Mailman 3 October 2015 - SciPy-Dev

Re: [SciPy-Dev] Setting up a dev environment with conda
by Luke Zoltan Kelley Oct. 17, 2015

Oct. 17, 2015

Charles, that's exactly what I'm trying to do. How do I install from source, to a specific anaconda environment?

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Re: [SciPy-Dev] Setting up a dev environment with conda
by Luke Zoltan Kelley Oct. 17, 2015

Oct. 17, 2015

Charles, that's exactly what I'm trying to do. How do I install from source, to a specific anaconda environment?

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Setting up a dev environment with conda
by Luke Zoltan Kelley Oct. 17, 2015

Oct. 17, 2015

I'm trying to play around with development for numpy. I've just switched over to using anaconda to make this easier, but I'm having trouble with the details. I've installed anaconda, and made an environment for numpy development: $ source activate numpy-py27 $ conda list -e # platform: osx-64 cython=0.23.4=py27_0 nose=1.3.7=py27_0 openssl=1.0.1k=1 pip=7.1.2=py27_0 python=2.7.10=1 readline=6.2=2 setuptools=18.4=py27_0 sqlite=3.8.4.1=1 tk=8.5.18=0 wheel=0.26.0=py27_1 zlib=1.2.8=0 I've cloned my fork of the numpy/numpy git repo to a local directory, and built the module in-place, i.e. $ git clone https://github.com/<USERNAME>/numpy.git $ cd numpy $ python setup.py build_ext --inplace But when I try to install, I get the error: $ python setup.py install Running from numpy source directory. Traceback (most recent call last): File "setup.py", line 264, in <module> setup_package() File "setup.py", line 248, in setup_package from numpy.distutils.core import setup File "/Users/lzkelley/Programs/public/numpy/numpy/distutils/__init__.py", line 21, in <module> from numpy.testing import Tester File "/Users/lzkelley/Programs/public/numpy/numpy/testing/__init__.py", line 14, in <module> from .utils import * File "/Users/lzkelley/Programs/public/numpy/numpy/testing/utils.py", line 17, in <module> from numpy.core import float32, empty, arange, array_repr, ndarray File "/Users/lzkelley/Programs/public/numpy/numpy/core/__init__.py", line 59, in <module> test = Tester().test File "/Users/lzkelley/Programs/public/numpy/numpy/testing/nosetester.py", line 180, in __init__ if raise_warnings is None and '.dev0' in np.__version__: AttributeError: 'module' object has no attribute '__version__' I can circumvent this by adding the `numpy` directory to my `PYTHONPATH` --- but that also prevents me from isolating the development environment... what is the standard procedure here? Thanks! Luke

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[ANN] SciPy India 2015: call for papers
by Prabhu Ramachandran Oct. 16, 2015

Oct. 16, 2015

Hello, [Apologies for the cross-posting!] The CFP and registration for SciPy India 2015 (http://scipy.in) is open. SciPy India 2015 will be held at IIT Bombay between December 14th to December 16th, 2015. Please spread the word! SciPy India is an annual conference on using Python for research and education. The conference is currently in its seventh year. Call for Papers ============= We look forward to your submissions on the use of Python for scientific computing and education. This includes pedagogy, exploration, modeling and analysis from both applied and developmental perspectives. We welcome contributions from academia as well as industry. For details on the paper submission please see here: http://scipy.in/2015/cfp/ Important Dates ================ - Call for proposals end: 24th November 2015 - List of accepted proposals will be published: 1st December 2015. We look forward to seeing you at SciPy India. Regards, Prabhu Ramachandran and Jarrod Millman

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welcome CJ Carey to the Scipy dev team
by Ralf Gommers Oct. 15, 2015

Oct. 15, 2015

Hi all, On behalf of the Scipy developers I'd like to welcome CJ Carey (@perimosocordiae) as a member of the core development team. CJ has been contributing for about 2 years, mainly to scipy.sparse. I'm looking forward to his continued contributions! Cheers, Ralf

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Re: [SciPy-Dev] [Numpy-discussion] Numpy 1.10.1 released.
by Nathaniel Smith Oct. 14, 2015

Oct. 14, 2015

On Oct 14, 2015 9:15 AM, "Chris Barker" <chris.barker(a)noaa.gov> wrote: > > On Mon, Oct 12, 2015 at 9:27 AM, Charles R Harris < charlesr.harris(a)gmail.com> wrote: >> >> * Compiling with msvc9 or msvc10 for 32 bit Windows now requires SSE2. >> This was the easiest fix for what looked to be some miscompiled code when >> SSE2 was not used. > > > Note that there is discusion right now on pyton-dev about requireing SSE2 for teh python.org build of python3.5 -- it does now, so it's fine for third party pacakges to also require it. But there is some talk of removing that requirement -- still a lot of old machines around, I guess -- particular at schools and the like. Note that the 1.10.1 release announcement is somewhat misleading -- apparently the affected builds have actually required SSE2 since numpy 1.8, and the change here just makes it even more required. I'm not sure if this is all 32 bit builds or only ones using msvc that have been needing SSE2 all along. The change in 1.10.1 only affects msvc, which is not what most people are using (IIUC Enthought Canopy uses msvc, but the pypi, gohlke, and Anaconda builds don't). I'm actually not sure if anyone even uses the 32 bit builds at all :-) > Ideally, any binary wheels on PyPi should be compatible with the python.org builds -- so not require SSE2, if the python.org builds don't. > > Though we had this discussion a while back -- and numpy could, and maybe should require more -- did we ever figure out a way to get a meaningful message to the user if they try to run an SSE2 build on a machine without SSE2? It's not that difficult in principle, just someone has to do it :-). -n

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Numpy 1.10.1 released.
by Charles R Harris Oct. 12, 2015

Oct. 12, 2015

Hi All, I'm pleased to announce the release of Numpy 1.10.1. This release fixes some build problems and serves to reset the release number on pipy to something usable. As a note for future release managers, I had to upload these files from the command line, as using the file upload option at pipy resulted in a failure to parse the version. NumPy 1.10.1 Release Notes ************************** This release deals with a few build problems that showed up in 1.10.0. Most users would not have seen these problems. The differences are: * Compiling with msvc9 or msvc10 for 32 bit Windows now requires SSE2. This was the easiest fix for what looked to be some miscompiled code when SSE2 was not used. If you need to compile for 32 bit Windows systems without SSE2 support, mingw32 should still work. * Make compiling with VS2008 python2.7 SDK easier * Change Intel compiler options so that code will also be generated to support systems without SSE4.2. * Some _config test functions needed an explicit integer return in order to avoid the openSUSE rpmlinter erring out. * We ran into a problem with pipy not allowing reuse of filenames and a resulting proliferation of *.*.*.postN releases. Not only were the names getting out of hand, some packages were unable to work with the postN suffix. Numpy 1.10.1 supports Python 2.6 - 2.7 and 3.2 - 3.5. Commits: 45a3d84 DEP: Remove warning for `full` when dtype is set. 0c1a5df BLD: import setuptools to allow compile with VS2008 python2.7 sdk 04211c6 BUG: mask nan to 1 in ordered compare 826716f DOC: Document the reason msvc requires SSE2 on 32 bit platforms. 49fa187 BLD: enable SSE2 for 32-bit msvc 9 and 10 compilers dcbc4cc MAINT: remove Wreturn-type warnings from config checks d6564cb BLD: do not build exclusively for SSE4.2 processors 15cb66f BLD: do not build exclusively for SSE4.2 processors c38bc08 DOC: fix var. reference in percentile docstring 78497f4 DOC: Sync 1.10.0-notes.rst in 1.10.x branch with master. Cheers, Chuck

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Scipy test-failures and absolute tolerance-levels
by Jamuar, Rohit Oct. 12, 2015

Oct. 12, 2015

Hi, I'm one of the engineers from Python Scripting team at Intel Corporation. One of the things that we've been trying to achieve is to improve performance of numerical and scientific computation packages - numpy and scipy, for starters. While building Scipy(v0.16) with Intel Compiler, we see failures that are being caused by stringent absolute tolerance-levels. It also seems that you ran into such problems with these tests earlier<https://github.com/scipy/scipy/pull/4243>. These are some of the failing tests : 1. test_j_roots() (from test_orthogonal in scipy.special) - a. vgq(rf(0.5, -0.5), ef(0.5, -0.5), wf(0.5, -0.5), -1., 1., 25, atol=1e-13) : If the tolerance is changed to 1e-12, the test passes 2. test_js_roots() (from test_orthogonal in scipy.special) - a. vgq(rf(1, 0.5), ef(1, 0.5), wf(1, 0.5), 0., 1., 25, atol=1e-13) : ) : If the tolerance is changed to 1e-12, the test passes b. vgq(rf(68.9, 2.25), ef(68.9, 2.25), wf(68.9, 2.25), 0., 1., 5, atol=2e-14) ) : If the tolerance is changed to 2e-13, the test passes I would really appreciate if you could share your rationale(s) behind altering tolerance-levels - does choosing a new tolerance-level depend on some theoretically defined range or is it chosen empirically? This information would help us better understand the ramifications of changing these values. Thanks, Rohit

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Matrix normal distribution
by Pete Bunch Oct. 12, 2015

Oct. 12, 2015

Hi scipy folks, I'd like to propose adding the matrix normal distribution to scipy.stats. https://github.com/scipy/scipy/pull/5296 It's useful for Bayesian learning of linear systems, especially in combination with the Wishart and inverse Wishart distributions which were recently added to stats. Any comments, questions, criticisms, suggestions? @drpeteb

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plan for 0.16.1 release
by Ralf Gommers Oct. 10, 2015

Oct. 10, 2015

Hi all, Quite a few fixes have accumulated, so it's time for a 0.16.1 bugfix release. I'd like to aim to get this done within two weeks. At the moment what will go in is all open and closed PRs/issues under: https://github.com/scipy/scipy/milestones/0.16.1 https://github.com/scipy/scipy/labels/backport-candidate If you think other things should go in, please speak up or add the PR to the milestone or backport-candidate label. Cheers, Ralf

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