Mailman 3 October 2002 - SciPy-User

jaja yerima
by jaja yerima Oct. 9, 2002

Oct. 9, 2002

CONFIDENTIAL BUSINESS PROPOSAL dear sir You may be suprise to receive this letter from me since you dont know me personally. The purpose of my introduction is that I am JAJA YERIMA, the first son of DAVID YERIMA , the most popular farmer in Zimbabwe who was recently murdered in the land dispute in my country. I got your contact through network online hence decide to write you. Before the death of my father, he had taken me to Johannesburg to deposit the sum of US$7,000,000.00(seven million united states of America dollars)in one security company as he forsaw the coming danger in zimbabwe. This money was deposited in a box as gemstones in to avoid much demurage from the security company.This amount was meart for the purchase of new machines and chemicals for the new farm and establishment in Swiztland. This land problems came when Zimbawean president ROBERT MUGABE introduced a new land act reform who holly affected the rich white farmers and some few black farmers. And this resulted to the killing and mob action by Zimbabwe war returns and some lunatics in the society. It is against this background that I and my family fled Zimbabwe for fear of our lives and currently staying in The Netherlands where we seek political asylum and mooreso have decided to transfer my father' money to more reliable foreign account sinces the law of The netherland prohibits a refugee to open any bank account or to be involveed in any financial transaction throughout the territorial zone of Netherland . As the eldest son of my father , I am saddled to which the respobility of seeking a genuine foreign account where this money could be transfered without the the knowledge of my government who are bert on taking everything we have got.The South Africa government seems to be playing along with them. I am faced with the delima of moving this amount of money out of South Africa for fear of going through the same experience in future, both countries have similar political history. I am seeking for a partner who I have to entrust my future and family in his hand, I must let you know that this transaction is risk free. If you accept to assist me and my family , all I want you to do for me , is to arrange with the security company to clear the consignment (funds) from their afiliate office here in the Netherlands as I have already given directives for the consignment to be brought to The Netherlands from South Africa. But before then all modalities will have to be put in place e.g change of ownership to the consignment and this money intend I intend to use for investment . I have two options for you , firstly you can choose to have certain percentage of the money or you can go into partnership with me for the proper profitable investment of the money in your country . Which ever the option you want , feel free to notify me. I have aslo mapped out 5% of the money for all kinds of expense incured in the process of this transaction. If you do not prefer a partnership I am willing to give you 15% of the money while the remaining 80% will be for my investment in your country. Contact me with the above email address while i imlore you to maintain the absolute secrecy required in this transaction. and your phone and fax number will be need for the transaction. Thanks God bless you JAJA YERIMA.

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my contribution
by Louis Cordier Oct. 8, 2002

Oct. 8, 2002

After experiencing a bit of difficulty to get everything {ATLAS,LAPACK,F2PY,Numeric,SciPy} working, I wrote this little script to automate the process for nodes on a cluster. I guess it can serve as a quick & dirty how-to for other newcomers. I used downloads from a local-network machine, just uncomment the original locations, etc. Feel free to use and redistribute it however you like. Regards, Louis. -------------------------------------------------------------- Louis Cordier, c:+27721472305, h:+27218865145, w:+27218084315 lcordier(a)dsp.sun.ac.za, http://www.dsp.sun.ac.za/~lcordier/ University of Stellenbosch - Electric & Electronic Engineering --------------------------------------------------------------

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Re: SciPy-user digest, Vol 1 #203 - 6 msgs
by Frank Gibbons Oct. 8, 2002

Oct. 8, 2002

Thanks to all of you for your suggestions. I get the mailing list in digest mode, which is why I had had no response - not enough volume. Looks like my last message kicked it over the limit. Anyway, I'm now happily SciPy-ing. My first task (once I get familiar with SciPy) will be to add this kind of help to the installation instructions! :) -Frank P.S. As a one-time FORTRAN programmer, it's kind of twilight-zonish to see odeint() and friends in Python ;) At 11:39 AM 10/8/2002, you wrote: >From: "Travis N. Vaught" <travis(a)enthought.com> >To: <scipy-user(a)scipy.net> >Subject: RE: [SciPy-user] Re: SciPy-user digest, Vol 1 #201 - 7 msgs >Date: Mon, 7 Oct 2002 15:23:29 -0500 >Reply-To: scipy-user(a)scipy.net > >Hey Frank, > >It sounds like you may be trying to import scipy from a python session >started in your build directory. Try switching to another dir (like ~/ or >/) and begin the python session and try an import. I won't tell you how >many times I have to force myself to remember this each week. PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons

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no module fastumath - how to fix it
by Frank Gibbons Oct. 8, 2002

Oct. 8, 2002

Got no response from the list on this, found it in the archives (Aug 2002) http://www.scipy.org/site_content/mailman?fn=scipy-user/2002-August/000561.… didn't quite understand the message, but got some hints from it. I'm sending this so that it's in the archive, and other people don't spend two hours trying to figure this out... After installing SciPy, you will be tempted to run python immediately, and import scipy (in fact, the docs suggest that, in INSTALL.txt). However, they don't mention that this may fail if you run it in the installation directory. So, go to another directory, then start python, then 'import scipy'. You may also want to check this message (I followed these instructions, but am not sure whether they helped or not): http://scipy.net/pipermail/scipy-user/2002-April/000302.html It may or may not also help to rename the directory from ~/cvs/SciPy to ~/cvs/SciPy_CVS (assuming that you, like most CVS users I know, have a cvs directory where you put all your projects). And to think I just about to throw in the towel on SciPy! -Frank P.S. If anyone has a better understanding of why this is a problem, I think it would be useful to put together a complete explanation (from the comments in the various emails, it seems to be a somewhat known problem). PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons

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Re: SciPy-user digest, Vol 1 #201 - 7 msgs
by Frank Gibbons Oct. 7, 2002

Oct. 7, 2002

Travis, I tried this, and it does allow me to finish building, but why are there no files in the xplt directory (except for setup_xplt.py), when I can see them on the CVS page. I see that someone else had a similar problem to me, with the downloaded tarball. Thanks for the tip. However.... I realized that I needed to get the full LAPACK installation (and therefore had to also build BLAS since I have no vendor-supplied version). My full LAPACK weighs in at a healthy 6MB, and I followed the procedures in the installation guide to replace ATLAS's wimpy version of LAPACK with the real one. So far, so good. Now the setup script runs to completion, but when I try to import scipy here's what happens: % ~/bin/python Python 2.1.1 (#1, Aug 9 2001, 11:10:31) [GCC egcs-2.91.66 19990314/Linux (egcs-1.1.2 release)] on linux2 Type "copyright", "credits" or "license" for more information. >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/home/fgibbons/lib/python2.1/site-packages/scipy/__init__.py", line 36, in ? from scipy_base import * File "scipy_base/__init__.py", line 99, in ? import fastumath ImportError: No module named fastumath To summarize my setup, I'm using the following: Python 2.1.1 Numeric 21.0 ATLAS 3.4.1 f2py 2.23.190... gcc 2.95.4 g77 (0.5.25 20010319) on a Debian Linux box. Since I've had to go back and forth in the build process a few times, I wonder if I might be able to just do the equivalent of 'make clean' and start it fresh. I'm not very familiar with setup.py (why is this better than make?) - can anyone tell me how to do the equivalent of 'make clean'? What is 'fastumath'? Where are the sources? How do I get them to build? Thanks a lot for the tips so far - I feel like I'm close, and I'm drooling at the possibility of having LAPACK/BLAS power available from Python! -Frank At 01:00 PM 10/5/2002, you wrote: >Message: 6 >From: "Travis N. Vaught" <travis(a)enthought.com> >To: <scipy-user(a)scipy.net> >Subject: RE: [SciPy-user] problems building - missing >cvs/SciPy/xplt/gistCmodule.c >Date: Fri, 4 Oct 2002 16:48:57 -0500 >Reply-To: scipy-user(a)scipy.net > >Frank, > >If you're OK with skipping xplt install (and it sounds like you are), you >may edit the scipy/setup.py file like so: > >Line 103 old: > unix_packages = ['xplt'] > >Line 103 new: > unix_packages = [] > >I haven't tried this, but it should work and costs little to test. > >Travis PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons

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overwriting Numeric on Windows is M$ policy :-)
by Gerard Vermeulen Oct. 6, 2002

Oct. 6, 2002

Hoping to do an easy install for a student, I tried to install SciPy on Windows and to port some of my NumPy extensions to Windows. (I am a Linux user, with very little Windows experience). The SciPy windows installer policy of overwriting a few modules, got me into trouble. This has the side effect that the Numerical header files (and C-API numbers) are out of sync with the binary modules. Consequently, my home cooked extensions started to return NumPy arrays of Complex instead of Float :-) >From your web site, I got the impression that SciPy for Windows has been built with Numeric-21.0, but this information looks dated. So, I have tried several versions (CVS included), but somehow the SciPy installer refused to overwrite the necessary modules (maybe because they were newer, or because my registry database is broken -- I am running Windows 98 with Win4Lin under Linux). IMHO, it is much more friendly to include a full NumPy (even if it is not the latest), instead of only a few binary modules. You are locking authors of NumPy based extension modules out of the 'market' ( I have written a Qt/Qwt based plotting package, see http://gerard.vermeulen.free.fr ). MicroSoft has been sued for a similar policy :-) Regards -- Gerard Vermeulen PS: your recipy for rebuilding SciPy on Windows looks pretty old. Did anybody try MinGW-2.O.O? And is MSYS-1.0.7 sufficient to build ATLAS? PPS: I am not rich enough to sue you.

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meshgrid_errors
by Karshi Oct. 5, 2002

Oct. 5, 2002

>>> from scipy import * >>> mgrid[0:5,05] Traceback (most recent call last): File "<pyshell#16>", line 1, in ? mgrid[0:5,05] File "C:\PYTHON22\Lib\site-packages\scipy_base\index_tricks.py", line 53, in __getitem__ step = key[k].step AttributeError: 'int' object has no attribute 'step' >>> ogrid[0:5,0:5] [array([[0], [1], [2], [3], [4]]), array([ [0, 1, 2, 3, 4]])] >>>

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help with scipy installation
by Viktor Hornak Oct. 5, 2002

Oct. 5, 2002

Hello, I am having trouble to get scipy compiled/installed on RedHat linux 7.3 (python2.2, numeric-22.0, atlas with full lapack in, wxPython-2.3.2, fftw-2.1.3). The binary installation (SciPy-0.2.0_alpha_105.3699.linux2_py2.2.tar.gz) seg faults on "from scipy import * " (or any scipy module) so I was trying to compile from CVS sources (SciPy-0.2.0_alpha_140.4284_src.tar.gz). I tried: % python2 setup.py build The compilation runs for a while but then it stops with the error: building 'scipy.xplt.gistC' extension error: file '.../scipy/SciPy-0.2.0_alpha_140.4284/xplt/gistCmodule.c' does not exist and the file 'gistCmodule.c' really is not there (or anywhere in the distribution). I wouldn't mind to skip xplt package (because I'd like to get Chaco working anyway) but I don't know how to specify which packages to skip during building. Thanks for help... Cheers, -Viktor -- =================================================================== Viktor Hornak Center for Structural Biology Phone: (631)632-1439 SUNY at Stony Brook Fax: (631)632-1555 Stony Brook, NY 11794-5115 E-mail: viktor.hornak(a)sunysb.edu ===================================================================

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problems building - missing cvs/SciPy/xplt/gistCmodule.c
by Frank Gibbons Oct. 4, 2002

Oct. 4, 2002

Hi, I've been using Python for about 5 months now, to write data-intensive bioinformatics code. Having had good luck with Numeric (and contributed features, bug-fixes and a test suite to its Jython counterpart, JNumeric), SciPy sounded like just what I need to go further. So I've just signed up, downloaded the source, and tried to build it. (I'm not root where I work, can't use RPMs etc.) I also got ATLAS and f2py and they apparently installed properly. I edited site.cfg to let SciPy know where to find ATLAS, and ran 'python setup.py install'. It runs through a bunch of stuff, but stops short at this: building 'scipy.xplt.gistC' extension error: file 'cvs/SciPy/xplt/gistCmodule.c' does not exist Anyone have any words of wisdom about how to get around this? If I were using make I'd give it a '-k' to ignore errors and keep going, in the hopes that I don't really need what I appear not to have. Is there something analogous in setup.py? Also, I may have overlooked this, but I couldn't find anything on the website listing specifically what functionality was available in SciPy - it lists packages, but not function names and descriptions. Please don't tell me I have to read the docstrings in each file, or pydoc them! A PDF file that covered the entire package would be really useful (yes, I saw the request for help setting up unit tests and working on docs - I'd be happy to, but first I need to get up and running). Thanks for any help, Frank Gibbons PhD, Computational Biologist, Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA. Tel: 617-432-3555 Fax: 617-432-3557 http://llama.med.harvard.edu/~fgibbons

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ANN: PyTables 0.1
by Francesc Alted Oct. 4, 2002

Oct. 4, 2002

Hi!, PyTables is a Python package which allows dealing with HDF5 tables. Such a table is defined as a collection of records whose values are stored in fixed-length fields. PyTables is intended to be easy-to-use, and tries to be a high-performance interface to HDF5. To achieve this, the newest improvements introduced in Python 2.2 (like generators or slots and metaclasses in new-brand classes) has been used. Pyrex creation extension tool has been chosen to access the HDF5 library. This package should be platform independent, but until now I've tested it only with Linux. It's the first public release (v 0.1), and it is in alpha state. You can get it from: http://sourceforge.net/projects/pytables/ There is still not a project home page. Perhaps in next days. Feedback welcome.! -- Francesc Alted PGP KeyID: 0x61C8C11F Scientific aplications developer Public PGP key available: http://www.openlc.org/falted_at_openlc.asc Key fingerprint = 1518 38FE 3A3D 8BE8 24A0 3E5B 1328 32CC 61C8 C11F

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