Woohoo! On Wed, Oct 25, 2017, 12:10 Charles R Harris <charlesr.har...@gmail.com> wrote:
> On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers <ralf.gomm...@gmail.com> > wrote: > >> Hi all, >> >> We are extremely pleased to announce the release of SciPy 1.0, 16 years >> after >> version 0.1 saw the light of day. It has been a long, productive journey >> to >> get here, and we anticipate many more exciting new features and releases >> in the >> future. >> >> >> Why 1.0 now? >> ------------ >> >> A version number should reflect the maturity of a project - and SciPy was >> a >> mature and stable library that is heavily used in production settings for >> a >> long time already. From that perspective, the 1.0 version number is long >> overdue. >> >> Some key project goals, both technical (e.g. Windows wheels and continuous >> integration) and organisational (a governance structure, code of conduct >> and a >> roadmap), have been achieved recently. >> >> Many of us are a bit perfectionist, and therefore are reluctant to call >> something "1.0" because it may imply that it's "finished" or "we are 100% >> happy >> with it". This is normal for many open source projects, however that >> doesn't >> make it right. We acknowledge to ourselves that it's not perfect, and >> there >> are some dusty corners left (that will probably always be the case). >> Despite >> that, SciPy is extremely useful to its users, on average has high quality >> code >> and documentation, and gives the stability and backwards compatibility >> guarantees that a 1.0 label imply. >> >> >> Some history and perspectives >> ----------------------------- >> >> - 2001: the first SciPy release >> - 2005: transition to NumPy >> - 2007: creation of scikits >> - 2008: scipy.spatial module and first Cython code added >> - 2010: moving to a 6-monthly release cycle >> - 2011: SciPy development moves to GitHub >> - 2011: Python 3 support >> - 2012: adding a sparse graph module and unified optimization interface >> - 2012: removal of scipy.maxentropy >> - 2013: continuous integration with TravisCI >> - 2015: adding Cython interface for BLAS/LAPACK and a benchmark suite >> - 2017: adding a unified C API with scipy.LowLevelCallable; removal of >> scipy.weave >> - 2017: SciPy 1.0 release >> >> >> **Pauli Virtanen** is SciPy's Benevolent Dictator For Life (BDFL). He >> says: >> >> *Truthfully speaking, we could have released a SciPy 1.0 a long time ago, >> so I'm >> happy we do it now at long last. The project has a long history, and >> during the >> years it has matured also as a software project. I believe it has well >> proved >> its merit to warrant a version number starting with unity.* >> >> *Since its conception 15+ years ago, SciPy has largely been written by >> and for >> scientists, to provide a box of basic tools that they need. Over time, >> the set >> of people active in its development has undergone some rotation, and we >> have >> evolved towards a somewhat more systematic approach to development. >> Regardless, >> this underlying drive has stayed the same, and I think it will also >> continue >> propelling the project forward in future. This is all good, since not long >> after 1.0 comes 1.1.* >> >> **Travis Oliphant** is one of SciPy's creators. He says: >> >> *I'm honored to write a note of congratulations to the SciPy developers >> and the >> entire SciPy community for the release of SciPy 1.0. This release >> represents >> a dream of many that has been patiently pursued by a stalwart group of >> pioneers >> for nearly 2 decades. Efforts have been broad and consistent over that >> time >> from many hundreds of people. From initial discussions to efforts >> coding and >> packaging to documentation efforts to extensive conference and community >> building, the SciPy effort has been a global phenomenon that it has been a >> privilege to participate in.* >> >> *The idea of SciPy was already in multiple people’s minds in 1997 when I >> first >> joined the Python community as a young graduate student who had just >> fallen in >> love with the expressibility and extensibility of Python. The internet >> was >> just starting to bringing together like-minded mathematicians and >> scientists in >> nascent electronically-connected communities. In 1998, there was a >> concerted >> discussion on the matrix-SIG, python mailing list with people like Paul >> Barrett, Joe Harrington, Perry Greenfield, Paul Dubois, Konrad Hinsen, >> David >> Ascher, and others. This discussion encouraged me in 1998 and 1999 to >> procrastinate my PhD and spend a lot of time writing extension modules to >> Python that mostly wrapped battle-tested Fortran and C-code making it >> available >> to the Python user. This work attracted the help of others like Robert >> Kern, >> Pearu Peterson and Eric Jones who joined their efforts with mine in 2000 >> so >> that by 2001, the first SciPy release was ready. This was long before >> Github >> simplified collaboration and input from others and the "patch" command and >> email was how you helped a project improve.* >> >> *Since that time, hundreds of people have spent an enormous amount of time >> improving the SciPy library and the community surrounding this library has >> dramatically grown. I stopped being able to participate actively in >> developing >> the SciPy library around 2010. Fortunately, at that time, Pauli Virtanen >> and >> Ralf Gommers picked up the pace of development supported by dozens of >> other key >> contributors such as David Cournapeau, Evgeni Burovski, Josef Perktold, >> and >> Warren Weckesser. While I have only been able to admire the development >> of >> SciPy from a distance for the past 7 years, I have never lost my love of >> the >> project and the concept of community-driven development. I remain >> driven >> even now by a desire to help sustain the development of not only the SciPy >> library but many other affiliated and related open-source projects. I am >> extremely pleased that SciPy is in the hands of a world-wide community of >> talented developers who will ensure that SciPy remains an example of how >> grass-roots, community-driven development can succeed.* >> >> **Fernando Perez** offers a wider community perspective: >> >> *The existence of a nascent Scipy library, and the incredible --if tiny by >> today's standards-- community surrounding it is what drew me into the >> scientific Python world while still a physics graduate student in 2001. >> Today, >> I am awed when I see these tools power everything from high school >> education to >> the research that led to the 2017 Nobel Prize in physics.* >> >> *Don't be fooled by the 1.0 number: this project is a mature cornerstone >> of the >> modern scientific computing ecosystem. I am grateful for the many who >> have >> made it possible, and hope to be able to contribute again to it in the >> future. >> My sincere congratulations to the whole team!* >> >> >> Highlights of this release >> -------------------------- >> >> 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. >> >> >> Upgrading and compatibility >> --------------------------- >> >> There have been a number of deprecations and API changes in this release, >> which >> are documented below. 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). >> >> 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. >> >> ``scipy.spatial.distance.matching`` is deprecated. It is an alias of >> `scipy.spatial.distance.hamming`, which should be used instead. >> >> Implementation of `scipy.spatial.distance.wminkowski` was based on a wrong >> interpretation of the metric definition. In scipy 1.0 it has been just >> deprecated in the documentation to keep retro-compatibility but is >> recommended >> to use the new version of `scipy.spatial.distance.minkowski` that >> implements >> the correct behaviour. >> >> Positional arguments of `scipy.spatial.distance.pdist` and >> `scipy.spatial.distance.cdist` should be replaced with their keyword >> version. >> >> >> 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 >> * Robert Cimrman >> * 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 >> * Juan Nunez-Iglesias >> * Arno Onken + >> * Nick Papior + >> * Dima Pasechnik + >> * Ashwin Pathak + >> * Oleksandr Pavlyk + >> * 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 >> * Nico Schlömer + >> * 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 121 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. >> >> >> Cheers, >> Ralf >> >> > Congratulations to all. SciPy provides wonderful tools that are free for > all to use. That those tools are available, and easily installed, is a > great boon to many who would otherwise be at a disadvantage for lack of > money or access; that, in itself, will have a major impact. > > Chuck > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@python.org > https://mail.python.org/mailman/listinfo/numpy-discussion >
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