Mailman 3 February 2006 - SciPy-Dev

Changing return types in C API
by David M. Cooke 19 Apr '06

19 Apr '06

One thing I like about numarray's "native" C API is that for functions that return arrays, the return type is PyArrayObject *, as opposed to the Numeric-compatible API, where the return types are PyObject *. Returning PyObject * in this case basically means you're *always* doing a cast like this: PyObject *o; PyArrayObject *a; a = (PyArrayObject *)PyArray_ContiguousFromObject(o, PyArray_DOUBLE, 2, 2); Could we change the API so that PyArrayObject * is used as the return type? On a similar note: the 'data' member of PyArrayObject's is a char *, where it really should be a void *. Being a void pointer would have the advantage of not needing the cast in cases like this: double *adata = (double)(a->data); It would also mean that accidentally dereferencing the pointer would be a compiler error: currently, a->data[0] is valid, but if a->data was a void *, it wouldn't be. Both of these changes wouldn't require recompiling extensions (since we're just relabelling what the pointer types are), and would be source-compatible with old code (since the casts used would now be superfluous). Newer code will also be easier to write. I'll work on the changes in a svn branch if people think this is a good idea. -- |>|\/|< /------------------------------------------------------------------\ |David M. Cooke http://arbutus.physics.mcmaster.ca/dmc/ |cookedm(a)physics.mcmaster.ca

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Numerical
by Manuel Metz 09 Mar '06

09 Mar '06

Hi, I know that development of Numeric has ceased and we should switch to numpy. Nevertheless there will be some code around which still uses Numeric, maybe for some years. Therefore: I found a memory leak in Numeric 24.2. I noticed it on Windows and Linux (Debian). The following code consumes lots of memory which it should not do !!! from Numeric import * for i in xrange(1000000): a = array( [1,2,3] ) b = a.tolist() # <- here seams to be the memory leak Could anyone fix that !? PLEASE ! Manuel

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Kuipers statistics
by Manuel Metz 03 Mar '06

03 Mar '06

Hi, I have attached a patch for the file /Lib/special/cephes/kolmogorov.c. This patch adds a function 'kuiper(y)' which is very similar to the function 'kolmogorov(y)', which is required for the K-S-Test. Kuipers statistics is a variant of K-S statistics which is invariant on a circle. I did not write an inverse function yet (is't not monotonic in it's first derivative) and also did not include patches for the corresponding .py files. Is there any interest to include the Kuiper statistics into SciPy ??? Manuel

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Scipy Homepage in Safari
by Brendan Simons 26 Feb '06

26 Feb '06

The gif fixes things, thanks. Weird though, I'm running Tiger. They must not have addressed the png bug completely yet. -Brendan > Brendan, > > Apparently it's a png-on-pre-tiger-Safari-issue--at least according > to this: > > http://hsivonen.iki.fi/png-gamma/ > > I've changed it from a png to a gif, hoping this will do the > trick. Let > me know how it looks. You may have to clear your cache or do other > things to get the .gif image. > > Thanks for pointing this out. > > Travis > > Brendan Simons wrote: > > Hello All. > > > > Sorry if this has been noticed before, but viewed with Safari, the > > logo on the new scipy.org page clashes with the header bar. In > > Firefox, the two match perfectly. I don't know enough about CSS to > > submit a patch. You can see a screenshot here: > > > > http://www.flickr.com/photos/28928816@N00/104426499/in/ > > set-72057594070348078/ > > > > Brendan > > __________________________________________________ > > Do You Yahoo!? > > Tired of spam? Yahoo! Mail has the best spam protection around > > http://mail.yahoo.com > > > > _______________________________________________ > > Scipy-dev mailing list > > Scipy-dev at scipy.net > > http://www.scipy.net/mailman/listinfo/scipy-dev > > > > -- > ........................ > Travis N. Vaught > CEO > Enthought, Inc. > http://www.enthought.com __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Scipy Homepage in Safari
by Brendan Simons 26 Feb '06

26 Feb '06

Hello All. Sorry if this has been noticed before, but viewed with Safari, the logo on the new scipy.org page clashes with the header bar. In Firefox, the two match perfectly. I don't know enough about CSS to submit a patch. You can see a screenshot here: http://www.flickr.com/photos/28928816@N00/104426499/in/ set-72057594070348078/ Brendan __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Conferences
by Steven H. Rogers 26 Feb '06

26 Feb '06

There doesn't seem to be any conference information on the new MorinMoin based web site. Are there plans for SciPy06? It would be nice to have conference page with an announcement for the next conference and links to the Plone pages for previous conferences/workshops. The conferences are helpful for promoting SciPy and the presentations have a lot of useful material. This information should be easy to find. I couldn't find anything on the new site and will start such a page if it doesn't already exist. I suppose it should go in the Developer Zone until it's reasonably polished? Regards Steve

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CHANGELOG for numpy/scipy ?
by Nils Wagner 25 Feb '06

25 Feb '06

Hi all, Is it possible to add a CHANGELOG to numpy/scipy ? Matplotlib comes with such a file and I find it useful w.r.t. to bugfixes, new features, etc. Any comment ? Nils

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rv_frozen for rv_discrete RVs?
by Eric Jonas 24 Feb '06

24 Feb '06

I've finally started playing around with the scipy.stats package, and I note that there doesn't appear to be a pmf function in rv_frozen. Thus, attempts to do: myrv = stats.poisson(0.5) x = myrv.pmf(r_[0:100]) yield: AttributeError: rv_frozen instance has no attribute 'pmf' Am I missing something here? I tried simply adding: def pmf(self,x): return self.dist.pmf(x,*self.args,**self.kwds) to stats/distributions.py and got the expected behavior, i.e. myrv.pmf now works as expected. I'm curious if I'm missing something, using this incorrectly, or if it's just a simple bug :) By the way, whoever came up with this distributions framework really rocks my socks! ...Eric

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scipy.io.read_array error reading from pipe
by Neal Becker 24 Feb '06

24 Feb '06

It seems read_array wants to seek. Is this really necessary? Is there a workaround? ~/remez/remez2 | ./plotfft.py Traceback (most recent call last): File "./plotfft.py", line 12, in ? x = scipy.io.read_array (sys.stdin) File "/usr/lib64/python2.4/site-packages/scipy/io/array_import.py", line 348, in read_array ascii_object = ascii_stream(fileobject, lines=lines, comment=comment, linesep=linesep) File "/usr/lib64/python2.4/site-packages/scipy/io/array_import.py", line 126, in __init__ self._pos = self.file.tell() IOError: [Errno 29] Illegal seek

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system_info problem
by Robert Cimrman 23 Feb '06

23 Feb '06

Hi, I am trying to (finally) move UMFPACK out of the sandbox to the scipy proper and so I need checking for its libraries via system_info.py of numpy distutils. I have added a new section to site.cfg: [umfpack] library_dirs = /home/share/software/packages/UMFPACK/UMFPACK/Lib:/home/share/software/packages/UMFPACK/AMD/Lib include_dirs = /home/share/software/packages/UMFPACK/UMFPACK/Include umfpack_libs = umfpack, amd the names of the libraries are libumfpack.a, libamd.a - they are correctly found in 'system_info._check_libs()' by 'self._lib_list(lib_dir, libs, exts)', but then the function fails, since 'len(found_libs) == len(libs)' which is wrong. Can some numpy.distutils expert help me? Below is the new umfpack_info class I have written using the blas_info class as template. yours clueless, r. PS: I do this because I prefer having the umfpack installed separately. It will be used, if present, to replace the default superLU-based sparse solver. Moving its sources under scipy/Lib/sparse would solve this issue, but Tim Davis recently changed the license of UMFPACK to GPL, and so the last version available for the direct inclusion is 4.4. (4.6 is the current one). Opinions are of course welcome. -- class umfpack_info(system_info): section = 'umfpack' dir_env_var = 'UMFPACK' _lib_names = ['umfpack', 'amd'] includes = 'umfpack.h' notfounderror = UmfpackNotFoundError def calc_info(self): info = {} lib_dirs = self.get_lib_dirs() print lib_dirs umfpack_libs = self.get_libs('umfpack_libs', self._lib_names) print umfpack_libs for d in lib_dirs: libs = self.check_libs(d,umfpack_libs,[]) print d, libs if libs is not None: dict_append(info,libraries=libs) break else: return include_dirs = self.get_include_dirs() print include_dirs h = (self.combine_paths(lib_dirs+include_dirs,includes) or [None])[0] if h: h = os.path.dirname(h) dict_append(info,include_dirs=[h]) print info self.set_info(**info)

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