Mailman 3 May 2009 - SciPy-Dev

Adding mpfit scipy optimize package, koposov@mpia-hd.mpg.de,
by william ratcliff May 8, 2009

May 8, 2009

Hi! For a long time, there has been a standard package used by IDL users for fitting functions to data called MPFIT: http://cow.physics.wisc.edu/~craigm/idl/fitting.html It allows the user to limit the domain (simple box limits), fix parameters, etc. It also returns errors on the parameters based on the covariance matrix. Essentially, it translates MINPACK to IDL and adds some nice features (like the ability to fix parameters). Some time later, Mark Rivers translated this to python for use with Numeric, and Sergei Koposov migrated the code to numpy and added several bug fixes from the Numeric version of the code. We've been working with the author of the IDL package, Craig Markwardt to include the additional bug fixes which he has added. I have written a nose-test compatible test. Could someone look at it and tell me if it meets the scipy style before I continue adding more tests from Craig's test-suite for the C version of his program? Also, what else would we need to do to include this in scipy? Mark Rivers, Craig, and Sergey have agreed to a BSD license for their contributions. Thanks, William

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docstrings in class.__init__
by josef.pktd＠gmail.com May 7, 2009

May 7, 2009

I just looked at the spline classes in scipy.interpolate. The docstring for the constructor is in the __init__ method, however this is currently not captured by the sphinx documentation. example: http://docs.scipy.org/scipy/docs/scipy.interpolate.fitpack2.UnivariateSplin… Is it possible to automatically add the __init__ docstring to the class docstring, or should we copy or move them over, or add __init__ method explicitly to the .rst files to be scanned by sphinx? help(interpolate.LSQUnivariateSpline) doesn't have this problem, as discussed last year. Josef

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Undefined NAN in amos_wrappers.c errors on Solaris amd64
by Dave Peterson May 7, 2009

May 7, 2009

When trying to build rev 5698 of SciPy's trunk on a Solaris amd64 system, I'm getting the a bunch of 'NAN undeclared' type errors in building the 'scipy.special._cephes' extension. Is this a known error by any chance? Or does anyone have an idea of what is going on? -- Dave Here's the GCC command being run: (build)-bash-3.00$ /home/dpeterson/local64/bin/gcc -m64 -DNDEBUG -O2 -DHAVE_NCURSES_H -I/home/dpeterson/py/build/include -I/home/dpeterson/py/build/include/ncurses -I/usr/include -I/home/dpeterson/py/build/include -m64 -g -O3 -pipe -fomit-frame-pointer -fPIC -I/home/dpeterson/py/build/trunk/recipes/install/numpy-1.3.0n1-py2.5-solaris-2.10-i86pc.egg/numpy/core/include -I/home/dpeterson/py/build/include/python2.5 -c scipy/special/amos_wrappers.c -o build/temp.solaris-2.10-i86pc-2.5/scipy/special/amos_wrappers.o And here's the error output: scipy/special/amos_wrappers.c: In function ‘set_nan_if_no_computation_done’: scipy/special/amos_wrappers.c:67: error: ‘NAN’ undeclared (first use in this function) scipy/special/amos_wrappers.c:67: error: (Each undeclared identifier is reported only once scipy/special/amos_wrappers.c:67: error: for each function it appears in.) scipy/special/amos_wrappers.c: In function ‘cairy_wrap_e_real’: scipy/special/amos_wrappers.c:177: error: ‘NAN’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesi_wrap’: scipy/special/amos_wrappers.c:218: error: ‘INFINITY’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesi_wrap_e_real’: scipy/special/amos_wrappers.c:275: error: ‘NAN’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesj_wrap’: scipy/special/amos_wrappers.c:300: error: ‘INFINITY’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesj_wrap_e_real’: scipy/special/amos_wrappers.c:340: error: ‘NAN’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesy_wrap’: scipy/special/amos_wrappers.c:365: error: ‘INFINITY’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesy_wrap_e’: scipy/special/amos_wrappers.c:396: error: ‘INFINITY’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesy_wrap_e_real’: scipy/special/amos_wrappers.c:414: error: ‘NAN’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesk_wrap’: scipy/special/amos_wrappers.c:438: error: ‘INFINITY’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesk_wrap_e’: scipy/special/amos_wrappers.c:461: error: ‘INFINITY’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesk_wrap_real’: scipy/special/amos_wrappers.c:472: error: ‘NAN’ undeclared (first use in this function) scipy/special/amos_wrappers.c: In function ‘cbesk_wrap_e_real’: scipy/special/amos_wrappers.c:484: error: ‘NAN’ undeclared (first use in this function)

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Status: optimize.fmin_slsqp
by Leon Adams May 6, 2009

May 6, 2009

Hi, I was wondering what the status is of the Slsqp extension to the optimize package. I am currently in need of the ability to place an equality constraint on some of my input variables, but the available documentation on slsqp seems insufficient. My Scenario: I have an objective fn: Obfn(x1,x2,x3,x4,x5,x6) that I would like to place the additional constrain of x1 + x2 + x3 = 1 x4 + x5 + x6 = 1 If there is a good usage example I can be pointed to, it would be appreciated Thanks in advance.

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erf, erfc and ndtr on OS X
by Tobias Wood May 5, 2009

May 5, 2009

Hi, I'm not sure whether this should go to the dev or users list, so sorry if it is in the wrong place. I'm using the lastest SVN Numpy/Scipy checkouts with Python 2.6 on Mac OS 10.5. I was trying to use the ndtr function in scipy.special and discovered that it returned 0.5 for all input values except +/-Inf. A little bit of searching pulled up the following bug ticket: http://projects.scipy.org/scipy/ticket/899 which hasn't been closed yet (I can't find any mention of it on the mailing lists though). I'd just like to report that I did manage to get erf and ndtr to return correct values by forcing the compiler to use the floating point constant values defined between #ifdef/endif UNK in both ndtr.c and const.c in scipy/special/cephes. I'm not totally sure which branch of the #ifdefs my compiler was going down before - is there an easy way to check? - but the constants it was getting were clearly wrong. SQRTH (1 over root 2) was defined as 0 previously. What is the likelihood of this being fixed in the SVN repository? I am happy to help in constructing a patch but don't understand the relationship between Cephes and Scipy. Thanks, Toby Wood

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NumPy Doc edit rights request
by David Goldsmith May 5, 2009

May 5, 2009

To whom it may concern: As per the instructions on the "Front Page," I'm emailing my NumPy Doc Editor registered username - dgoldsmith - and requesting edit rights. Thanks! David Goldsmith Olympia, WA

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How to handle code contribution with GSoC students ?
by David Cournapeau May 5, 2009

May 5, 2009

Hi, I was wondering about the best way to handle code by students for the upcoming GSoC. The year I participated, I already had write access, so the question did not come up. I think I would prefer starting with code reviews, before giving them svn write access later. Do people have better suggestions ? cheers, David

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Please hammer scipy.io.matlab routines
by Matthew Brett May 5, 2009

May 5, 2009

Hi, We are getting very close to a scipy point release, and I have just been putting together fixes for the matlab routines. I would be very grateful if anyone who was having problems, or is not having problems, could update to latest scipy SVN and try on the worst possible files to see if it is working and at reasonable speed. Please let me know if not; thanks to all those who have posted files, please keep doing so. Thanks a lot, Matthew

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RFR: refactor line searches out of optimize.py
by Pauli Virtanen May 4, 2009

May 4, 2009

Hi, I'd like to refactor line searches in optimize.py a bit, so that they can be easily used for solving nonlinear equations. Code review here: http://codereview.appspot.com/52096 http://github.com/pv/scipy-work/commits/linesearch-refactor This is a part of the scipy.optimize.nonlin rewrite: http://github.com/pv/scipy-work/commits/ticket/791-optimize-nonlin-rewrite -- Pauli Virtanen

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RFR: New iterative sparse solver: LGMRES
by Pauli Virtanen May 4, 2009

May 4, 2009

Hi, I'd like to submit a new iterative (pure-Python) sparse solver to Scipy: http://codereview.appspot.com/53096/show http://github.com/pv/scipy-work/commits/lgmres This is a part of a new Newton-Krylov solver in the scipy.optimize.nonlin rewrite. (For those interested, it's almost done, http://github.com/pv/scipy-work/commits/ticket/791-optimize-nonlin-rewrite but still needs tests for the line searches since I needed to refactor them out of optimize.py.) -- Pauli Virtanen

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