Mailman 3 June 2009 - SciPy-Dev

Summer NumPy Doc Marathon (Reply-to: scipy-dev@scipy.org)
by David Goldsmith June 9, 2009

June 9, 2009

Dear SciPy Community Members: Hi! My name is David Goldsmith. I've been hired for the summer by Joe Harrington to further progress on NumPy documentation and ultimately, pending funding, SciPy documentation. Joe and I are reviving last summer’s enthusiasm in the community for this mission and enlisting as many of you as possible in the effort. On that note, please peruse the NumPy Doc Wiki (http://docs.scipy.org/numpy/Front Page/) and, in particular, the master list of functions/objects (“items”) needing work (http://docs.scipy.org/numpy/Milestones/). Our goal is to have every item to the ready-for-first-review stage (or better) by August 18 (i.e., the start of SciPyCon09). To accomplish this, we're forming teams to attack each doc category on the Milestones page. From the Milestones page: "To speed things up, get more uniformity in the docs, and add a social element, we're attacking these categories as teams. A team lead takes responsibility for getting a category to "Needs review" within one month [we expect that some categories will require less time – please furnish your most ‘optimistically realistic’ deadline when ‘claiming’ a category], but no later than 18 August 2009. As leader, you commit to working with anyone who signs up in your category, and vice versa. The scipy-dev mailing list is a great place to recruit helpers. "Major doc contributors will be listed in NumPy's contributors file, THANKS.txt. Anyone writing more than 1000 words will get a T-shirt (while supplies last, etc.). Teams that reach their goals in time will get special mention in THANKS.txt. "Of course, you don't have to join a team. If you'd like to work on your own, please choose docstrings from an unclaimed category, and put your name after docstrings you are editing in the list below. If someone later claims that category, please coordinate with them or finish up your current docstrings and move to another category." Please note that, to edit anything on the Wiki (including the doc itself), you’ll need “edit rights” – how you get these is Item 5 under “Before you start” on the “Front Page,” but for your convenience, I’ll quote that here: "Register a username on [docs.scipy.org]. Send an e-mail with your username to the scipy-dev mailing list (requires subscribing to the mailing list first, [which can be done at http://mail.scipy.org/mailman/listinfo/scipy-dev]), so that we can give you edit rights. If you are not subscribed to the mailing-list, you can also send an email to gael dot varoquaux at normalesup dot org, but this will take longer [and you’ll want to subscribe to scipy-dev anyway, because that’s the place to post questions and comments about this whole doc development project]." Also, I’ll be holding a weekly Skype (www.skype.com) telecon – Wednesdays at 4:30pm US Eastern Daylight Time - to review progress and discuss any roadblocks we may have encountered (or anticipate encountering). If you’d like to participate and haven’t already downloaded and installed Skype and registered a Skype ID, you should do those things; then, you'll be able to join in simply by "Skyping" me (Skype ID: d.l.goldsmith) and I'll add you to the call. So, thanks for your time reading this, and please make time this summer to help us meet (or beat) the goal. Sincerely, David Goldsmith, Technical Editor Olympia, WA

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more with SVD wrapping
by M Trumpis June 9, 2009

June 9, 2009

Hi all, While I was playing with the f2py wrappings for SVD routines, I went ahead and beefed up the *gesdd and *gesvd interfaces, and added a wrapping for the "generalized SVD" wrappings, *ggsvd. improvements to svd: * can query the lapack drivers for best workspace size--this eliminates the need for the code in "calc_lwork.f". * can ask the drivers to return compact matrices: a = (m x n) ==> u = (m x min(m,n)), vh = (min(m,n) x n) Use of the *gesvd driver can be toggled with an argument: scipy.linalg.svd( ... , fast_svd=False) I made two scipy interpretations of the GSVD, one corresponding to the lapack docs, and one that is more like the matlab version. This ticket supercedes ticket 957. http://projects.scipy.org/scipy/ticket/964 Kind regards, Mike

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The SciPy Doc Marathon continues
by Joe Harrington June 8, 2009

June 8, 2009

Let's Finish Documenting SciPy! Last year, we began the SciPy Documentation Marathon to write reference pages ("docstrings") for NumPy and SciPy. It was a huge job, bigger than we first imagined, with NumPy alone having over 2,000 functions. We created the doc wiki (now at docs.scipy.org), where you write, review, and proofread docs that then get integrated into the source code. In September, we had over 55% of NumPy in the "first draft" stage, and about 25% to the "needs review" stage. The PDF NumPy Reference Guide was over 300 pages, nicely formatted by ReST, which makes an HTML version as well. The PDF document now has over 500 pages, with the addition of sections from Travis Oliphant's book Guide to NumPy. That's an amazing amount of work, possible through the contributions of over 30 volunteers. It came back to us as the vastly-expanded help pages in NumPy 1.2, released last September. With your help, WE CAN FINISH! This summer we can: - Write all the "important" NumPy pages to the "Needs Review" stage - Start documenting the SciPy package - Get the SciPy User Manual started - Implement dual review - technical and presentation - on the doc wiki - Get NumPy docs and packaging on a sound financial footing We'll start with the first two. UCF has hired David Goldsmith to lead this summer's doc effort. David will write a lot of docs himself, but more importantly, he will organize our efforts toward completing doc milestones. There will be rewards, T-shirts, and likely other fun stuff for those who contribute the most. David will start the ball rolling shortly. This is a big vision, and it will require YOUR help to make it happen! The main need now is for people to work on the reference pages. Here's how: 1. Go to http://docs.scipy.org/NumPy 2. Read the intro and doc standards, and some docstrings on the wiki 3. Make an account 4. Ask the scipy-dev(a)scipy.org email list for editor access 5. EDIT! All doc discussions (except announcements like this one) should happen on the scipy-dev(a)scipy.org email list. You can browse the archives and sign up for the list at http://scipy.org/Mailing_Lists . That's where we will announce sprints on topic areas and so on. We'll also meet online every week, Wednesdays at 4:30pm US Eastern Time, on Skype. David will give the details. Welcome back to the Marathon! --jh-- Prof. Joseph Harrington Planetary Sciences Group Department of Physics MAP 414 4000 Central Florida Blvd. University of Central Florida Orlando, FL 32816-2385 jh(a)physics.ucf.edu planets.ucf.edu

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Definitions of pv, fv, nper, pmt, and rate
by David Goldsmith June 8, 2009

June 8, 2009

Hi, folks. Unable to find a printed reference for the definition we use to compute each of these functions, I posted a couple queries for help in this regard in the Discussion for fv (http://docs.scipy.org/numpy/docs/numpy.lib.financial.fv/#discussion-sec). josef Pktd's reply (thanks!) just makes me even more doubtful that we're using the definition that most users from the financial community would be expecting. At this point, I'd have to say, my position is: someone needs to refer me to a printed reference documenting this definition, or I contend that our implementation is "wrong" (or at least inconsistent with what's used in financial circles). DG PS: Some of the financial functions' help doc says they're unimplemented - are there plans to implement them, and if not, why do we have help doc for them?

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Trac-ing backports
by Pauli Virtanen June 5, 2009

June 5, 2009

Hi, I noticed that keeping track of bugs to backport is a bit painful. Also Trac isn't currently too helpful about this. So, how should we deal with backports within Trac: a) For each bug you think could be useful to backport, before closing the ticket, file a new "Backport #xxx to 0.y.z" ticket. Easy to forget, though, and a bit nasty with Numpy with its 1.0.x, 1.1.x, 1.2.x, 1.3.x, branches... b) Add a custom field "Branches" that contains some custom format, such as "-1.3.x" before and "+1.3.x" after backporting. Add corresponding queries to Trac's roadmap. -- Pauli Virtanen

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Re: [SciPy-dev] important word document
by David Goldsmith June 3, 2009

June 3, 2009

Okee, dokee, thanks! DG --- On Wed, 6/3/09, David Warde-Farley <dwf(a)cs.toronto.edu> wrote: > From: David Warde-Farley <dwf(a)cs.toronto.edu> > Subject: Re: [SciPy-dev] important word document > To: "SciPy Developers List" <scipy-dev(a)scipy.org> > Date: Wednesday, June 3, 2009, 12:43 PM > On 3-Jun-09, at 1:12 PM, Charles R > Harris wrote: > > > Important word document? Surely it's spam. Why > you received it is > > another > > question, I haven't seen it. > > Me neither. Moreover it looks like Travis uses an enthought > email > address these days. > > David > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-dev >

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Re: [SciPy-dev] important word document
by David Goldsmith June 3, 2009

June 3, 2009

Hi, Travis. My virus guard tells me there's a virus in this file - did you mean to send it, or did the virus do so "unilaterally"? If you meant to, obviously, please sanitize and resend. Thanks! DG --- On Wed, 6/3/09, oliphant(a)ee.byu.edu <oliphant(a)ee.byu.edu> wrote: > From: oliphant(a)ee.byu.edu <oliphant(a)ee.byu.edu> > Subject: Re: [SciPy-dev] important word document > To: scipy-dev(a)scipy.org > Date: Wednesday, June 3, 2009, 4:38 AM > Please see the attached file for > details. > > > -----Inline Attachment Follows----- > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-dev >

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scipy.stats._chk_asarray
by ctw June 3, 2009

June 3, 2009

I just wanted to give you a heads up that I came across a bug in scipy.stats._chk_asarray. I have updated the corresponding review page ( http://projects.scipy.org/scipy/ticket/44 ) with the following comment: _chk_asarray does not respect the class of the input. If the input is a subclass of numpy.ndarray _chk_asarray will transform it into an ndarray. This can lead to undesirable consequences in functions that call _chk_asarray (e.g., scipy.stats.nanmean). Simple example: >>> tst = matrix(range(4)) >>> scipy.stats.nanmean(tst) array([0., 1., 2., 3.]) >>> np.mean(tst,0) matrix([[0., 1., 2., 3.]]) The problem is the call to np.asarray() which should only be made for input that is not an ndarray instance. I just committed a corresponding fix via SVN.

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Re: [SciPy-dev] important word document
by oliphant＠ee.byu.edu June 3, 2009

June 3, 2009

Please see the attached file for details.

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Setup doesn't pickup Intel Fortran compiler
by Matthieu Brucher June 3, 2009

June 3, 2009

Hi, I have trouble getting Scipy (and numpy) using the correct Fortran compiler : Found executable /appli/intel/10.1.018/intel64/cce/bin/icc customize GnuFCompiler Found executable /appli/intel/10.1.018/intel64/fce/bin/ifort gnu: no Fortran 90 compiler found Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found customize IntelFCompiler customize LaheyFCompiler Could not locate executable lf95 lahey: no Fortran 90 compiler found lahey: no Fortran 90 compiler found customize PGroupFCompiler Could not locate executable pgf90 pg: no Fortran 90 compiler found pg: no Fortran 90 compiler found customize AbsoftFCompiler Could not locate executable f90 absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found customize NAGFCompiler Found executable /usr/bin/f95 customize VastFCompiler customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize CompaqFCompiler Could not locate executable fort compaq: no Fortran 90 compiler found compaq: no Fortran 90 compiler found customize IntelItaniumFCompiler customize IntelEM64TFCompiler customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize UnixCCompiler customize UnixCCompiler using scons Found executable /appli/intel/10.1.018/intel64/cce/bin/icpc Why is it trying to search for another Fortran compiler when it actually found the Intel one? I used python setup.py install or python setup.py install --fcompiler=intelem, but the output was the same :| Matthieu -- Information System Engineer, Ph.D. Website: http://matthieu-brucher.developpez.com/ Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92 LinkedIn: http://www.linkedin.com/in/matthieubrucher

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