[SciPy-User] finite elements tools in python
Guillaume Gay
guillaume at damcb.com
Mon Dec 11 07:27:55 EST 2017
Hi,
Have you tried using the conda-forge channel, ie
conda install -c conda-forge sfepy
It is often more up-to-date than the base channel.
Best
Guillaume
Le 11/12/2017 à 12:11, Kai Lähteenmäki a écrit :
> Hi,
> I'm interested in FEM -programs (since 70')
> Which Python FEM program is easy to install?
> I tried to install SfePy on Anaconda3, but it failed?
> I'm novise on Python and Anaconda, I have used SciPy some months though.
> Thanks for help,
> regards,
> Kai
>
>
> 2017-10-25 20:09 GMT+03:00 Charles R Harris <charlesr.harris at gmail.com
> <mailto:charlesr.harris at gmail.com>>:
>
>
>
> On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers
> <ralf.gommers at gmail.com <mailto: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
> <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
>
> _______________________________________________
> SciPy-User mailing list
> SciPy-User at python.org <mailto:SciPy-User at python.org>
> https://mail.python.org/mailman/listinfo/scipy-user
> <https://mail.python.org/mailman/listinfo/scipy-user>
>
>
>
>
> _______________________________________________
> SciPy-User mailing list
> SciPy-User at python.org
> https://mail.python.org/mailman/listinfo/scipy-user
--
Guillaume Gay, PhD
Morphgénie Logiciels SAS
http://morphogenie.fr
12 rue Camoin Jeune
13004 Marseille
+336 51 95 94 00
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