Update scipy to 1.0.1 - Githubissues

This PR updates scipy from 0.19.1 to 1.0.1.

Changelog

### 1.0.0 ``` 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. Moreover, our development attention will now shift to bug-fix releases on the 1.0.x branch, and on adding new features on the master branch. Some of the highlights of this release are: - Major build improvements. Windows wheels are available on PyPI for the first time, and continuous integration has been set up on Windows and OS X in addition to Linux. - A set of new ODE solvers and a unified interface to them (`scipy.integrate.solve_ivp`). - Two new trust region optimizers and a new linear programming method, with improved performance compared to what `scipy.optimize` offered previously. - Many new BLAS and LAPACK functions were wrapped. The BLAS wrappers are now complete. This release requires Python 2.7 or 3.4+ and NumPy 1.8.2 or greater. This is also the last release to support LAPACK 3.1.x - 3.3.x. Moving the lowest supported LAPACK version to >3.2.x was long blocked by Apple Accelerate providing the LAPACK 3.2.1 API. We have decided that it's time to either drop Accelerate or, if there is enough interest, provide shims for functions added in more recent LAPACK versions so it can still be used. New features ============ `scipy.cluster` improvements ---------------------------- `scipy.cluster.hierarchy.optimal_leaf_ordering`, a function to reorder a linkage matrix to minimize distances between adjacent leaves, was added. `scipy.fftpack` improvements ---------------------------- N-dimensional versions of the discrete sine and cosine transforms and their inverses were added as ``dctn``, ``idctn``, ``dstn`` and ``idstn``. `scipy.integrate` improvements ------------------------------ A set of new ODE solvers have been added to `scipy.integrate`. The convenience function `scipy.integrate.solve_ivp` allows uniform access to all solvers. The individual solvers (``RK23``, ``RK45``, ``Radau``, ``BDF`` and ``LSODA``) can also be used directly. `scipy.linalg` improvements ---------------------------- The BLAS wrappers in `scipy.linalg.blas` have been completed. Added functions are ``*gbmv``, ``*hbmv``, ``*hpmv``, ``*hpr``, ``*hpr2``, ``*spmv``, ``*spr``, ``*tbmv``, ``*tbsv``, ``*tpmv``, ``*tpsv``, ``*trsm``, ``*trsv``, ``*sbmv``, ``*spr2``, Wrappers for the LAPACK functions ``*gels``, ``*stev``, ``*sytrd``, ``*hetrd``, ``*sytf2``, ``*hetrf``, ``*sytrf``, ``*sycon``, ``*hecon``, ``*gglse``, ``*stebz``, ``*stemr``, ``*sterf``, and ``*stein`` have been added. The function `scipy.linalg.subspace_angles` has been added to compute the subspace angles between two matrices. The function `scipy.linalg.clarkson_woodruff_transform` has been added. It finds low-rank matrix approximation via the Clarkson-Woodruff Transform. The functions `scipy.linalg.eigh_tridiagonal` and `scipy.linalg.eigvalsh_tridiagonal`, which find the eigenvalues and eigenvectors of tridiagonal hermitian/symmetric matrices, were added. `scipy.ndimage` improvements ---------------------------- Support for homogeneous coordinate transforms has been added to `scipy.ndimage.affine_transform`. The ``ndimage`` C code underwent a significant refactoring, and is now a lot easier to understand and maintain. `scipy.optimize` improvements ----------------------------- The methods ``trust-region-exact`` and ``trust-krylov`` have been added to the function `scipy.optimize.minimize`. These new trust-region methods solve the subproblem with higher accuracy at the cost of more Hessian factorizations (compared to dogleg) or more matrix vector products (compared to ncg) but usually require less nonlinear iterations and are able to deal with indefinite Hessians. They seem very competitive against the other Newton methods implemented in scipy. `scipy.optimize.linprog` gained an interior point method. Its performance is superior (both in accuracy and speed) to the older simplex method. `scipy.signal` improvements --------------------------- An argument ``fs`` (sampling frequency) was added to the following functions: ``firwin``, ``firwin2``, ``firls``, and ``remez``. This makes these functions consistent with many other functions in `scipy.signal` in which the sampling frequency can be specified. `scipy.signal.freqz` has been sped up significantly for FIR filters. `scipy.sparse` improvements --------------------------- Iterating over and slicing of CSC and CSR matrices is now faster by up to ~35%. The ``tocsr`` method of COO matrices is now several times faster. The ``diagonal`` method of sparse matrices now takes a parameter, indicating which diagonal to return. `scipy.sparse.linalg` improvements ---------------------------------- A new iterative solver for large-scale nonsymmetric sparse linear systems, `scipy.sparse.linalg.gcrotmk`, was added. It implements ``GCROT(m,k)``, a flexible variant of ``GCROT``. `scipy.sparse.linalg.lsmr` now accepts an initial guess, yielding potentially faster convergence. SuperLU was updated to version 5.2.1. `scipy.spatial` improvements ---------------------------- Many distance metrics in `scipy.spatial.distance` gained support for weights. The signatures of `scipy.spatial.distance.pdist` and `scipy.spatial.distance.cdist` were changed to ``*args, **kwargs`` in order to support a wider range of metrics (e.g. string-based metrics that need extra keywords). Also, an optional ``out`` parameter was added to ``pdist`` and ``cdist`` allowing the user to specify where the resulting distance matrix is to be stored `scipy.stats` improvements -------------------------- The methods ``cdf`` and ``logcdf`` were added to `scipy.stats.multivariate_normal`, providing the cumulative distribution function of the multivariate normal distribution. New statistical distance functions were added, namely `scipy.stats.wasserstein_distance` for the first Wasserstein distance and `scipy.stats.energy_distance` for the energy distance. Deprecated features =================== The following functions in `scipy.misc` are deprecated: ``bytescale``, ``fromimage``, ``imfilter``, ``imread``, ``imresize``, ``imrotate``, ``imsave``, ``imshow`` and ``toimage``. Most of those functions have unexpected behavior (like rescaling and type casting image data without the user asking for that). Other functions simply have better alternatives. ``scipy.interpolate.interpolate_wrapper`` and all functions in that submodule are deprecated. This was a never finished set of wrapper functions which is not relevant anymore. The ``fillvalue`` of `scipy.signal.convolve2d` will be cast directly to the dtypes of the input arrays in the future and checked that it is a scalar or an array with a single element. Backwards incompatible changes ============================== The following deprecated functions have been removed from `scipy.stats`: ``betai``, ``chisqprob``, ``f_value``, ``histogram``, ``histogram2``, ``pdf_fromgamma``, ``signaltonoise``, ``square_of_sums``, ``ss`` and ``threshold``. The following deprecated functions have been removed from `scipy.stats.mstats`: ``betai``, ``f_value_wilks_lambda``, ``signaltonoise`` and ``threshold``. The deprecated ``a`` and ``reta`` keywords have been removed from `scipy.stats.shapiro`. The deprecated functions ``sparse.csgraph.cs_graph_components`` and ``sparse.linalg.symeig`` have been removed from `scipy.sparse`. The following deprecated keywords have been removed in `scipy.sparse.linalg`: ``drop_tol`` from ``splu``, and ``xtype`` from ``bicg``, ``bicgstab``, ``cg``, ``cgs``, ``gmres``, ``qmr`` and ``minres``. The deprecated functions ``expm2`` and ``expm3`` have been removed from `scipy.linalg`. The deprecated keyword ``q`` was removed from `scipy.linalg.expm`. And the deprecated submodule ``linalg.calc_lwork`` was removed. The deprecated functions ``C2K``, ``K2C``, ``F2C``, ``C2F``, ``F2K`` and ``K2F`` have been removed from `scipy.constants`. The deprecated ``ppform`` class was removed from `scipy.interpolate`. The deprecated keyword ``iprint`` was removed from `scipy.optimize.fmin_cobyla`. The default value for the ``zero_phase`` keyword of `scipy.signal.decimate` has been changed to True. The ``kmeans`` and ``kmeans2`` functions in `scipy.cluster.vq` changed the method used for random initialization, so using a fixed random seed will not necessarily produce the same results as in previous versions. `scipy.special.gammaln` does not accept complex arguments anymore. The deprecated functions ``sph_jn``, ``sph_yn``, ``sph_jnyn``, ``sph_in``, ``sph_kn``, and ``sph_inkn`` have been removed. Users should instead use the functions ``spherical_jn``, ``spherical_yn``, ``spherical_in``, and ``spherical_kn``. Be aware that the new functions have different signatures. The cross-class properties of `scipy.signal.lti` systems have been removed. The following properties/setters have been removed: Name - (accessing/setting has been removed) - (setting has been removed) * StateSpace - (``num``, ``den``, ``gain``) - (``zeros``, ``poles``) * TransferFunction (``A``, ``B``, ``C``, ``D``, ``gain``) - (``zeros``, ``poles``) * ZerosPolesGain (``A``, ``B``, ``C``, ``D``, ``num``, ``den``) - () ``signal.freqz(b, a)`` with ``b`` or ``a`` >1-D raises a ``ValueError``. This was a corner case for which it was unclear that the behavior was well-defined. The method ``var`` of `scipy.stats.dirichlet` now returns a scalar rather than an ndarray when the length of alpha is 1. Other changes ============= SciPy now has a formal governance structure. It consists of a BDFL (Pauli Virtanen) and a Steering Committee. See `the governance document <https://github.com/scipy/scipy/blob/master/doc/source/dev/governance/governance.rst>`_ for details. It is now possible to build SciPy on Windows with MSVC + gfortran! Continuous integration has been set up for this build configuration on Appveyor, building against OpenBLAS. Continuous integration for OS X has been set up on TravisCI. The SciPy test suite has been migrated from ``nose`` to ``pytest``. ``scipy/_distributor_init.py`` was added to allow redistributors of SciPy to add custom code that needs to run when importing SciPy (e.g. checks for hardware, DLL search paths, etc.). Support for PEP 518 (specifying build system requirements) was added - see ``pyproject.toml`` in the root of the SciPy repository. In order to have consistent function names, the function ``scipy.linalg.solve_lyapunov`` is renamed to `scipy.linalg.solve_continuous_lyapunov`. The old name is kept for backwards-compatibility. Authors ======= * arcady + * xoviat + * Anton Akhmerov * Dominic Antonacci + * Alessandro Pietro Bardelli * Ved Basu + * Michael James Bedford + * Ray Bell + * Juan M. Bello-Rivas + * Sebastian Berg * Felix Berkenkamp * Jyotirmoy Bhattacharya + * Matthew Brett * Jonathan Bright * Bruno Jiménez + * Evgeni Burovski * Patrick Callier * Mark Campanelli + * CJ Carey * Adam Cox + * Michael Danilov + * David Haberthür + * Andras Deak + * Philip DeBoer * Anne-Sylvie Deutsch * Cathy Douglass + * Dominic Else + * Guo Fei + * Roman Feldbauer + * Yu Feng * Jaime Fernandez del Rio * Orestis Floros + * David Freese + * Adam Geitgey + * James Gerity + * Dezmond Goff + * Christoph Gohlke * Ralf Gommers * Dirk Gorissen + * Matt Haberland + * David Hagen + * Charles Harris * Lam Yuen Hei + * Jean Helie + * Gaute Hope + * Guillaume Horel + * Franziska Horn + * Yevhenii Hyzyla + * Vladislav Iakovlev + * Marvin Kastner + * Mher Kazandjian * Thomas Keck * Adam Kurkiewicz + * Ronan Lamy + * J.L. Lanfranchi + * Eric Larson * Denis Laxalde * Gregory R. Lee * Felix Lenders + * Evan Limanto * Julian Lukwata + * François Magimel * Syrtis Major + * Charles Masson + * Nikolay Mayorov * Tobias Megies * Markus Meister + * Roman Mirochnik + * Jordi Montes + * Nathan Musoke + * Andrew Nelson * M.J. Nichol * Nico Schlömer + * Juan Nunez-Iglesias * Arno Onken + * Dima Pasechnik + * Ashwin Pathak + * Stefan Peterson * Ilhan Polat * Andrey Portnoy + * Ravi Kumar Prasad + * Aman Pratik * Eric Quintero * Vedant Rathore + * Tyler Reddy * Joscha Reimer * Philipp Rentzsch + * Antonio Horta Ribeiro * Ned Richards + * Kevin Rose + * Benoit Rostykus + * Matt Ruffalo + * Eli Sadoff + * Pim Schellart * Klaus Sembritzki + * Nikolay Shebanov + * Jonathan Tammo Siebert * Scott Sievert * Max Silbiger + * Mandeep Singh + * Michael Stewart + * Jonathan Sutton + * Deep Tavker + * Martin Thoma * James Tocknell + * Aleksandar Trifunovic + * Paul van Mulbregt + * Jacob Vanderplas * Aditya Vijaykumar * Pauli Virtanen * James Webber * Warren Weckesser * Eric Wieser + * Josh Wilson * Zhiqing Xiao + * Evgeny Zhurko * Nikolay Zinov + * Zé Vinícius + A total of 118 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. ``` ### 1.0.0b1 ``` *This is the beta release for SciPy 1.0.0* ```

Links

- PyPI: https://pypi.python.org/pypi/scipy - Changelog: https://pyup.io/changelogs/scipy/ - Repo: https://github.com/scipy/scipy/releases - Homepage: https://www.scipy.org

ClimateImpactLab / DataFS

Update scipy to 1.0.1 #514