Mailman 3 September 2003 - SciPy-User

Re: [SciPy-user] Installation on Mac OSX, again
by Andrew Straw Sept. 10, 2003

Sept. 10, 2003

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday, Sep 10, 2003, at 15:49 Australia/Adelaide, Bob Ippolito wrote: > On Tuesday, Sep 9, 2003, at 23:18 America/New_York, Andrew Straw wrote: > >> In the meantime, I exist quite happily by grabbing ATLAS from fink, >> but using the "official" MacPython-2.3 from Jack Jansen and compiling >> scipy (and other python modules not available through Package >> Manager) from CVS sources. I posted some stuff to this list about a >> few tweaks to scipy's build system -- I think site.cfg or something. > > I can't seem to find your previous thread about the tweaks to scipy's > build system in the archives, can you forward me the message? Looks like I actually posted solutions to pythonmac-sig. Sorry for the confusion. http://mail.python.org/pipermail/pythonmac-sig/2003-April/007617.html In a nutshell, my method is: 0) installing prerequisites 1) Create scipy_core/scipy_distutils/site.cfg for ATLAS et al. 2) remove xplt from the build process (I just haven't put in the effort to get it to compile - I can't see why it shouldn't) by commenting it out of setup.py. 3) python setup.py install > Also, I'd be interested to know what modules you're using that aren't > covered by either my PackageManager repository or Jack's, so I can > package them and make everyone's life easier. A quick browse down the memory lane called 'site-packages' shows that in addition to many packages in your and Jack's PackMan databases, I most frequently use scipy (including chaco), biggles, Gnuplot, IPython, mysql, reportlab, piddle, rpy, pyro, pytables, and numarray. (Actually, some of these might be in the databases, but I remember building them myself...) -----BEGIN PGP SIGNATURE----- iD8DBQE/Xs4R1xWcCSPVbpgRAnKLAKCYrBsU57K1426B0C9V2zAyiIZgewCfa6TG c2umoTzSgvDBs9EUoY8cw28= =6XOw -----END PGP SIGNATURE-----

2 1

IPython completion
by Jeffery D. Collins Sept. 9, 2003

Sept. 9, 2003

Filename completion for IPython does not work for me under Python-2.3, but does for Python-2.2. That is, typing a <tab> does nothing. It seems to work fine for everything else. Startup dialog: Python 2.3 (#11, Sep 5 2003, 13:12:43) Type "copyright", "credits" or "license" for more information. IPython 0.4.0 -- An enhanced Interactive Python. ? -> Introduction to IPython's features. @magic -> Information about IPython's 'magic' @ functions. help -> Python's own help system. object? -> Details about 'object'. ?object also works, ?? prints more. IPython profile: numeric Activating auto-logging. Current session state plus future input saved to: ipython.log Logging mode: rotate *** Your version of Gnuplot appears not to have mouse support. *** Type `gphelp` for help on the Gnuplot integration features. -- Jeffery Collins

2 5

SciPy 2003 Parking?
by ChuckEsterbrook＠yahoo.com Sept. 9, 2003

Sept. 9, 2003

Can anyone tell me what SciPy 2003 parking is going to be like? The CalTech site has a parking form, but I don't know if I'm supposed to get back a sticker or what... Do I just snail mail them the form here? http://atc.caltech.edu/CIT_parking/visit_reg.pdf -Chuck -- http://ChuckEsterbrook.com/

3 3

[weave] newbie : installation problem
by Jean-Baptiste Richet - AREAS Sept. 8, 2003

Sept. 8, 2003

Hello, weave could be highly usefull to me, but I can't have it work correctly on my PC, and I don't know what to do. Could you help me ? I installed the latest zip package by "python setup.py install", on a python 2.3 installation (OS = Windows ME), and here is a result when trying it : ========================= IDLE 1.0 >>> import weave >>> a = 123 >>> weave.inline('printf("%d\\n",a);',['a']) Exception exceptions.AttributeError: "DbfilenameShelf instance has no attribute 'writeback'" in Traceback (most recent call last): File "<pyshell#2>", line 1, in -toplevel- weave.inline('printf("%d\\n",a);',['a']) File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\inline_tools.py", line 327, in inline auto_downcast = auto_downcast, File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\inline_tools.py", line 426, in compile_function verbose=verbose, **kw) File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\ext_tools.py", line 349, in compile verbose = verbose, **kw) File "C:\DEVELOPPEMENT\PYTHON23\Lib\site-packages\weave\build_tools.py", line 194, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "c:\developpement\python23\lib\distutils\core.py", line 166, in setup raise SystemExit, "error: " + str(msg) CompileError: error: command 'g++' failed with exit status 1 >>> =========================== The gcc I use comes from MinGW and is version 3.2. I tried out gcc 2.95, and it was nearly the same (error at the same place, but 'cc' was blaimed). I tried cygwin, and it was not different. I tried python 2.2, and the result was similar. Any idea ? thanks a lot for your help. -- Jean-Baptiste Richet AREAS _________________________________ Association régionale pour l'étude et l'amélioration des sols 2, avenue Foch 76460 Saint Valéry en Caux tél : +33 2 35 97 25 12 fax : +33 2 35 97 25 73 _________________________________

1 0

Announce: Python 2.3 for Windows (Enthought Edition) now available
by David C. Morrill Sept. 6, 2003

Sept. 6, 2003

Just a quick heads up that Python 2.3 for Windows (Enthought Edition) is now available at: http://www.enthought.com This is in addition to the Python 2.2.3 for Windows (Enthought Edition) that was previously announced. Besides the obvious feature of being based on Python 2.3, this new version also includes updates to several other packages, such as wxPython So if you've been putting off giving Python 2.3 a spin, now might be a good time to upgrade. And if you do decide to give it a try, we'd also appreciate hearing from you either on the mailing lists or on the bug tracker concerning what you think about the new Python distribution. Enjoy! The Python guys at Enthought, Inc.

4 5

Nelson and siegel codes
by Wassim Dbouk Sept. 5, 2003

Sept. 5, 2003

Hello Daniel, I need to use matlab to compute the yield curve using Nelson and siegel approach. However, i don't find enough resources to the the matlab codes for such a topic.I am starting from scratch with matlab and i am facing difficulties in progressing. I was searching the web and I found your post where you were saying that you have used matlab with Nelson and Siegel. I am wondering if you can email me the M-file. I hope I am not asking too much but this would really help me a lot. Best wishes wassim

1 0

how to build with NetCDF?
by al.danial＠ngc.com Sept. 5, 2003

Sept. 5, 2003

Hello, I'm an old-time Perl guy trying out Python. I'm not having luck building SciPy with NetCDF support. The "python setup.py install" step goes fine and scipy.test(level=1) within Python looks pretty good, +700 tests pass and two failures. However it did not build the NetCDF IO stuff because "from Scientific.IO.NetCDF import NetCDFFile" produces: Traceback (most recent call last): File "./cmp_nc.py", line 32, in ? from Scientific.IO.NetCDF import NetCDFFile ImportError: No module named Scientific.IO.NetCDF (I'm using cmp_nc.py from http://starship.python.net/~hinsen/ScientificPython/netcdf_example2.tar.gz to check the NetCDF module witin SciPy.) Can any one give me clues on how to make the build process see my NetCDF lib and include directories? They are not in the usual places like /usr/lib or /usr/local/lib so I figure I need to help SciPy find them but don't know. The INSTALL.txt file doesn't give any hints on how to make extra packages visible during the build. Details: x86 RedHat Linux v8.0 Python v2.3 GCC v3.2 netcdf-3.5.1-beta13 SciPy-0.2.0_alpha_200.4161_src.tar.gz -- Al

1 0

unhelpful error messages in weave
by Christopher Fonnesbeck Sept. 5, 2003

Sept. 5, 2003

Thanks for the help. Unfortunately, I need to be working in Python2.3, so perhaps I will try coding the thing in Fortran and use f2py. Incidentally, following your second point, there is wierd stuff in the .cpp file, namely the following: catch(...) { return_val = py::object(); exception_occured = 1; } which appears without a try statement. cjf Christopher Fonnesbeck wrote: > Hi Everyone, >>I'm trying to move some C++ code over to weave, but am running into >some problems that are difficult to debug. Specifically, there are >try/catch messages referring to lines of code in my module that do not >exist. Here is the error message: A couple of general tips: 1. try first with python 2.2. I've seen weird messages pop up using py2.3 which don't appear with 2.2 (and weave.inline, of course). I haven't had the time to make a small, clean test case to submit for Eric to look at, though. 2. use the verbose option in inline() and look directly at the ~/.python_compiled2.2/NNNNNNNNNNNNNNNNNNN.cpp file which weave auto-generates. It's big, but once you learn how it gets organized, you'll navigate it pretty quickly. You can try to compile it separately yourself. I've debugged weave.inlined modules this way before. Best, f. -- Christopher J. Fonnesbeck (chris at fonnesbeck dot org) GA Coop. Fish & Wildlife Research Unit, University of Georgia

1 0

unhelpful error messages in weave
by Christopher Fonnesbeck Sept. 5, 2003

Sept. 5, 2003

Hi Everyone, I'm trying to move some C++ code over to weave, but am running into some problems that are difficult to debug. Specifically, there are try/catch messages referring to lines of code in my module that do not exist. Here is the error message: [Histrionicus:python/Biometric/tmp] chris% python2.3 Blackduck.py file changed Compiling code... Blackduck.py: In function `PyObject* compiled_func(PyObject*, PyObject*)': Blackduck.py:426: parse error before `catch' Blackduck.py:432: must have at least one catch per try block Traceback (most recent call last): File "Blackduck.py", line 833, in ? nxt_state = weave.inline(sd_code,['cur_state','dec','wtp'],verbose=1) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/inline_tools.py", line 335, in inline auto_downcast = auto_downcast, File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/inline_tools.py", line 439, in compile_function verbose=verbose, **kw) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/ext_tools.py", line 340, in compile verbose = verbose, **kw) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/weave/build_tools.py", line 272, in build_extension setup(name = module_name, ext_modules = [ext],verbose=verb) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/site- packages/scipy_distutils/core.py", line 42, in setup return old_setup(**new_attr) File "/Library/Frameworks/Python.framework/Versions/2.3/lib/python2.3/ distutils/core.py", line 166, in setup raise SystemExit, "error: " + str(msg) weave.build_tools.CompileError: error: command 'gcc' failed with exit status 1 My inline code ends at line 420, but I get error messages from weave outside those lines. I dont use 'catch' anywhere in my code, yet I am given an error message referring to it. Here is the call and the code for those willing to look into this: sd_code = ''' #line 56 "Blackduck.py" #define NPOP 3 #define NPROD 2 #define NSURV 2 #define NAGE 2 #define NSEX 2 #define NHARV 6 py::list nxt_state(NPOP); double Harv[NHARV][NPROD][NAGE][NSEX][NPOP], Spr_A[NSEX][NPOP],ss[NSEX], wts[NSURV] = {0.881, 0.119},//production model weights Harv_S[NPROD][NAGE][NSEX][NPOP], Harv_N[NPROD][NAGE][NSEX][NPOP], next[NPROD][NSURV][NAGE][NSEX][NPOP], Fall_Pre[NPROD][NAGE][NSEX][NPOP], Fall_N[NPROD][NAGE][NSEX][NPOP], movekill[NAGE][NSEX][NPOP][NHARV], //objective function values Value [2] = {1., 0.} , //values for bd and mallard harvest cripple [2] = {0.20, 0.20} ; int i = 0, j = 0, k = 0, q = 0, m = 0, n = 0, age = 0, sex = 0, pop = 0, pop0 = 0, pop1 = 0, harv = 0, prod = 0, surv = 0, init = 1, done = 0, debug = 0; static const double P_am = 0.543 , DV[NAGE][NSEX]={ {1,0.94}, {2.03, 1.88} }, b[NPROD][NPOP][3] ={ { {1.755, -0.2455, -0.2345}, { 1.164, -0.2455, -0.2345}, {0.9171, -0.2455, -0.2345} }, { {1.463, -0.2392, 0}, {1.674, -0.7436, 0}, {0.8289, -0.2009, 0} } }, Ac[NSURV][2]= { {1.033288, 0}, {1.033288, -0.000001} }, move_n[NAGE][NSEX][NPOP][3] ={ { { {0.984, .016, 0}, {.081, 0.904, .015}, {0, .026, .974} }, { {.974, .026, 0}, {.052, .93, .018}, {0 ,.014 ,.986} } }, { { {0.984, .016, 0}, {.081, 0.904, .015}, {0, .026, .974} }, { {.974, .026, 0}, {.052, .93, .018}, {0 ,.014 ,.986} } } }, move_s[NAGE][NSEX][NPOP][3]= { { { {.506, .214, .280}, {.048, .689, .263}, {.002, .914, .084} }, { {.451, .262, 0.287}, {.062, .686, .252}, { 0.002, .89, .108} } }, { { {.506, .214, .280}, {.048, .689, .263}, {.002, .914, .084} }, { {.451, .262, 0.287}, {.062, .686, .252}, { 0.002, .89, .108} } } }, fidel[NAGE][NSEX][NPOP][NPOP]= { { { {0.89,0.055,0.055}, {0.065,0.87,0.065}, {0.06,0.06,0.88} }, { {0.88,0.06,0.06}, {0.07,0.86,0.07}, {0.075,0.075,0.85} } }, { { {0.39,0.305,0.305}, {0.32,0.36,0.32}, {0.325,0.325, 0.35} }, { {0.41,0.295,0.295}, {0.31,0.38,0.31}, {0.295,0.295, 0.41} } } }, ssf=0.75; double temp; double N[NPOP],M[NPOP], A[NPROD][NPOP], H[NHARV][NAGE][NSEX], K[NHARV][NAGE][NSEX], Kill_N[NPROD][NAGE][NSEX][NPOP], Kill_S[NPROD][NAGE][NSEX][NPOP], Wint[NPROD][NAGE][NSEX][NPOP], Wint_T[NPROD][NPOP], SS_m[NPROD][NSURV][NPOP], SS[NPROD][NSURV][NPOP][NAGE][NSEX], surv_joint[NPROD][NSURV][NAGE][NSEX][NPOP], spring_pre[NPROD][NSURV][NAGE][NSEX][NPOP], next_[NPROD][NSURV][NAGE][NSEX][NPOP][NPOP], pwt,nval,mval,harv_dec,state, wnext[NPROD][NSURV][NAGE][NSEX][NPOP], hss[NAGE][NSEX][NPOP]; // Index constant values. //Jianping add ss[1]=ssf; ss[0]=ssf*(P_am/(1.-P_am)); //Loop over breeding populations for (pop=0;pop<3;pop++) { // Scaled population sizes nval = py_to_float(PyList_GetItem(cur_state,pop),"nval"); N[pop] = nval; mval = py_to_float(PyList_GetItem(cur_state,pop+3),"mval"); M[pop] = mval; // Spring adults Spr_A [0][pop]=P_am *N[pop]; Spr_A [1][pop]=(1-P_am)*N[pop]; //Fall adults -- loop over production models for (prod=0;prod<2;prod++) { // Calculate fall age ratio A[prod][pop]= b[prod][pop][0] + b[prod][pop][1]*N[pop]/100000. + b[prod][pop][2]*M[pop]/100000. ; A[prod][pop] =exp(A[prod][pop]); for (sex=0;sex<2;sex++) { // Spring survival Fall_Pre[prod][0][sex][pop] =Spr_A[sex][pop]*ss[sex]; // Recruitment Fall_Pre[prod][1][sex][pop]= 0.5*A[prod][pop]* (Fall_Pre[prod][0][0][pop]+Fall_Pre[prod][0][1][pop]); } } for (k=0;k<6;k++) { for (age=0;age<2;age++) { for (sex=0;sex<2;sex++) { // Harvest rates harv_dec = py_to_float(PyList_GetItem(dec,k),"harv_dec"); H[k][age][sex]=DV[age][sex]*harv_dec; K[k][age][sex]=H[k][age][sex]/(1-cripple[0]); } } } //Joint movement and kill rates for (age=0;age<2;age++) { for (sex=0;sex<2;sex++) { // Loop over breeding areas for (pop=0;pop<3;pop++) { // Loop over harvest areas for (harv=0;harv<3;harv++) { movekill[age][sex][pop][harv]=move_n[age][sex][pop][harv] *K[harv][age][sex]; // age and sex specific? } for (harv=0;harv<3;harv++) { movekill[age][sex][pop][harv+3]= move_s[age][sex][pop][harv]*K[harv+3][age][sex]; } //Suvival of southern hunting hss[age][sex][pop]=1- (movekill[age][sex][pop][3]+movekill[age][sex][pop][4] +movekill[age][sex][pop][5]); } } } // Movement to northern harvest areas and harvest // Loop over production models for (prod=0;prod<2;prod++) { for (age=0;age<2;age++) { for (sex=0;sex<2;sex++) { //Loop over pop areas // these are survivors of northern breeding areas for (pop=0;pop<3;pop++) { // Loop over northern harvest areas Kill_N[prod][age][sex][pop]=0; Kill_S[prod][age][sex][pop]=0; //Nothern kill Kill_N[prod][age][sex][pop]=Fall_Pre[prod][age][sex][pop]* (movekill[age][sex][pop][0]+movekill[age][sex][pop][1]+movekill[age][sex ][pop][2]); for(harv=0;harv<3;harv++) { Harv[harv][prod][age][sex][pop]=Fall_Pre[prod][age][sex][pop]* movekill[age][sex][pop][harv]*(1-cripple[0]); } //population after northern harvest with respect to breeding area Fall_N[prod][age][sex][pop]=Fall_Pre[prod][age][sex][pop]- Kill_N[prod][age][sex][pop]; //Convert kill to harvest Harv_N[prod][age][sex][pop]=Kill_N[prod][age][sex][pop]*(1- cripple[0]); //Southern kill Kill_S[prod][age][sex][pop]=Fall_N[prod][age][sex][pop]* (movekill[age][sex][pop][3]+movekill[age][sex][pop][4]+movekill[age][sex ][pop][5]); for(harv=3;harv<6;harv++) { Harv[harv][prod][age][sex][pop]=Fall_Pre[prod][age][sex][pop]* movekill[age][sex][pop][harv]*(1-cripple[1]); } //population after southern harvest Wint[prod][age][sex][pop]=Fall_N[prod][age][sex][pop]- Kill_S[prod][age][sex][pop]; //convert kill to harvest Harv_S[prod][age][sex][pop]=Kill_S[prod][age][sex][pop]*(1- cripple[1]); } }//end of for (sex=0;sex<2;sex++) } //end of for (age=0;age<2;age++) for (pop=0; pop < NPOP; pop++) { Wint_T[prod][pop]=0; for (age=0;age<2;age++) { for (sex=0;sex<2;sex++) { // Sum populations over age and sex, Wint_T[prod][pop]+=Wint[prod][age][sex][pop]; } } } for (surv=0;surv<2;surv++) { for (pop=0;pop<3;pop++) { // Winter survival, males SS_m[prod][surv][pop] = Ac[surv][0] + Ac[surv][1]*3*Wint_T[prod][pop]; temp=SS_m[prod][surv][pop]; SS_m[prod][surv][pop]=exp(temp)/(1+exp(temp)); for (age=0;age<2;age++) { for (sex=0;sex<2;sex++) { // # Survival by age and sex SS[prod][surv][pop][age][sex] =SS_m[prod][surv][pop]/ss[sex]; // # Joint survival of Southern hunting surv_joint[prod][surv][age][sex][pop] =SS[prod][surv][pop][age][sex] * hss[age][sex][pop]; // # Spring population pre-movement spring_pre[prod][surv][age][sex][pop] = Fall_N[prod][age][sex][pop] * surv_joint[prod][surv][age][sex][pop] ; }//for(sex= }//for age= }//for pop= for (age=0;age<2;age++) { for (sex=0;sex<2;sex++) { // # Migrate back to breeding areas to determine next years populations for (pop1=0;pop1<3; pop1++) { //next_[pop][prod][surv][age][sex]=0; for (pop0=0;pop0<3; pop0++) { next_[prod][surv][age][sex][pop1][pop0]=spring_pre[prod][surv][age][sex] [pop0] * fidel[age][sex][pop0][pop1]; } //aggregate t return breeding area next[prod][surv][age][sex][pop1]=next_[prod][surv][age][sex][pop1][0]+ next_[prod][surv][age][sex][pop1][1]+ next_[prod][surv][age][sex][pop1][2]; //# Weighted next year pwt = py_to_float(PyList_GetItem(wtp,prod),"pwt"); wnext[prod][surv][age][sex][pop1]=next[prod][surv][age][sex][pop1]*pwt*w ts[surv]; }//edn pop1 }//end of for (sex=0;sex<2;sex++) }//end of for (age=0;age<2;age++) }//end of for (surv=0;surv<3;surv++) }//end of for (prod=0;prod<2;prod++) // # Sum across age sex and models to get next year's populations for (pop=0;pop < NPOP;pop++) { //nxt_state[pop]=0; for (prod=0;prod < NPROD;prod++) { for (age=0;age < NAGE;age++) { for(surv=0;surv<2;surv++) { for (sex=0;sex < NSEX;sex++) { state = py_to_float(PyList_GetItem(nxt_state,pop),"state"); PyList_SetItem(nxt_state,pop,PyFloat_FromDouble(state + wnext[prod][surv][age][sex][pop])); } } } } } return_val = nxt_state; ''' if __name__=='__main__': n = [100000,100000,100000] m = [10000,1000,1000] cur_state = n+m dec = [0.1]*6 wtp = [0.5,0.5] nxt_state = weave.inline(sd_code,['cur_state','dec','wtp'],verbose=1) print nxt_state thanks a bunch in advance, cjf -- Christopher J. Fonnesbeck (chris at fonnesbeck dot org) GA Coop. Fish & Wildlife Research Unit, University of Georgia

2 1

STFT implementations in Python
by Andrew Nesbit Sept. 4, 2003

Sept. 4, 2003

Does anybody know if there exist any Python implementations for STFT and inverse STFT? I can code it myself, but I just wanted to know if anybody has already done this, as it seems like it would be a pretty common thing. Thanks. Andrew.

3 2