Congrats everybody!
2017-10-25 12:14 GMT+02:00 Ralf Gommers <ralf.gomm...@gmail.com>: > 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 > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion@python.org > https://mail.python.org/mailman/listinfo/numpy-discussion > > -- Francesc Alted
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