From renaud.geoffroy at univ-lr.fr Tue Dec 5 03:32:03 2017 From: renaud.geoffroy at univ-lr.fr (Renaud Geoffroy) Date: Tue, 5 Dec 2017 09:32:03 +0100 Subject: [SciPy-User] Help about a function on Python - Renaud GEOFFROY Message-ID: <0241302b-42bb-02e0-c1d0-13046d65dd07@univ-lr.fr> Hello, my name's Renaud Geoffroy and I'm a PhD in a laboratory named "LaSIE" at La Rochelle, France. My subject is about the use of rainwater on a roof as a passive cooling for builidings. I'm working on Python on a simplified model to represent the roof temperatures, coupled itself with a simplified model of building modelizing. I resolve the differential equation with the function "scipy.integrate.odeint". The issue appeared when I integrate the building model in the core module : instead of resolving the equations on all the time period, my program "stops" way before. No error but no results on all the time period. I don't know how to resolve it because perhaps it concerns the source code of the function "odeint". Yours faithfully, Renaud GEOFFROY From guillaume at damcb.com Tue Dec 5 03:35:58 2017 From: guillaume at damcb.com (Guillaume Gay) Date: Tue, 05 Dec 2017 09:35:58 +0100 Subject: [SciPy-User] Help about a function on Python - Renaud GEOFFROY In-Reply-To: <0241302b-42bb-02e0-c1d0-13046d65dd07@univ-lr.fr> References: <0241302b-42bb-02e0-c1d0-13046d65dd07@univ-lr.fr> Message-ID: <8FA5EA63-2C7B-4AED-BF9C-DA8D796AA3EB@damcb.com> Hi Renaud, Can you share your code somewhere, or try to reproduce your issue with a simplified code? It is hard to help you with your description only Best Guillaume Le 5 d?cembre 2017 09:32:03 GMT+01:00, Renaud Geoffroy a ?crit : >Hello, my name's Renaud Geoffroy and I'm a PhD in a laboratory named >"LaSIE" at La Rochelle, France. My subject is about the use of >rainwater on a roof as a passive cooling for builidings. I'm working on >Python on a simplified model to represent the roof temperatures, >coupled itself >with a simplified model of building modelizing. I resolve the >differential equation with the function "scipy.integrate.odeint". The >issue appeared when I integrate the building model in the core module : >instead of resolving the equations on all the time period, my program >"stops" way before. No error but no results on all the time period. I >don't know how to resolve it because perhaps it concerns the source >code of the function "odeint". > >Yours faithfully, > >Renaud GEOFFROY > >_______________________________________________ >SciPy-User mailing list >SciPy-User at python.org >https://mail.python.org/mailman/listinfo/scipy-user -- Morphog?nie Logiciels 12 rue Camoin Jeune, 13004 Marseille. +33 651 95 94 00 -------------- next part -------------- An HTML attachment was scrubbed... URL: From chimmulas at usgs.gov Wed Dec 6 14:30:50 2017 From: chimmulas at usgs.gov (Chimmula, Sumani) Date: Wed, 6 Dec 2017 13:30:50 -0600 Subject: [SciPy-User] calculating 3D surface elevation volume difference Message-ID: I'm trying to calculate difference between two interpolated grids. The grids are irregular and of different shapes, so cannot use np.subtract to calculate the difference. Any help on how to calculate the difference? Another important information is these are spatial grids with overlapping spatial extents. If we just broadcast/extend array shapes, would that be enough? I do not want to subtract the grids at wrong x/y locations. So basically like in GIS/Arcmap how we calculate raster difference at each cell at a particular xy cell location. #create two interpolated grids from two set of xyz points and calculate difference ixx = np.array(self.ix) iyy = np.array(self.iy) izz = np.array(self.iz) iminx = min(ixx.flat) imaxx = max(ixx.flat) iminy = min(iyy.flat) imaxy = max(iyy.flat) # post surface - get extents pxx = np.array(self.px) pyy = np.array(self.py) pzz = np.array(self.pz) pminx = min(pxx.flat) pmaxx = max(pxx.flat) pminy = min(pyy.flat) pmaxy = max(pyy.flat) ixi = np.arange(iminx, imaxx, self.cellsize) iyi = np.arange(iminy, imaxy, self.cellsize) iX,iY = np.meshgrid(ixi,iyi) iextent = (min(ixi), max(ixi), min(iyi), max(iyi)) pxi = np.arange(pminx, pmaxx, self.cellsize) pyi = np.arange(pminy, pmaxy, self.cellsize) pX,pY = np.meshgrid(pxi,pyi) pextent = (min(pxi), max(pxi), min(pyi), max(pyi)) igrid = griddata((ixx, iyy), izz, (iX, iY), method='linear') pgrid = griddata((pxx, pyy), pzz, (pX, pY), method='linear') # would like to calcualte difference, but this wont work, due to different shapes changegrid = np.subtract(pgrid, igrid) igrid shape is (181, 130), pgrid shape is (184, 126). Thanks. From stevenbocco at gmail.com Thu Dec 7 08:23:30 2017 From: stevenbocco at gmail.com (Steven Bocco) Date: Thu, 7 Dec 2017 08:23:30 -0500 Subject: [SciPy-User] Announcing Theano 1.0.1 Message-ID: Announcing Theano 1.0.1 This is a maintenance release of Theano, version 1.0.1, with no new features, but some important bug fixes. Upgrading to Theano 1.0.1 is recommended for everyone. For those using the bleeding edge version in the git repository, we encourage you to update to the rel-1.0.1 tag. What's New Highlights (since 1.0.0): - Fixed compilation and improved float16 support for topK on GPU - *NB*: topK support on GPU is experimental and may not work for large input sizes on certain GPUs - Fixed cuDNN reductions when axes to reduce have size 1 - Attempted to prevent re-initialization of the GPU in a child process - Fixed support for temporary paths with spaces in Theano initialization - Spell check pass on the documentation Download and Install You can download Theano from http://pypi.python.org/pypi/Theano Installation instructions are available at http://deeplearning.net/software/theano/install.html Description Theano is a Python library that allows you to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. It is built on top of NumPy. Theano features: - tight integration with NumPy: a similar interface to NumPy's. numpy.ndarrays are also used internally in Theano-compiled functions. - transparent use of a GPU: perform data-intensive computations much faster than on a CPU. - efficient symbolic differentiation: Theano can compute derivatives for functions of one or many inputs. - speed and stability optimizations: avoid nasty bugs when computing expressions such as log(1+ exp(x)) for large values of x. - dynamic C code generation: evaluate expressions faster. - extensive unit-testing and self-verification: includes tools for detecting and diagnosing bugs and/or potential problems. Theano has been powering large-scale computationally intensive scientific research since 2007, but it is also approachable enough to be used in the classroom (IFT6266 at the University of Montreal). Resources About Theano: http://deeplearning.net/software/theano/ Theano-related projects: http://github.com/Theano/Theano/wiki/Related-projects About NumPy: http://numpy.scipy.org/ About SciPy: http://www.scipy.org/ Machine Learning Tutorial with Theano on Deep Architectures: http://deeplearning.net/tutorial/ Acknowledgments I would like to thank all contributors of Theano. Since release 1.0.0, many people have helped, notably (in alphabetical order): - Arnaud Bergeron - Edward Betts - Frederic Bastien - Sam Johnson - Simon Lefrancois - Steven Bocco Also, thank you to all NumPy and Scipy developers as Theano builds on their strengths. All questions/comments are always welcome on the Theano mailing-lists ( http://deeplearning.net/software/theano/#community ) -- Steven Bocco -------------- next part -------------- An HTML attachment was scrubbed... URL: From larry.martell at gmail.com Fri Dec 8 22:13:29 2017 From: larry.martell at gmail.com (Larry Martell) Date: Sat, 09 Dec 2017 03:13:29 +0000 Subject: [SciPy-User] install problem In-Reply-To: References: Message-ID: Trying to install scipy on ubuntu-trusty-64 running Python 2.7.6. It's failing with: $ sudo pip install scipy Downloading/unpacking scipy Downloading scipy-1.0.0.tar.gz (15.2MB): 15.2MB downloaded Running setup.py (path:/tmp/pip_build_root/scipy/setup.py) egg_info for package scipy /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires' Followed by many screens full of errors. Is that just a warning or is that the issue? I've installed many other packages without a problem on this same system. What is the issue here? -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Fri Dec 8 23:25:41 2017 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Sat, 9 Dec 2017 17:25:41 +1300 Subject: [SciPy-User] install problem In-Reply-To: References: Message-ID: On Sat, Dec 9, 2017 at 4:13 PM, Larry Martell wrote: > > Trying to install scipy on ubuntu-trusty-64 running Python 2.7.6. It's > failing with: > > $ sudo pip install scipy > "sudo pip" is a bad idea, you're installing to the same place that your package manager installs things to. If you want to install from source for a Python installed by APT, use `pip install scipy --user`. Downloading/unpacking scipy > Downloading scipy-1.0.0.tar.gz (15.2MB): 15.2MB downloaded > Running setup.py (path:/tmp/pip_build_root/scipy/setup.py) egg_info > for package scipy > /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown > distribution option: 'python_requires' > This is just a warning, not an error. We cannot tell what is wrong from that. Please provide a full build log, preferably as a gist. Cheers, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Sat Dec 9 04:37:19 2017 From: matthew.brett at gmail.com (Matthew Brett) Date: Sat, 9 Dec 2017 09:37:19 +0000 Subject: [SciPy-User] install problem In-Reply-To: References: Message-ID: Hi, On Sat, Dec 9, 2017 at 4:25 AM, Ralf Gommers wrote: > > > On Sat, Dec 9, 2017 at 4:13 PM, Larry Martell > wrote: >> >> >> Trying to install scipy on ubuntu-trusty-64 running Python 2.7.6. It's >> failing with: >> >> $ sudo pip install scipy > > > "sudo pip" is a bad idea, you're installing to the same place that your > package manager installs things to. If you want to install from source for a > Python installed by APT, use `pip install scipy --user`. > >> Downloading/unpacking scipy >> Downloading scipy-1.0.0.tar.gz (15.2MB): 15.2MB downloaded >> Running setup.py (path:/tmp/pip_build_root/scipy/setup.py) egg_info >> for package scipy >> /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown >> distribution option: 'python_requires' > > > This is just a warning, not an error. We cannot tell what is wrong from > that. Please provide a full build log, preferably as a gist. Also - I suspect you have a really old version of pip - because it doesn't recognize 'python_requires' and is not downloading the binary wheel. Your life would be much easier if you reinstall pip with: wget https://bootstrap.pypa.io/get-pip.py python get-pip.py --user Then make sure that $HOME/.local/bin is on your path and hash -r to make sure that you get the new pip command. Cheers, Matthew From guillaume at damcb.com Sat Dec 9 05:43:50 2017 From: guillaume at damcb.com (Guillaume Gay) Date: Sat, 9 Dec 2017 11:43:50 +0100 Subject: [SciPy-User] install problem In-Reply-To: References: Message-ID: Also, it should be pointed out at that point that python 2.7 will not be supported long, so if you have the option on that machine (which should be the case if you are a sudoer), prefer a python 3.6 install, it will play out much better in the long run. You might also want to have a look at the conda package manager... Best, Guillaume Le 09/12/2017 ? 10:37, Matthew Brett a ?crit?: > Hi, > > On Sat, Dec 9, 2017 at 4:25 AM, Ralf Gommers wrote: >> >> On Sat, Dec 9, 2017 at 4:13 PM, Larry Martell >> wrote: >>> >>> Trying to install scipy on ubuntu-trusty-64 running Python 2.7.6. It's >>> failing with: >>> >>> $ sudo pip install scipy >> >> "sudo pip" is a bad idea, you're installing to the same place that your >> package manager installs things to. If you want to install from source for a >> Python installed by APT, use `pip install scipy --user`. >> >>> Downloading/unpacking scipy >>> Downloading scipy-1.0.0.tar.gz (15.2MB): 15.2MB downloaded >>> Running setup.py (path:/tmp/pip_build_root/scipy/setup.py) egg_info >>> for package scipy >>> /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown >>> distribution option: 'python_requires' >> >> This is just a warning, not an error. We cannot tell what is wrong from >> that. Please provide a full build log, preferably as a gist. > Also - I suspect you have a really old version of pip - because it > doesn't recognize 'python_requires' and is not downloading the binary > wheel. Your life would be much easier if you reinstall pip with: > > wget https://bootstrap.pypa.io/get-pip.py > python get-pip.py --user > > Then make sure that $HOME/.local/bin is on your path and > > hash -r > > to make sure that you get the new pip command. > > Cheers, > > Matthew > _______________________________________________ > SciPy-User mailing list > SciPy-User at python.org > https://mail.python.org/mailman/listinfo/scipy-user > -- Guillaume Gay, PhD Morphg?nie Logiciels SAS http://morphogenie.fr 12 rue Camoin Jeune 13004 Marseille +336 51 95 94 00 From larry.martell at gmail.com Sat Dec 9 11:14:36 2017 From: larry.martell at gmail.com (Larry Martell) Date: Sat, 9 Dec 2017 11:14:36 -0500 Subject: [SciPy-User] install problem In-Reply-To: References: Message-ID: On Sat, Dec 9, 2017 at 4:37 AM, Matthew Brett wrote: > Hi, > > On Sat, Dec 9, 2017 at 4:25 AM, Ralf Gommers wrote: >> >> >> On Sat, Dec 9, 2017 at 4:13 PM, Larry Martell >> wrote: >>> >>> >>> Trying to install scipy on ubuntu-trusty-64 running Python 2.7.6. It's >>> failing with: >>> >>> $ sudo pip install scipy >> >> >> "sudo pip" is a bad idea, you're installing to the same place that your >> package manager installs things to. If you want to install from source for a >> Python installed by APT, use `pip install scipy --user`. >> >>> Downloading/unpacking scipy >>> Downloading scipy-1.0.0.tar.gz (15.2MB): 15.2MB downloaded >>> Running setup.py (path:/tmp/pip_build_root/scipy/setup.py) egg_info >>> for package scipy >>> /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown >>> distribution option: 'python_requires' >> >> >> This is just a warning, not an error. We cannot tell what is wrong from >> that. Please provide a full build log, preferably as a gist. > > Also - I suspect you have a really old version of pip - because it > doesn't recognize 'python_requires' and is not downloading the binary > wheel. Your life would be much easier if you reinstall pip with: > > wget https://bootstrap.pypa.io/get-pip.py > python get-pip.py --user > > Then make sure that $HOME/.local/bin is on your path and > > hash -r > > to make sure that you get the new pip command. Thank you very much. That worked perfectly. From kai.j.lahteenmaki at gmail.com Mon Dec 11 06:11:24 2017 From: kai.j.lahteenmaki at gmail.com (=?UTF-8?B?S2FpIEzDpGh0ZWVubcOka2k=?=) Date: Mon, 11 Dec 2017 13:11:24 +0200 Subject: [SciPy-User] [Numpy-discussion] SciPy 1.0 released! In-Reply-To: References: Message-ID: 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 : > > > On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers > 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 >> > 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 Jim?nez + >> * Evgeni Burovski >> * Patrick Callier >> * Mark Campanelli + >> * CJ Carey >> * Robert Cimrman >> * Adam Cox + >> * Michael Danilov + >> * David Haberth?r + >> * 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 + >> * Fran?ois 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 Schl?mer + >> * 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 + >> * Z? Vin?cius + >> >> 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 > https://mail.python.org/mailman/listinfo/scipy-user > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guillaume at damcb.com Mon Dec 11 07:27:55 2017 From: guillaume at damcb.com (Guillaume Gay) Date: Mon, 11 Dec 2017 13:27:55 +0100 Subject: [SciPy-User] finite elements tools in python In-Reply-To: References: Message-ID: 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 ? 12:11, Kai L?hteenm?ki a ?crit?: > 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 >: > > > > On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers > > 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 > >`_ > 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 Jim?nez + > * Evgeni Burovski > * Patrick Callier > * Mark Campanelli + > * CJ Carey > * Robert Cimrman > * Adam Cox + > * Michael Danilov + > * David Haberth?r + > * 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 + > * Fran?ois 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 Schl?mer + > * 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 + > * Z? Vin?cius + > > 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 > 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 Morphg?nie Logiciels SAS http://morphogenie.fr 12 rue Camoin Jeune 13004 Marseille +336 51 95 94 00 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sandeep.nagar at gmail.com Mon Dec 11 08:11:29 2017 From: sandeep.nagar at gmail.com (Sandeep Nagar) Date: Mon, 11 Dec 2017 18:41:29 +0530 Subject: [SciPy-User] [Numpy-discussion] SciPy 1.0 released! In-Reply-To: References: Message-ID: Hi, Have you tried FEniCS ? Running in a container does not require additional installation and dependency requirements. Its book explains the working very neatly. cheers --------- My books My Amazon Author Profile Training profile: http://sandeepnagar4.wix.com/compuski Research profile: Google Scholar , Linkedin , Researchgate --------- *Dr. Sandeep Nagar * On Mon, Dec 11, 2017 at 4:41 PM, Kai L?hteenm?ki < kai.j.lahteenmaki at gmail.com> wrote: > 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 : > >> >> >> On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers >> 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 >>> >> overnance/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 Jim?nez + >>> * Evgeni Burovski >>> * Patrick Callier >>> * Mark Campanelli + >>> * CJ Carey >>> * Robert Cimrman >>> * Adam Cox + >>> * Michael Danilov + >>> * David Haberth?r + >>> * 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 + >>> * Fran?ois 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 Schl?mer + >>> * 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 + >>> * Z? Vin?cius + >>> >>> 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 >> 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From contact at nicolas-cellier.net Mon Dec 11 08:48:40 2017 From: contact at nicolas-cellier.net (Nicolas Cellier) Date: Mon, 11 Dec 2017 14:48:40 +0100 Subject: [SciPy-User] [Numpy-discussion] SciPy 1.0 released! In-Reply-To: References: Message-ID: I haven't found yet a great FDM solver "easy" to install : easier may be Sfepy, otherwise you fall to Fenics. This is a great tool but installation is not that easy. As said previously, running it with Docker make it easier. There is a conda channel too, but I have not be able to make it work yet.. Nicolas Cellier 2017-12-11 14:11 GMT+01:00 Sandeep Nagar : > Hi, > > Have you tried FEniCS ? Running in a container > does not require additional > installation and dependency requirements. Its book > explains > the working very neatly. > > cheers > > --------- > My books > My Amazon Author Profile > > Training profile: http://sandeepnagar4.wix.com/compuski > Research profile: Google Scholar > , > Linkedin , Researchgate > > --------- > *Dr. Sandeep Nagar * > > > > On Mon, Dec 11, 2017 at 4:41 PM, Kai L?hteenm?ki < > kai.j.lahteenmaki at gmail.com> wrote: > >> 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 : >> >>> >>> >>> On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers >>> 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 >>>> >>> overnance/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 Jim?nez + >>>> * Evgeni Burovski >>>> * Patrick Callier >>>> * Mark Campanelli + >>>> * CJ Carey >>>> * Robert Cimrman >>>> * Adam Cox + >>>> * Michael Danilov + >>>> * David Haberth?r + >>>> * 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 + >>>> * Fran?ois 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 Schl?mer + >>>> * 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 + >>>> * Z? Vin?cius + >>>> >>>> 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 >>> 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 >> >> > > _______________________________________________ > SciPy-User mailing list > SciPy-User at python.org > https://mail.python.org/mailman/listinfo/scipy-user > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From me at fredt.org Tue Dec 12 20:33:52 2017 From: me at fredt.org (me at fredt.org) Date: Tue, 12 Dec 2017 17:33:52 -0800 Subject: [SciPy-User] scipy.signal.spectrogram level in DB Message-ID: Hi, does anyone how to convert the power level in DB out of scipy.signal.spectrogram? I'm trying to match what I see in audacity in term of spectral power at various frequency. Thanks FredT From nicholdav at gmail.com Tue Dec 12 22:52:42 2017 From: nicholdav at gmail.com (David Nicholson) Date: Tue, 12 Dec 2017 22:52:42 -0500 Subject: [SciPy-User] scipy.signal.spectrogram level in DB In-Reply-To: References: Message-ID: I think at a very high level to convert to dB you would do: 20 * np.log10 ( your_spectrogram / np.max(your_spectrogram)) Apparently Audacity uses dBFS so to get the exact same thing as Audacity, you would need to know what Audacity thinks the maximum peak value of amplitude is and then put that in place of np.max(your_spectrogram) http://wiki.audacityteam.org/wiki/HowAudacityWorks https://en.wikipedia.org/wiki/DBFS That's my best guess but someone who knows more digital signal processing might be able to give you a better answer On Tue, Dec 12, 2017 at 8:33 PM, wrote: > Hi, does anyone how to convert the power level in DB out of > scipy.signal.spectrogram? I'm trying to match what I see in audacity in > term of spectral power at various frequency. > > Thanks > FredT > _______________________________________________ > SciPy-User mailing list > SciPy-User at python.org > https://mail.python.org/mailman/listinfo/scipy-user > -- David Nicholson, Ph.D. Sober Lab , Emory Neuroscience Program. www.nicholdav.info; https://github.com/NickleDave -------------- next part -------------- An HTML attachment was scrubbed... URL: From bnsn.babu at gmail.com Wed Dec 13 01:53:00 2017 From: bnsn.babu at gmail.com (binson babu) Date: Wed, 13 Dec 2017 12:23:00 +0530 Subject: [SciPy-User] Free Live Webinar on "How to Use Git" Message-ID: Hello, Knowing how to use Git for version control and collaboration is an essential skill to have. We are organizing a Free Live Webinar on "How to Use Git". When: 16th Dec 2017 (Timings will be announced to Registered participants soon) Where: Online, Live Webinar Fees: The webinar is completely Free Sign up using this Google Form (https://goo.gl/forms/IM6t8WJgbxU8s6to2) and you will receive further instructions (Software Requirements, Installation Help, Timings etc) as well as the final link to the Live webinar. Regards, Arjinium Team -------------- next part -------------- An HTML attachment was scrubbed... URL: From me at fredt.org Wed Dec 13 02:34:57 2017 From: me at fredt.org (me at fredt.org) Date: Tue, 12 Dec 2017 23:34:57 -0800 Subject: [SciPy-User] scipy.signal.spectrogram level in DB In-Reply-To: References: Message-ID: Thanks for your input. However, I should have been more clear, I meant the spectrum view like here: http://manual.audacityteam.org/man/plot_spectrum.html If I do a spectrogram and look at a time interval, I should be able to get the same view however, getting the same scale seems to be a challenge. Perhaps the solution is in what you provided but in this case the np.max would be a static number? On 2017-12-12 19:52, David Nicholson wrote: > I think at a very high level to convert to dB you would do: > > 20 * np.log10 ( your_spectrogram / np.max(your_spectrogram)) > > Apparently Audacity uses dBFS so to get the exact same thing as > Audacity, you would need to know what Audacity thinks the maximum peak > value of amplitude is and then put that in place of > np.max(your_spectrogram) > > http://wiki.audacityteam.org/wiki/HowAudacityWorks [2] > > https://en.wikipedia.org/wiki/DBFS [3] > > That's my best guess but someone who knows more digital signal > processing might be able to give you a better answer > > On Tue, Dec 12, 2017 at 8:33 PM, wrote: > >> Hi, does anyone how to convert the power level in DB out of >> scipy.signal.spectrogram? I'm trying to match what I see in audacity >> in term of spectral power at various frequency. >> >> Thanks >> FredT >> _______________________________________________ >> SciPy-User mailing list >> SciPy-User at python.org >> https://mail.python.org/mailman/listinfo/scipy-user [1] > > -- > > David Nicholson, Ph.D. > Sober Lab [4], Emory Neuroscience Program. [5] > > www.nicholdav.info; [6]https://github.com/NickleDave [7] > > > Links: > ------ > [1] https://mail.python.org/mailman/listinfo/scipy-user > [2] http://wiki.audacityteam.org/wiki/HowAudacityWorks > [3] https://en.wikipedia.org/wiki/DBFS > [4] http://www.biology.emory.edu/research/Sober/Home.html > [5] http://www.emory.edu/NEUROSCIENCE/ > [6] http://www.nicholdav.info > [7] https://github.com/NickleDave > > _______________________________________________ > SciPy-User mailing list > SciPy-User at python.org > https://mail.python.org/mailman/listinfo/scipy-user From kai.j.lahteenmaki at gmail.com Wed Dec 13 05:42:45 2017 From: kai.j.lahteenmaki at gmail.com (=?UTF-8?B?S2FpIEzDpGh0ZWVubcOka2k=?=) Date: Wed, 13 Dec 2017 12:42:45 +0200 Subject: [SciPy-User] [Numpy-discussion] SciPy 1.0 released! In-Reply-To: References: Message-ID: Thanks for help,but ... I think I must use ELMER etc compact special tool, I hope that SfePy and other FEM- py tools are integrated well to SciPy ? reg Kai 2017-12-11 15:48 GMT+02:00 Nicolas Cellier : > I haven't found yet a great FDM solver "easy" to install : easier may be > Sfepy, otherwise you fall to Fenics. This is a great tool but installation > is not that easy. As said previously, running it with Docker make it > easier. There is a conda channel too, but I have not be able to make it > work yet.. > > Nicolas Cellier > > 2017-12-11 14:11 GMT+01:00 Sandeep Nagar : > >> Hi, >> >> Have you tried FEniCS ? Running in a >> container does not require >> additional installation and dependency requirements. Its book >> explains >> the working very neatly. >> >> cheers >> >> --------- >> My books >> My Amazon Author Profile >> >> Training profile: http://sandeepnagar4.wix.com/compuski >> Research profile: Google Scholar >> , >> Linkedin , Researchgate >> >> --------- >> *Dr. Sandeep Nagar * >> >> >> >> On Mon, Dec 11, 2017 at 4:41 PM, Kai L?hteenm?ki < >> kai.j.lahteenmaki at gmail.com> wrote: >> >>> 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 : >>> >>>> >>>> >>>> On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers >>>> 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 >>>>> >>>> overnance/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 Jim?nez + >>>>> * Evgeni Burovski >>>>> * Patrick Callier >>>>> * Mark Campanelli + >>>>> * CJ Carey >>>>> * Robert Cimrman >>>>> * Adam Cox + >>>>> * Michael Danilov + >>>>> * David Haberth?r + >>>>> * 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 + >>>>> * Fran?ois 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 Schl?mer + >>>>> * 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 + >>>>> * Z? Vin?cius + >>>>> >>>>> 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 >>>> 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 >>> >>> >> >> _______________________________________________ >> SciPy-User mailing list >> SciPy-User at python.org >> 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmkleffner at gmail.com Wed Dec 13 07:48:44 2017 From: cmkleffner at gmail.com (Carl Kleffner) Date: Wed, 13 Dec 2017 13:48:44 +0100 Subject: [SciPy-User] [Numpy-discussion] SciPy 1.0 released! In-Reply-To: References: Message-ID: You may take a look at: (not limited for python) What_is_the_best_open_source_finite_element_software_for_mechanical_problems for EM (2D) there is Agros2d or FreeFem++ that is scriptable to some extend by python. Carl 2017-12-13 11:42 GMT+01:00 Kai L?hteenm?ki : > Thanks for help,but ... > I think I must use ELMER etc compact special tool, > I hope that SfePy and other FEM- py tools are integrated well to SciPy ? > reg Kai > > 2017-12-11 15:48 GMT+02:00 Nicolas Cellier : > >> I haven't found yet a great FDM solver "easy" to install : easier may be >> Sfepy, otherwise you fall to Fenics. This is a great tool but installation >> is not that easy. As said previously, running it with Docker make it >> easier. There is a conda channel too, but I have not be able to make it >> work yet.. >> >> Nicolas Cellier >> >> 2017-12-11 14:11 GMT+01:00 Sandeep Nagar : >> >>> Hi, >>> >>> Have you tried FEniCS ? Running in a >>> container does not require >>> additional installation and dependency requirements. Its book >>> explains >>> the working very neatly. >>> >>> cheers >>> >>> --------- >>> My books >>> My Amazon Author Profile >>> >>> Training profile: http://sandeepnagar4.wix.com/compuski >>> Research profile: Google Scholar >>> , >>> Linkedin , Researchgate >>> >>> --------- >>> *Dr. Sandeep Nagar * >>> >>> >>> >>> On Mon, Dec 11, 2017 at 4:41 PM, Kai L?hteenm?ki < >>> kai.j.lahteenmaki at gmail.com> wrote: >>> >>>> 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 >>>> : >>>> >>>>> >>>>> >>>>> On Wed, Oct 25, 2017 at 4:14 AM, Ralf Gommers >>>>> 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 >>>>>> >>>>> overnance/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 Jim?nez + >>>>>> * Evgeni Burovski >>>>>> * Patrick Callier >>>>>> * Mark Campanelli + >>>>>> * CJ Carey >>>>>> * Robert Cimrman >>>>>> * Adam Cox + >>>>>> * Michael Danilov + >>>>>> * David Haberth?r + >>>>>> * 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 + >>>>>> * Fran?ois 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 Schl?mer + >>>>>> * 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 + >>>>>> * Z? Vin?cius + >>>>>> >>>>>> 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 >>>>> 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 >>>> >>>> >>> >>> _______________________________________________ >>> SciPy-User mailing list >>> SciPy-User at python.org >>> 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 >> >> > > _______________________________________________ > SciPy-User mailing list > SciPy-User at python.org > https://mail.python.org/mailman/listinfo/scipy-user > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Wed Dec 13 17:54:17 2017 From: charlesr.harris at gmail.com (Charles R Harris) Date: Wed, 13 Dec 2017 15:54:17 -0700 Subject: [SciPy-User] NumPy 1.14.0rc1 release Message-ID: Hi All, On behalf of the NumPy team, I am pleased to announce NumPy 1.14.0rc1. Numpy 1.14.0rc1 is the result of seven months of work and contains a large number of bug fixes and new features, along with several changes with potential compatibility issues. The major change that users will notice are the stylistic changes in the way numpy arrays and scalars are printed, a change that will affect doctests. See the release notes for details on how to preserve the old style printing when needed. A major decision affecting future development concerns the schedule for dropping Python 2.7 support in the runup to 2020. The decision has been made to support 2.7 for all releases made in 2018, with the last release being designated a long term release with support for bug fixes extending through the end of 2019. Starting from January, 2019 support for 2.7 will be dropped in all new releases. More details can be found in the relevant NEP . This release supports Python 2.7 and 3.4 - 3.6. Wheels for the pre-release are available on PyPI. Source tarballs, zipfiles, release notes, and the changelog are available on github . *Highlights* - The ``np.einsum`` function uses BLAS when possible - ``genfromtxt``, ``loadtxt``, ``fromregex`` and ``savetxt`` can now handle files with arbitrary Python supported encoding. - Major improvements to printing of NumPy arrays and scalars. *New functions* - ``parametrize``: decorator added to numpy.testing - ``chebinterpolate``: Interpolate function at Chebyshev points. - ``format_float_positional`` and ``format_float_scientific`` : format floating-point scalars unambiguously with control of rounding and padding. - ``PyArray_ResolveWritebackIfCopy`` and ``PyArray_SetWritebackIfCopyBase``, new C-API functions useful in achieving PyPy compatibity. *Contributors* A total of 101 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Alexey Brodkin + - Allan Haldane - Andras Deak + - Andrew Lawson + - Antoine Pitrou - Bernhard M. Wiedemann + - Bob Eldering + - Brandon Carter - CJ Carey - Charles Harris - Chris Lamb - Christoph Boeddeker + - Christoph Gohlke - Daniel Hrisca + - Daniel Smith - Danny Hermes - David Freese - David Hagen - David Linke + - David Schaefer + - Dillon Niederhut + - Egor Panfilov + - Emilien Kofman - Eric Wieser - Erik Bray + - Erik Quaeghebeur + - Garry Polley + - Gunjan + - Henke Adolfsson + - Hidehiro NAGAOKA + - Hong Xu + - Iryna Shcherbina + - Jaime Fernandez - James Bourbeau + - Jamie Townsend + - Jarrod Millman - Jean Helie + - Jeroen Demeyer + - John Goetz + - John Kirkham - John Zwinck - Jonathan Helmus - Joseph Fox-Rabinovitz - Joseph Paul Cohen + - Joshua Leahy + - Julian Taylor - J?rg D?pfert + - Keno Goertz + - Kevin Sheppard + - Kexuan Sun + - Konrad Kapp + - Kristofor Maynard + - Licht Takeuchi + - Lo?c Est?ve - Lukas Mericle + - Marten van Kerkwijk - Matheus Portela + - Matthew Brett - Matti Picus - Michael Lamparski + - Michael Odintsov + - Michael Schnaitter + - Michael Seifert - Mike Nolta - Nathaniel J. Smith - Nelle Varoquaux + - Nicholas Del Grosso + - Nico Schl?mer + - Oleg Zabluda + - Oleksandr Pavlyk - Pauli Virtanen - Pim de Haan + - Ralf Gommers - Robert T. McGibbon + - Roland Kaufmann - Sebastian Berg - Serhiy Storchaka + - Shitian Ni + - Spencer Hill + - Srinivas Reddy Thatiparthy + - Stefan Winkler + - Stephan Hoyer - Steven Maude + - SuperBo + - Thomas K?ppe + - Toon Verstraelen - Vedant Misra + - Warren Weckesser - Wirawan Purwanto + - Yang Li + - Ziyan + - chaoyu3 + - hemildesai + - k_kapp at yahoo.com + - nickdg + - orbit-stabilizer + - schnaitterm + - solarjoe - wufangjie + - xoviat + - ?lie Gouzien + Enjoy, Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From chris.barker at noaa.gov Thu Dec 14 12:15:58 2017 From: chris.barker at noaa.gov (Chris Barker - NOAA Federal) Date: Thu, 14 Dec 2017 09:15:58 -0800 Subject: [SciPy-User] [Numpy-discussion] NumPy 1.14.0rc1 release In-Reply-To: References: Message-ID: <-5551096436323765362@unknownmsgid> Thanks Chuck! And a huge thanks to that awesome list of contributors!!! -Chris Sent from my iPhone On Dec 13, 2017, at 2:55 PM, Charles R Harris wrote: Hi All, On behalf of the NumPy team, I am pleased to announce NumPy 1.14.0rc1. Numpy 1.14.0rc1 is the result of seven months of work and contains a large number of bug fixes and new features, along with several changes with potential compatibility issues. The major change that users will notice are the stylistic changes in the way numpy arrays and scalars are printed, a change that will affect doctests. See the release notes for details on how to preserve the old style printing when needed. A major decision affecting future development concerns the schedule for dropping Python 2.7 support in the runup to 2020. The decision has been made to support 2.7 for all releases made in 2018, with the last release being designated a long term release with support for bug fixes extending through the end of 2019. Starting from January, 2019 support for 2.7 will be dropped in all new releases. More details can be found in the relevant NEP . This release supports Python 2.7 and 3.4 - 3.6. Wheels for the pre-release are available on PyPI. Source tarballs, zipfiles, release notes, and the changelog are available on github . *Highlights* - The ``np.einsum`` function uses BLAS when possible - ``genfromtxt``, ``loadtxt``, ``fromregex`` and ``savetxt`` can now handle files with arbitrary Python supported encoding. - Major improvements to printing of NumPy arrays and scalars. *New functions* - ``parametrize``: decorator added to numpy.testing - ``chebinterpolate``: Interpolate function at Chebyshev points. - ``format_float_positional`` and ``format_float_scientific`` : format floating-point scalars unambiguously with control of rounding and padding. - ``PyArray_ResolveWritebackIfCopy`` and ``PyArray_SetWritebackIfCopyBase``, new C-API functions useful in achieving PyPy compatibity. *Contributors* A total of 101 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Alexey Brodkin + - Allan Haldane - Andras Deak + - Andrew Lawson + - Antoine Pitrou - Bernhard M. Wiedemann + - Bob Eldering + - Brandon Carter - CJ Carey - Charles Harris - Chris Lamb - Christoph Boeddeker + - Christoph Gohlke - Daniel Hrisca + - Daniel Smith - Danny Hermes - David Freese - David Hagen - David Linke + - David Schaefer + - Dillon Niederhut + - Egor Panfilov + - Emilien Kofman - Eric Wieser - Erik Bray + - Erik Quaeghebeur + - Garry Polley + - Gunjan + - Henke Adolfsson + - Hidehiro NAGAOKA + - Hong Xu + - Iryna Shcherbina + - Jaime Fernandez - James Bourbeau + - Jamie Townsend + - Jarrod Millman - Jean Helie + - Jeroen Demeyer + - John Goetz + - John Kirkham - John Zwinck - Jonathan Helmus - Joseph Fox-Rabinovitz - Joseph Paul Cohen + - Joshua Leahy + - Julian Taylor - J?rg D?pfert + - Keno Goertz + - Kevin Sheppard + - Kexuan Sun + - Konrad Kapp + - Kristofor Maynard + - Licht Takeuchi + - Lo?c Est?ve - Lukas Mericle + - Marten van Kerkwijk - Matheus Portela + - Matthew Brett - Matti Picus - Michael Lamparski + - Michael Odintsov + - Michael Schnaitter + - Michael Seifert - Mike Nolta - Nathaniel J. Smith - Nelle Varoquaux + - Nicholas Del Grosso + - Nico Schl?mer + - Oleg Zabluda + - Oleksandr Pavlyk - Pauli Virtanen - Pim de Haan + - Ralf Gommers - Robert T. McGibbon + - Roland Kaufmann - Sebastian Berg - Serhiy Storchaka + - Shitian Ni + - Spencer Hill + - Srinivas Reddy Thatiparthy + - Stefan Winkler + - Stephan Hoyer - Steven Maude + - SuperBo + - Thomas K?ppe + - Toon Verstraelen - Vedant Misra + - Warren Weckesser - Wirawan Purwanto + - Yang Li + - Ziyan + - chaoyu3 + - hemildesai + - k_kapp at yahoo.com + - nickdg + - orbit-stabilizer + - schnaitterm + - solarjoe - wufangjie + - xoviat + - ?lie Gouzien + Enjoy, Chuck _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion at python.org https://mail.python.org/mailman/listinfo/numpy-discussion -------------- next part -------------- An HTML attachment was scrubbed... URL: From cimrman3 at ntc.zcu.cz Fri Dec 29 07:47:17 2017 From: cimrman3 at ntc.zcu.cz (Robert Cimrman) Date: Fri, 29 Dec 2017 13:47:17 +0100 Subject: [SciPy-User] ANN: SfePy 2017.4 Message-ID: I am pleased to announce release 2017.4 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method or by the isogeometric analysis (limited support). It is distributed under the new BSD license. Home page: http://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - basic support for penalty-based contacts - support for user-defined contexts in all solvers and preconditioners - new example: dispersion analysis of heterogeneous periodic materials For full release notes see http://docs.sfepy.org/doc/release_notes.html#id1 (rather long and technical). Cheers, Robert Cimrman --- Contributors to this release in alphabetical order: Robert Cimrman Jan Heczko Lubos Kejzlar Jan Kopacka Vladimir Lukes Matyas Novak