Mailman 3 May 2008 - SciPy-Dev

Re: [SciPy-dev] ANN: NumPy/SciPy Documentation Marathon 2008
by Pauli Virtanen 18 May '08

18 May '08

Hi, su, 2008-05-18 kello 13:40 +0200, Johann Cohen-Tanugi kirjoitti: > one quesiton, the preliminary doc refers to saving the pages locally, > then editing, and in the end uploading everything. I do not understand > how the wiki or any page thereof can be saved on a local machine. I > tried a wget but clearly the wiki system gets broken this way. You can wget pages by adding ?action=raw at the end of the url. But I think Joe's idea was that for larger rewriting, it is more convenient to copy-and-paste the text for the docstring you want to edit, edit it on your own machine until you are happy with the result, and after that put it to the wiki. > P.S. I logged out and in again but the page > http://sd-2116.dedibox.fr/doc/EditorGroup tells me that I am not > allowed to see this page. I do not know whether this is expected. It's expected; you should be able to edit other pages. But I just changed this to reduce confusion. -- Pauli Virtanen

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Re: [SciPy-dev] [Numpy-discussion] [SciPy-user] ANN: NumPy/SciPy Documentation Marathon 2008
by Anne Archibald 18 May '08

18 May '08

2008/5/17 Joe Harrington <jh(a)physics.ucf.edu>: > Ryan writes: >> This is very good news. I will find some way to get involved. > > Great! Please dive right in, and sign up on the Developer_Zone page > so we can keep track of who's involved. > > One thing I forgot to mention in my too-wordy announcement was that > discussion of documentation is on the scipy-dev mailing list. We had > to pick one spot and decided that since we are going after scipy as > soon as numpy is done, we'd like to use that list rather than > numpy-discussion. We also wanted to keep it on a development list > rather than polluting the new users' discussion space. This sounds like a great idea! I have a few questions, though: * Am I supposed to be able to edit the wiki? If I go to, for example, http://sd-2116.dedibox.fr/doc/Docstrings/numpy/core/multiarray/empty and click on any of the "edit" links I am told I don't have permission to edit the page, in spite of having registered. * How and when are merges back from the wiki into the docstrings going to happen? Presumably, since any examples will become doctests, this will require substantial human intervention to fix all the broken tests (and remove instances of "shutil.deltree('/')" and the like). * Is there some special format the wiki markup needs to be in to ensure that the reST docstrings are properly formatted? * What fate is planned for the Numpy Example List and its progeny? Presumably everything in the basic Example List should be moved into docstrings (and therefore become doctests)? The categorized example list would presumably then develop links to the function documentation pages instead... Anne

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asscalar and asarray in numpy
by Hoyt Koepke 17 May '08

17 May '08

Hello, Perhaps I'm misunderstanding things, I'm a bit surprised that asscalar cannot take a scalar argument, i.e. d = asscalar(1.0) doesn't work. Although the doc string specifies that it returns the scalar part of a single element array, my assumption about this method's behavior based on how asarray is used is that it should accept anything that can be turned into a scalar and do the conversion based on that, i.e. we can use it to ensure that a particular type is a scalar. The current code in the function is: def asscalar(a): """Convert an array of size 1 to its scalar equivalent. """ return a.item() I'm thinking it would be reasonable to replace this by something more robust, perhaps: def asscalar(a): """Convert the input to its scalar equivalent, if possible. """ if numpy.isscalar(a): return a elif isinstance(a, numpy.ndarray): return a.item() else: raise TypeError("Argument cannot be converted to a scalar.") This is untested, and I may be missing subtleties in how I'm doing this -- if so, let me know. I'd be happy to write a unit test if people want this change. Those worried about speed can just use the a.item() method directly. Am I misunderstanding the reasoning behind the as* functions, or is this reasonable? Thanks, --Hoyt -- +++++++++++++++++++++++++++++++++++ Hoyt Koepke UBC Department of Computer Science http://www.cs.ubc.ca/~hoytak/ hoytak(a)gmail.com +++++++++++++++++++++++++++++++++++

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fftpack: building all backends and setting them at runtime (was dropping djbfft)
by David Cournapeau 17 May '08

17 May '08

Hi, After some more work, I have modified scipy.fftpack such as backends are truely independent code-wise, and can be selected at runtime. I hope it adresses all remarks comments made in the previous thread: http://projects.scipy.org/scipy/scipy/browser/branches/refactor_fft/ Concretely: - all fftw/fftw3/djbfft/mkl code has been put in scipy/fftpack/backends directory. - fftpack is always build and used by default for all functions - for each backend, if the corresponding libraries are available, the module is built (so if you have mkl, fftw, fftw3 and djbfft, all backends will always be built) - fftpack module now uses some magic to set up functions from one backend or the other (scipy/fftpack/common.py). Basically, the functions are defined at runtime depending on which backend is selected. If the function is not available, the default backend is used as a fallback. TODO: - I have not implemented any registration method, because I was not sure how to do it (config file, monkey patching, import magic ?). - The convolution module is not done yet. - I have not implemented djbfft backend yet (all the other ones should work), because it needs a bit more logic, but nothing serious. - All module .pyf files are almost duplication, but since we want to have them independent, I am not sure how to do better. It should be possible to put all the code in backends out of scipy once the registration system is in place. cheers, David

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ANN: NumPy/SciPy Documentation Marathon 2008
by Joe Harrington 16 May '08

16 May '08

NUMPY/SCIPY DOCUMENTATION MARATHON 2008 As we all know, the state of the numpy and scipy reference documentation (aka the docstrings) is best described as "incomplete". Most functions have docstrings shorter than 5 lines, whereas our competitors IDL and Matlab usually have a concise and well-written page or two per function. The (wonderful) categorized list of functions is very new and isn't included in the package yet. There isn't even a "Getting Started"-type of document you can hand a new user so they can dive right in. Documentation tools are limited to plain-text paginators, while our competition enjoys HTML-based documents with formulae, images, search capability, and cross linking. Tales of woe abound. A university class switched to Numpy and got hopelessly bogged down because students couldn't find out how to call the functions. A developer looked something up while giving a presentation and the words "Blah, Blah, Blah" stared down at the audience in response. To head off another pedagogical meltdown, the University of Central Florida has hired Stefan van der Walt full time to coordinate a community documentation effort to write reference documentation and tools. The project starts now and continues through the summer. The goals: 1. Produce complete docstrings for all numpy functions and as much of scipy as possible, 2. Produce an 8-15 page Getting Started tutorial that is not discipline-specific, 3. Write reference sections on topics in numpy, such as slicing and the use principles of the modules, 4. Complete a first edition, in both PDF and HTML, of a NumPy Reference Manual, and 5. Check everything into the sources by 1 August 2008 so that the Packaging Team can cut a release and have it available in time for Fall 2008 classes. Even Stefan could not document the hundreds of functions that need it by himself, and in any case such a large contribution requires community review. To make it easy for everyone to contribute, Pauli Virtanen and Emmanuelle Guillart have provided a wiki system for editing reference documentation. The idea was developed by Fernando Perez, Stefan, and Gael Varoquaux. We encourage community members to write, review, and proofread reference pages on this wiki. Stefan will check updates into the sources roughly weekly. Near the end of the project, we will put these wiki pages through a vetting process and then check them into the sources a final time for a release hopefully to occur in early August. Meanwhile, Perry Greenfield has taken the lead on on task 3, writing reference docs for things that currently don't have docstrings, such as basic concepts like slicing. We have proposed two small extensions to the current docstring format, for images (to be used sparingly) and indexing. These appear in updated versions of the doc standard, which are linked from the wiki frontpage. Please take a look and comment on these if you like. All docstrings will remain readable in plain text, but we are now generating a full reference guide in PDF and HTML (you guessed it, linked from the wiki). These are searchable formats. There are several ways you can help: 1. Write some docstrings on the wiki! Many people can do this, many more than can write code for the package itself. However, you must know numpy, the function group, and the function you are writing well. You should be familiar with the concept of a reference page and write in that concise style. We'll do tutorial docs in another project at a later date. See the instructions on the wiki for guidelines and format. 2. Review others' docstrings and leave comments on their wiki pages. 3. Proofread docstrings. Make sure they are correct, complete, and concise. Fix grammar. 4. Write examples ("doctests"). Even if you are not a top-notch English writer, you can help by producing a code snippet of a few lines that demonstrates a function. It is fine for them to go into the docstring templates before the actual text. 5. Write a new help function that optionally produces ASCII or points the user's PDF or HTML reader to the right page (either local or global). 6. If you are in a position to hire someone, such as a knowledgeable student or short-term consultant, hire them to work on the tasks above for the summer. We can provide supervision to them or guidance to you if you like. The home for this project is here: http://scipy.org/Developer_Zone/DocMarathon2008 This is not a sprint. It is a marathon, and this time we are going to finish. We hope you will join us! --jh-- and Stefan and Perry and Pauli and Emmanuelle...and you! Joe Harrington Stefan van der Walt Perry Greenfield Pauli Virtanen Emmanuelle Guillart ...and you!

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[IT] Maintenance and scheduled downtime this evening and weekend
by Peter Wang 16 May '08

16 May '08

Hi everyone, This evening and this weekend, we will be doing a major overhaul of Enthought's internal network infrastructure. We will be cleaning up a large amount of legacy structure and transitioning to a more maintainable, better documented configuration. We have planned the work so that externally-facing servers will experience a minimum of downtime. In the event of unforeseen difficulties that cause outages to extend beyond the times given below, we will update the network status page, located at http://dr0.enthought.com/status/ . This page will remain available and be unaffected by any network outages. Downtimes: Friday May 2, 2008, 8pm - 10pm Central time (= 9pm - 11pm Eastern time) (= 1am - 3am UTC Sat. May 3) Saturday May 2, 2008, 10am - 11am Central time (= 11am - 12 noon Eastern time) (= 3pm - 4pm UTC) To reach us during the downtime, please use the contact information provided on the network status page. Please let me know if you have any questions or concerns. We will send out another email once the outage is complete. Thanks for your patience! -Peter

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Dropping djbfft ?
by David Cournapeau 13 May '08

13 May '08

Hi, I would like to ask again about dropping djbfft support. Djbfft is a fft implementation, which has not been updated since 1999, and is not packaged by most linux distributions (I quite doubt anyone on windows is using it). Also, because it only supports 2^n sizes, it has to be used simultaneously with another backend (fftpack, fftw, fftw3, etc....). The later is why I would like to drop it: it is quite a PITA to test all combinations, and it takes a lot of time for maybe one or two users out there. I would much prefer spending times on improving things like our fftw3 support, float support, etc... cheers, David

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Test
by Travis E. Oliphant 12 May '08

12 May '08

This is a test. -teo

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bug: indexing CSR matrix, 64bits
by Robert Cimrman 12 May '08

12 May '08

Hi, indexing by slices is broken on a 64 bit machine. On a 32 bit one, all is ok. Is something missing in the INSTANTIATE_ALL macro in sparsetools.i? r. In [1]: import scipy In [2]: scipy.__version__ Out[2]: '0.7.0.dev4195' In [3]: import numpy In [4]: numpy.__version__ Out[4]: '1.1.0.dev5106' (Pdb) mtx <12160x12160 sparse matrix of type '<type 'numpy.float64'>' with 235578 stored elements in Compressed Sparse Row format> (Pdb) mtx.data array([ 0. , 0. , 0. , ..., -0.00540995, -0.00636418, 0.0202062 ]) (Pdb) mtx.data.dtype dtype('float64') (Pdb) mtx.indices array([ 0, 1, 36, ..., 12136, 12155, 12159], dtype=int32) (Pdb) mtx.indptr array([ 0, 15, 30, ..., 235543, 235560, 235578], dtype=int32) (Pdb) ir slice(8974, 12160, None) (Pdb) ic slice(8974, 12160, None) (Pdb) mtx[ir,ic] *** NotImplementedError: Wrong number of arguments for overloaded function 'get_csr_submatrix'. Possible C/C++ prototypes are: get_csr_submatrix< int,signed char >(int const,int const,int const [],int const [],signed char const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< signed char > *) get_csr_submatrix< int,unsigned char >(int const,int const,int const [],int const [],unsigned char const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< unsigned char > *) get_csr_submatrix< int,short >(int const,int const,int const [],int const [],short const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< short > *) get_csr_submatrix< int,unsigned short >(int const,int const,int const [],int const [],unsigned short const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< unsigned short > *) get_csr_submatrix< int,int >(int const,int const,int const [],int const [],int const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< int > *) get_csr_submatrix< int,unsigned int >(int const,int const,int const [],int const [],unsigned int const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< unsigned int > *) get_csr_submatrix< int,long long >(int const,int const,int const [],int const [],long long const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< long long > *) get_csr_submatrix< int,unsigned long long >(int const,int const,int const [],int const [],unsigned long long const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< unsigned long long > *) get_csr_submatrix< int,float >(int const,int const,int const [],int const [],float const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< float > *) get_csr_submatrix< int,double >(int const,int const,int const [],int const [],double const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< double > *) get_csr_submatrix< int,long double >(int const,int const,int const [],int const [],long double const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< long double > *) get_csr_submatrix< int,npy_cfloat_wrapper >(int const,int const,int const [],int const [],npy_cfloat_wrapper const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< npy_cfloat_wrapper > *) get_csr_submatrix< int,npy_cdouble_wrapper >(int const,int const,int const [],int const [],npy_cdouble_wrapper const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< npy_cdouble_wrapper > *) get_csr_submatrix< int,npy_clongdouble_wrapper >(int const,int const,int const [],int const [],npy_clongdouble_wrapper const [],int const,int const,int const,int const,std::vector< int > *,std::vector< int > *,std::vector< npy_clongdouble_wrapper > *)

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Patch (weave): Fix warnings about missing const
by Norbet Namec 08 May '08

08 May '08

Hi there, I tried to submit this as trac-ticket but the system gave me a "500 Server Error". Could someone please check it into SVN, so I can forget about it. The change is trivial and obvious. Thanks, Norbert -- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer

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