Mailman 3 March 2003 - SciPy-User

SciPy and PyGSL
by Richard Muller April 1, 2003

April 1, 2003

I've been spending a little time getting to know the Gnu Scientific Library. It shares a lot of the strengths with SciPy. I notice that there is a fledgling effort to make python wrappers to the GSL, and I now wonder how the SciPy community sees such an effort: competition, fellow warriors, or potential successor? I for one would like to see the GSL become more of a standard in the scientific computing field, so I'd like to see PyGSL get support. But not necessarily at the expense of SciPy. Thoughts? Rick Rick Muller rpm(a)wag.caltech.edu http://wag.caltech.edu/home/rpm

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never mind ...
by Christopher Fonnesbeck March 31, 2003

March 31, 2003

I referred to some of the updated examples and saw that things like mydict.ptr() are no longer used. My updated code now compiles, with only the following warning: exceptions.ImportError: /usr/lib/python2.2/site-packages/scipy/linalg/_flinalg.so: undefined symbol: dlaswp_ Cheers, cjf -- Christopher J. Fonnesbeck (chris at fonnesbeck.org) GA Coop. Fish & Wildlife Research Unit, University of Georgia Oh my friend, what a time is this To trade the handshake for the fist -- Joni Mitchell

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strange weave.inline errors in weave using gcc3.2
by Christopher Fonnesbeck March 31, 2003

March 31, 2003

I have installed weave from cvs, and with gcc3.2 all of the tests run fine. However, when I run it with some of my code, Bad Things happen. Here are the relevant parts of the code, followed by the error messages: code = ''' #line 610 "ReinforcementLearning.py" PyObject *key, *qval, *traceval = NULL; Py::List keys = qfunction.keys(); for (int i=0; i<keys.length(); i++) { key = PyList_GET_ITEM(keys.ptr(),i); /* Grab and convert current Q-value */ qval = PyDict_GetItem(qfunction.ptr(),key); double qval_raw = py_to_float(qval,"qval_raw"); /* Grab and convert current elegibility value */ traceval = PyDict_GetItem(etrace.ptr(),key); double traceval_raw = py_to_float(traceval,"traceval_raw"); /* Calculate new Q-value */ qval_raw += alpha * delta * traceval_raw; /* Return new Q-value to Q-function */ PyObject* qval_new = PyFloat_FromDouble(qval_raw); PyDict_SetItem( qfunction.ptr(), key, qval_new ); /* Cleanup */ Py_DECREF(qval_new); /* Only update nonzero e-trace values */ if (traceval_raw>0.0) { /* Only interested in sizeable values */ if (traceval_raw>=tolerance) { /* Calculate new elegibility value */ traceval_raw = gamma * lamda * traceval_raw; /* Return new elegibility value to trace */ PyObject* traceval_new = PyFloat_FromDouble(traceval_raw); PyDict_SetItem( etrace.ptr(), key, traceval_new ); /* Cleanup */ Py_DECREF(traceval_new); } /* Set very small values to zero */ else PyDict_SetItem( etrace.ptr(), key, PyFloat_FromDouble(0.0) ); } } ''' 'Call to weave' weave.inline(code, ['qfunction', 'alpha','delta','etrace', 'gamma','lamda','tolerance']) This yields: ReinforcementLearning.py: In function `PyObject* compiled_func(PyObject*, PyObject*)': ReinforcementLearning.py:612: `Py' undeclared (first use this function) ReinforcementLearning.py:612: (Each undeclared identifier is reported only once for each function it appears in.) ReinforcementLearning.py:612: parse error before `::' token ReinforcementLearning.py:613: `keys' undeclared (first use this function) ReinforcementLearning.py:617: no matching function for call to `py::dict::ptr() ' ReinforcementLearning.py:621: no matching function for call to `py::dict::ptr() ' ReinforcementLearning.py:629: no matching function for call to `py::dict::ptr() ' ReinforcementLearning.py:646: no matching function for call to `py::dict::ptr() ' ReinforcementLearning.py:653: no matching function for call to `py::dict::ptr() ' Traceback (most recent call last): File "ReinforcementLearning.py", line 931, in __call__ s==maxsteps-1) File "ReinforcementLearning.py", line 678, in update_qfunction ['qfunction', File "/usr/lib/python2.2/site-packages/weave/inline_tools.py", line 335, in inline auto_downcast = auto_downcast, File "/usr/lib/python2.2/site-packages/weave/inline_tools.py", line 439, in compile_function verbose=verbose, **kw) File "/usr/lib/python2.2/site-packages/weave/ext_tools.py", line 340, in compile verbose = verbose, **kw) File "/usr/lib/python2.2/site-packages/weave/build_tools.py", line 272, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/usr/lib/python2.2/site-packages/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "//usr/lib/python2.2/distutils/core.py", line 157, in setup raise SystemExit, "error: " + str(msg) CompileError: error: command 'gcc' failed with exit status 1 Any ideas what is happening? -- Christopher J. Fonnesbeck (chris at fonnesbeck.org) GA Coop. Fish & Wildlife Research Unit, University of Georgia Oh my friend, what a time is this To trade the handshake for the fist -- Joni Mitchell

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RE: Re: [SciPy-user] SciPy and PyGSL
by Nadav Horesh March 30, 2003

March 30, 2003

As much as I know, a wrapper around a GPL library should not be "infected" by the GPL, since it does not include a copy of the GPLed source code. Am I wrong? Nadav. >"RM" == Richard Muller <rpm(a)wag.caltech.edu> writes: > > > > RM> I've been spending a little time getting to know the Gnu > RM> Scientific Library. It shares a lot of the strengths with > RM> SciPy. I notice that there is a fledgling effort to make > RM> python wrappers to the GSL, and I now wonder how the SciPy > RM> community sees such an effort: competition, fellow warriors, > RM> or potential successor? > > RM> I for one would like to see the GSL become more of a standard > RM> in the scientific computing field, so I'd like to see PyGSL > RM> get support. But not necessarily at the expense of > RM> SciPy. Thoughts? > >IIRC, the biggest issue with GSL is the GPL license. SciPy uses a BSD >style license. Since the GPL is so restrictive, if SciPy even linked >to libgsl, SciPy would need to be released as GPL. Dual licensing as >GPL/BSD is meaningless. > > We are the Borg of FSF, non-GPL is futile, you will be GPL'd! > >Sorry could not resist that one! > >cheers, >prabhu > >--__--__-- >

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cannot build SciPy on Redhat 8.0
by Christopher Fonnesbeck March 29, 2003

March 29, 2003

Hi folks, I am trying to build SciPy on a new installation of RedHat 8.0, but am ahving trouble getting out of the gate. I have installed all of the prerequisite packages, but when I try and run "python setup.py install", I get the following: Traceback (most recent call last): File "setup.py", line 111, in ? setup_package() File "setup.py", line 90, in setup_package config_list += map(get_separate_package_config,separate_packages) File "setup.py", line 74, in get_separate_package_config return get_package_config(name,'') File "setup.py", line 67, in get_package_config mod = __import__('setup_'+os.path.basename(name)) ImportError: No module named setup_scipy_distutils I clearly have a setup_scipy_distutils in my /usr/lib/python2.2/site-packages/scipy_distutils, so I don't know why I am getting this error. I hope someone can clarify this for me. Has anyone ever tried putting together rpm packages? Thanks, Chris Fonnesbeck

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URGENT RESPONSES NEEDED
by MICHEAL SANKOH JNR. March 29, 2003

March 29, 2003

URGENT ASSISTANCE NEEDED WITH ABSOLUTE TRUST IN GOD AND DUE RESPECT TO YOU, I WRITE TO YOU THIS LETTER WHICH I BELIEVE YOU WOULD BE OF GREAT ASSISTANCE TO ME AND WOULD KEEP THE INFORMATION CONFIDENTIAL. I AM MICHEAL SANKOH, A SON TO FODAY SANKOH, THE REBEL LEADER IN SIERRA LEONE WARRING FACTIONS, I AM ABSOLUTELY AGAINST THE UNENDING POLITICAL CRISES IN MY COUNTRY THAT HAS RESULTED TO A MISSIVE DESTRUCTION OF HUMAN LIVES AND PROPERTY WHICH IS CURRENTLY IN THE WORLD NEWS. ON THIS LAST ASSAULT BY THE FORCES. I ESCAPED TO THE NETHERLAND THROUGH THE HELP OF UNITED NATIONS SOLDIERS WHO ARE THERE ON A PEACE MISSION. ON ARRIVAL TO AMSTERDAM, I WENT DIRECTLY TO THE ASSYLUM CAMP, TO SEEK FOR POLITICAL ASSYLUM, I WAS ASCEPTED, and BEFORE THE WAR HE DEPOSITED A TOTAL SUM $10.500 MILLION USD IN TWO TRUNK BOXES WITH A SAFE DEPOSIT WITH FINANCE HOUSE. HE DEPOSITED THEM AS FAMILY VALUABLES IN THE NAME OF HIS SON MICHAEL SANKOH. I AM LOOKING FOR A RELIABLE AND TRUST WORTHY PARTNER FROM A DIFFERENT COUNTRIES FROM THE NETHERLANDS SINCE THE LAW OF THE NETHERLANDS PROHIBIT A REFUGEE (ASYLUM SEEKER) TO OPEN ACCOUNT OR TO BE INVOLVED IN ANY FINANCIAL TRANSACTION.MOREOVER, THE NETHERLANDS FOREIGN EXCHANGE POLICY DOES NOT ALLOW SUCH INVESTMENT FROM ASYLUM SEEKERS.I AM FACED WITH THE DILEMA OF INVESTING THIS AMOUNT OF MONEY IN THE NETHERLANDS FOR THE FEAR OF GOING THROUGH THE SAME EXPERIENCE IN FUTURE SINCE BOTH COUNTRIES HAVE SIMILAR HISTORY. I HUMBLY SOLICIT FOR YOUR ASSISTANCE IN THE FOLLOWING: 1) PAY A SHORT WORKING DAY VISIT TO AMSTERDAM THE NETHERLANDS SO THAT WE SEE FACE TO FACE, HAVE A TABLE TALK THAT WOULD CREATE CONFIDENCE IN ME THAT THE FUND WOULD BE SAFE IN YOUR HANDS AND HAVE HAVE AN AGREEMENT FROM A ADVOCATE, WHICH WILL BE DULY AND LEGALLY SIGN IN HIS CHAMBERS BEFORE TAKEN ANY STEP IN THIS TRANSACTION. 2GET ALL THE NECESSARY DOCUMENT REGARDING THIS TRANSACTION AND CLAIM THE BOXES FROM THE SECURITY COMPANY, OPEN AN ACCOUNT IN YOUR NAME WITH A LOCAL BANK HERE AND DEPOSIT THE MONEY FOR ONWARD TRANSFER TO YOUR DESIGNATED ACCOUNTS OVERSEAS. 3) MAKE A GOOD ARRANGEMENT FOR INVESTMENT AND DO INVEST THE MONEY FOR ME. I AM WILLING TO GIVE YOU SOME PERCENTAGE FOR YOUR ASSISTANCE AND ON THIS, I OFFER YOU 15%. 5% WOULD BE USED TO OFFSET EVERY EXPENSES TO BE INCURRED AND TAXES OR CHARGES TO BE PAID IN THE COURSE ON THE TRANSACTION WHILE 80% WOULD BE INVESTED AND YOU GET YOUR WAGE MONTHLY FOR MANAGING THE 80%. I ASSURE YOU THAT THE TRANSACTION IS RISK FREE AND COULD BE COMPLETED UPON YOUR ARRIVAL IF YOU WOULD BE OF ASSISTANCE TO ME, PLEASE FORWARD YOUR REPLY THROUGH MY PRIVATE EMAIL ADDRESS AND CALL ME ON MY TELEPHONE LINE: 0031629343835 FOR FURTHER DISCUSSION, AND REMEMBER CONFIDENTIAL SINCE I AM STILL WITH THE NETHERLANDS GOVERNMENT. THANKS AND GOD BLESS MICHEAL SANKOH JNR.

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Resultant of two polynomials - Sylvester matrix
by Thomas M. Zavist March 28, 2003

March 28, 2003

Dear scipy-user: I stumbled upon a request on the internet by Nils Wagner. The request is "I am looking for a function which computes the resultant of two polynomials. It is defined to be the determinant of their Sylvester matrix. A small example would be appreciated." About 15 years ago I read what looks like the answer to the question in the Fondren Library at Rice University in a book by Yitzhak Katznelson entitled "Yale Lecture Series," or something like that, published in 1960. If you have two polynomials A + Bx + Cx^2 + Dx^3 and E + Fx + Gx^2, then the resultant of the two is the determinant of the 5 x 5 matrix with the following elements: A 0 E 0 0 B A F E 0 C B G F E D C 0 G F 0 D 0 0 G The polynomials have a common root if and only if the determinant--the resultant is zero. The resultant is related to the product of the difference of each pair of roots--one from each polynomial. You can define the resultant for any pair of polynomials in one variable. A polynomial of degree m and another of degree n lead to an (m+n) x (m+n) determinant as their resultant. Katznelson's lecture, which is described above, pertains to two polynomials of one variable. If you have two polynomials of more than one variable, you can treat them as polynomials of one variable--treating the additional variables as constants and dropping them into the resultant. The result is one polynomial that has one fewer variable than the two polynomials you had originally. By iterating this process you can take a system of polynomial equations in several variables and eliminate as many variables as there are equations in excess of one. Besides this recursive procedure, there are other ways to generalize the resultant to solve any system of polynomial equations. You can also use the resultant to define a polynomial whose roots are the sum, difference, product or quotient of the roots of other polynomials. I hope this is helpful. Sincerely, Tom Zavist

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Re: [SciPy-user] IPython, a new SciPy.org netizen
by Eric Jones March 28, 2003

March 28, 2003

Hey Fernando, Cool! Glad to hear this is all set up. I look forward to a bright future for ipython and pycrust integration. By the way, I'm at PyCon right now, and the conference is going very well. They've done a great job of organizing it. see ya, eric Fernando Perez <fperez(a)colorado.edu> wrote .. > Hi all, > > I'd like start by publicly thanking Eric Jones, Joe Cooper and the rest > of the > SciPy team for hosting IPython. Some of you are already users of ipython > and > may have received a message earlier today about this. My apologies for > the > double mail, this one is short :) > > For those who are not previous ipython users, I encourage you to take a > look > at IPython at: > > http://ipython.scipy.org > > This will be IPython's new home on the net, and it will have the usual > scipy.org accoutrements in due time. But right now the most important > things, > anonymous CVS access and mailing lists, are already up. > > I really hope that this will not only enable me to develop ipython further, > but also help the whole community to provide the scipy project with a good > interactive shell. Scipy is heavily using PyCrust already, and I have > a lot > of interest in moving ipython in the direction of integrating (optionally) > with pycrust. > > For further discussion of ipython issues, I encourage those interested > to sign > up at the ipython-specific mailing lists, located at: > > - User list: http://scipy.net/mailman/listinfo/ipython-user > - Dev list: http://scipy.net/mailman/listinfo/ipython-dev > > This will keep the scipy-* lists focused on scipy-specific issues. > > Those interested in integration with PyCrust should also sign up for the > PyCrust list at https://lists.sourceforge.net/lists/listinfo/pycrust-users, > following Patrick O'Brien's suggestion. Knowledgeable WxPython developers > would be most welcome. > > Hope to see you all on the lists! > > Best regards, > > f. > > _______________________________________________ > SciPy-user mailing list > SciPy-user(a)scipy.net > http://www.scipy.net/mailman/listinfo/scipy-user

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Overflow Errors
by Edward Hartley March 28, 2003

March 28, 2003

Hi I'm using python 2.2.2 I know there are some issues with overflow errors So should this version be reompiled with -lieee as I've seen suggested on another thread and if so does this mean I have to adjust the Makefile or can it be done through the configure script Regards Ed Hartley

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scipy to C ?
by Agustin Lobo March 28, 2003

March 28, 2003

Is there a tool to convert a (sci)python program into a C program? something like what the Matlab compiler is supossed to do (never tried) with matlab scripts? My interest is on improving the performance of scipy scripts that use (unavoidable, at least for me) "for loops". Thanks Agus Dr. Agustin Lobo Instituto de Ciencias de la Tierra (CSIC) Lluis Sole Sabaris s/n 08028 Barcelona SPAIN tel 34 93409 5410 fax 34 93411 0012 alobo(a)ija.csic.es

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