Mailman 3 August 2009 - SciPy-Dev

Problems packaging GSoC statsmodels code as scikit
by Skipper Seabold 23 Aug '09

23 Aug '09

Hello all, I have been trying to package the models code using the scikits template and have run into a problem. On linux, both Kubuntu 64-bit and openSuSE 32-bit, I can install the package (sudo python setup.py install), but when I do from scikits import statsmodels statsmodels.test() I get Running unit tests for scikits.statsmodels NumPy version 1.4.0.dev7303 NumPy is installed in /usr/local/lib/python2.6/dist-packages/numpy Python version 2.6.2 (release26-maint, Apr 19 2009, 01:58:18) [GCC 4.3.3] nose version 0.11.1 ---------------------------------------------------------------------- Ran 0 tests in 0.003s OK Out[2]: <nose.result.TextTestResult run=0 errors=0 failures=0> Similarly if I try to use nosetests from the command line on the installed tests folder, I get nothing skipper@linux-desktop:~$ nosetests -v /usr/local/lib/python2.6/dist-packages/scikits.statsmodels-0.1.1dev-py2.6.egg/scikits/statsmodels/tests/ ---------------------------------------------------------------------- Ran 0 tests in 0.003s OK However, if I run the nosetests either from the source directory or if I import the directory statsmodels the tests return errors (which I expect at this point, due to incomplete refactoring). skipper@linux-desktop:~$ nosetests -w /home/skipper/nipy/statsmodels/scikits/statsmodels/tests/ <snip> ---------------------------------------------------------------------- Ran 6 tests in 0.188s FAILED (errors=6) Josef is able to install the package and run the tests (statsmodels.test()) and return these errors on Windows with Python 2.5. Is there anyone who would be willing to have a look at my setup.py and see if they spot a problem, because I am at a loss. My attempt is here. Also I don't think the tester.py is correct, though I've tried with and without (and don't think it would affect this issue). <http://bazaar.launchpad.net/~scipystats/%2Bjunk/statsmodels/files/1859> Cheers, Skipper

5 12

setup.py sdist and bzr
by josef.pktd＠gmail.com 23 Aug '09

23 Aug '09

I had problems including data files in the source distribution generated with setup.py sdist . After spending some time with google, I figured out that setuptools only includes files under svn version control by default, but not under bzr config.add_data_files(filename) config.add_data_dir('scikits/statsmodels/tests') worked with bdist_egg and bdist but not with sdist I finally added a MANIFEST.in file with almost include * Is the MANIFEST.in the only way or is there a better way similar to the case with svn? Josef

3 4

Sprinting at SciPy2009 today and tomorrow
by Stéfan van der Walt 22 Aug '09

22 Aug '09

Hey everyone, The SciPy2009 sprints are underway, and you are welcome to take part! Topics include NumPy, SciPy, Mayavi, Traits, IPython, Documentation and the image processing toolbox. Join us on irc in channel #scipy, server irc.freenode.net. The timezone here is GMT-7, and we'll be around both days from 10:00am till late. See you there, Stéfan

1 0

Sprints
by David Goldsmith 22 Aug '09

22 Aug '09

Hi, folks. So, I'm "signed-up" to participate in the Sprint(s), but I haven't been able to successfully install mayavi - given this, will I be able to be helpful in the Sprint(s)? DG __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

3 7

I just do what Joe tell me to (Docs)
by Paul Ivanov 22 Aug '09

22 Aug '09

Please give me permission to edit and proofread. thank you, Paul Ivanov (ivanov)

3 3

Re: [SciPy-dev] draft: NumPy User Guide introduction
by Neil Crighton 21 Aug '09

21 Aug '09

Andrew Hawryluk <HAWRYLA <at> novachem.com> writes: > > I have posted a first draft of a NumPy User Guide introduction. > Hopefully it is both useful and factually correct, but please jump in > where you see room for improvement. > > I am assuming familiarity with Python programming, but no prior > knowledge of NumPy. > > http://docs.scipy.org/numpy/docs/numpy-docs/user/introduction.rst/ > > Andrew > It looks good, thanks for putting it together! A nitpick - say 'dictionaries' rather than 'dicts'. I think it would help to explicitly give a and b lists (something like [1, 2, 3, 4]). This will give an example of a possible data type (integers), and make the following examples more clear. If this is going to be the first stop for anyone wanting to know what numpy can do, it would also be great to give an example of reading columns of data from a text file into arrays with np.genfromtxt. Neil

4 3

munkres (Hungarian algorithm or the Kuhn-Munkres algorithm)
by Neal Becker 21 Aug '09

21 Aug '09

I am trying to use munkres. I found munkres on pypi. It doesn't currently work with numpy. I started trying to convert it, but so far only managed to break it (mysteriously). Anyone have a version that works with numpy array?

1 0

Deprecate chararray [was Plea for help]
by David Goldsmith 20 Aug '09

20 Aug '09

--- On Thu, 8/20/09, Christopher Hanley <chanley(a)stsci.edu> wrote: > I'd like to respectfully request that we move any > discussion of what > to do with the numpy.char module to the numpy list. NP, done. > I'm a little concerned about some of the assumptions that > are being > made about the number of users of the module. I would > also like to > better understand the reasons for wanting to dump it. I think Ralf did a pretty good job of synopsizing the reasons for deprecation, but since we're moving the thread, I'll reprint them here: 0) "it gets very little use" (an assumption you presumably dispute); 1) "is pretty much undocumented" (less true than a week ago, but still true for several of the attributes, with another handful or so falling into the category of "poorly documented"); 2) "probably more buggy than most other parts of NumPy" ("probably" being a euphemism, IMO); 3) "there is not a really good use-case for it" (a conjecture, but one that has yet to be challenged by counter-example); 4) it's not the first time its presence in NumPy has been questioned ("as Stefan pointed out when asking this same question last year") 5) NumPy already has a (perhaps superior) alternative ("object arrays would do nicely if one needs this functionality"); to which I'll add: 6) it is, on its face, "counter to the spirit" of NumPy. So far, IIRC, the only reason in favor of its continued inclusion is inertia. > Let me be > clear. I'm not opposed to change. However > breaking other people's > code just for the sake of change seems like a poor reason So, I don't think we're proposing this "just for the sake of change" > and a mean > thing to do to our customers. Apologies, but it is not proposed maliciously. The only other things I would add by way of "review" from the scipy-dev thread: a compromise proposal (made by Ralf): "Put clearly in the docs that this module exists for backwards compatibility reasons, and is not recommended for new development" and a clarification of deprecation process (provided by Robert): "[asked by the present author] How has deprecation in Numpy worked in the past - by dictum, vote, or consensus? [Robert's answer] Consensus or dictum without major objection. Voting is pointless except to inform one of those." Thanks for your time and consideration. David Goldsmith > Thank you for your time and help, > Chris > > > -- > Christopher Hanley > Senior Systems Software Engineer > Space Telescope Science Institute > 3700 San Martin Drive > Baltimore MD, 21218 > (410) 338-4338 > > On Aug 20, 2009, at 1:35 AM, Robert Kern wrote: > > > On Wed, Aug 19, 2009 at 20:03, David > > Goldsmith<d_l_goldsmith(a)yahoo.com> > wrote: > >> I'm going to take it a step further: "breakage" is > always the > >> deterrent to change, and yet "change we must" > (i.e., "adapt or > >> die"). It's certainly not without precedent > - even within Numpy, I > >> believe - for things (though perhaps not whole > namespaces) to be > >> deemed "to-be-deprecated," have a warning to this > effect > >> established in one x.[even #].0 release, and then > be removed by the > >> x.[even # + 2 or + 4].0 release. How has > deprecation in Numpy > >> worked in the past - by dictum, vote, or > consensus? > > > > Consensus or dictum without major objection. Voting is > pointless > > except to inform one of those. > > > > -- > > Robert Kern > > > > "I have come to believe that the whole world is an > enigma, a harmless > > enigma that is made terrible by our own mad attempt to > interpret it as > > though it had an underlying truth." > > -- Umberto Eco > > _______________________________________________ > > Scipy-dev mailing list > > Scipy-dev(a)scipy.org > > http://mail.scipy.org/mailman/listinfo/scipy-dev > > _______________________________________________ > Scipy-dev mailing list > Scipy-dev(a)scipy.org > http://mail.scipy.org/mailman/listinfo/scipy-dev >

3 3

Questions about scikits: 1) What is the best way to translate nosetests into numpy testing framework? 2) How can I get an svn account?
by John Salvatier 20 Aug '09

20 Aug '09

Hello All, My name is John Salvatier and I am building the scikit scikit.bvp_solver<http://pypi.python.org/pypi/scikits.bvp_solver/>which is for solving two-point boundary value problem. Anyway, I have two questions about how scikits work: 1) What is the best way to translate tests which are arranged so for nose to the configuration required for scikits http://www.scipy.org/scipy/scikits/wiki/ScikitsForDevelopers#Testing? Is there any easy way? 2) How can I get an svn account for svn.scipy.org/svn/? Best Regards, John Salvatier

3 2

Can I add an *.rst file via the Wiki?
by Andrew Hawryluk 20 Aug '09

20 Aug '09

I have drafted an introduction to the NumPy User Guide. I could not see a way to create a new *.rst file through the Wiki. If I am correct that the Wiki is only designed to edit existing pages, how do I create a file doc/source/user/introduction.rst? Thanks, Andrew

2 3