SciPy 1.0 released!

[Paul Dubois]

The DNA of this work goes much further back. After some discussion as
mentioned, Jim Hugunin wrote a numerical extension (called Numerical) and
after a bit I took over as its coordinator with financial support for my
work from Lawrence Livermore National Laboratory. They also supported the
Foundation. I do not remember the exact timing but certainly Numerical was
running before the 4th International was held at the Lab in the early 90s.
Guido put in the complex type and other things to help us. We had endless
discussion amongst us as how to spell it: 1i or 1j!

One should note that the Lab was breaking new ground in supporting an open
source project. SciPy was born to try to improve and extend a product that
was already crucial to a lot of people. Indeed, it is a big part of several
ongoing projects. Even non-numerical applications are important there.

I retired in 2005, and everyone who writes software knows that what they do
is ephemeral, but I don’t want history to be lost so soon.

Paul Dubois
... moving as we speak to La Mesa, CA



On Wed, Oct 25, 2017 at 5:05 AM Ralf Gommers <ralf.gommers at 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
> --
> https://mail.python.org/mailman/listinfo/python-announce-list
>
>         Support the Python Software Foundation:
>         http://www.python.org/psf/donations/
>