[Numpy-discussion] [SciPy-Dev] ANN: SciPy 1.3.0rc1 -- please test
Mark Mikofski
mikofski at berkeley.edu
Sat Apr 27 14:46:21 EDT 2019
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.reddy at 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
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--
Mark Mikofski, PhD (2005)
*Fiat Lux*
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