Mailman 3 January 2007 - NumPy-Discussion

Re: [Numpy-discussion] failed to build numpy and Numeric in Windows
by Zhou, Mi Jan. 12, 2007

Jan. 12, 2007

Hi, Python on the same machine was built with MSVS2005. I think it is capable of building python modules. Interestingly, if I replace "floor" with "ceil" in that line of code. It will build just fine, and of course, the Numeric.floor() will work just like Numeric.ceil(): static void * floor_data[] = { (void *)ceil, (void *)ceil, (void *)"floor", }; Thanks, Mi -----Original Message----- From: numpy-discussion-bounces(a)scipy.org [mailto:numpy-discussion-bounces@scipy.org] On Behalf Of Robert Kern Sent: Friday, January 12, 2007 1:55 PM To: Discussion of Numerical Python Subject: Re: [Numpy-discussion] failed to build numpy and Numeric in Windows Zhou, Mi wrote: > Hi, > > I am trying to build Numpy-1.01 in windows using "python setup.py > build". My C compiler is MSVS2005. Hmm. I was pretty sure that MSVS2005 was not capable of building Python extension modules that work with the official Python interpreter builds. That doesn't explain or solve the problem that you state, but if the problem is restricted to MSVS2005, it may not be worth solving. -- 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 _______________________________________________ Numpy-discussion mailing list Numpy-discussion(a)scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion

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failed to build numpy and Numeric in Windows
by Zhou, Mi Jan. 12, 2007

Jan. 12, 2007

Hi, I am trying to build Numpy-1.01 in windows using "python setup.py build". My C compiler is MSVS2005. The compiler throws an error about umathmodule.c: "__umath_generated.c(72): error C2099: initializer is not a constant." Tried with Numeric-24.2, it gives the same error. The line of code it complains about is: static void * floor_data[] = { (void *)floor, (void *)floor, (void *)"floor", }; Does anybody know how to fix it? Thanks, Mi Zhou

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failed to build numpy and Numeric in Windows
by Zhou, Mi Jan. 12, 2007

Jan. 12, 2007

Hi, I am trying to build Numpy-1.01 in windows using "python setup.py build". My C compiler is MSVS2005. The compiler throws an error about umathmodule.c: "__umath_generated.c(72): error C2099: initializer is not a constant." Tried with Numeric-24.2, it gives the same error. The line of code it complains about is: static void * floor_data[] = { (void *)floor, (void *)floor, (void *)"floor", }; Does anybody know how to fix it? Thanks, Mi Zhou

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Installation
by Bernhard Voigt Jan. 12, 2007

Jan. 12, 2007

Dear all, I've recently installed the last releases of numpy and scipy (tar archives from scipy.org). I encountered two problems: 1) During the configuration it seems the information from my site.cfg is not read. 2) Installation using atlas optimized lapack/blas libraries didn't work 1) My site.cfg is in numpy-1.0.1/ (same as the setup.py file) and has the following contents: [blas] library_dirs = ~/apps/usr/local/lib/ blas_libs = blas [lapack] library_dirs= ~/apps/usr/local/lib lapack_libs = lapack The output of the python setup.py config lists this: .... blas_info: FOUND: libraries = ['blas'] library_dirs = ['/afs/ifh.de/user/b/bvoigt/apps/lib'] language = f77 lapack_info: FOUND: libraries = ['lapack'] library_dirs = ['/afs/ifh.de/user/b/bvoigt/apps/lib'] language = f77 Which acutally aren't the libs from the path I quoted in site.cfg. I've put links to ~/apps/lib in order to get it run and this works. ~/apps/libs might be take from some python standard library path since this is where my python lives. 2) In addition to that I had another problem using ATLAS optimized blas and lapack libraries. Installation worked the same way that I had to put a link in ~/apps/lib/atlas. However, I got an unresolved symbold error that ATL_dgemm was not found, when I imported numpy.linalg. I searched for that type of failure when using altas and I found that the order of the libraries might be of importance when the numpy fortran wrappers are compiled: Taken from ( http://groups.google.com/group/sci.math.num-analysis/browse_frm/thread/8b62… ): <snip> my problem was the order of the invication of the librarys ! if i use g77 dgt.f libf77blas.a libatlas.a i get no errormessage. but if i use g77 dgt.f libatlas.a libf77blas.a </snip> In this case quoted here, the compiler complained already about unresolved symbols, so I don't know if this is the same reason for the problem I observer. Anyway, I sorted the list of libraries in the numpy/distutils/system_info.py file in the method at the bottom. This had an effect, however another symbol couldn't be resolved :-( and I stopped playing around. Thanks for any suggestions/help solving those problems. Bernhard

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How do I test if an array contains NaN ?
by Sebastian Haase Jan. 12, 2007

Jan. 12, 2007

Hi! Simple question: How do I test if an array contains NaN ? Or others like inf ...? Thanks, Sebastian Haase

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No test file found
by Keith Goodman Jan. 11, 2007

Jan. 11, 2007

I see a lot of 'No test file found' warnings when running numpy.test(). What does that mean? >> M.__version__ '1.0.1' >> M.test(10,10) Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core.info' from '...e-packages/numpy/core/info.pyc'> Found 13 tests for numpy.core.umath Found 9 tests for numpy.lib.arraysetops Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils.info' from '...kages/numpy/distutils/info.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/fft/tests for module <module 'numpy.fft.fftpack_lite' from '...ages/numpy/fft/fftpack_lite.so'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils' from '...s/numpy/distutils/__init__.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/lib/tests for module <module 'numpy.lib._compiled_base' from '...es/numpy/lib/_compiled_base.so'> Found 3 tests for numpy.fft.helper Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils.__version__' from '...umpy/distutils/__version__.pyc'> Found 1 tests for numpy.lib.ufunclike Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core._internal' from '...kages/numpy/core/_internal.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy.dual' from '...4/site-packages/numpy/dual.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/testing/tests for module <module 'numpy.testing.info' from '...ackages/numpy/testing/info.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/testing/tests for module <module 'numpy.testing.utils' from '...ckages/numpy/testing/utils.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core.fromnumeric' from '...ges/numpy/core/fromnumeric.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy.ctypeslib' from '...e-packages/numpy/ctypeslib.pyc'> Found 2 tests for numpy.lib.polynomial Found 9 tests for numpy.core.records Found 26 tests for numpy.core.numeric Found 5 tests for numpy.distutils.misc_util Found 4 tests for numpy.lib.getlimits Found 31 tests for numpy.core.numerictypes Found 4 tests for numpy.core.scalarmath Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/linalg/tests for module <module 'numpy.linalg.info' from '...packages/numpy/linalg/info.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy.add_newdocs' from '...packages/numpy/add_newdocs.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/random/tests for module <module 'numpy.random' from '...ages/numpy/random/__init__.pyc'> Found 12 tests for numpy.lib.twodim_base Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core.arrayprint' from '...ages/numpy/core/arrayprint.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/lib/tests for module <module 'numpy.lib.scimath' from '...packages/numpy/lib/scimath.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy.__config__' from '...-packages/numpy/__config__.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy.matlib' from '...site-packages/numpy/matlib.pyc'> Found 47 tests for numpy.lib.shape_base Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy._import_tools' from '...ckages/numpy/_import_tools.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/fft/tests for module <module 'numpy.fft.info' from '...te-packages/numpy/fft/info.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils.log' from '...ckages/numpy/distutils/log.pyc'> Found 4 tests for numpy.lib.index_tricks Found 32 tests for numpy.linalg.linalg Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/random/tests for module <module 'numpy.random.mtrand' from '...ackages/numpy/random/mtrand.so'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils.ccompiler' from '.../numpy/distutils/ccompiler.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy.version' from '...ite-packages/numpy/version.pyc'> Found 42 tests for numpy.lib.type_check Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/lib/tests for module <module 'numpy.lib.info' from '...te-packages/numpy/lib/info.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core._sort' from '...e-packages/numpy/core/_sort.so'> Found 1 tests for numpy.fft.fftpack Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils.unixccompiler' from '...py/distutils/unixccompiler.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/tests for module <module 'numpy' from '...te-packages/numpy/__init__.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/lib/tests for module <module 'numpy.lib' from '...ackages/numpy/lib/__init__.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core' from '...ckages/numpy/core/__init__.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/lib/tests for module <module 'numpy.lib.utils' from '...e-packages/numpy/lib/utils.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/lib/tests for module <module 'numpy.lib.machar' from '...-packages/numpy/lib/machar.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/random/tests for module <module 'numpy.random.info' from '...packages/numpy/random/info.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/testing/tests for module <module 'numpy.testing' from '...ges/numpy/testing/__init__.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils.exec_command' from '...mpy/distutils/exec_command.pyc'> Found 188 tests for numpy.core.multiarray Found 36 tests for numpy.core.ma Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core.memmap' from '...packages/numpy/core/memmap.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/linalg/tests for module <module 'numpy.linalg.lapack_lite' from '...es/numpy/linalg/lapack_lite.so'> Found 10 tests for numpy.core.defmatrix Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/fft/tests for module <module 'numpy.fft' from '...ackages/numpy/fft/__init__.pyc'> Found 41 tests for numpy.lib.function_base Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/distutils/tests for module <module 'numpy.distutils.__config__' from '...numpy/distutils/__config__.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core._dotblas' from '...ackages/numpy/core/_dotblas.so'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/testing/tests for module <module 'numpy.testing.numpytest' from '...es/numpy/testing/numpytest.pyc'> Warning: No test file found in /usr/lib/python2.4/site-packages/numpy/core/tests for module <module 'numpy.core.defchararray' from '...es/numpy/core/defchararray.pyc'> Found 0 tests for __main__

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Fwd: Advanced selection, duplicate indices, and augmented assignment
by Timothy Hochberg Jan. 11, 2007

Jan. 11, 2007

On 1/6/07, Robert Kern <robert.kern(a)gmail.com> wrote: > > Sean R. Lynch wrote: > > >>>> x = zeros((3,)) > >>>> x[array([0, 1, 1])] += array([1, 1, 1]) > >>>> x > > array([ 1., 1., 0.]) > > > > If this worked the way I was hoping, the output would be [1 2 0] because > > > it would add to element 1 twice due to its duplication in the advanced > > selection array. > > > > Is the current behavior intentional or is it an accident of > > implementation? > > It is an unavoidable consequence of the way Python interprets that code > and the > way numpy arrays are fundamentally implemented. See Travis Oliphant's, Tim > Hochberg's and my posts in the thread "Histograms via indirect index > arrays" for > more details. > > > http://projects.scipy.org/pipermail/numpy-discussion/2006-March/thread.html… Do we have to revisit that thread? I seem to recall it getting kind of cranky. To avoid reliving that, I will attempt dredge up the relevant issue: "a[indx]+=b" should be the same as "a[indx]=a[indx]+b". All else follow from that. If staring at that for a while doesn't enlighten you, then you will have to read that thread. [ I suspect that in theory we could make the += form behave as you expect, but that would break the identity above, which would confuse a bunch of people] -tim

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Warning messages after upgrading to 1.0.1
by Keith Goodman Jan. 11, 2007

Jan. 11, 2007

I get lots of warning messages after upgrading from 1.0rc1 to 1.0.1: Warning: divide by zero encountered in divide Warning: invalid value encountered in log Warning: invalid value encountered in subtract Warning: invalid value encountered in multiply What's a good way to turn off the warnings?

2 1

Docstring standards for NumPy and SciPy
by Travis Oliphant Jan. 11, 2007

Jan. 11, 2007

There was a lively discussion on the SciPy List before Christmas regarding establishing a standard for documentation strings for NumPy / SciPy. I am very interested in establishing such a standard. A hearty thanks goes to William Stein for encouraging the discussion. I hope it is very clear that the developers of NumPy / SciPy are quite interested in good documentation strings but recognize that producing them can be fairly tedious and un-interesting work. This is the best explanation I can come up with for the relative paucity of documentation rather than some underlying agenda *not* to produce them. I suspect a standard has not been established largely because of all the discussions taking place within the documentation communities of epydoc, docutils, etc. and a relative unclarity on what to do about Math in docstrings. I'd like to get something done within the next few days (like placing the standard on a wiki and/or placing a HOWTO_DOCUMENT file in the distribution of NumPy). My preference is to use our own basic format for documentation with something that will translate the result into something that the epydoc package can process (like epytext or reStructuredText). The reason, I'd like to use our own simple syntax, is that I'm not fully happy with either epytext or reStructuredText. In general, I don't like a lot of line-noise and "formatting" extras. Unfortuntately both epytext and reStructuredText seem to have their fair share of such things. Robert wrote some great documentation for a few functions (apparently following a reStructuredText format). While I liked that he did this, it showed me that I don't very much like all the line-noise needed for structured text. I've looked through a large number of documentation strings that I've written over the years and believe that the following format suffices. I would like all documentation to follow this format. This format attempts to be a combination of epytext and restructured text with additions for latex-math. The purpose is to make a docstring readable but also allowing for some structured text directives. At some point we will have a sub-routine that will translate docstrings in this format to pure epytext or pure restructured text. """ one-line summary not using variable names or the function name A few sentences giving an extended description. Inputs: var1 -- Explanation variable2 -- Explanation Outputs: named, list, of, outputs named -- explanation list -- more detail of -- blah, blah. outputs -- even more blah Additional Inputs: kwdarg1 -- A little-used input not always needed. kwdarg2 -- Some keyword arguments can and should be given in Inputs Section. This is just for "little-used" inputs. Algorithm: Notes about the implemenation algorithm (if needed). This can have multiple paragraphs as can all sections. Notes: Additional notes if needed Authors: name (date): notes about what was done name (date): major documentation updates can be included here also. See also: * func1 -- any notes about the relationship * func2 -- * func3 -- (or this can be a comma separated list) func1, func2, func3 (For NumPy functions, these do not need to have numpy. namespace in front of them) (For SciPy they don't need the scipy. namespace in front of them). (Use np and sp for abbreviations to numpy and scipy if you need to reference the other package). Examples: examples in doctest format Comments: This section should include anything that should not be displayed in a help or other hard-copy output. Such things as substitution-directed directives should go here. """ Additional Information: For paragraphs, indentation is significant and indicates indentation in the output. New paragraphs are marked with blank line. Text-emphasis: Use *italics*, **bold**, and `courier` if needed in any explanations (but not for variable names and doctest code or multi-line code) Math: Use \[...\] or $...$ for math in latex format (remember to use the raw-format for your text string in such cases). Place it in a new-paragraph for displaystyle or in-line for inline style. References: Use L{reference-link} for any code links (except in the see-also section). The reference-link should contain the full path-name (unless the function is in the same name-space as this one is. Use http:// for any URL's Lists: * item1 - subitem + subsubitem * item2 * item3 or 1. item1 a. subitem i. subsubitem1 ii. subsubitem2 2. item2 3. item3 for lists. Definitions: descripition This is my description for any definitions needed. Addtional Code-blocks: {{{ for multi-line code-blocks that are not examples to be run but should be formatted as code. }}} Tables: Tables should be constructed as either: +------------------------+------------+----------+ | Header row, column 1 | Header 2 | Header 3 | +========================+============+==========+ | body row 1, column 1 | column 2 | column 3 | +------------------------+------------+----------+ | body row 2 | Cells may span | +------------------------+-----------------------+ or || Header row, column 1 || Header 2 || Header 3 || ------------------------------------------------------- || body row, column 1 || column 2 || column 3 || || body row 2 |||| Cells may span columns || Footnotes: [1] or [CITATION3] for Footnotes which are placed at the bottom of the docstring as [1] Footnote [CITATION3] Additional note. Substitution: Use |somename|{optional text} with (the next line is placed at the bottom of the docstring in the Comments: section) .. |somename| image::myfile.png or .. |somename| somedirective:: {optional text} for placing restructured text directives in the main text. Please address comments to this proposal, very soon. I'd like to finalize it within a few days. -Travis

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Scipy - Numpy incompatiblility when calling upon Old Numeric
by frbeaxs Jan. 11, 2007

Jan. 11, 2007

Matplotlib ver 0.87.4. was the problem. An update to matplotlib-0.87.7 was all that was necessary.

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