Mailman 3 February 2013 - NumPy-Discussion

A new webpage promoting Compiler technology for CPython
by Travis Oliphant Feb. 16, 2013

Feb. 16, 2013

Hey all, With Numba and Blaze we have been doing a lot of work on what essentially is compiler technology and realizing more and more that we are treading on ground that has been plowed before with many other projects. So, we wanted to create a web-site and perhaps even a mailing list or forum where people could coordinate and communicate about compiler projects, compiler tools, and ways to share efforts and ideas. The website is: http://compilers.pydata.org/ This page is specifically for Compiler projects that either integrate with or work directly with the CPython run-time which is why PyPy is not presently listed. The PyPy project is a great project but we just felt that we wanted to explicitly create a collection of links to compilation projects that are accessible from CPython which are likely less well known. But that is just where we started from. The website is intended to be a community website constructed from a github repository. So, we welcome pull requests from anyone who would like to see the website updated to reflect their related project. Jon Riehl (Mython, PyFront, ROFL, and many other interesting projects) and Stephen Diehl (Blaze) and I will be moderating the pull requests to begin with. But, we welcome others with similar interests to participate in that effort of moderation. The github repository is here: https://github.com/pydata/compilers-webpage This is intended to be a community website for information spreading, and so we welcome any and all contributions. Thank you, Travis Oliphant

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Re: [Numpy-discussion] A proposed change to rollaxis() behavior for negative 'start' values
by Thomas Coffee Feb. 16, 2013

Feb. 16, 2013

Adding to an old discussion thread (see below) ... an implementation of the proposed functionality: from numpy import rollaxis def moveaxis(a, i, j = 0): """ move axis i of array a to position j """ n = a.ndim i = i if i >= 0 else i + n if j > i: return rollaxis(a, i, j + 1) elif j >= 0: return rollaxis(a, i, j) elif j == -1: return rollaxis(a, i, n) elif j >= -i: return rollaxis(a, i, j + 1) else: return rollaxis(a, i, j) Examples: In [464]: a = numpy.ones((3,4,5,6)) In [465]: moveaxis(a,2,0).shape Out[465]: (5, 3, 4, 6) In [466]: moveaxis(a,2,1).shape Out[466]: (3, 5, 4, 6) In [467]: moveaxis(a,2,2).shape Out[467]: (3, 4, 5, 6) In [468]: moveaxis(a,2,3).shape Out[468]: (3, 4, 6, 5) In [469]: moveaxis(a,2,4).shape --------------------------------------------------------------------------- ValueError: rollaxis: start (5) must be >=0 and < 5 In [470]: moveaxis(a,2,-1).shape Out[470]: (3, 4, 6, 5) In [471]: moveaxis(a,2,-2).shape Out[471]: (3, 4, 5, 6) In [472]: moveaxis(a,2,-3).shape Out[472]: (3, 5, 4, 6) In [473]: moveaxis(a,2,-4).shape Out[473]: (5, 3, 4, 6) In [474]: moveaxis(a,2,-5).shape --------------------------------------------------------------------------- ValueError: rollaxis: start (-1) must be >=0 and < 5 On Thu, Sep 23, 2010 at 11:33 AM, Nathaniel Smith wrote: > > On Tue, Sep 21, 2010 at 12:48 PM, Ken Basye <kbasye1(a)jhu.edu> wrote: > > If that's going to break too much code, here's a pathway that might be > > acceptable: Add a new function moveaxis() which works the way > > rollaxis() does for positive arguments but in the new way for negative > > arguments. Eventually, rollaxis could be deprecated to keep things > > tidy. This has the added advantage of using a name that seems to fit > > what the function does better - 'rollaxis' suggests a behavior like the > > roll() function which affects other axes, which isn't what happens. > > My 2 cents: +1 on a new function, but I'd change the behavior for > positive arguments too. > > Currently, the API is (AFAICT): You give the index of the axis you > want to move, and you give the index of the axis that you want the > first axis to be moved in front of. This is super confusing! > > I propose that a much better API would be: You give the index of the > axis you want to move, and you give the index you *want* that axis to > have. So we'd have the invariant: > b = np.moveaxis(a, i, j) > assert a.shape[i] == b.shape[j] > This is way easier to think about, at least for me. And it solves the > problem with negative indices too. > > BTW, note that that the documentation for rollaxis is actually > self-contradictory at the moment: > http://docs.scipy.org/doc/numpy/reference/generated/numpy.rollaxis.html > At the top it seems to document the behavior that I propose ("Roll the > specified axis backwards, until it lies *in a given* position."), and > then in the details it describes the actual behavior("The axis is > rolled until it lies *before* this position"). I take this as further > evidence that the current behavior is unnatural and confusing :-). > > -- Nathaniel

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NumPy 1.7.0 for MeeGo Harmattan OS
by Roberto Colistete Jr. Feb. 16, 2013

Feb. 16, 2013

Hi, It is my first participation here. About NumPy on Mobile OS : - NumPy 1.7.0 was released today (11/02/2013) for MeeGo Harmattan OS (for Nokia N9/N950), just 1 day after the mainstream release. See the Talk Maemo.org topic : http://talk.maemo.org/showthread.php?p=1322503 MeeGo Harmattan OS also has NumPy 1.4.1 from Nokia repositories : http://wiki.maemo.org/Python/Harmattan - Maemo 5 OS (Nokia N900) has NumPy 1.4.0 : http://maemo.org/packages/view/python-numpy/ Also for MeeGo Harmattan OS : - MatPlotLib 1.2.0 was released (in 09/02/2013) for MeeGo Harmattan OS. Including Qt4/PySide backend : http://talk.maemo.org/showthread.php?p=1128672 - IPython 0.13.1, including Notebook and Qt console interfaces, was released in 22/01/2013. See the Talk Maemo.org topic : http://talk.maemo.org/showthread.php?p=1123672 It can work as an IPython Notebook server , with web clients running on Android, desktop OS, etc via via WiFi hotspot of Nokia N9/N950. See my blog article comparing scientific Python tools for computers, tablets and smartphones : http://translate.google.com/translate?hl=pt-BR&sl=pt&tl=en&u=http%3A%2F%2Fr… The conclusion is very simple : real mobile Linux OS (with glibc, X11, dependencies, etc) are better for scientific Python. Like Maemo 5 OS and MeeGo Harmattan OS. And future Sailfish OS and Ubuntu Phone OS can follow the same path. Best regards, Roberto Colistete Jr.

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confused about tensordot
by Neal Becker Feb. 15, 2013

Feb. 15, 2013

In the following code c = np.multiply (a, b.conj()) d = np.abs (np.sum (c, axis=0)/rows) d2 = np.abs (np.tensordot (a, b.conj(), ((0,),(0,)))/rows) print a.shape, b.shape, d.shape, d2.shape The 1st compute steps, where I do multiply and then sum give the result I want. I wanted to try to combine these 2 steps using tensordot, but it's not doing what I want. The print statement outputs this: (1004, 13) (1004, 13) (13,) (13, 13) The correct output should be (13,), but the tensordot output is (13,13). It's supposed to take 2 matrixes, each (1004, 13) and do element-wise multiply, then sum over axis 0.

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Purpose of this list
by Juan Luis Cano Feb. 15, 2013

Feb. 15, 2013

Hello all, I have a brief question about the general purpose of Numpy-discussion. I suscribed a month ago more or less to keep an eye on NumPy development (and perhaps contributing eventually), for I saw that some decisions about the roadmap were discussed here, but 90 % of the emails that arrive through the list are related to support. Whats is actually the scope/purpose of the list? I am not critizicing anyone, just asking for a clarification on this point, to manage my mail client filters etc. Best regards, Juan Luis Cano

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SciPy 2013 Announcement -- June 24 - 29, 2013, Austin, TX!
by Anthony Scopatz Feb. 15, 2013

Feb. 15, 2013

Hello All, As this years conference communications co-chair, it is my extreme pleasure to announce the *SciPy 2013 conference from June 24th - 29th in sunny Austin, Texas, USA.* Please see our website<http://conference.scipy.org/scipy2013/about.php>(or below) for more details. A call for presentations, tutorials, and papers will be coming out very soon. Please make sure to sign up on our mailing list<http://eepurl.com/dyoeL>, follow us on twitter <https://twitter.com/SciPy2013>, or Google Plus<https://plus.google.com/u/0/100948873231627513165/posts> so that you don't miss out on any important updates. I sincerely hope that you can attend this year and make 2013 the best year for SciPy yet! Happy Hacking! Anthony Scopatz SciPy 2013 Conference Announcement ---------------------------------- SciPy 2013, the twelfth annual Scientific Computing with Python conference, will be held this June 24th-29th in Austin, Texas. SciPy is a community dedicated to the advancement of scientific computing through open source Python software for mathematics, science, and engineering. The annual SciPy Conference allows participants from academic, commercial, and governmental organizations to showcase their latest projects, learn from skilled users and developers, and collaborate on code development. The conference consists of two days of tutorials by followed by two days of presentations, and concludes with two days of developer sprints on projects of interest to the attendees. Specialized Tracks ------------------ This year we are happy to announce two specialized tracks run in parallel to the general conference: *Machine Learning* In recent years, Python's machine learning libraries rapidly matured with a flurry of new libraries and cutting-edge algorithm implement and development occurring within Python. As Python makes these algorithms more accessible, machine learning algorithm application has spread across disciplines. Showcase your favorite machine learning library or how it has been used as an effective tool in your work! *Reproducible Science* Over recent years, the Open Science movement has stoked a renewed acknowledgement of the importance of reproducible research. The goals of this movement include improving the dissemination of progress, prevent fraud through transparency, and enable deeper/wider development and collaboration. This track is to discuss the tools and methods used to achieve reproducible scientific computing. Domain-specific Mini-symposia ----------------------------- Introduced in 2012, mini-symposia are held to discuss scientific computing applied to a specific scientific domain/industry during a half afternoon after the general conference. Their goal is to promote industry specific libraries and tools, and gather people with similar interests for discussions. Mini-symposia on the following topics will take place this year: - Meteorology, climatology, and atmospheric and oceanic science - Astronomy and astrophysics - Medical imaging - Bio-informatics Tutorials --------- Multiple interactive half-day tutorials will be taught by community experts. The tutorials provide conceptual and practical coverage of tools that have broad interest at both an introductory or advanced level. This year, a third track will be added, targeting specifically programmers with no prior knowledge of scientific python. Developer Sprints ----------------- A hackathon environment is setup for attendees to work on the core SciPy packages or their own personal projects. The conference is an opportunity for developers that are usually physically separated to come together and engage in highly productive sessions. It is also an occasion for new community members to introduce themselves and recieve tips from community experts. This year, some of the sprints will be scheduled and announced ahead of the conference. Birds-of-a-Feather (BOF) Sessions --------------------------------- Birds-of-a-Feather sessions are self-organized discussions that run parallel to the main conference. The BOFs sessions cover primary, tangential, or unrelated topics in an interactive, discussion setting. This year, some of the BOF sessions will be scheduled and announced ahead of the conference. Important Dates --------------- - March 18th: Presentation abstracts, poster, tutorial submission deadline. Application for sponsorship deadline. - April 15th: Speakers selected - April 22nd: Sponsorship acceptance deadline - May 1st: Speaker schedule announced - May 5th: Paper submission deadline - May 6th: Early-bird registration ends - June 24th-29th: 2 days of tutorials, 2 days of conference, 2 days of sprints We look forward to a very exciting conference and hope to see you all at the conference. The SciPy2013 organization team: * Andy Terrel, Co-chair * Jonathan Rocher, Co-chair * Katy Huff, Program Committee co-chair * Matt McCormick, Program Committee co-chair * Dharhas Pothina, Tutorial co-chair * Francesc Alted, Tutorial co-chair * Corran Webster, Sprint co-chair * Peter Wang, Sprint co-chair * Matthew Turk, BoF co-chair * Jarrod Millman, Proceeding co-chair * Stéfan van der Walt, Proceeding co-chair * Anthony Scopatz, Communications co-chair * Majken Tranby, Communications co-chair * Jeff Daily, Financial Aid co-chair * John Wiggins, Financial Aid co-chair * Leah Jones, Operations chair * Brett Murphy, Sponsor chair * Bill Cowan, Financial chair

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Trouble building numpy on different version of OSX.
by Steve Spicklemire Feb. 14, 2013

Feb. 14, 2013

Hi Numpy Folks! When I try to build numpy on MacOSX 10.6 with Xcode 3.2.5 installed (python3.2 setup.py build) things go great! At some point I get this: -------------------- Generating build/src.macosx-10.6-intel-3.2/numpy/core/include/numpy/config.h C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c' gcc-4.2: _configtest.c success! removing: _configtest.c _configtest.o C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -------------------- Keeping everything as nearly as possible the same on MacOSX 10.7 with Xcode 4.6 installed I get this: -------------------- Generating build/src.macosx-10.6-intel-3.2/numpy/core/include/numpy/config.h C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -c' gcc-4.2: _configtest.c _configtest.c:1:20: error: Python.h: No such file or directory _configtest.c:1:20: error: Python.h: No such file or directory lipo: can't figure out the architecture type of: /var/folders/4h/7kcqgdb55yjdtfs6dpwjytjh0000gn/T//ccIEwAT5.out _configtest.c:1:20: error: Python.h: No such file or directory _configtest.c:1:20: error: Python.h: No such file or directory lipo: can't figure out the architecture type of: /var/folders/4h/7kcqgdb55yjdtfs6dpwjytjh0000gn/T//ccIEwAT5.out failure. removing: _configtest.c _configtest.o -------------------- Obviously the -I/Library/Frameworks/etc... is missing. I get the same thing with Xcode 4.6 on 10.8. ;-(. I can *run* my numpy build from 10.6 on 10.7 and 10.8, but I'd really like to be able to build it without having to reboot from an old backup disk. ;-) For what it's worth, on 10.7 and 10.8 (and 10.6 for that matter) python3.2-config works and returns reasonable results. Where does setup.py decide about which paths to include in the compile options string? thanks! -steve

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Python trademark in legal trouble in Europe, please help
by Fernando Perez Feb. 14, 2013

Feb. 14, 2013

Hi all, please do NOT respond to this thread or to me directly. This is strictly to spread this message as widely as possible, so that anyone who receives it and can act on it does so. Needless to say, do forward this to anyone you think might be in a position to take useful action. The Python trademark is in serious risk across Europe due to the actions of a UK-based IP troll. If you operate in Europe, please help the Python Software Foundation gather evidence in the legal battle to protect the Python trademark across the EU. You can find the official blog post from the PSF with instructions on how to help here: http://pyfound.blogspot.com/2013/02/python-trademark-at-risk-in-europe-we.h… and this thread on Hacker News is being monitored by the PSF Chairman Van Lindberg in case you want to ask the team directly any questions: http://news.ycombinator.com/item?id=5221093 Cheers, f

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How to upload to pypi
by Ondřej Čertík Feb. 14, 2013

Feb. 14, 2013

Hi, I have uploaded the NumPy 1.7.0 source distribution to pypi: http://pypi.python.org/pypi/numpy/1.7.0 I did it by uploading the file PKG-INFO from numpy-1.7.0.tar.gz. It said "Error processing form. Form Failure; reset form submission" about 3x times, but on the 4th try it went through. I reported the issue here: https://sourceforge.net/tracker/?func=detail&aid=3604194&group_id=66150&ati… I then attached the numpy-1.7.0.tar.gz and numpy-1.7.0.zip source files. Now I am having trouble attaching the windows installers, just like they are here: http://pypi.python.org/pypi/numpy/1.6.2 but whenever I upload the file numpy-1.7.0-win32-superpack-python2.5.exe (and set it as "MS Windows installer"), it uploads and then I get a blank page with the text: """ Error processing form invalid distribution file """ That's it.... Not very useful. Do you know if the sources of pypi are somewhere online? (I didn't find them, only a similar package https://github.com/schmir/pypiserver, but that doesn't seem to be it.) Anyway, so I at least reported the bug here: http://sourceforge.net/tracker/?func=detail&aid=3604193&group_id=66150&atid… Finally, should we try to upload the Windows installers to pypi at all? I am probably doing something wrong if I am hitting these pypi bugs. Many thanks, Ondrej

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Fwd: Package: scipy-0.11.0-0.1.rc2.fc18 Tag: f18-updates-candidate Status: failed Built by: orion
by Orion Poplawski Feb. 13, 2013

Feb. 13, 2013

This is a plea for some help. We've been having trouble getting scipy to pass all of the tests in the Fedora 18 build with python 3.3 (although it seems to build okay in Fedora 19). Below are the logs of the build. There appears to be some kind of memory corruption that manifests itself a little differently on 32-bit vs. 64-bit. I really have no idea myself how to pursue debugging this, though I'm happy to provide any more needed information. Thanks, Orion -------- Original Message -------- Subject: Package: scipy-0.11.0-0.1.rc2.fc18 Tag: f18-updates-candidate Status: failed Built by: orion Date: Thu, 20 Sep 2012 21:01:54 +0000 (UTC) From: Fedora Koji Build System <buildsys(a)fedoraproject.org> To: ausil(a)fedoraproject.org, jspaleta(a)fedoraproject.org, voronov(a)fedoraproject.org, torwangjl(a)fedoraproject.org, alagunambi(a)fedoraproject.org, urkle(a)fedoraproject.org, orion(a)fedoraproject.org Package: scipy-0.11.0-0.1.rc2.fc18 Tag: f18-updates-candidate Status: failed Built by: orion ID: 350761 Started: Thu, 20 Sep 2012 20:39:45 UTC Finished: Thu, 20 Sep 2012 21:01:32 UTC scipy-0.11.0-0.1.rc2.fc18 (350761) failed on buildvm-33.phx2.fedoraproject.org (x86_64), buildvm-35.phx2.fedoraproject.org (i386), buildvm-34.phx2.fedoraproject.org (noarch): BuildError: error building package (arch x86_64), mock exited with status 1; see build.log for more information SRPMS: scipy-0.11.0-0.1.rc2.fc18.src.rpm Failed tasks: ------------- Task 4509076 on buildvm-33.phx2.fedoraproject.org Task Type: buildArch (scipy-0.11.0-0.1.rc2.fc18.src.rpm, x86_64) logs: http://koji.fedoraproject.org/koji/getfile?taskID=4509076&name=build.log http://koji.fedoraproject.org/koji/getfile?taskID=4509076&name=mock_output.… http://koji.fedoraproject.org/koji/getfile?taskID=4509076&name=root.log http://koji.fedoraproject.org/koji/getfile?taskID=4509076&name=state.log Task 4509077 on buildvm-35.phx2.fedoraproject.org Task Type: buildArch (scipy-0.11.0-0.1.rc2.fc18.src.rpm, i686) logs: http://koji.fedoraproject.org/koji/getfile?taskID=4509077&name=build.log http://koji.fedoraproject.org/koji/getfile?taskID=4509077&name=mock_output.… http://koji.fedoraproject.org/koji/getfile?taskID=4509077&name=root.log http://koji.fedoraproject.org/koji/getfile?taskID=4509077&name=state.log Task 4509063 on buildvm-34.phx2.fedoraproject.org Task Type: build (f18-candidate, /scipy:cb69bd06f0d930fbe8840d89b918b617e28af63f) Closed tasks: ------------- Task 4509064 on buildvm-30.phx2.fedoraproject.org Task Type: buildSRPMFromSCM (/scipy:cb69bd06f0d930fbe8840d89b918b617e28af63f) logs: http://koji.fedoraproject.org/koji/getfile?taskID=4509064&name=build.log http://koji.fedoraproject.org/koji/getfile?taskID=4509064&name=checkout.log http://koji.fedoraproject.org/koji/getfile?taskID=4509064&name=mock_output.… http://koji.fedoraproject.org/koji/getfile?taskID=4509064&name=root.log http://koji.fedoraproject.org/koji/getfile?taskID=4509064&name=state.log Task Info: http://koji.fedoraproject.org/koji/taskinfo?taskID=4509063 Build Info: http://koji.fedoraproject.org/koji/buildinfo?buildID=350761

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