`` to > `stats.ks_2samp`. > > Backwards incompatible changes > ============================== > > `scipy.interpolate` changes > --------------------------- > > Functions from ``scipy.interpolate`` (``spleval``, ``spline``, ``splmake``, > and ``spltopp``) and functions from ``scipy.misc`` (``bytescale``, > ``fromimage``, ``imfilter``, ``imread``, ``imresize``, ``imrotate``, > ``imsave``, ``imshow``, ``toimage``) have been removed. The former set has > been deprecated since v0.19.0 and the latter has been deprecated since v1.0.0. > Similarly, aliases from ``scipy.misc`` (``comb``, ``factorial``, > ``factorial2``, ``factorialk``, ``logsumexp``, ``pade``, ``info``, ``source``, > ``who``) which have been deprecated since v1.0.0 are removed. > `SciPy documentation for > v1.1.0 <https://docs.scipy.org/doc/scipy-1.1.0/reference/misc.html>`__ > can be used to track the new import locations for the relocated functions. > > `scipy.linalg` changes > ---------------------- > > For ``pinv``, ``pinv2``, and ``pinvh``, the default cutoff values are changed > for consistency (see the docs for the actual values). > > `scipy.stats` changes > --------------------- > > Previously, ``ks_2samp(data1, data2)`` would run a two-sided test and return > the approximated p-value. The new signature, ``ks_2samp(data1, data2, > alternative="two-sided", method="auto")``, still runs the two-sided test by > default but returns the exact p-value for small samples and the approximated > value for large samples. ``method="asymp"`` would be equivalent to the > old version but ``auto`` is the better choice. > > Other changes > ============= > > Our tutorial has been expanded with a new section on global optimizers > > There has been a rework of the ``stats.distributions`` tutorials. > > `scipy.optimize` now correctly sets the convergence flag of the result to > ``CONVERR``, a convergence error, for bounded scalar-function root-finders > if the maximum iterations has been exceeded, ``disp`` is false, and > ``full_output`` is true. > > `scipy.optimize.curve_fit` no longer fails if ``xdata`` and ``ydata`` dtypes > differ; they are both now automatically cast to ``float64``. > > `scipy.ndimage` functions including ``binary_erosion``, ``binary_closing``, > and > ``binary_dilation`` now require an integer value for the number of iterations, > which alleviates a number of reported issues. > > Fixed normal approximation in case ``zero_method == "pratt"`` in > `scipy.stats.wilcoxon`. > > Fixes for incorrect probabilities, broadcasting issues and thread-safety > related to stats distributions setting member variables inside > ``_argcheck()``. > > `scipy.optimize.newton` now correctly raises a ``RuntimeError``, when default > arguments are used, in the case that a derivative of value zero is obtained, > which is a special case of failing to converge. > > A draft toolchain roadmap is now available, laying out a compatibility plan > including Python versions, C standards, and NumPy versions. > > > Authors > ======= > > * ananyashreyjain + > * ApamNapat + > * Scott Calabrese Barton + > * Christoph Baumgarten > * Peter Bell + > * Jacob Blomgren + > * Doctor Bob + > * Mana Borwornpadungkitti + > * Matthew Brett > * Evgeni Burovski > * CJ Carey > * Vega Theil Carstensen + > * Robert Cimrman > * Forrest Collman + > * Pietro Cottone + > * David + > * Idan David + > * Christoph Deil > * Dieter Werthmüller > * Conner DiPaolo + > * Dowon > * Michael Dunphy + > * Peter Andreas Entschev + > * Gökçen Eraslan + > * Johann Faouzi + > * Yu Feng > * Piotr Figiel + > * Matthew H Flamm > * Franz Forstmayr + > * Christoph Gohlke > * Richard Janis Goldschmidt + > * Ralf Gommers > * Lars Grueter > * Sylvain Gubian > * Matt Haberland > * Yaroslav Halchenko > * Charles Harris > * Lindsey Hiltner > * JakobStruye + > * He Jia + > * Jwink3101 + > * Greg Kiar + > * Julius Bier Kirkegaard > * John Kirkham + > * Thomas Kluyver > * Vladimir Korolev + > * Joseph Kuo + > * Michael Lamparski + > * Eric Larson > * Denis Laxalde > * Katrin Leinweber > * Jesse Livezey > * ludcila + > * Dhruv Madeka + > * Magnus + > * Nikolay Mayorov > * Mark Mikofski > * Jarrod Millman > * Markus Mohrhard + > * Eric Moore > * Andrew Nelson > * Aki Nishimura + > * OGordon100 + > * Petar Mlinarić + > * Stefan Peterson > * Matti Picus + > * Ilhan Polat > * Aaron Pries + > * Matteo Ravasi + > * Tyler Reddy > * Ashton Reimer + > * Joscha Reimer > * rfezzani + > * Riadh + > * Lucas Roberts > * Heshy Roskes + > * Mirko Scholz + > * Taylor D. Scott + > * Srikrishna Sekhar + > * Kevin Sheppard + > * Sourav Singh > * skjerns + > * Kai Striega > * SyedSaifAliAlvi + > * Gopi Manohar T + > * Albert Thomas + > * Timon + > * Paul van Mulbregt > * Jacob Vanderplas > * Daniel Vargas + > * Pauli Virtanen > * VNMabus + > * Stefan van der Walt > * Warren Weckesser > * Josh Wilson > * Nate Yoder + > * Roman Yurchak > > A total of 97 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 1.3.0 > ----------------------- > > * `#1320 <https://github.com/scipy/scipy/issues/1320>`__: > scipy.stats.distribution: problem with self.a, self.b if they... > * `#2002 <https://github.com/scipy/scipy/issues/2002>`__: members set in > scipy.stats.distributions.##._argcheck (Trac #1477) > * `#2823 <https://github.com/scipy/scipy/issues/2823>`__: distribution > methods add tmp > * `#3220 <https://github.com/scipy/scipy/issues/3220>`__: > Scipy.opimize.fmin_powell direc argument syntax unclear > * `#3728 <https://github.com/scipy/scipy/issues/3728>`__: > scipy.stats.pearsonr: possible bug with zero variance input > * `#6805 <https://github.com/scipy/scipy/issues/6805>`__: > error-in-scipy-wilcoxon-signed-rank-test-for-equal-series > * `#6873 <https://github.com/scipy/scipy/issues/6873>`__: 'stats.boxcox' > return all same values > * `#7117 <https://github.com/scipy/scipy/issues/7117>`__: Warn users when > using float32 input data to curve_fit and friends > * `#7632 <https://github.com/scipy/scipy/issues/7632>`__: it's not possible > to tell the \`optimize.least_squares\` solver... > * `#7730 <https://github.com/scipy/scipy/issues/7730>`__: stats.pearsonr: > Potential division by zero for dataset of length... > * `#7933 <https://github.com/scipy/scipy/issues/7933>`__: stats.truncnorm > fails when providing values outside truncation... > * `#8033 <https://github.com/scipy/scipy/issues/8033>`__: Add standard filter > types to firwin to set pass_zero intuitively... > * `#8600 <https://github.com/scipy/scipy/issues/8600>`__: lfilter.c.src zfill > has erroneous header > * `#8692 <https://github.com/scipy/scipy/issues/8692>`__: Non-negative values > of \`stats.hypergeom.logcdf\` > * `#8734 <https://github.com/scipy/scipy/issues/8734>`__: Enable pip build > isolation > * `#8861 <https://github.com/scipy/scipy/issues/8861>`__: scipy.linalg.pinv > gives wrong result while scipy.linalg.pinv2... > * `#8915 <https://github.com/scipy/scipy/issues/8915>`__: need to fix macOS > build against older numpy versions > * `#8980 <https://github.com/scipy/scipy/issues/8980>`__: > scipy.stats.pearsonr overflows with high values of x and y > * `#9226 <https://github.com/scipy/scipy/issues/9226>`__: BUG: signal: > SystemError: <built-in function _linear_filter>... > * `#9254 <https://github.com/scipy/scipy/issues/9254>`__: BUG: root finders > brentq, etc, flag says "converged" even if... > * `#9308 <https://github.com/scipy/scipy/issues/9308>`__: Test failure - > test_initial_constraints_as_canonical > * `#9353 <https://github.com/scipy/scipy/issues/9353>`__: > scipy.stats.pearsonr returns r=1 if r_num/r_den = inf > * `#9359 <https://github.com/scipy/scipy/issues/9359>`__: Planck distribution > is a geometric distribution > * `#9381 <https://github.com/scipy/scipy/issues/9381>`__: linregress should > warn user in 2x2 array case > * `#9406 <https://github.com/scipy/scipy/issues/9406>`__: BUG: stats: In > pearsonr, when r is nan, the p-value must also... > * `#9437 <https://github.com/scipy/scipy/issues/9437>`__: Cannot create > sparse matrix from size_t indexes > * `#9518 <https://github.com/scipy/scipy/issues/9518>`__: Relational > attributes in loadarff > * `#9551 <https://github.com/scipy/scipy/issues/9551>`__: BUG: > scipy.optimize.newton says the root of x^2+1 is zero. > * `#9564 <https://github.com/scipy/scipy/issues/9564>`__: rv_sample accepts > invalid input in scipy.stats > * `#9565 <https://github.com/scipy/scipy/issues/9565>`__: improper handling > of multidimensional input in stats.rv_sample > * `#9581 <https://github.com/scipy/scipy/issues/9581>`__: Least-squares > minimization fails silently when x and y data are... > * `#9587 <https://github.com/scipy/scipy/issues/9587>`__: Outdated value for > scipy.constants.au > * `#9611 <https://github.com/scipy/scipy/issues/9611>`__: Overflow error with > new way of p-value calculation in kendall... > * `#9645 <https://github.com/scipy/scipy/issues/9645>`__: > \`scipy.stats.mode\` crashes with variable length arrays (\`dtype=object\`) > * `#9734 <https://github.com/scipy/scipy/issues/9734>`__: > PendingDeprecationWarning for np.matrix with pytest > * `#9786 <https://github.com/scipy/scipy/issues/9786>`__: stats.ks_2samp() > misleading for small data sets. > * `#9790 <https://github.com/scipy/scipy/issues/9790>`__: Excessive memory > usage on detrend > * `#9801 <https://github.com/scipy/scipy/issues/9801>`__: dual_annealing does > not set the success attribute in OptimizeResult > * `#9833 <https://github.com/scipy/scipy/issues/9833>`__: IntegrationWarning > from mielke.stats() during build of html doc. > * `#9835 <https://github.com/scipy/scipy/issues/9835>`__: scipy.signal.firls > seems to be inefficient versus MATLAB firls > * `#9864 <https://github.com/scipy/scipy/issues/9864>`__: Curve_fit does not > check for empty input data if called with... > * `#9869 <https://github.com/scipy/scipy/issues/9869>`__: > scipy.ndimage.label: Minor documentation issue > * `#9882 <https://github.com/scipy/scipy/issues/9882>`__: format at the wrong > paranthesis in scipy.spatial.transform > * `#9889 <https://github.com/scipy/scipy/issues/9889>`__: > scipy.signal.find_peaks minor documentation issue > * `#9890 <https://github.com/scipy/scipy/issues/9890>`__: Minkowski p-norm > Issues in cKDTree For Values Other Than 2 Or... > * `#9896 <https://github.com/scipy/scipy/issues/9896>`__: > scipy.stats._argcheck sets (not just checks) values > * `#9905 <https://github.com/scipy/scipy/issues/9905>`__: Memory error in > ndimage.binary_erosion > * `#9909 <https://github.com/scipy/scipy/issues/9909>`__: > binary_dilation/erosion/closing crashes when iterations is float > * `#9919 <https://github.com/scipy/scipy/issues/9919>`__: BUG: \`coo_matrix\` > does not validate the \`shape\` argument. > * `#9982 <https://github.com/scipy/scipy/issues/9982>`__: lsq_linear > hangs/infinite loop with 'trf' method > * `#10003 <https://github.com/scipy/scipy/issues/10003>`__: exponnorm.pdf > returns NAN for small K > * `#10011 <https://github.com/scipy/scipy/issues/10011>`__: Incorrect check > for invalid rotation plane in scipy.ndimage.rotate > * `#10024 <https://github.com/scipy/scipy/issues/10024>`__: Fails to build > from git > * `#10048 <https://github.com/scipy/scipy/issues/10048>`__: DOC: > scipy.optimize.root_scalar > * `#10068 <https://github.com/scipy/scipy/issues/10068>`__: DOC: > scipy.interpolate.splev > * `#10074 <https://github.com/scipy/scipy/issues/10074>`__: BUG: \`expm\` > calculates the wrong coefficients in the backward... > > > Pull requests for 1.3.0 > ----------------------- > > * `#7827 <https://github.com/scipy/scipy/pull/7827>`__: ENH: sparse: overhaul > of sparse matrix indexing > * `#8431 <https://github.com/scipy/scipy/pull/8431>`__: ENH: Cython optimize > zeros api > * `#8743 <https://github.com/scipy/scipy/pull/8743>`__: DOC: Updated > linalg.pinv, .pinv2, .pinvh docstrings > * `#8744 <https://github.com/scipy/scipy/pull/8744>`__: DOC: added examples > to remez docstring > * `#9227 <https://github.com/scipy/scipy/pull/9227>`__: DOC: update > description of "direc" parameter of "fmin_powell" > * `#9263 <https://github.com/scipy/scipy/pull/9263>`__: ENH: optimize: added > "revised simplex" for scipy.optimize.linprog > * `#9325 <https://github.com/scipy/scipy/pull/9325>`__: DEP: Remove > deprecated functions for 1.3.0 > * `#9330 <https://github.com/scipy/scipy/pull/9330>`__: Add note on push and > pull affine transformations > * `#9423 <https://github.com/scipy/scipy/pull/9423>`__: DOC: Clearly state > how 2x2 input arrays are handled in stats.linregress > * `#9428 <https://github.com/scipy/scipy/pull/9428>`__: ENH: parallelised > brute > * `#9438 <https://github.com/scipy/scipy/pull/9438>`__: BUG: Initialize coo > matrix with size_t indexes > * `#9455 <https://github.com/scipy/scipy/pull/9455>`__: MAINT: Speed up > get_(lapack,blas)_func > * `#9465 <https://github.com/scipy/scipy/pull/9465>`__: MAINT: Clean up > optimize.zeros C solvers interfaces/code. > * `#9477 <https://github.com/scipy/scipy/pull/9477>`__: DOC: linalg: fix > lstsq docstring on residues shape > * `#9478 <https://github.com/scipy/scipy/pull/9478>`__: DOC: Add docstring > examples for rosen functions > * `#9479 <https://github.com/scipy/scipy/pull/9479>`__: DOC: Add docstring > example for ai_zeros and bi_zeros > * `#9480 <https://github.com/scipy/scipy/pull/9480>`__: MAINT: linalg: lstsq > clean up > * `#9489 <https://github.com/scipy/scipy/pull/9489>`__: DOC: roadmap update > for changes over the last year. > * `#9492 <https://github.com/scipy/scipy/pull/9492>`__: MAINT: stats: Improve > implementation of chi2 ppf method. > * `#9497 <https://github.com/scipy/scipy/pull/9497>`__: DOC: Improve > docstrings sparse.linalg.isolve > * `#9499 <https://github.com/scipy/scipy/pull/9499>`__: DOC: Replace "Scipy" > with "SciPy" in the .rst doc files for consistency. > * `#9500 <https://github.com/scipy/scipy/pull/9500>`__: DOC: Document the > toolchain and its roadmap. > * `#9505 <https://github.com/scipy/scipy/pull/9505>`__: DOC: specify which > definition of skewness is used > * `#9511 <https://github.com/scipy/scipy/pull/9511>`__: DEP: interpolate: > remove deprecated interpolate_wrapper > * `#9517 <https://github.com/scipy/scipy/pull/9517>`__: BUG: improve error > handling in stats.iqr > * `#9522 <https://github.com/scipy/scipy/pull/9522>`__: ENH: Add Fiedler and > fiedler companion to special matrices > * `#9526 <https://github.com/scipy/scipy/pull/9526>`__: TST: relax precision > requirements in signal.correlate tests > * `#9529 <https://github.com/scipy/scipy/pull/9529>`__: DOC: fix missing > random seed in optimize.newton example > * `#9533 <https://github.com/scipy/scipy/pull/9533>`__: MAINT: Use list > comprehension when possible > * `#9537 <https://github.com/scipy/scipy/pull/9537>`__: DOC: add a "big > picture" roadmap > * `#9538 <https://github.com/scipy/scipy/pull/9538>`__: DOC: Replace "Numpy" > with "NumPy" in .py, .rst and .txt doc files... > * `#9539 <https://github.com/scipy/scipy/pull/9539>`__: ENH: add two-sample > test (Epps-Singleton) to scipy.stats > * `#9559 <https://github.com/scipy/scipy/pull/9559>`__: DOC: add section on > global optimizers to tutorial > * `#9561 <https://github.com/scipy/scipy/pull/9561>`__: ENH: remove > noprefix.h, change code appropriately > * `#9562 <https://github.com/scipy/scipy/pull/9562>`__: MAINT: stats: Rewrite > pearsonr. > * `#9563 <https://github.com/scipy/scipy/pull/9563>`__: BUG: Minor bug fix > Callback in linprog(method='simplex') > * `#9568 <https://github.com/scipy/scipy/pull/9568>`__: MAINT: raise runtime > error for newton with zeroder if disp true,... > * `#9570 <https://github.com/scipy/scipy/pull/9570>`__: Correct docstring in > show_options in optimize. Fixes #9407 > * `#9573 <https://github.com/scipy/scipy/pull/9573>`__: BUG fixes range of pk > variable pre-check > * `#9577 <https://github.com/scipy/scipy/pull/9577>`__: TST: fix minor issue > in a signal.stft test. > * `#9580 <https://github.com/scipy/scipy/pull/9580>`__: Included blank line > before list - Fixes #8658 > * `#9582 <https://github.com/scipy/scipy/pull/9582>`__: MAINT: drop Python > 2.7 and 3.4 > * `#9588 <https://github.com/scipy/scipy/pull/9588>`__: MAINT: update > \`constants.astronomical_unit\` to new 2012 value. > * `#9592 <https://github.com/scipy/scipy/pull/9592>`__: TST: Add 32-bit > testing to CI > * `#9593 <https://github.com/scipy/scipy/pull/9593>`__: DOC: Replace > cumulative density with cumulative distribution > * `#9596 <https://github.com/scipy/scipy/pull/9596>`__: TST: remove VC 9.0 > from Azure CI > * `#9599 <https://github.com/scipy/scipy/pull/9599>`__: Hyperlink DOI to > preferred resolver > * `#9601 <https://github.com/scipy/scipy/pull/9601>`__: DEV: try to limit GC > memory use on PyPy > * `#9603 <https://github.com/scipy/scipy/pull/9603>`__: MAINT: improve logcdf > and logsf of hypergeometric distribution > * `#9605 <https://github.com/scipy/scipy/pull/9605>`__: Reference to pylops > in LinearOperator notes and ARPACK example > * `#9617 <https://github.com/scipy/scipy/pull/9617>`__: TST: reduce max > memory usage for sparse.linalg.lgmres test > * `#9619 <https://github.com/scipy/scipy/pull/9619>`__: FIX: Sparse matrix > addition/subtraction eliminates explicit zeros > * `#9621 <https://github.com/scipy/scipy/pull/9621>`__: bugfix in rv_sample > in scipy.stats > * `#9622 <https://github.com/scipy/scipy/pull/9622>`__: MAINT: Raise error in > directed_hausdorff distance > * `#9623 <https://github.com/scipy/scipy/pull/9623>`__: DOC: Build docs with > warnings as errors > * `#9625 <https://github.com/scipy/scipy/pull/9625>`__: Return the number of > calls to 'hessp' (not just 'hess') in trust... > * `#9627 <https://github.com/scipy/scipy/pull/9627>`__: BUG: ignore empty > lines in mmio > * `#9637 <https://github.com/scipy/scipy/pull/9637>`__: Function to calculate > the MAD of an array > * `#9646 <https://github.com/scipy/scipy/pull/9646>`__: BUG: stats: mode for > objects w/ndim > 1 > * `#9648 <https://github.com/scipy/scipy/pull/9648>`__: Add > \`stats.contingency\` to refguide-check > * `#9650 <https://github.com/scipy/scipy/pull/9650>`__: ENH: many lobpcg() > algorithm improvements > * `#9652 <https://github.com/scipy/scipy/pull/9652>`__: Move misc.doccer to > _lib.doccer > * `#9660 <https://github.com/scipy/scipy/pull/9660>`__: ENH: add pearson, > tippett, and mudholkar-george to combine_pvalues > * `#9661 <https://github.com/scipy/scipy/pull/9661>`__: BUG: Fix ksone > right-hand endpoint, documentation and tests. > * `#9664 <https://github.com/scipy/scipy/pull/9664>`__: ENH: adding > multi-target dijsktra performance enhancement > * `#9670 <https://github.com/scipy/scipy/pull/9670>`__: MAINT: link planck > and geometric distribution in scipy.stats > * `#9676 <https://github.com/scipy/scipy/pull/9676>`__: ENH: optimize: change > default linprog method to interior-point > * `#9685 <https://github.com/scipy/scipy/pull/9685>`__: Added reference to > ndimage.filters.median_filter > * `#9705 <https://github.com/scipy/scipy/pull/9705>`__: Fix coefficients in > expm helper function > * `#9711 <https://github.com/scipy/scipy/pull/9711>`__: Release the GIL > during sosfilt processing for simple types > * `#9721 <https://github.com/scipy/scipy/pull/9721>`__: ENH: Convexhull > visiblefacets > * `#9723 <https://github.com/scipy/scipy/pull/9723>`__: BLD: Modify > rv_generic._construct_doc to print out failing distribution... > * `#9726 <https://github.com/scipy/scipy/pull/9726>`__: BUG: Fix small issues > with \`signal.lfilter' > * `#9729 <https://github.com/scipy/scipy/pull/9729>`__: BUG: Typecheck > iterations for binary image operations > * `#9730 <https://github.com/scipy/scipy/pull/9730>`__: ENH: reduce > sizeof(NI_WatershedElement) by 20% > * `#9731 <https://github.com/scipy/scipy/pull/9731>`__: ENH: remove > suspicious sequence of type castings > * `#9739 <https://github.com/scipy/scipy/pull/9739>`__: BUG: qr_updates fails > if u is exactly in span Q > * `#9749 <https://github.com/scipy/scipy/pull/9749>`__: BUG: > MapWrapper.__exit__ should terminate > * `#9753 <https://github.com/scipy/scipy/pull/9753>`__: ENH: Added exact > computation for Kolmogorov-Smirnov two-sample... > * `#9755 <https://github.com/scipy/scipy/pull/9755>`__: DOC: Added example > for signal.impulse, copied from impulse2 > * `#9756 <https://github.com/scipy/scipy/pull/9756>`__: DOC: Added docstring > example for iirdesign > * `#9757 <https://github.com/scipy/scipy/pull/9757>`__: DOC: Added examples > for step functions > * `#9759 <https://github.com/scipy/scipy/pull/9759>`__: ENH: Allow pass_zero > to act like btype > * `#9760 <https://github.com/scipy/scipy/pull/9760>`__: DOC: Added docstring > for lp2bs > * `#9761 <https://github.com/scipy/scipy/pull/9761>`__: DOC: Added docstring > and example for lp2bp > * `#9764 <https://github.com/scipy/scipy/pull/9764>`__: BUG: Catch internal > warnings for matrix > * `#9766 <https://github.com/scipy/scipy/pull/9766>`__: ENH: Speed up > _gaussian_kernel1d by removing dependence on np.polynomial > * `#9769 <https://github.com/scipy/scipy/pull/9769>`__: BUG: Fix Cubic Spline > Read Only issues > * `#9773 <https://github.com/scipy/scipy/pull/9773>`__: DOC: Several > docstrings > * `#9774 <https://github.com/scipy/scipy/pull/9774>`__: TST: bump Azure CI > OpenBLAS version to match wheels > * `#9775 <https://github.com/scipy/scipy/pull/9775>`__: DOC: Improve clarity > of cov_x documentation for scipy.optimize.leastsq > * `#9779 <https://github.com/scipy/scipy/pull/9779>`__: ENH: dual_annealing > vectorise visit_fn > * `#9788 <https://github.com/scipy/scipy/pull/9788>`__: TST, BUG: > f2py-related issues with NumPy < 1.14.0 > * `#9791 <https://github.com/scipy/scipy/pull/9791>`__: BUG: fix amax > constraint not enforced in scalar_search_wolfe2 > * `#9792 <https://github.com/scipy/scipy/pull/9792>`__: ENH: Allow inplace > copying in place in "detrend" function > * `#9795 <https://github.com/scipy/scipy/pull/9795>`__: DOC: Fix/update > docstring for dstn and dst > * `#9796 <https://github.com/scipy/scipy/pull/9796>`__: MAINT: Allow None > tolerances in least_squares > * `#9798 <https://github.com/scipy/scipy/pull/9798>`__: BUG: fixes abort trap > 6 error in scipy issue 9785 in unit tests > * `#9807 <https://github.com/scipy/scipy/pull/9807>`__: MAINT: improve doc > and add alternative keyword to wilcoxon in... > * `#9808 <https://github.com/scipy/scipy/pull/9808>`__: Fix PPoly integrate > and test for CubicSpline > * `#9810 <https://github.com/scipy/scipy/pull/9810>`__: ENH: Add the > geometric standard deviation function > * `#9811 <https://github.com/scipy/scipy/pull/9811>`__: MAINT: remove invalid > derphi default None value in scalar_search_wolfe2 > * `#9813 <https://github.com/scipy/scipy/pull/9813>`__: Adapt hamming > distance in C to support weights > * `#9817 <https://github.com/scipy/scipy/pull/9817>`__: DOC: Copy solver > description to solver modules > * `#9829 <https://github.com/scipy/scipy/pull/9829>`__: ENH: Add FOH and > equivalent impulse response discretizations... > * `#9831 <https://github.com/scipy/scipy/pull/9831>`__: ENH: Implement > RotationSpline > * `#9834 <https://github.com/scipy/scipy/pull/9834>`__: DOC: Change mielke > distribution default parameters to ensure... > * `#9838 <https://github.com/scipy/scipy/pull/9838>`__: ENH: Use faster > solvers for firls > * `#9854 <https://github.com/scipy/scipy/pull/9854>`__: ENH: loadarff now > supports relational attributes. > * `#9856 <https://github.com/scipy/scipy/pull/9856>`__: integrate.bvp - > improve handling of nonlinear boundary conditions > * `#9862 <https://github.com/scipy/scipy/pull/9862>`__: TST: reduce Appveyor > CI load > * `#9874 <https://github.com/scipy/scipy/pull/9874>`__: DOC: Update > requirements in release notes > * `#9883 <https://github.com/scipy/scipy/pull/9883>`__: BUG: fixed > parenthesis in spatial.rotation > * `#9884 <https://github.com/scipy/scipy/pull/9884>`__: ENH: Use Sparsity in > Clarkson-Woodruff Sketch > * `#9888 <https://github.com/scipy/scipy/pull/9888>`__: MAINT: Replace NumPy > aliased functions > * `#9892 <https://github.com/scipy/scipy/pull/9892>`__: BUG: Fix 9890 > query_ball_point returns wrong result when p is... > * `#9893 <https://github.com/scipy/scipy/pull/9893>`__: BUG: curve_fit > doesn't check for empty input if called with bounds > * `#9894 <https://github.com/scipy/scipy/pull/9894>`__: > scipy.signal.find_peaks documentation error > * `#9898 <https://github.com/scipy/scipy/pull/9898>`__: BUG: Set success > attribute in OptimizeResult. See #9801 > * `#9900 <https://github.com/scipy/scipy/pull/9900>`__: BUG: Restrict > rv_generic._argcheck() and its overrides from setting... > * `#9906 <https://github.com/scipy/scipy/pull/9906>`__: fixed a bug in kde > logpdf > * `#9911 <https://github.com/scipy/scipy/pull/9911>`__: DOC: replace example > for "np.select" with the one from numpy... > * `#9912 <https://github.com/scipy/scipy/pull/9912>`__: BF(DOC): point to > numpy.select instead of plain (python) .select > * `#9914 <https://github.com/scipy/scipy/pull/9914>`__: DOC: change > ValueError message in _validate_pad of signaltools. > * `#9915 <https://github.com/scipy/scipy/pull/9915>`__: cKDTree > query_ball_point improvements > * `#9918 <https://github.com/scipy/scipy/pull/9918>`__: Update ckdtree.pyx > with boxsize argument in docstring > * `#9920 <https://github.com/scipy/scipy/pull/9920>`__: BUG: sparse: Validate > explicit shape if given with dense argument... > * `#9924 <https://github.com/scipy/scipy/pull/9924>`__: BLD: add back > pyproject.toml > * `#9931 <https://github.com/scipy/scipy/pull/9931>`__: Fix empty constraint > * `#9935 <https://github.com/scipy/scipy/pull/9935>`__: DOC: fix references > for stats.f_oneway > * `#9936 <https://github.com/scipy/scipy/pull/9936>`__: Revert gh-9619: "FIX: > Sparse matrix addition/subtraction eliminates... > * `#9937 <https://github.com/scipy/scipy/pull/9937>`__: MAINT: fix PEP8 > issues and update to pycodestyle 2.5.0 > * `#9939 <https://github.com/scipy/scipy/pull/9939>`__: DOC: correct > \`structure\` description in \`ndimage.label\` docstring > * `#9940 <https://github.com/scipy/scipy/pull/9940>`__: MAINT: remove > extraneous distutils copies > * `#9945 <https://github.com/scipy/scipy/pull/9945>`__: ENH: > differential_evolution can use Bounds object > * `#9949 <https://github.com/scipy/scipy/pull/9949>`__: Added 'std' to add > doctstrings since it is a \`known_stats\`... > * `#9953 <https://github.com/scipy/scipy/pull/9953>`__: DOC: Documentation > cleanup for stats tutorials. > * `#9962 <https://github.com/scipy/scipy/pull/9962>`__: __repr__ for Bounds > * `#9971 <https://github.com/scipy/scipy/pull/9971>`__: ENH: Improve > performance of lsmr > * `#9987 <https://github.com/scipy/scipy/pull/9987>`__: CI: pin Sphinx > version to 1.8.5 > * `#9990 <https://github.com/scipy/scipy/pull/9990>`__: ENH: constraint > violation > * `#9991 <https://github.com/scipy/scipy/pull/9991>`__: BUG: Avoid inplace > modification of input array in newton > * `#9995 <https://github.com/scipy/scipy/pull/9995>`__: MAINT: > sparse.csgraph: Add cdef to stop build warning. > * `#9996 <https://github.com/scipy/scipy/pull/9996>`__: BUG: Make > minimize_quadratic_1d work with infinite bounds correctly > * `#10004 <https://github.com/scipy/scipy/pull/10004>`__: BUG: Fix unbound > local error in linprog - simplex. > * `#10007 <https://github.com/scipy/scipy/pull/10007>`__: BLD: fix Python 3.7 > build with build isolation > * `#10009 <https://github.com/scipy/scipy/pull/10009>`__: BUG: Make sure that > _binary_erosion only accepts an integer number... > * `#10016 <https://github.com/scipy/scipy/pull/10016>`__: Update link to > airspeed-velocity > * `#10017 <https://github.com/scipy/scipy/pull/10017>`__: DOC: Update > \`interpolate.LSQSphereBivariateSpline\` to include... > * `#10018 <https://github.com/scipy/scipy/pull/10018>`__: MAINT: special: Fix > a few warnings that occur when compiling... > * `#10019 <https://github.com/scipy/scipy/pull/10019>`__: TST: Azure > summarizes test failures > * `#10021 <https://github.com/scipy/scipy/pull/10021>`__: ENH: Introduce > CubicHermiteSpline > * `#10022 <https://github.com/scipy/scipy/pull/10022>`__: BENCH: Increase > cython version in asv to fix benchmark builds > * `#10023 <https://github.com/scipy/scipy/pull/10023>`__: BUG: Avoid > exponnorm producing nan for small K values. > * `#10025 <https://github.com/scipy/scipy/pull/10025>`__: BUG: optimize: > tweaked linprog status 4 error message > * `#10026 <https://github.com/scipy/scipy/pull/10026>`__: ENH: optimize: use > SuiteSparse in linprog interior-point when... > * `#10027 <https://github.com/scipy/scipy/pull/10027>`__: MAINT: cluster: > clean up the use of malloc() in the function... > * `#10028 <https://github.com/scipy/scipy/pull/10028>`__: Fix rotate invalid > plane check > * `#10040 <https://github.com/scipy/scipy/pull/10040>`__: MAINT: fix pratt > method of wilcox test in scipy.stats > * `#10041 <https://github.com/scipy/scipy/pull/10041>`__: MAINT: special: Fix > a warning generated when building the AMOS... > * `#10044 <https://github.com/scipy/scipy/pull/10044>`__: DOC: fix up > spatial.transform.Rotation docstrings > * `#10047 <https://github.com/scipy/scipy/pull/10047>`__: MAINT: interpolate: > Fix a few build warnings. > * `#10051 <https://github.com/scipy/scipy/pull/10051>`__: Add project_urls to > setup > * `#10052 <https://github.com/scipy/scipy/pull/10052>`__: don't set flag to > "converged" if max iter exceeded > * `#10054 <https://github.com/scipy/scipy/pull/10054>`__: MAINT: signal: Fix > a few build warnings and modernize some C... > * `#10056 <https://github.com/scipy/scipy/pull/10056>`__: BUG: Ensure > factorial is not too large in kendaltau > * `#10058 <https://github.com/scipy/scipy/pull/10058>`__: Small speedup in > samping from ortho and special_ortho groups > * `#10059 <https://github.com/scipy/scipy/pull/10059>`__: BUG: optimize: fix > #10038 by increasing tol > * `#10061 <https://github.com/scipy/scipy/pull/10061>`__: BLD: DOC: make > building docs easier by parsing python version. > * `#10064 <https://github.com/scipy/scipy/pull/10064>`__: ENH: Significant > speedup for ortho and special ortho group > * `#10065 <https://github.com/scipy/scipy/pull/10065>`__: DOC: Reword > parameter descriptions in \`optimize.root_scalar\` > * `#10066 <https://github.com/scipy/scipy/pull/10066>`__: BUG: signal: Fix > error raised by savgol_coeffs when deriv > polyorder. > * `#10067 <https://github.com/scipy/scipy/pull/10067>`__: MAINT: Fix the > cutoff value inconsistency for pinv2 and pinvh > * `#10072 <https://github.com/scipy/scipy/pull/10072>`__: BUG: stats: Fix > boxcox_llf to avoid loss of precision. > * `#10075 <https://github.com/scipy/scipy/pull/10075>`__: ENH: Add wrappers > for ?syconv routines > * `#10076 <https://github.com/scipy/scipy/pull/10076>`__: BUG: optimize: fix > curve_fit for mixed float32/float64 input > * `#10077 <https://github.com/scipy/scipy/pull/10077>`__: DOC: Replace > undefined \`k\` in \`interpolate.splev\` docstring > * `#10079 <https://github.com/scipy/scipy/pull/10079>`__: DOC: Fixed typo, > rearranged some doc of stats.morestats.wilcoxon. > * `#10080 <https://github.com/scipy/scipy/pull/10080>`__: TST: install > scikit-sparse for full TravisCI tests > * `#10083 <https://github.com/scipy/scipy/pull/10083>`__: Clean > \`\`_clean_inputs\`\` in optimize.linprog > * `#10088 <https://github.com/scipy/scipy/pull/10088>`__: ENH: optimize: > linprog test CHOLMOD/UMFPACK solvers when available > * `#10090 <https://github.com/scipy/scipy/pull/10090>`__: MAINT: Fix > CubicSplinerInterpolator for pandas > * `#10091 <https://github.com/scipy/scipy/pull/10091>`__: MAINT: improve > logcdf and logsf of hypergeometric distribution > * `#10095 <https://github.com/scipy/scipy/pull/10095>`__: MAINT: Clean > \`\`_clean_inputs\`\` in linprog > > Checksums > ========= > > MD5 > ~~~ > > 5a71a217fa4ff372097f501daf816f3b > scipy-1.3.0rc1-cp35-cp35m-macosx_10_6_intel.macosx_10_9_int > el.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl > c154ca8eee9ebafe04575b316e41ed85 > scipy-1.3.0rc1-cp35-cp35m-manylinux1_i686.whl > 36a91fa4ae6eeceeb79bf97b9bd013eb > scipy-1.3.0rc1-cp35-cp35m-manylinux1_x86_64.whl > f1f4259b373332d6edc6bef123b0dc7c scipy-1.3.0rc1-cp35-cp35m-win32.whl > c81d78bed8e2176cf0168785b7e1b692 scipy-1.3.0rc1-cp35-cp35m-win_amd64.whl > c43dd24f349c9d37a6c996e7c0674141 > scipy-1.3.0rc1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_int > el.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl > 8188210e0fd710f4544f314306b76313 > scipy-1.3.0rc1-cp36-cp36m-manylinux1_i686.whl > 0cf317ee185a8f5736b479d1c8b5f415 > scipy-1.3.0rc1-cp36-cp36m-manylinux1_x86_64.whl > e46e5b38288d79321d8d6ffa15a8f54e scipy-1.3.0rc1-cp36-cp36m-win32.whl > 85a79e9be408de72056c6efc1eef7d46 scipy-1.3.0rc1-cp36-cp36m-win_amd64.whl > 2436169658f74e03b4037142e51a8f86 > scipy-1.3.0rc1-cp37-cp37m-macosx_10_6_intel.macosx_10_9_int > el.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl > 1b9e2caa5994ee227b4ad8e46b45ad7e > scipy-1.3.0rc1-cp37-cp37m-manylinux1_i686.whl > 05a51b40471abdf4e9020183ad449bf2 > scipy-1.3.0rc1-cp37-cp37m-manylinux1_x86_64.whl > debecbc0e54fe4e737971b0a6d9f24f5 scipy-1.3.0rc1-cp37-cp37m-win32.whl > 79c725144fa59566d8ebd3bf556533aa scipy-1.3.0rc1-cp37-cp37m-win_amd64.whl > 0b9fa3583bcf2c8190b277cddb287132 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2ab6d6f940b6b09cbee6d7cb2de5914a50f459cbc612b4328b033f67452fd1d6 > scipy-1.3.0rc1-cp37-cp37m-win_amd64.whl > d09e6fae7434aa9e1422d95bbee28f0b66ba97ab770fec24f31c75a873823cd6 > scipy-1.3.0rc1.tar.gz > ba49645a693f6e70e690cf6e2175865b7bf0182cf59bdce872968f47546f4269 > scipy-1.3.0rc1.tar.xz > f1cdb4651f3d150f5c145dc930a627f09aa2afc5275c6c5da97a9a5df274c531 > scipy-1.3.0rc1.zip > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1 > > iQIcBAEBAgAGBQJcw54gAAoJELD/41ZX0J71zbEQAKaapoUb0gbLvljeLL+FZmaZ > Ha8OecYf7Fsdgj9kiGk2kKgrvz5nkoRyJDpxi4BOzPua+HBUhECoH3DBL5kA6sbv > VsMAhTb5HFPiKmC78LHEUNSY1fPJrdK7s99pIgedjQFR5diODHqqtB54awbRsTOs > Vdq45I7JoCd+DUMqQWIA3TZyjrZzw2V1KBFS8mHFdcop71Q1RqRNf3rVw7Rpydob > uegbae42cJ2Hej4+viU8hsCM+JIgkCuZaQEN2wp4W9pmHsDCzJcoyQjulTjZQAeG > W3L/F5O1p9A9nHIPk+wvS3D2ageKOhYmVSgB6dznXnFRsjwIKH4O4k0TCzYAamsd > HvcKnncGAzc+95o2k+v46575O3pBPRYCmOKz6LlFfFGNr/PWkxPYuG49nGIwQZU+ > /w0RYvu2NIPyd05gQQfwyEAATmwbYQfCelbQtHtPehDrtwMINZF4ZCqVg8D7d2ns > 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