From vs at it.uu.se Sat Jan 2 14:40:10 2016 From: vs at it.uu.se (Virgil Stokes) Date: Sat, 2 Jan 2016 20:40:10 +0100 Subject: [SciPy-User] ANN: first release candidate for scipy 0.17.0 In-Reply-To: References: <568007F1.5080106@it.uu.se> Message-ID: <5688279A.8020705@it.uu.se> On 2015-Dec-29 10:59, Ralf Gommers wrote: > > - -------------------------- > > > I agree with you logic in supplying source code only. Can you provide > detailed instructions how to create the necessary modules for Python 2.7 > on a windows 32-bit platform (Vista)? > > > This is a detailed guide, with the current best option (Intel compilers and > MKL): > https://software.intel.com/en-us/articles/building-numpyscipy-with-intel-mkl-and-intel-fortran-on-windows > > Ralf > > > > > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-user This link looks promising Ralf. I will look into this in more detail --- thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Thu Jan 7 13:39:21 2016 From: charlesr.harris at gmail.com (Charles R Harris) Date: Thu, 7 Jan 2016 11:39:21 -0700 Subject: [SciPy-User] Numpy 1.10.4 release. Message-ID: Hi All, I'm pleased the release of the Numpy 1.10.4 (bugs stomped) release. This release was motivated by a reported segfault, but a few additional fixes were made: * gh-6922 BUG: numpy.recarray.sort segfaults on Windows, * gh-6937 BUG: busday_offset does the wrong thing with modifiedpreceding roll, * gh-6949 BUG: Type is lost when slicing a subclass of recarray, together with one minor enhancement * gh-6950 BUG trace is not subclass aware, np.trace(ma) != ma.trace(). The sources and documentation are available on Sourceforge, but no binaries. The usual windows binaries were ommitted due to problems with the toolchain. We hope that will be remedied in the future. Mac binaries can be installed from pypi. "Where is numpy 1.10.3?", you may ask. There were glitches with the uploads to pypi for that version that necessitated a version upgrade. A release manager's life is not a happy one. Many thanks to Marten van Kerkwijk, Sebastian Seberg, and Mark Wiebe for the quick bug fixes. Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From evgeny.burovskiy at gmail.com Thu Jan 7 18:24:48 2016 From: evgeny.burovskiy at gmail.com (Evgeni Burovski) Date: Thu, 7 Jan 2016 23:24:48 +0000 Subject: [SciPy-User] ANN: second release candidate for scipy 0.17.0 Message-ID: Hi, I'm pleased to announce the availability of the second release candidate for Scipy 0.17.0. It's two days ahead of the original schedule: based on typical development patterns, I'd like to have two weekends and a full working week before January 17th, when this rc2 is supposed to become the final release. Please try this rc and report any issues on Github tracker or scipy-dev mailing list. Source tarballs and full release notes are available from Github Releases: https://github.com/scipy/scipy/releases/tag/v0.17.0rc2 Compared to rc1, the following PRs were merged: - - `#5624 `__: FIX: Fix interpolate - - `#5625 `__: BUG: msvc9 binaries crash when indexing std::vector of size 0 - - `#5635 `__: BUG: misspelled __dealloc__ in cKDTree. - - `#5642 `__: STY: minor fixup of formatting of 0.17.0 release notes. - - `#5643 `__: BLD: fix a build issue in special/Faddeeva.cc with isnan. - - `#5661 `__: TST: linalg tests used stdlib random instead of numpy.random. There is a bit of an unusual change in this rc. In short, in testing rc1 we found that 1) interpolate.interp1d had an undocumented feature of allowing an array-valued fill_value to be broadcast against the data being interpolated, and 2) we broke it in 0.17.0rc1. (See PR 5624 for details.) We now *think* we fixed it so that no existing code is broken. Nevertheless, I would like to encourage everyone to test their code against this rc2, especially all code which uses interp1d. Cheers, Evgeni From matthew.brett at gmail.com Thu Jan 7 22:10:04 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Fri, 8 Jan 2016 03:10:04 +0000 Subject: [SciPy-User] [Numpy-discussion] ANN: second release candidate for scipy 0.17.0 In-Reply-To: References: Message-ID: Hi, On Thu, Jan 7, 2016 at 11:24 PM, Evgeni Burovski wrote: > Hi, > > I'm pleased to announce the availability of the second release > candidate for Scipy 0.17.0. It's two days ahead of the original > schedule: based on typical development patterns, I'd like to have two > weekends and a full working week before January 17th, when this rc2 is > supposed to become the final release. > > Please try this rc and report any issues on Github tracker or > scipy-dev mailing list. > Source tarballs and full release notes are available from Github > Releases: https://github.com/scipy/scipy/releases/tag/v0.17.0rc2 > > Compared to rc1, the following PRs were merged: > > - - `#5624 `__: FIX: Fix interpolate > - - `#5625 `__: BUG: msvc9 > binaries crash when indexing std::vector of size 0 > - - `#5635 `__: BUG: > misspelled __dealloc__ in cKDTree. > - - `#5642 `__: STY: minor > fixup of formatting of 0.17.0 release notes. > - - `#5643 `__: BLD: fix a > build issue in special/Faddeeva.cc with isnan. > - - `#5661 `__: TST: linalg > tests used stdlib random instead of numpy.random. > > There is a bit of an unusual change in this rc. In short, in testing > rc1 we found that 1) interpolate.interp1d had an undocumented feature > of allowing an array-valued fill_value to be broadcast against the > data being interpolated, and 2) we broke it in 0.17.0rc1. (See PR > 5624 for details.) > We now *think* we fixed it so that no existing code is broken. > Nevertheless, I would like to encourage everyone to test their code > against this rc2, especially all code which uses interp1d. Thanks for doing this. Testing builds of OSX wheels via https://github.com/MacPython/scipy-wheels, I found this problem : https://github.com/scipy/scipy/issues/5689 Cheers, Matthew From ndbecker2 at gmail.com Fri Jan 8 07:49:35 2016 From: ndbecker2 at gmail.com (Neal Becker) Date: Fri, 8 Jan 2016 07:49:35 -0500 Subject: [SciPy-User] [pythran] Pythran 0.7.4 is out! In-Reply-To: <20160107195139.GA23778@lakota> References: <20160107195139.GA23778@lakota> Message-ID: How do I build pythran3? On Thu, Jan 7, 2016 at 2:51 PM, serge guelton < serge.guelton at telecom-bretagne.eu> wrote: > (sorry for the double posting, if any) > > Dear pythraners and pythonists, > > The pythran team (a great total of 2 active developers) is delighted to > announce the release of Pythran 0.7.4, available on the traditional > channels: > > - pypi: https://pypi.python.org/pypi/pythran > - conda: https://anaconda.org/serge-sans-paille/pythran > - github: https://github.com/serge-sans-paille/pythran > > As usual, here is a (new) code sample, once again adapted from a > stackoverflow question[0] that showcases pythran capability: > > > #pythran export check_mask(bool[][], bool[]) > # ^~~~~~~ non intrusive top-level annotation > > import numpy as np > # ^~~~~~ numpy support (partial) > def check_mask(db, out, mask=[1, 0, 1]): > for idx, line in enumerate(db): > target, vector = line[0], line[1:] > # ^~~~~ type destructuring, array view > if (mask == np.bitwise_and(mask, vector)).all(): > # ^~~~~~~ optimization of high level construct > if target == 1: > out[idx] = 1 > return out > > > Compiled with: > > % pythran check_mask.py > > And benchmarked with: > > % python -m timeit -s 'n=10e3 ; import numpy as np;db = > np.array(np.random.randint(2, size=(n, 4)), dtype=bool); out = > np.zeros(int(n),dtype=bool); from eq import check_mask' 'check_mask(db, > out)' > > On average, the CPython version runs in 137 msec while the pythran version > run in 450us on my laptop :-) > > > Here is an extract of the changelog: > > 2016-01-05 Serge Guelton > > * IPython's magic for pythran now supports extra compile flags > > * Pythran's C++ output is compatible with Python3 and pythran3 can > compile it! > > * More syntax checks (and less template traceback) > > * Improved UI (multiline pythran exports, better setup.py...) > > * Pythonic leaning / bugfixing (this tends to be a permanent item) > > * More generic support for numpy's dtype > > * Simpler install (no more boost.python deps, nor nt2 > configuration) > > * Faster compilation (no more boost.python deps, smarter pass > manager) > > * Better testing (gcc + clang) > > Again, thanks a lot to Pierrick for his continuous top-quality work, and > to the OpenDreamKit[1] project that funded (most of) the recent > developments! > > Special thanks to @hainm, @nbecker, @pkoch, @fsteinmetz, @Suor for their > feedbacks. *You* give us the motivation to go on! > > > [0] > http://stackoverflow.com/questions/34500913/numba-slower-for-numpy-bitwise-and-on-boolean-arrays > [1] http://opendreamkit.org/ > -- *Those who don't understand recursion are doomed to repeat it* -------------- next part -------------- An HTML attachment was scrubbed... URL: From marek.jagielski at gmail.com Sat Jan 16 11:18:14 2016 From: marek.jagielski at gmail.com (Marek Jagielski) Date: Sat, 16 Jan 2016 17:18:14 +0100 Subject: [SciPy-User] SciPy with workflow processing Message-ID: Hi, I am developing a modeling tool for my start-up: systemincloud.com. Tool enables users creating data ?ow diagrams consisting of prede?ned or user-written blocks and execute them on their local machine. I added lastly a python support: Now, it is possible to define custom blocks using python language: http://systemincloud.com/tasks/#0.8.0/commons/pythontask. Blocks can be executed with cpython or jython. It is also possible to integrate external libraries like NumPy. Example can be watched here (NumPy + Matplotlib): https://www.youtube.com/watch?v=qvY3V9Ujoa0 I am looking forward for any feedback from you. Do you find such a tool interesting for you? Thanks, Marek Jagielski -------------- next part -------------- An HTML attachment was scrubbed... URL: From msarahan at gmail.com Mon Jan 18 17:29:42 2016 From: msarahan at gmail.com (Michael Sarahan) Date: Mon, 18 Jan 2016 22:29:42 +0000 Subject: [SciPy-User] Build on Win32-x86 / Intel fortran Message-ID: Greetings, I'm bumping into a strange issue building SciPy 0.16.1 for Python 3.5 with Visual Studio 2015. The 64-bit build completes successfully. The 32-bit build, not so much. It dies at linking fftpack: C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe /nologo /INCREMENTAL:NO /LTCG /nodefaultlib:libucrt.lib ucrt.lib /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\aroot\stage\libs /LIBPATH:C:\aroot\stage\PCbuild\win32 /LIBPATH:build\temp.win32-3.5 /LIBPATH:C:\aroot\stage\libs /LIBPATH:C:\aroot\stage\PCbuild\win32 /LIBPATH:build\temp.win32-3.5 /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" /LIBPATH:"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" dfftpack.lib fftpack.lib /EXPORT:PyInit__fftpack build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib Creating library build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib and object build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use of other libs; use /NODEFAULTLIB:library MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved external symbol __except_handler4_common build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : fatal error LNK1120: 1 unresolved externals Is this a problem with Intel's libraries linking with /MT rather than /MD? I haven't been able to find any /MT or /MD stuff in the SciPy build stuff. Pointers much appreciated. Best, Michael -------------- next part -------------- An HTML attachment was scrubbed... URL: From ralf.gommers at gmail.com Mon Jan 18 18:03:07 2016 From: ralf.gommers at gmail.com (Ralf Gommers) Date: Tue, 19 Jan 2016 00:03:07 +0100 Subject: [SciPy-User] Build on Win32-x86 / Intel fortran In-Reply-To: References: Message-ID: On Mon, Jan 18, 2016 at 11:29 PM, Michael Sarahan wrote: > Greetings, > > I'm bumping into a strange issue building SciPy 0.16.1 for Python 3.5 with > Visual Studio 2015. The 64-bit build completes successfully. The 32-bit > build, not so much. It dies at linking fftpack: > > C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe > /nologo /INCREMENTAL:NO /LTCG /nodefaultlib:libucrt.lib ucrt.lib /DLL > /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\aroot\stage\libs > /LIBPATH:C:\aroot\stage\PCbuild\win32 /LIBPATH:build\temp.win32-3.5 > /LIBPATH:C:\aroot\stage\libs /LIBPATH:C:\aroot\stage\PCbuild\win32 > /LIBPATH:build\temp.win32-3.5 /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows > Kits\8.1\lib\winv6.3\um\x86" dfftpack.lib fftpack.lib > /EXPORT:PyInit__fftpack > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj > /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd > /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > Creating library > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > and object > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp > LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use of other > libs; use /NODEFAULTLIB:library > MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved external symbol > __except_handler4_common > build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : fatal error > LNK1120: 1 unresolved externals > > Is this a problem with Intel's libraries linking with /MT rather than > /MD? I haven't been able to find any /MT or /MD stuff in the SciPy build > stuff. > > Pointers much appreciated. > The MT/MD flags should come from here: https://github.com/numpy/numpy/blob/master/numpy/distutils/fcompiler/intel.py#L162 We made some changes recently, so it may depend on the version of numpy you're building against. Hope that helps, Ralf -------------- next part -------------- An HTML attachment was scrubbed... URL: From msarahan at gmail.com Mon Jan 18 18:20:11 2016 From: msarahan at gmail.com (Michael Sarahan) Date: Mon, 18 Jan 2016 23:20:11 +0000 Subject: [SciPy-User] Build on Win32-x86 / Intel fortran In-Reply-To: References: Message-ID: Hi Ralf, Thanks for the fast reply! I looked back at the history of that file, and that part seems pretty stable. I don't think your recent changes are making the difference here. Here's a little more of the build output that might be relevant: C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe /c /nologo /Ox /W3 /GL /DNDEBUG /MT -Iscipy\fftpack\src -Ibuild\src.win32-3.5 -IC:\aroot\stage\lib\site-packages\numpy\core\include -IC:\aroot\stage\include -IC:\aroot\stage\include -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" -I"C:\Program Files (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows Kits\8.1\include\winrt" /Tcbuild\src.win32-3.5\fortranobject.c /Fobuild\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj could not find library 'dfftpack' in directories [] could not find library 'fftpack' in directories [] This has the /MT flag - so the fftpack stuff is being compiled for the static MSVC runtime. However, at the linker stage just afterwards, it seems we actively prevent the static UCRT runtime (libucrt.lib), and instead force it to use the dynamic UCRT (ucrt.lib). Am I understanding this correctly? C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe /nologo /INCREMENTAL:NO /LTCG /nodefaultlib:libucrt.lib ucrt.lib /DLL [snip] /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" dfftpack.lib fftpack.lib /EXPORT:PyInit__fftpack build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib Creating library build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib and object build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use of other libs; use /NODEFAULTLIB:library MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved external symbol __except_handler4_common build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : fatal error LNK1120: 1 unresolved externals Best, Michael On Mon, Jan 18, 2016 at 5:03 PM Ralf Gommers wrote: > On Mon, Jan 18, 2016 at 11:29 PM, Michael Sarahan > wrote: > >> Greetings, >> >> I'm bumping into a strange issue building SciPy 0.16.1 for Python 3.5 >> with Visual Studio 2015. The 64-bit build completes successfully. The >> 32-bit build, not so much. It dies at linking fftpack: >> >> C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe >> /nologo /INCREMENTAL:NO /LTCG /nodefaultlib:libucrt.lib ucrt.lib /DLL >> /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\aroot\stage\libs >> /LIBPATH:C:\aroot\stage\PCbuild\win32 /LIBPATH:build\temp.win32-3.5 >> /LIBPATH:C:\aroot\stage\libs /LIBPATH:C:\aroot\stage\PCbuild\win32 >> /LIBPATH:build\temp.win32-3.5 /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> /LIBPATH:"C:\Program Files >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\LIB" >> /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\10\lib\10.0.10150.0\ucrt\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files (x86)\Windows >> Kits\8.1\lib\winv6.3\um\x86" dfftpack.lib fftpack.lib >> /EXPORT:PyInit__fftpack >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj >> build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj >> build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj >> build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj >> build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj >> build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj >> /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd >> /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib >> Creating library >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib >> and object >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp >> LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use of other >> libs; use /NODEFAULTLIB:library >> MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved external symbol >> __except_handler4_common >> build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : fatal error >> LNK1120: 1 unresolved externals >> >> Is this a problem with Intel's libraries linking with /MT rather than >> /MD? I haven't been able to find any /MT or /MD stuff in the SciPy build >> stuff. >> >> Pointers much appreciated. >> > > The MT/MD flags should come from here: > https://github.com/numpy/numpy/blob/master/numpy/distutils/fcompiler/intel.py#L162 > We made some changes recently, so it may depend on the version of numpy > you're building against. > > Hope that helps, > Ralf > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-user > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cgohlke at uci.edu Mon Jan 18 19:12:32 2016 From: cgohlke at uci.edu (Christoph Gohlke) Date: Mon, 18 Jan 2016 16:12:32 -0800 Subject: [SciPy-User] Build on Win32-x86 / Intel fortran In-Reply-To: References: Message-ID: <569D7F70.1040202@uci.edu> Could it be that you are building with an older RC (non-final) version of Python 3.5? Those versions were using `/MT` and `/nodefaultlib:libucrt.lib ucrt.lib` flags, which were reverted in the last RC and final. Christoph On 1/18/2016 3:20 PM, Michael Sarahan wrote: > Hi Ralf, > > Thanks for the fast reply! I looked back at the history of that file, > and that part seems pretty stable. I don't think your recent changes > are making the difference here. Here's a little more of the build > output that might be relevant: > > C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe /c > /nologo /Ox /W3 /GL /DNDEBUG /MT -Iscipy\fftpack\src > -Ibuild\src.win32-3.5 > -IC:\aroot\stage\lib\site-packages\numpy\core\include > -IC:\aroot\stage\include -IC:\aroot\stage\include -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" > -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" -I"C:\Program > Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files > (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program > Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program > Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files > (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\winrt" -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" > -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" > -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" > -I"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows > Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\winrt" -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" > -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" -I"C:\Program > Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files > (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program > Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program > Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files > (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\winrt" -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" > -I"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" > -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" > -I"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows > Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > Kits\8.1\include\winrt" /Tcbuild\src.win32-3.5\fortranobject.c > /Fobuild\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj > could not find library 'dfftpack' in directories [] > could not find library 'fftpack' in directories [] > > This has the /MT flag - so the fftpack stuff is being compiled for the > static MSVC runtime. However, at the linker stage just afterwards, it > seems we actively prevent the static UCRT runtime (libucrt.lib), and > instead force it to use the dynamic UCRT (ucrt.lib). Am I understanding > this correctly? > > C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe > /nologo /INCREMENTAL:NO /LTCG /nodefaultlib:libucrt.lib ucrt.lib /DLL > > [snip] > > /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" > dfftpack.lib fftpack.lib /EXPORT:PyInit__fftpack > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj > /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd > /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > Creating library > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > and object > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp > LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use of other > libs; use /NODEFAULTLIB:library > MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved external > symbol __except_handler4_common > build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : fatal error > LNK1120: 1 unresolved externals > > Best, > Michael > > On Mon, Jan 18, 2016 at 5:03 PM Ralf Gommers > wrote: > > On Mon, Jan 18, 2016 at 11:29 PM, Michael Sarahan > > wrote: > > Greetings, > > I'm bumping into a strange issue building SciPy 0.16.1 for > Python 3.5 with Visual Studio 2015. The 64-bit build completes > successfully. The 32-bit build, not so much. It dies at > linking fftpack: > > C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\BIN\link.exe /nologo /INCREMENTAL:NO /LTCG > /nodefaultlib:libucrt.lib ucrt.lib /DLL /MANIFEST:EMBED,ID=2 > /MANIFESTUAC:NO /LIBPATH:C:\aroot\stage\libs > /LIBPATH:C:\aroot\stage\PCbuild\win32 > /LIBPATH:build\temp.win32-3.5 /LIBPATH:C:\aroot\stage\libs > /LIBPATH:C:\aroot\stage\PCbuild\win32 > /LIBPATH:build\temp.win32-3.5 /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program > Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program > Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program > Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > /LIBPATH:"C:\Program Files > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > /LIBPATH:"C:\Program Files (x86)\Windows > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" dfftpack.lib > fftpack.lib /EXPORT:PyInit__fftpack > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj > build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj > build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj > /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd > /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > Creating library > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > and object > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp > LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use > of other libs; use /NODEFAULTLIB:library > MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved > external symbol __except_handler4_common > build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : > fatal error LNK1120: 1 unresolved externals > > Is this a problem with Intel's libraries linking with /MT rather > than /MD? I haven't been able to find any /MT or /MD stuff in > the SciPy build stuff. > > Pointers much appreciated. > > > The MT/MD flags should come from here: > https://github.com/numpy/numpy/blob/master/numpy/distutils/fcompiler/intel.py#L162 > We made some changes recently, so it may depend on the version of > numpy you're building against. > > Hope that helps, > Ralf > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-user > > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-user > From msarahan at gmail.com Mon Jan 18 19:14:26 2016 From: msarahan at gmail.com (Michael Sarahan) Date: Tue, 19 Jan 2016 00:14:26 +0000 Subject: [SciPy-User] Build on Win32-x86 / Intel fortran In-Reply-To: <569D7F70.1040202@uci.edu> References: <569D7F70.1040202@uci.edu> Message-ID: Thanks, Christoph. I am reading your contributions to that discussion ( https://bugs.python.org/issue24872) now. That certainly looks like where the issue is. I'm not sure where we're picking up those old flags, but I'm pretty sure finding out will fix things. Best, Michael On Mon, Jan 18, 2016 at 6:12 PM Christoph Gohlke wrote: > Could it be that you are building with an older RC (non-final) version > of Python 3.5? Those versions were using `/MT` and > `/nodefaultlib:libucrt.lib ucrt.lib` flags, which were reverted in the > last RC and final. > > Christoph > > > On 1/18/2016 3:20 PM, Michael Sarahan wrote: > > Hi Ralf, > > > > Thanks for the fast reply! I looked back at the history of that file, > > and that part seems pretty stable. I don't think your recent changes > > are making the difference here. Here's a little more of the build > > output that might be relevant: > > > > C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe /c > > /nologo /Ox /W3 /GL /DNDEBUG /MT -Iscipy\fftpack\src > > -Ibuild\src.win32-3.5 > > -IC:\aroot\stage\lib\site-packages\numpy\core\include > > -IC:\aroot\stage\include -IC:\aroot\stage\include -I"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" > > -I"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" > -I"C:\Program > > Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files > > (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program > > Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program > > Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files > > (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\winrt" -I"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" > > -I"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" > > -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" > > -I"C:\Program Files (x86)\Microsoft Visual Studio > > 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows > > Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows > > Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\winrt" -I"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" > > -I"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" > -I"C:\Program > > Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files > > (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program > > Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program > > Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files > > (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\winrt" -I"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" > > -I"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" > > -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" > > -I"C:\Program Files (x86)\Microsoft Visual Studio > > 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows > > Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows > > Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows > > Kits\8.1\include\winrt" /Tcbuild\src.win32-3.5\fortranobject.c > > /Fobuild\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj > > could not find library 'dfftpack' in directories [] > > could not find library 'fftpack' in directories [] > > > > This has the /MT flag - so the fftpack stuff is being compiled for the > > static MSVC runtime. However, at the linker stage just afterwards, it > > seems we actively prevent the static UCRT runtime (libucrt.lib), and > > instead force it to use the dynamic UCRT (ucrt.lib). Am I understanding > > this correctly? > > > > C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe > > /nologo /INCREMENTAL:NO /LTCG /nodefaultlib:libucrt.lib ucrt.lib /DLL > > > > [snip] > > > > /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" > > dfftpack.lib fftpack.lib /EXPORT:PyInit__fftpack > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj > > build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj > > /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd > > > /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > > Creating library > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > > and object > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp > > LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use of other > > libs; use /NODEFAULTLIB:library > > MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved external > > symbol __except_handler4_common > > build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : fatal error > > LNK1120: 1 unresolved externals > > > > Best, > > Michael > > > > On Mon, Jan 18, 2016 at 5:03 PM Ralf Gommers > > wrote: > > > > On Mon, Jan 18, 2016 at 11:29 PM, Michael Sarahan > > > wrote: > > > > Greetings, > > > > I'm bumping into a strange issue building SciPy 0.16.1 for > > Python 3.5 with Visual Studio 2015. The 64-bit build completes > > successfully. The 32-bit build, not so much. It dies at > > linking fftpack: > > > > C:\Program Files (x86)\Microsoft Visual Studio > > 14.0\VC\BIN\link.exe /nologo /INCREMENTAL:NO /LTCG > > /nodefaultlib:libucrt.lib ucrt.lib /DLL /MANIFEST:EMBED,ID=2 > > /MANIFESTUAC:NO /LIBPATH:C:\aroot\stage\libs > > /LIBPATH:C:\aroot\stage\PCbuild\win32 > > /LIBPATH:build\temp.win32-3.5 /LIBPATH:C:\aroot\stage\libs > > /LIBPATH:C:\aroot\stage\PCbuild\win32 > > /LIBPATH:build\temp.win32-3.5 /LIBPATH:"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > > /LIBPATH:"C:\Program Files (x86)\Windows > > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program > > Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" > > /LIBPATH:"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" > > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > > /LIBPATH:"C:\Program Files (x86)\Windows > > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program > > Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > > /LIBPATH:"C:\Program Files (x86)\Windows > > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program > > Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" > > /LIBPATH:"C:\Program Files > > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" > > /LIBPATH:"C:\Program Files > > > (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" > > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio > > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual > > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" > > /LIBPATH:"C:\Program Files (x86)\Windows > > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files > > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" dfftpack.lib > > fftpack.lib /EXPORT:PyInit__fftpack > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj > > build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj > > > build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj > > /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd > > > /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > > Creating library > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib > > and object > > > build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp > > LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use > > of other libs; use /NODEFAULTLIB:library > > MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved > > external symbol __except_handler4_common > > build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : > > fatal error LNK1120: 1 unresolved externals > > > > Is this a problem with Intel's libraries linking with /MT rather > > than /MD? I haven't been able to find any /MT or /MD stuff in > > the SciPy build stuff. > > > > Pointers much appreciated. > > > > > > The MT/MD flags should come from here: > > > https://github.com/numpy/numpy/blob/master/numpy/distutils/fcompiler/intel.py#L162 > > We made some changes recently, so it may depend on the version of > > numpy you're building against. > > > > Hope that helps, > > Ralf > > > > _______________________________________________ > > SciPy-User mailing list > > SciPy-User at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-user > > > > > > > > _______________________________________________ > > SciPy-User mailing list > > SciPy-User at scipy.org > > https://mail.scipy.org/mailman/listinfo/scipy-user > > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-user > -------------- next part -------------- An HTML attachment was scrubbed... URL: From msarahan at gmail.com Mon Jan 18 20:03:33 2016 From: msarahan at gmail.com (Michael Sarahan) Date: Tue, 19 Jan 2016 01:03:33 +0000 Subject: [SciPy-User] Build on Win32-x86 / Intel fortran In-Reply-To: References: <569D7F70.1040202@uci.edu> Message-ID: Indeed, I had read Steve Dower's blog post ( http://stevedower.id.au/blog/building-for-python-3-5-part-two/) before, but I should have re-read it: =====================Always statically link The build options are updated to statically link the DLL if PY_VCRUNTIME_REDIST is empty. If you set DISTUTILS_USE_SDK but not PY_VCRUNTIME_REDIST, you will get statically linked vcruntime140.dll. This is probably the biggest surprise from the change. ========================== By setting the PY_VCRUNTIME_REDIST environment variable, everything works. Thanks everyone. Michael On Mon, Jan 18, 2016 at 6:14 PM Michael Sarahan wrote: > Thanks, Christoph. I am reading your contributions to that discussion ( > https://bugs.python.org/issue24872) now. That certainly looks like where > the issue is. I'm not sure where we're picking up those old flags, but I'm > pretty sure finding out will fix things. > > Best, > Michael > > On Mon, Jan 18, 2016 at 6:12 PM Christoph Gohlke wrote: > >> Could it be that you are building with an older RC (non-final) version >> of Python 3.5? Those versions were using `/MT` and >> `/nodefaultlib:libucrt.lib ucrt.lib` flags, which were reverted in the >> last RC and final. >> >> Christoph >> >> >> On 1/18/2016 3:20 PM, Michael Sarahan wrote: >> > Hi Ralf, >> > >> > Thanks for the fast reply! I looked back at the history of that file, >> > and that part seems pretty stable. I don't think your recent changes >> > are making the difference here. Here's a little more of the build >> > output that might be relevant: >> > >> > C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe /c >> > /nologo /Ox /W3 /GL /DNDEBUG /MT -Iscipy\fftpack\src >> > -Ibuild\src.win32-3.5 >> > -IC:\aroot\stage\lib\site-packages\numpy\core\include >> > -IC:\aroot\stage\include -IC:\aroot\stage\include -I"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" >> > -I"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" >> -I"C:\Program >> > Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files >> > (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program >> > Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program >> > Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files >> > (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\winrt" -I"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" >> > -I"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" >> > -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" >> > -I"C:\Program Files (x86)\Microsoft Visual Studio >> > 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows >> > Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows >> > Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\winrt" -I"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include" >> > -I"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\include\ia32" >> -I"C:\Program >> > Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" -I"C:\Program Files >> > (x86)\Microsoft Visual Studio 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program >> > Files (x86)\Windows Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program >> > Files (x86)\Windows Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files >> > (x86)\Windows Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\winrt" -I"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\include" >> > -I"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\daal\include" >> > -I"C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\INCLUDE" >> > -I"C:\Program Files (x86)\Microsoft Visual Studio >> > 14.0\VC\ATLMFC\INCLUDE" -I"C:\Program Files (x86)\Windows >> > Kits\10\include\10.0.10150.0\ucrt" -I"C:\Program Files (x86)\Windows >> > Kits\NETFXSDK\4.6\include\um" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\shared" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\um" -I"C:\Program Files (x86)\Windows >> > Kits\8.1\include\winrt" /Tcbuild\src.win32-3.5\fortranobject.c >> > /Fobuild\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj >> > could not find library 'dfftpack' in directories [] >> > could not find library 'fftpack' in directories [] >> > >> > This has the /MT flag - so the fftpack stuff is being compiled for the >> > static MSVC runtime. However, at the linker stage just afterwards, it >> > seems we actively prevent the static UCRT runtime (libucrt.lib), and >> > instead force it to use the dynamic UCRT (ucrt.lib). Am I understanding >> > this correctly? >> > >> > C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe >> > /nologo /INCREMENTAL:NO /LTCG /nodefaultlib:libucrt.lib ucrt.lib /DLL >> > >> > [snip] >> > >> > /LIBPATH:"C:\Program Files (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" >> > dfftpack.lib fftpack.lib /EXPORT:PyInit__fftpack >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj >> > build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj >> > /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd >> > >> /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib >> > Creating library >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib >> > and object >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp >> > LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use of other >> > libs; use /NODEFAULTLIB:library >> > MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved external >> > symbol __except_handler4_common >> > build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : fatal error >> > LNK1120: 1 unresolved externals >> > >> > Best, >> > Michael >> > >> > On Mon, Jan 18, 2016 at 5:03 PM Ralf Gommers > > > wrote: >> > >> > On Mon, Jan 18, 2016 at 11:29 PM, Michael Sarahan >> > > wrote: >> > >> > Greetings, >> > >> > I'm bumping into a strange issue building SciPy 0.16.1 for >> > Python 3.5 with Visual Studio 2015. The 64-bit build completes >> > successfully. The 32-bit build, not so much. It dies at >> > linking fftpack: >> > >> > C:\Program Files (x86)\Microsoft Visual Studio >> > 14.0\VC\BIN\link.exe /nologo /INCREMENTAL:NO /LTCG >> > /nodefaultlib:libucrt.lib ucrt.lib /DLL /MANIFEST:EMBED,ID=2 >> > /MANIFESTUAC:NO /LIBPATH:C:\aroot\stage\libs >> > /LIBPATH:C:\aroot\stage\PCbuild\win32 >> > /LIBPATH:build\temp.win32-3.5 /LIBPATH:C:\aroot\stage\libs >> > /LIBPATH:C:\aroot\stage\PCbuild\win32 >> > /LIBPATH:build\temp.win32-3.5 /LIBPATH:"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual >> > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" >> > /LIBPATH:"C:\Program Files (x86)\Windows >> > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program >> > Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" >> > /LIBPATH:"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" >> > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual >> > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" >> > /LIBPATH:"C:\Program Files (x86)\Windows >> > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program >> > Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual >> > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" >> > /LIBPATH:"C:\Program Files (x86)\Windows >> > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" /LIBPATH:"C:\Program >> > Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32\vc_mt" >> > /LIBPATH:"C:\Program Files >> > (x86)\IntelSWTools\compilers_and_libraries\windows\mkl\lib\ia32" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\daal\lib\ia32_win" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\compiler\lib\ia32_win" >> > /LIBPATH:"C:\Program Files >> > >> (x86)\IntelSWTools\compilers_and_libraries\windows\tbb\lib\ia32_win\vc_mt" >> > /LIBPATH:"C:\Program Files (x86)\Microsoft Visual Studio >> > 14.0\VC\LIB" /LIBPATH:"C:\Program Files (x86)\Microsoft Visual >> > Studio 14.0\VC\ATLMFC\LIB" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\10\lib\10.0.10150.0\ucrt\x86" >> > /LIBPATH:"C:\Program Files (x86)\Windows >> > Kits\NETFXSDK\4.6\lib\um\x86" /LIBPATH:"C:\Program Files >> > (x86)\Windows Kits\8.1\lib\winv6.3\um\x86" dfftpack.lib >> > fftpack.lib /EXPORT:PyInit__fftpack >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpackmodule.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\zfft.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\drfft.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\zrfft.obj >> > build\temp.win32-3.5\Release\scipy\fftpack\src\zfftnd.obj >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dct.obj >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\src\dst.obj >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\fortranobject.obj >> > /OUT:build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd >> > >> /IMPLIB:build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib >> > Creating library >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.lib >> > and object >> > >> build\temp.win32-3.5\Release\build\src.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.exp >> > LINK : warning LNK4098: defaultlib 'MSVCRT' conflicts with use >> > of other libs; use /NODEFAULTLIB:library >> > MSVCRT.lib(_chandler4gs_.obj) : error LNK2001: unresolved >> > external symbol __except_handler4_common >> > build\lib.win32-3.5\scipy\fftpack\_fftpack.cp35-win32.pyd : >> > fatal error LNK1120: 1 unresolved externals >> > >> > Is this a problem with Intel's libraries linking with /MT rather >> > than /MD? I haven't been able to find any /MT or /MD stuff in >> > the SciPy build stuff. >> > >> > Pointers much appreciated. >> > >> > >> > The MT/MD flags should come from here: >> > >> https://github.com/numpy/numpy/blob/master/numpy/distutils/fcompiler/intel.py#L162 >> > We made some changes recently, so it may depend on the version of >> > numpy you're building against. >> > >> > Hope that helps, >> > Ralf >> > >> > _______________________________________________ >> > SciPy-User mailing list >> > SciPy-User at scipy.org >> > https://mail.scipy.org/mailman/listinfo/scipy-user >> > >> > >> > >> > _______________________________________________ >> > SciPy-User mailing list >> > SciPy-User at scipy.org >> > https://mail.scipy.org/mailman/listinfo/scipy-user >> > >> _______________________________________________ >> SciPy-User mailing list >> SciPy-User at scipy.org >> https://mail.scipy.org/mailman/listinfo/scipy-user >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erwin at amsterdamoptimization.com Tue Jan 19 09:51:06 2016 From: erwin at amsterdamoptimization.com (Erwin Kalvelagen) Date: Tue, 19 Jan 2016 14:51:06 +0000 (UTC) Subject: [SciPy-User] minimize SLSQP return code when model is infeasible Message-ID: Here is small model that is infeasible: min x^2 + y^2 x+y=1 x>=2 x,y>=0 However when I try this with SLSQP I get a return code that seems to indicate everything is hunky-dory: x = [1,2] optimize.minimize( lambda x: x[0]**2+x[1]**2, x, constraints = ( {'type':'eq','fun': lambda x: x[0]+x[1]-1}, {'type':'ineq','fun': lambda x: x[0]-2} ), bounds = ((0,None),(0,None)), method='SLSQP') nfev: 8 fun: 2.77777777777712 nit: 6 jac: array([ 3.33333334e+00, 2.98023224e-08, 0.00000000e+00]) x: array([ 1.66666667e+00, 1.39888101e-14]) success: True message: 'Optimization terminated successfully.' status: 0 njev: 2 R has a similar interface to SLSQP, so I tried that also. We see that a number of flags are raised. slsqp(c(1,2), function(x) {x[1]^2+x[2]^2}, heq=function(x){x[1]+x[2]-1}, hin=function(x){x[1]-2}, lower=c(0,0)) $par [1] 1.666667e+00 4.773719e-11 $value [1] 2.777778 $iter [1] 105 $convergence [1] -4 $message [1] "NLOPT_ROUNDOFF_LIMITED: Roundoff errors led to a breakdown of the optimization algorithm. In this case, the returned minimum may still be useful. (e.g. this error occurs in NEWUOA if one tries to achieve a tolerance too close to machine precision.)" I am not very familiar with this solver (so I may be doing something wrong or misinterpreting something) but it looks like the scipy version does not return a correct return code. Thanks, Erwin From shoyer at gmail.com Thu Jan 21 22:05:55 2016 From: shoyer at gmail.com (Stephan Hoyer) Date: Thu, 21 Jan 2016 19:05:55 -0800 Subject: [SciPy-User] ANN: xarray (formerly xray) v0.7.0 released Message-ID: I am pleased to announce version v0.7.0 of xarray, the project formerly known as xray. xarray is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. These data structures are based on the data model of the netCDF file format. In this latest release, we have renamed the project from "xray" to "xarray". This avoids a namespace conflict with the entire field of X-ray science. We have new URLs for our documentation, source code and mailing list: http://xarray.pydata.org/ http://github.com/pydata/xarray/ https://groups.google.com/forum/#!forum/xarray Highlights of this release: * An internal refactor of DataArray internals * New methods for reshaping, rolling and shifting data * Preliminary support for pandas.MultiIndex * Support for reading GRIB, HDF4 and other file formats via PyNIO For more details, read the full release notes: http://xarray.pydata.org/en/stable/whats-new.html Contributors to this release: Antony Lee Fabien Maussion Joe Hamman Maximilian Roos Stephan Hoyer Takeshi Kanmae femtotrader I'd also like to highlight the contributions of Clark Fitzgerald, who added a plotting module to xray in v0.6, and Dave Brown, for his assistance adding PyNIO support. Best, Stephan -------------- next part -------------- An HTML attachment was scrubbed... URL: From erwin at amsterdamoptimization.com Fri Jan 22 07:57:19 2016 From: erwin at amsterdamoptimization.com (Erwin Kalvelagen) Date: Fri, 22 Jan 2016 12:57:19 +0000 (UTC) Subject: [SciPy-User] minimize SLSQP return code when model is infeasible References: Message-ID: Added to bug tracker: https://github.com/scipy/scipy/issues/5743 From evgeny.burovskiy at gmail.com Sat Jan 23 07:51:58 2016 From: evgeny.burovskiy at gmail.com (Evgeni Burovski) Date: Sat, 23 Jan 2016 12:51:58 +0000 Subject: [SciPy-User] ANN: scipy 0.17.0 release Message-ID: Hi, On behalf of the Scipy development team I am pleased to announce the availability of Scipy 0.17.0. This release contains several new features, detailed in the release notes below. 101 people contributed to this release over the course of six months. This release requires Python 2.6, 2.7 or 3.2-3.4 and NumPy 1.6.2 or greater. Source tarballs and release notes can be found at https://github.com/scipy/scipy/releases/tag/v0.17.0. Thanks to everyone who contributed to this release. Cheers, Evgeni -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 ========================== SciPy 0.17.0 Release Notes ========================== .. contents:: SciPy 0.17.0 is the culmination of 6 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Moreover, our development attention will now shift to bug-fix releases on the 0.17.x branch, and on adding new features on the master branch. This release requires Python 2.6, 2.7 or 3.2-3.5 and NumPy 1.6.2 or greater. Release highlights: - New functions for linear and nonlinear least squares optimization with constraints: `scipy.optimize.lsq_linear` and `scipy.optimize.least_squares` - Support for fitting with bounds in `scipy.optimize.curve_fit`. - Significant improvements to `scipy.stats`, providing many functions with better handing of inputs which have NaNs or are empty, improved documentation, and consistent behavior between `scipy.stats` and `scipy.stats.mstats`. - Significant performance improvements and new functionality in `scipy.spatial.cKDTree`. New features ============ `scipy.cluster` improvements - ---------------------------- A new function `scipy.cluster.hierarchy.cut_tree`, which determines a cut tree from a linkage matrix, was added. `scipy.io` improvements - ----------------------- `scipy.io.mmwrite` gained support for symmetric sparse matrices. `scipy.io.netcdf` gained support for masking and scaling data based on data attributes. `scipy.optimize` improvements - ----------------------------- Linear assignment problem solver ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ `scipy.optimize.linear_sum_assignment` is a new function for solving the linear sum assignment problem. It uses the Hungarian algorithm (Kuhn-Munkres). Least squares optimization ~~~~~~~~~~~~~~~~~~~~~~~~~~ A new function for *nonlinear* least squares optimization with constraints was added: `scipy.optimize.least_squares`. It provides several methods: Levenberg-Marquardt for unconstrained problems, and two trust-region methods for constrained ones. Furthermore it provides different loss functions. New trust-region methods also handle sparse Jacobians. A new function for *linear* least squares optimization with constraints was added: `scipy.optimize.lsq_linear`. It provides a trust-region method as well as an implementation of the Bounded-Variable Least-Squares (BVLS) algorithm. `scipy.optimize.curve_fit` now supports fitting with bounds. `scipy.signal` improvements - --------------------------- A ``mode`` keyword was added to `scipy.signal.spectrogram`, to let it return other spectrograms than power spectral density. `scipy.stats` improvements - -------------------------- Many functions in `scipy.stats` have gained a ``nan_policy`` keyword, which allows specifying how to treat input with NaNs in them: propagate the NaNs, raise an error, or omit the NaNs. Many functions in `scipy.stats` have been improved to correctly handle input arrays that are empty or contain infs/nans. A number of functions with the same name in `scipy.stats` and `scipy.stats.mstats` were changed to have matching signature and behavior. See `gh-5474 `__ for details. `scipy.stats.binom_test` and `scipy.stats.mannwhitneyu` gained a keyword ``alternative``, which allows specifying the hypothesis to test for. Eventually all hypothesis testing functions will get this keyword. For methods of many continuous distributions, complex input is now accepted. Matrix normal distribution has been implemented as `scipy.stats.matrix_normal`. `scipy.sparse` improvements - --------------------------- The `axis` keyword was added to sparse norms, `scipy.sparse.linalg.norm`. `scipy.spatial` improvements - ---------------------------- `scipy.spatial.cKDTree` was partly rewritten for improved performance and several new features were added to it: - - the ``query_ball_point`` method became significantly faster - - ``query`` and ``query_ball_point`` gained an ``n_jobs`` keyword for parallel execution - - build and query methods now release the GIL - - full pickling support - - support for periodic spaces - - the ``sparse_distance_matrix`` method can now return and sparse matrix type `scipy.interpolate` improvements - -------------------------------- Out-of-bounds behavior of `scipy.interpolate.interp1d` has been improved. Use a two-element tuple for the ``fill_value`` argument to specify separate fill values for input below and above the interpolation range. Linear and nearest interpolation kinds of `scipy.interpolate.interp1d` support extrapolation via the ``fill_value="extrapolate"`` keyword. ``fill_value`` can also be set to an array-like (or a two-element tuple of array-likes for separate below and above values) so long as it broadcasts properly to the non-interpolated dimensions of an array. This was implicitly supported by previous versions of scipy, but support has now been formalized and gets compatibility-checked before use. For example, a set of ``y`` values to interpolate with shape ``(2, 3, 5)`` interpolated along the last axis (2) could accept a ``fill_value`` array with shape ``()`` (singleton), ``(1,)``, ``(2, 1)``, ``(1, 3)``, ``(3,)``, or ``(2, 3)``; or it can be a 2-element tuple to specify separate below and above bounds, where each of the two tuple elements obeys proper broadcasting rules. `scipy.linalg` improvements - --------------------------- The default algorithm for `scipy.linalg.leastsq` has been changed to use LAPACK's function ``*gelsd``. Users wanting to get the previous behavior can use a new keyword ``lapack_driver="gelss"`` (allowed values are "gelss", "gelsd" and "gelsy"). ``scipy.sparse`` matrices and linear operators now support the matmul (``@``) operator when available (Python 3.5+). See [PEP 465](http://legacy.python.org/dev/peps/pep-0465/) A new function `scipy.linalg.ordqz`, for QZ decomposition with reordering, has been added. Deprecated features =================== ``scipy.stats.histogram`` is deprecated in favor of ``np.histogram``, which is faster and provides the same functionality. ``scipy.stats.threshold`` and ``scipy.mstats.threshold`` are deprecated in favor of ``np.clip``. See issue #617 for details. ``scipy.stats.ss`` is deprecated. This is a support function, not meant to be exposed to the user. Also, the name is unclear. See issue #663 for details. ``scipy.stats.square_of_sums`` is deprecated. This too is a support function not meant to be exposed to the user. See issues #665 and #663 for details. ``scipy.stats.f_value``, ``scipy.stats.f_value_multivariate``, ``scipy.stats.f_value_wilks_lambda``, and ``scipy.mstats.f_value_wilks_lambda`` are deprecated. These are related to ANOVA, for which ``scipy.stats`` provides quite limited functionality and these functions are not very useful standalone. See issues #660 and #650 for details. ``scipy.stats.chisqprob`` is deprecated. This is an alias. ``stats.chi2.sf`` should be used instead. ``scipy.stats.betai`` is deprecated. This is an alias for ``special.betainc`` which should be used instead. Backwards incompatible changes ============================== The functions ``stats.trim1`` and ``stats.trimboth`` now make sure the elements trimmed are the lowest and/or highest, depending on the case. Slicing without at least partial sorting was previously done, but didn't make sense for unsorted input. When ``variable_names`` is set to an empty list, ``scipy.io.loadmat`` now correctly returns no values instead of all the contents of the MAT file. Element-wise multiplication of sparse matrices now returns a sparse result in all cases. Previously, multiplying a sparse matrix with a dense matrix or array would return a dense matrix. The function ``misc.lena`` has been removed due to license incompatibility. The constructor for ``sparse.coo_matrix`` no longer accepts ``(None, (m,n))`` to construct an all-zero matrix of shape ``(m,n)``. This functionality was deprecated since at least 2007 and was already broken in the previous SciPy release. Use ``coo_matrix((m,n))`` instead. The Cython wrappers in ``linalg.cython_lapack`` for the LAPACK routines ``*gegs``, ``*gegv``, ``*gelsx``, ``*geqpf``, ``*ggsvd``, ``*ggsvp``, ``*lahrd``, ``*latzm``, ``*tzrqf`` have been removed since these routines are not present in the new LAPACK 3.6.0 release. With the exception of the routines ``*ggsvd`` and ``*ggsvp``, these were all deprecated in favor of routines that are currently present in our Cython LAPACK wrappers. Because the LAPACK ``*gegv`` routines were removed in LAPACK 3.6.0. The corresponding Python wrappers in ``scipy.linalg.lapack`` are now deprecated and will be removed in a future release. The source files for these routines have been temporarily included as a part of ``scipy.linalg`` so that SciPy can be built against LAPACK versions that do not provide these deprecated routines. Other changes ============= Html and pdf documentation of development versions of Scipy is now automatically rebuilt after every merged pull request. `scipy.constants` is updated to the CODATA 2014 recommended values. Usage of `scipy.fftpack` functions within Scipy has been changed in such a way that `PyFFTW `__ can easily replace `scipy.fftpack` functions (with improved performance). See `gh-5295 `__ for details. The ``imread`` functions in `scipy.misc` and `scipy.ndimage` were unified, for which a ``mode`` argument was added to `scipy.misc.imread`. Also, bugs for 1-bit and indexed RGB image formats were fixed. ``runtests.py``, the development script to build and test Scipy, now allows building in parallel with ``--parallel``. Authors ======= * @cel4 + * @chemelnucfin + * @endolith * @mamrehn + * @tosh1ki + * Joshua L. Adelman + * Anne Archibald * Herv? Audren + * Vincent Barrielle + * Bruno Beltran + * Sumit Binnani + * Joseph Jon Booker * Olga Botvinnik + * Michael Boyle + * Matthew Brett * Zaz Brown + * Lars Buitinck * Pete Bunch + * Evgeni Burovski * CJ Carey * Ien Cheng + * Cody + * Jaime Fernandez del Rio * Ales Erjavec + * Abraham Escalante * Yves-R?mi Van Eycke + * Yu Feng + * Eric Firing * Francis T. O'Donovan + * Andr? Gaul * Christoph Gohlke * Ralf Gommers * Alex Griffing * Alexander Grigorievskiy * Charles Harris * J?rn Hees + * Ian Henriksen * Derek Homeier + * David Men?ndez Hurtado * Gert-Ludwig Ingold * Aakash Jain + * Rohit Jamuar + * Jan Schl?ter * Johannes Ball? * Luke Zoltan Kelley + * Jason King + * Andreas Kopecky + * Eric Larson * Denis Laxalde * Antony Lee * Gregory R. Lee * Josh Levy-Kramer + * Sam Lewis + * Fran?ois Magimel + * Mart?n Gait?n + * Sam Mason + * Andreas Mayer * Nikolay Mayorov * Damon McDougall + * Robert McGibbon * Sturla Molden * Will Monroe + * Eric Moore * Maniteja Nandana * Vikram Natarajan + * Andrew Nelson * Marti Nito + * Behzad Nouri + * Daisuke Oyama + * Giorgio Patrini + * Fabian Paul + * Christoph Paulik + * Mad Physicist + * Irvin Probst * Sebastian Pucilowski + * Ted Pudlik + * Eric Quintero * Yoav Ram + * Joscha Reimer + * Juha Remes * Frederik Rietdijk + * R?my L?one + * Christian Sachs + * Skipper Seabold * Sebastian Skoup? + * Alex Seewald + * Andreas Sorge + * Bernardo Sulzbach + * Julian Taylor * Louis Tiao + * Utkarsh Upadhyay + * Jacob Vanderplas * Gael Varoquaux + * Pauli Virtanen * Fredrik Wallner + * Stefan van der Walt * James Webber + * Warren Weckesser * Raphael Wettinger + * Josh Wilson + * Nat Wilson + * Peter Yin + A total of 101 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. Issues closed for 0.17.0 - ------------------------ - - `#1923 `__: problem with numpy 0's in stats.poisson.rvs (Trac #1398) - - `#2138 `__: scipy.misc.imread segfaults on 1 bit png (Trac #1613) - - `#2237 `__: distributions do not accept complex arguments (Trac #1718) - - `#2282 `__: scipy.special.hyp1f1(0.5, 1.5, -1000) fails (Trac #1763) - - `#2618 `__: poisson.pmf returns NaN if mu is 0 - - `#2957 `__: hyp1f1 precision issue - - `#2997 `__: FAIL: test_qhull.TestUtilities.test_more_barycentric_transforms - - `#3129 `__: No way to set ranges for fitting parameters in Optimize functions - - `#3191 `__: interp1d should contain a fill_value_below and a fill_value_above... - - `#3453 `__: PchipInterpolator sets slopes at edges differently than Matlab's... - - `#4106 `__: ndimage._ni_support._normalize_sequence() fails with numpy.int64 - - `#4118 `__: `scipy.integrate.ode.set_solout` called after `scipy.integrate.ode.set_initial_value` fails silently - - `#4233 `__: 1D scipy.interpolate.griddata using method=nearest produces nans... - - `#4375 `__: All tests fail due to bad file permissions - - `#4580 `__: scipy.ndimage.filters.convolve documenation is incorrect - - `#4627 `__: logsumexp with sign indicator - enable calculation with negative... - - `#4702 `__: logsumexp with zero scaling factor - - `#4834 `__: gammainc should return 1.0 instead of NaN for infinite x - - `#4838 `__: enh: exprel special function - - `#4862 `__: the scipy.special.boxcox function is inaccurate for denormal... - - `#4887 `__: Spherical harmonic incongruences - - `#4895 `__: some scipy ufuncs have inconsistent output dtypes? - - `#4923 `__: logm does not aggressively convert complex outputs to float - - `#4932 `__: BUG: stats: The `fit` method of the distributions silently ignores... - - `#4956 `__: Documentation error in `scipy.special.bi_zeros` - - `#4957 `__: Docstring for `pbvv_seq` is wrong - - `#4967 `__: block_diag should look at dtypes of all arguments, not only the... - - `#5037 `__: scipy.optimize.minimize error messages are printed to stdout... - - `#5039 `__: Cubic interpolation: On entry to DGESDD parameter number 12 had... - - `#5163 `__: Base case example of Hierarchical Clustering (offer) - - `#5181 `__: BUG: stats.genextreme.entropy should use the explicit formula - - `#5184 `__: Some? wheels don't express a numpy dependency - - `#5197 `__: mstats: test_kurtosis fails (ULP max is 2) - - `#5260 `__: Typo causing an error in splrep - - `#5263 `__: Default epsilon in rbf.py fails for colinear points - - `#5276 `__: Reading empty (no data) arff file fails - - `#5280 `__: 1d scipy.signal.convolve much slower than numpy.convolve - - `#5326 `__: Implementation error in scipy.interpolate.PchipInterpolator - - `#5370 `__: Test issue with test_quadpack and libm.so as a linker script - - `#5426 `__: ERROR: test_stats.test_chisquare_masked_arrays - - `#5427 `__: Automate installing correct numpy versions in numpy-vendor image - - `#5430 `__: Python3 : Numpy scalar types "not iterable"; specific instance... - - `#5450 `__: BUG: spatial.ConvexHull triggers a seg. fault when given nans. - - `#5478 `__: clarify the relation between matrix normal distribution and `multivariate_normal` - - `#5539 `__: lstsq related test failures on windows binaries from numpy-vendor - - `#5560 `__: doc: scipy.stats.burr pdf issue - - `#5571 `__: lstsq test failure after lapack_driver change - - `#5577 `__: ordqz segfault on Python 3.4 in Wine - - `#5578 `__: scipy.linalg test failures on python 3 in Wine - - `#5607 `__: Overloaded ?isnan(double&)? is ambiguous when compiling with... - - `#5629 `__: Test for lstsq randomly failed - - `#5630 `__: memory leak with scipy 0.16 spatial cKDEtree - - `#5689 `__: isnan errors compiling scipy/special/Faddeeva.cc with clang++ - - `#5694 `__: fftpack test failure in test_import - - `#5719 `__: curve_fit(method!="lm") ignores initial guess Pull requests for 0.17.0 - ------------------------ - - `#3022 `__: hyp1f1: better handling of large negative arguments - - `#3107 `__: ENH: Add ordered QZ decomposition - - `#4390 `__: ENH: Allow axis and keepdims arguments to be passed to scipy.linalg.norm. - - `#4671 `__: ENH: add axis to sparse norms - - `#4796 `__: ENH: Add cut tree function to scipy.cluster.hierarchy - - `#4809 `__: MAINT: cauchy moments are undefined - - `#4821 `__: ENH: stats: make distribution instances picklable - - `#4839 `__: ENH: Add scipy.special.exprel relative error exponential ufunc - - `#4859 `__: Logsumexp fixes - allows sign flags and b==0 - - `#4865 `__: BUG: scipy.io.mmio.write: error with big indices and low precision - - `#4869 `__: add as_inexact option to _lib._util._asarray_validated - - `#4884 `__: ENH: Finite difference approximation of Jacobian matrix - - `#4890 `__: ENH: Port cKDTree query methods to C++, allow pickling on Python... - - `#4892 `__: how much doctesting is too much? - - `#4896 `__: MAINT: work around a possible numpy ufunc loop selection bug - - `#4898 `__: MAINT: A bit of pyflakes-driven cleanup. - - `#4899 `__: ENH: add 'alternative' keyword to hypothesis tests in stats - - `#4903 `__: BENCH: Benchmarks for interpolate module - - `#4905 `__: MAINT: prepend underscore to mask_to_limits; delete masked_var. - - `#4906 `__: MAINT: Benchmarks for optimize.leastsq - - `#4910 `__: WIP: Trimmed statistics functions have inconsistent API. - - `#4912 `__: MAINT: fix typo in stats tutorial. Closes gh-4911. - - `#4914 `__: DEP: deprecate `scipy.stats.ss` and `scipy.stats.square_of_sums`. - - `#4924 `__: MAINT: if the imaginary part of logm of a real matrix is small,... - - `#4930 `__: BENCH: Benchmarks for signal module - - `#4941 `__: ENH: update `find_repeats`. - - `#4942 `__: MAINT: use np.float64_t instead of np.float_t in cKDTree - - `#4944 `__: BUG: integer overflow in correlate_nd - - `#4951 `__: do not ignore invalid kwargs in distributions fit method - - `#4958 `__: Add some detail to docstrings for special functions - - `#4961 `__: ENH: stats.describe: add bias kw and empty array handling - - `#4963 `__: ENH: scipy.sparse.coo.coo_matrix.__init__: less memory needed - - `#4968 `__: DEP: deprecate ``stats.f_value*`` and ``mstats.f_value*`` functions. - - `#4969 `__: ENH: review `stats.relfreq` and `stats.cumfreq`; fixes to `stats.histogram` - - `#4971 `__: Extend github source links to line ranges - - `#4972 `__: MAINT: impove the error message in validate_runtests_log - - `#4976 `__: DEP: deprecate `scipy.stats.threshold` - - `#4977 `__: MAINT: more careful dtype treatment in block diagonal matrix... - - `#4979 `__: ENH: distributions, complex arguments - - `#4984 `__: clarify dirichlet distribution error handling - - `#4992 `__: ENH: `stats.fligner` and `stats.bartlett` empty input handling. - - `#4996 `__: DOC: fix stats.spearmanr docs - - `#4997 `__: Fix up boxcox for underflow / loss of precision - - `#4998 `__: DOC: improved documentation for `stats.ppcc_max` - - `#5000 `__: ENH: added empty input handling `scipy.moment`; doc enhancements - - `#5003 `__: ENH: improves rankdata algorithm - - `#5005 `__: scipy.stats: numerical stability improvement - - `#5007 `__: ENH: nan handling in functions that use `stats._chk_asarray` - - `#5009 `__: remove coveralls.io - - `#5010 `__: Hypergeometric distribution log survival function - - `#5014 `__: Patch to compute the volume and area of convex hulls - - `#5015 `__: DOC: Fix mistaken variable name in sawtooth - - `#5016 `__: DOC: resample example - - `#5017 `__: DEP: deprecate `stats.betai` and `stats.chisqprob` - - `#5018 `__: ENH: Add test on random inpu to volume computations - - `#5026 `__: BUG: Fix return dtype of lil_matrix.getnnz(axis=0) - - `#5030 `__: DOC: resample slow for prime output too - - `#5033 `__: MAINT: integrate, special: remove unused R1MACH and Makefile - - `#5034 `__: MAINT: signal: lift max_len_seq validation out of Cython - - `#5035 `__: DOC/MAINT: refguide / doctest drudgery - - `#5041 `__: BUG: fixing some small memory leaks detected by cppcheck - - `#5044 `__: [GSoC] ENH: New least-squares algorithms - - `#5050 `__: MAINT: C fixes, trimmed a lot of dead code from Cephes - - `#5057 `__: ENH: sparse: avoid densifying on sparse/dense elementwise mult - - `#5058 `__: TST: stats: add a sample distribution to the test loop - - `#5061 `__: ENH: spatial: faster 2D Voronoi and Convex Hull plotting - - `#5065 `__: TST: improve test coverage for `stats.mvsdist` and `stats.bayes_mvs` - - `#5066 `__: MAINT: fitpack: remove a noop - - `#5067 `__: ENH: empty and nan input handling for `stats.kstat` and `stats.kstatvar` - - `#5071 `__: DOC: optimize: Correct paper reference, add doi - - `#5072 `__: MAINT: scipy.sparse cleanup - - `#5073 `__: DOC: special: Add an example showing the relation of diric to... - - `#5075 `__: DOC: clarified parameterization of stats.lognorm - - `#5076 `__: use int, float, bool instead of np.int, np.float, np.bool - - `#5078 `__: DOC: Rename fftpack docs to README - - `#5081 `__: BUG: Correct handling of scalar 'b' in lsmr and lsqr - - `#5082 `__: loadmat variable_names: don't confuse [] and None. - - `#5083 `__: Fix integrate.fixed_quad docstring to indicate None return value - - `#5086 `__: Use solve() instead of inv() for gaussian_kde - - `#5090 `__: MAINT: stats: add explicit _sf, _isf to gengamma distribution - - `#5094 `__: ENH: scipy.interpolate.NearestNDInterpolator: cKDTree configurable - - `#5098 `__: DOC: special: fix typesetting in ``*_roots quadrature`` functions - - `#5099 `__: DOC: make the docstring of stats.moment raw - - `#5104 `__: DOC/ENH fixes and micro-optimizations for scipy.linalg - - `#5105 `__: enh: made l-bfgs-b parameter for the maximum number of line search... - - `#5106 `__: TST: add NIST test cases to `stats.f_oneway` - - `#5110 `__: [GSoC]: Bounded linear least squares - - `#5111 `__: MAINT: special: Cephes cleanup - - `#5118 `__: BUG: FIR path failed if len(x) < len(b) in lfilter. - - `#5124 `__: ENH: move the filliben approximation to a publicly visible function - - `#5126 `__: StatisticsCleanup: `stats.kruskal` review - - `#5130 `__: DOC: update PyPi trove classifiers. Beta -> Stable. Add license. - - `#5131 `__: DOC: differential_evolution, improve docstring for mutation and... - - `#5132 `__: MAINT: differential_evolution improve init_population_lhs comments... - - `#5133 `__: MRG: rebased mmio refactoring - - `#5135 `__: MAINT: `stats.mstats` consistency with `stats.stats` - - `#5139 `__: TST: linalg: add a smoke test for gh-5039 - - `#5140 `__: EHN: Update constants.codata to CODATA 2014 - - `#5145 `__: added ValueError to docstring as possible error raised - - `#5146 `__: MAINT: Improve implementation details and doc in `stats.shapiro` - - `#5147 `__: [GSoC] ENH: Upgrades to curve_fit - - `#5150 `__: Fix misleading wavelets/cwt example - - `#5152 `__: BUG: cluster.hierarchy.dendrogram: missing font size doesn't... - - `#5153 `__: add keywords to control the summation in discrete distributions... - - `#5156 `__: DOC: added comments on algorithms used in Legendre function - - `#5158 `__: ENH: optimize: add the Hungarian algorithm - - `#5162 `__: FIX: Remove lena - - `#5164 `__: MAINT: fix cluster.hierarchy.dendrogram issues and docs - - `#5166 `__: MAINT: changed `stats.pointbiserialr` to delegate to `stats.pearsonr` - - `#5167 `__: ENH: add nan_policy to `stats.kendalltau`. - - `#5168 `__: TST: added nist test case (Norris) to `stats.linregress`. - - `#5169 `__: update lpmv docstring - - `#5171 `__: Clarify metric parameter in linkage docstring - - `#5172 `__: ENH: add mode keyword to signal.spectrogram - - `#5177 `__: DOC: graphical example for KDTree.query_ball_point - - `#5179 `__: MAINT: stats: tweak the formula for ncx2.pdf - - `#5188 `__: MAINT: linalg: A bit of clean up. - - `#5189 `__: BUG: stats: Use the explicit formula in stats.genextreme.entropy - - `#5193 `__: BUG: fix uninitialized use in lartg - - `#5194 `__: BUG: properly return error to fortran from ode_jacobian_function - - `#5198 `__: TST: Fix TestCtypesQuad failure on Python 3.5 for Windows - - `#5201 `__: allow extrapolation in interp1d - - `#5209 `__: MAINT: Change complex parameter to boolean in Y_() - - `#5213 `__: BUG: sparse: fix logical comparison dtype conflicts - - `#5216 `__: BUG: sparse: fixing unbound local error - - `#5218 `__: DOC and BUG: Bessel function docstring improvements, fix array_like,... - - `#5222 `__: MAINT: sparse: fix COO ctor - - `#5224 `__: DOC: optimize: type of OptimizeResult.hess_inv varies - - `#5228 `__: ENH: Add maskandscale support to netcdf; based on pupynere and... - - `#5229 `__: DOC: sparse.linalg.svds doc typo fixed - - `#5234 `__: MAINT: sparse: simplify COO ctor - - `#5235 `__: MAINT: sparse: warn on todia() with many diagonals - - `#5236 `__: MAINT: ndimage: simplify thread handling/recursion + constness - - `#5239 `__: BUG: integrate: Fixed issue 4118 - - `#5241 `__: qr_insert fixes, closes #5149 - - `#5246 `__: Doctest tutorial files - - `#5247 `__: DOC: optimize: typo/import fix in linear_sum_assignment - - `#5248 `__: remove inspect.getargspec and test python 3.5 on Travis CI - - `#5250 `__: BUG: Fix sparse multiply by single-element zero - - `#5261 `__: Fix bug causing a TypeError in splrep when a runtime warning... - - `#5262 `__: Follow up to 4489 (Addition LAPACK routines in linalg.lstsq) - - `#5264 `__: ignore zero-length edges for default epsilon - - `#5269 `__: DOC: Typos and spell-checking - - `#5272 `__: MAINT: signal: Convert array syntax to memoryviews - - `#5273 `__: DOC: raw strings for docstrings with math - - `#5274 `__: MAINT: sparse: update cython code for MST - - `#5278 `__: BUG: io: Stop guessing the data delimiter in ARFF files. - - `#5289 `__: BUG: misc: Fix the Pillow work-around for 1-bit images. - - `#5291 `__: ENH: call np.correlate for 1d in scipy.signal.correlate - - `#5294 `__: DOC: special: Remove a potentially misleading example from the... - - `#5295 `__: Simplify replacement of fftpack by pyfftw - - `#5296 `__: ENH: Add matrix normal distribution to stats - - `#5297 `__: Fixed leaf_rotation and leaf_font_size in Python 3 - - `#5303 `__: MAINT: stats: rewrite find_repeats - - `#5307 `__: MAINT: stats: remove unused Fortran routine - - `#5313 `__: BUG: sparse: fix diags for nonsquare matrices - - `#5315 `__: MAINT: special: Cephes cleanup - - `#5316 `__: fix input check for sparse.linalg.svds - - `#5319 `__: MAINT: Cython code maintenance - - `#5328 `__: BUG: Fix place_poles return values - - `#5329 `__: avoid a spurious divide-by-zero in Student t stats - - `#5334 `__: MAINT: integrate: miscellaneous cleanup - - `#5340 `__: MAINT: Printing Error Msg to STDERR and Removing iterate.dat - - `#5347 `__: ENH: add Py3.5-style matmul operator (e.g. A @ B) to sparse linear... - - `#5350 `__: FIX error, when reading 32-bit float wav files - - `#5351 `__: refactor the PCHIP interpolant's algorithm - - `#5354 `__: MAINT: construct csr and csc matrices from integer lists - - `#5359 `__: add a fast path to interp1d - - `#5364 `__: Add two fill_values to interp1d. - - `#5365 `__: ABCD docstrings - - `#5366 `__: Fixed typo in the documentation for scipy.signal.cwt() per #5290. - - `#5367 `__: DOC updated scipy.spatial.Delaunay example - - `#5368 `__: ENH: Do not create a throwaway class at every function call - - `#5372 `__: DOC: spectral: fix reference formatting - - `#5375 `__: PEP8 amendments to ffpack_basic.py - - `#5377 `__: BUG: integrate: builtin name no longer shadowed - - `#5381 `__: PEP8ified fftpack_pseudo_diffs.py - - `#5385 `__: BLD: fix Bento build for changes to optimize and spatial - - `#5386 `__: STY: PEP8 amendments to interpolate.py - - `#5387 `__: DEP: deprecate stats.histogram - - `#5388 `__: REL: add "make upload" command to doc/Makefile. - - `#5389 `__: DOC: updated origin param of scipy.ndimage.filters.convolve - - `#5395 `__: BUG: special: fix a number of edge cases related to `x = np.inf`. - - `#5398 `__: MAINT: stats: avoid spurious warnings in lognorm.pdf(0, s) - - `#5407 `__: ENH: stats: Handle mu=0 in stats.poisson - - `#5409 `__: Fix the behavior of discrete distributions at the right-hand... - - `#5412 `__: TST: stats: skip a test to avoid a spurious log(0) warning - - `#5413 `__: BUG: linalg: work around LAPACK single-precision lwork computation... - - `#5414 `__: MAINT: stats: move creation of namedtuples outside of function... - - `#5415 `__: DOC: fix up sections in ToC in the pdf reference guide - - `#5416 `__: TST: fix issue with a ctypes test for integrate on Fedora. - - `#5418 `__: DOC: fix bugs in signal.TransferFunction docstring. Closes gh-5287. - - `#5419 `__: MAINT: sparse: fix usage of NotImplementedError - - `#5420 `__: Raise proper error if maxiter < 1 - - `#5422 `__: DOC: changed documentation of brent to be consistent with bracket - - `#5444 `__: BUG: gaussian_filter, BPoly.from_derivatives fail on numpy int... - - `#5445 `__: MAINT: stats: fix incorrect deprecation warnings and test noise - - `#5446 `__: DOC: add note about PyFFTW in fftpack tutorial. - - `#5459 `__: DOC: integrate: Some improvements to the differential equation... - - `#5465 `__: BUG: Relax mstats kurtosis test tolerance by a few ulp - - `#5471 `__: ConvexHull should raise ValueError for NaNs. - - `#5473 `__: MAINT: update decorators.py module to version 4.0.5 - - `#5476 `__: BUG: imsave searches for wrong channel axis if image has 3 or... - - `#5477 `__: BLD: add numpy to setup/install_requires for OS X wheels - - `#5479 `__: ENH: return Jacobian/Hessian from BasinHopping - - `#5484 `__: BUG: fix ttest zero division handling - - `#5486 `__: Fix crash on kmeans2 - - `#5491 `__: MAINT: Expose parallel build option to runtests.py - - `#5494 `__: Sort OptimizeResult.__repr__ by key - - `#5496 `__: DOC: update the author name mapping - - `#5497 `__: Enhancement to binned_statistic: option to unraveled returned... - - `#5498 `__: BUG: sparse: fix a bug in sparsetools input dtype resolution - - `#5500 `__: DOC: detect unprintable characters in docstrings - - `#5505 `__: BUG: misc: Ensure fromimage converts mode 'P' to 'RGB' or 'RGBA'. - - `#5514 `__: DOC: further update the release notes - - `#5515 `__: ENH: optionally disable fixed-point acceleration - - `#5517 `__: DOC: Improvements and additions to the matrix_normal doc - - `#5518 `__: Remove wrappers for LAPACK deprecated routines - - `#5521 `__: TST: skip a linalg.orth memory test on 32-bit platforms. - - `#5523 `__: DOC: change a few floats to integers in docstring examples - - `#5524 `__: DOC: more updates to 0.17.0 release notes. - - `#5525 `__: Fix to minor typo in documentation for scipy.integrate.ode - - `#5527 `__: TST: bump arccosh tolerance to allow for inaccurate numpy or... - - `#5535 `__: DOC: signal: minor clarification to docstring of TransferFunction. - - `#5538 `__: DOC: signal: fix find_peaks_cwt documentation - - `#5545 `__: MAINT: Fix typo in linalg/basic.py - - `#5547 `__: TST: mark TestEig.test_singular as knownfail in master. - - `#5550 `__: MAINT: work around lstsq driver selection issue - - `#5556 `__: BUG: Fixed broken dogbox trust-region radius update - - `#5561 `__: BUG: eliminate warnings, exception (on Win) in test_maskandscale;... - - `#5567 `__: TST: a few cleanups in the test suite; run_module_suite and clearer... - - `#5568 `__: MAINT: simplify poisson's _argcheck - - `#5569 `__: TST: bump GMean test tolerance to make it pass on Wine - - `#5572 `__: TST: lstsq: bump test tolerance for TravisCI - - `#5573 `__: TST: remove use of np.fromfile from cluster.vq tests - - `#5576 `__: Lapack deprecations - - `#5579 `__: TST: skip tests of linalg.norm axis keyword on numpy <= 1.7.x - - `#5582 `__: Clarify language of survival function documentation - - `#5583 `__: MAINT: stats/tests: A bit of clean up. - - `#5588 `__: DOC: stats: Add a note that stats.burr is the Type III Burr distribution. - - `#5595 `__: TST: fix test_lamch failures on Python 3 - - `#5600 `__: MAINT: Ignore spatial/ckdtree.cxx and .h - - `#5602 `__: Explicitly numbered replacement fields for maintainability - - `#5605 `__: MAINT: collection of small fixes to test suite - - `#5614 `__: Minor doc change. - - `#5624 `__: FIX: Fix interpolate - - `#5625 `__: BUG: msvc9 binaries crash when indexing std::vector of size 0 - - `#5635 `__: BUG: misspelled __dealloc__ in cKDTree. - - `#5642 `__: STY: minor fixup of formatting of 0.17.0 release notes. - - `#5643 `__: BLD: fix a build issue in special/Faddeeva.cc with isnan. - - `#5661 `__: TST: linalg tests used stdlib random instead of numpy.random. - - `#5682 `__: backports for 0.17.0 - - `#5696 `__: Minor improvements to least_squares' docstring. - - `#5697 `__: BLD: fix for isnan/isinf issues in special/Faddeeva.cc - - `#5720 `__: TST: fix for file opening error in fftpack test_import.py - - `#5722 `__: BUG: Make curve_fit respect an initial guess with bounds - - `#5726 `__: Backports for v0.17.0rc2 - - `#5727 `__: API: Changes to least_squares API Checksums ========= MD5 ~~~ 5ff2971e1ce90e762c59d2cd84837224 scipy-0.17.0.tar.gz ef0949640ee73f845dde6dd7f84d7691 scipy-0.17.0.tar.xz 28a4fe29e980804db162524f10873211 scipy-0.17.0.zip SHA256 ~~~~~~ f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089 scipy-0.17.0.tar.gz 2bc03ea36cd55bfd80869d87f690334b4cad240373e05857ddfa7a4d1e2f9a7a scipy-0.17.0.tar.xz ede6820030b2e5796126aa1571d86738b14bbd670d68c83378877b1d9eb9894d scipy-0.17.0.zip -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) iQEcBAEBAgAGBQJWokWbAAoJEIp0pQ0zQcu+JUgH/16Qqurptl3jUU11+4pl+8ji 3AFZN+dgzGLyiMz9s+V+OyL4hcdZY4++WM2QizF5uD3hDDFNi+aJRHAYySMAZeIZ O8y//v+DXDVOLZpKwcPFq5E5ZebTDh1jO4zZzpuyi1PnKgTAEKZeSyBSMd0RMx/p kZ0URTcAa/tPgkNZz3+i8By9b/zBWOlbI+v6fCVwV8E20YWfGBSp2s0KAtQk787D Q88ylnc3Zfv4IR1hgCFZz6oJA0RgmpH4USKi7guyg+fIKjf1nFe64zIuV3C2r/Uj y9Qbs/8x/HTteDp5owkRiSwnpTZHOtx/jqeh2z/w9aQe0i8Nag5Ere6JZ2kixG4= =jZUn -----END PGP SIGNATURE----- From mviljamaa at kapsi.fi Sat Jan 23 13:01:02 2016 From: mviljamaa at kapsi.fi (mviljamaa) Date: Sat, 23 Jan 2016 20:01:02 +0200 Subject: [SciPy-User] freqs parameter in scipy.signal.lombscargle? Message-ID: <83c93a1ee2fd0a1addfab2be7246d56e@kapsi.fi> What's the freqs parameter in scipy.signal.lombscargle? How can they be computed/generated if my data is e.g. 2D or a time series? From gnurser at gmail.com Tue Jan 26 05:14:54 2016 From: gnurser at gmail.com (George Nurser) Date: Tue, 26 Jan 2016 10:14:54 +0000 Subject: [SciPy-User] ANN: xarray (formerly xray) v0.7.0 released In-Reply-To: References: Message-ID: It's a very nice package. Pip install works fine, but the new version doesn't seem to be up on conda yet: ~ $ conda install xarray dask netCDF4 bottleneck Using Anaconda Cloud api site https://api.anaconda.org Fetching package metadata: .... Error: No packages found in current linux-64 channels matching: xarray Best regards, George Nurser On 22 January 2016 at 03:05, Stephan Hoyer wrote: > I am pleased to announce version v0.7.0 of xarray, the project formerly > known as xray. > > xarray is an open source project and Python package that aims to bring > the labeled data power of pandas to the physical sciences, by providing > N-dimensional variants of the core pandas data structures. These data > structures are based on the data model of the netCDF file format. > > In this latest release, we have renamed the project from "xray" to > "xarray". This avoids a namespace conflict with the entire field of X-ray > science. We have new URLs for our documentation, source code and mailing > list: > http://xarray.pydata.org/ > http://github.com/pydata/xarray/ > https://groups.google.com/forum/#!forum/xarray > > Highlights of this release: > > * An internal refactor of DataArray internals > * New methods for reshaping, rolling and shifting data > * Preliminary support for pandas.MultiIndex > * Support for reading GRIB, HDF4 and other file formats via PyNIO > > For more details, read the full release notes: > http://xarray.pydata.org/en/stable/whats-new.html > > Contributors to this release: > > Antony Lee > Fabien Maussion > Joe Hamman > Maximilian Roos > Stephan Hoyer > Takeshi Kanmae > femtotrader > > I'd also like to highlight the contributions of Clark Fitzgerald, who > added a plotting module to xray in v0.6, and Dave Brown, for his assistance > adding PyNIO support. > > Best, > Stephan > > _______________________________________________ > SciPy-User mailing list > SciPy-User at scipy.org > https://mail.scipy.org/mailman/listinfo/scipy-user > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From charlesr.harris at gmail.com Tue Jan 26 15:49:30 2016 From: charlesr.harris at gmail.com (Charles R Harris) Date: Tue, 26 Jan 2016 13:49:30 -0700 Subject: [SciPy-User] Numpy 1.11.0b1 is out Message-ID: Hi All, I'm pleased to announce that Numpy 1.11.0b1 is now available on sourceforge. This is a source release as the mingw32 toolchain is broken. Please test it out and report any errors that you discover. Hopefully we can do better with 1.11.0 than we did with 1.10.0 ;) Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From nadavh at visionsense.com Wed Jan 27 06:19:02 2016 From: nadavh at visionsense.com (Nadav Horesh) Date: Wed, 27 Jan 2016 11:19:02 +0000 Subject: [SciPy-User] [Numpy-discussion] Numpy 1.11.0b1 is out In-Reply-To: References: Message-ID: Why the dot function/method is slower than @ on python 3.5.1? Tested from the latest 1.11 maintenance branch. np.__version__ Out[39]: '1.11.0.dev0+Unknown' %timeit A @ c 10000 loops, best of 3: 185 ?s per loop %timeit A.dot(c) 1000 loops, best of 3: 526 ?s per loop %timeit np.dot(A,c) 1000 loops, best of 3: 527 ?s per loop A.dtype, A.shape, A.flags Out[43]:? (dtype('float32'), (100, 100, 3), ? C_CONTIGUOUS : True ? ?F_CONTIGUOUS : False ? ?OWNDATA : True ? ?WRITEABLE : True ? ?ALIGNED : True ? ?UPDATEIFCOPY : False) c.dtype, c.shape, c.flags Out[44]:? (dtype('float32'), (3, 3), ? C_CONTIGUOUS : True ? ?F_CONTIGUOUS : False ? ?OWNDATA : True ? ?WRITEABLE : True ? ?ALIGNED : True ? ?UPDATEIFCOPY : False) From: NumPy-Discussion on behalf of Charles R Harris Sent: 26 January 2016 22:49 To: numpy-discussion; SciPy Developers List; SciPy Users List Subject: [Numpy-discussion] Numpy 1.11.0b1 is out ? Hi All, I'm pleased to announce that Numpy 1.11.0b1 is now available on sourceforge. This is a source release as the mingw32 toolchain is broken. Please test it out and report any errors that you discover. Hopefully we can do better with 1.11.0 than we did with 1.10.0 ;) Chuck From charlesr.harris at gmail.com Thu Jan 28 15:51:49 2016 From: charlesr.harris at gmail.com (Charles R Harris) Date: Thu, 28 Jan 2016 13:51:49 -0700 Subject: [SciPy-User] Numpy 1.11.0b2 released Message-ID: Hi All, I hope I am pleased to announce the Numpy 1.11.0b2 release. The first beta was a damp squib due to missing files in the released source files, this release fixes that. The new source filese may be downloaded from sourceforge, no binaries will be released until the mingw tool chain problems are sorted. Please test and report any problem. Chuck -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.brett at gmail.com Thu Jan 28 16:29:11 2016 From: matthew.brett at gmail.com (Matthew Brett) Date: Thu, 28 Jan 2016 13:29:11 -0800 Subject: [SciPy-User] [Numpy-discussion] Numpy 1.11.0b2 released In-Reply-To: References: Message-ID: Hi, On Thu, Jan 28, 2016 at 12:51 PM, Charles R Harris wrote: > Hi All, > > I hope I am pleased to announce the Numpy 1.11.0b2 release. The first beta > was a damp squib due to missing files in the released source files, this > release fixes that. The new source filese may be downloaded from > sourceforge, no binaries will be released until the mingw tool chain > problems are sorted. > > Please test and report any problem. OSX wheels build OK: https://travis-ci.org/MacPython/numpy-wheels/builds/105521850 Y'all can test with: pip install --pre --trusted-host wheels.scipy.org -f http://wheels.scipy.org numpy Cheers, Matthew From novosirj at ca.rutgers.edu Fri Jan 29 13:08:29 2016 From: novosirj at ca.rutgers.edu (Novosielski, Ryan) Date: Fri, 29 Jan 2016 13:08:29 -0500 Subject: [SciPy-User] Build Questions, Intel Compilers/MKL (16), CentOS 7.2 Message-ID: Hi there, 1) I?m trying to get an answer to something that isn?t explained in any of the documentation I?ve found about building NumPy/SciPy with the Intel compilers. What I?ve been looking at is both here: https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl ?and here: http://www.scipy.org/scipylib/building/linux.html#intel-mkl-11-0-updated-dec-2012 ?which agree with one another. If you look at these, both say to build NumPy, do this: $ python setup.py config --compiler=intelem build_clib --compiler=intelem build_ext --compiler=intelem install For SciPy, they say to do this: $ python setup.py config --compiler=intelem --fcompiler=intelem build_clib --compiler=intelem --fcompiler=intelem build_ext --compiler=intelem --fcompiler=intelem install ?but neither one says why we?re not using the Intel Fortran compiler for NumPy. I assumed at first it might be because NumPy doesn?t have Fortran code or something, but I see during the build process, gfortran is definitely used. Can anyone shed some light on this one? It builds fine if I use the same command to build NumPy as the recommended one for SciPy. Somewhat related, the Intel link above recommends a set of compiler flags: self.cc_exe = 'icc -O3 -g -fPIC -fp-model strict -fomit-frame-pointer -openmp -xhost? ?which does work to build NumPy. However, when I build SciPy, I?m seeing a lot of -xSSE4.2 on the Fortran compiles: compiling Fortran sources Fortran f77 compiler: /opt/intel/compilers_and_libraries_2016.1.150/linux/bin/intel64/ifort -FI -fPIC -openmp -fp-model strict -xSSE4.2 Fortran f90 compiler: /opt/intel/compilers_and_libraries_2016.1.150/linux/bin/intel64/ifort -FR -fPIC -openmp -fp-model strict -xSSE4.2 Fortran fix compiler: /opt/intel/compilers_and_libraries_2016.1.150/linux/bin/intel64/ifort -FI -fPIC -openmp -fp-model strict -xSSE4.2 2) Ideally I?d want to use -xAVX if it were possible (which is what -xhost is doing since I?m building on an AVX-capable machine). There doesn?t seem to be anyplace to set this in SciPy, and there is some indication from reading about SciPy that it uses NumPy?s build setup somehow. Any idea why this is happening? Thanks! -- ____ *Note: UMDNJ is now Rutgers-Biomedical and Health Sciences* || \\UTGERS |---------------------*O*--------------------- ||_// Biomedical | Ryan Novosielski - Senior Technologist || \\ and Health | novosirj at rutgers.edu - 973/972.0922 (2x0922) || \\ Sciences | OIRT/High Perf & Res Comp - MSB C630, Newark `' -------------- next part -------------- A non-text attachment was scrubbed... Name: signature.asc Type: application/pgp-signature Size: 204 bytes Desc: Message signed with OpenPGP using GPGMail URL: