Mailman 3 July 2005 - SciPy-Dev

SciPy CVS to Subversion migration
by Joe Cooper Aug. 4, 2005

Aug. 4, 2005

Hi all, The issues with converting our CVS repository to Subversion have been resolved, and so I'd like to make the switch tomorrow (Friday) afternoon. If you have anything you'd like to check-in before the CVS repository is gone forever, please do so before then. You will have to check out a new working copy after the conversion occurs. If the timing of this outage will cause anyone discomfort, please let me know, and I will re-schedule for another day. Just FYI: History will be maintained from the old CVS tree. Once the migration occurs, branching, merging, and reorganizing the tree will become trivially simple and reliable (and anyone with commit access can make those kinds of changes without system administrator intervention). I know there is a contingent of SciPy developers that would like to do some long-desired serious cleanups and purges within the tree--the new Subversion repository will easily allow these kinds of changes without having to throw out all of the old history and start fresh. If, after the migration, you find you still want to start fresh, let me know and I'll create a new Subversion repo for you to work in. Holler if you have any further questions or concerns. Thanks, Joe

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Re: [Numpy-discussion] Suggested Addition to the new array PEP
by Travis Oliphant July 31, 2005

July 31, 2005

Chris Barker wrote: > Hi all, but particularly Travis, > > I just took the time to read the new array PEP: > > http://numeric.scipy.org/PEP.txt > > It looks great. > > I do have one suggestion for an addition method: > > change_type(NewType) # or some other name: > > Change the type that the bytes in the array represent, without > changing the data at. Dimensions will change if the new type has a > different itemsize than the old. > Actually, I think this functionality is supported by attribute assignment. Anyway, it is a good suggestion and one that should be supported ( I know I wanted it to be supported at some time, I don't know if it is). > > By the way, I'm also not seeing tostring() or tobuffer() listed in the > PEP The are still there just attributes now... a.data is always a buffer object a.data[:] is a string (because [:] on a buffer object always produces the string)

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edit scipy zwiki using emacs?
by John Hunter July 28, 2005

July 28, 2005

Has anyone gotten emacs working with the zwiki/plone on scipy.org? I have used it in the past with zwiki-mode and ange-ftp, but I think this requires direct ftp access to the server, and the plone site appears to have its own authentication system http://zwiki.org/FAQs#How%20do%20I%20edit%20with%20Emacs? http://zwiki.org/EmacsAndWiki The link below details an approach that can work with xmlrpc, but requires some server side code in the extensions dir http://www.zope.org/Members/alburt/zwiki_mode Any pointers? JDH

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ANN: SciPy 2005 Conf: Abstracts and early registration due 7/29/05
by Janet M. Swisher July 28, 2005

July 28, 2005

Friday, July 29, 2005 is the deadline for abstract submission for the 2005 Scientific Computing in Python Conference, scheduled for September 22 and 23, at Caltech. More information on the conference, including abstract guidelines, can be found at <http://www.scipy.org/wikis/scipy05> The 29th is also the deadline for early registration for the conference. The early registration fee is US$100; regular registration is US$150. The conference fee includes breakfast and lunch both days, and dinner on the first day. -- Janet Swisher --- Senior Technical Writer Enthought, Inc. http://www.enthought.com

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matplotlib cookbook wiki on scipy.org ?
by John Hunter July 28, 2005

July 28, 2005

I wanted to setup a wiki for matplotlib where I and others can post snippets, recipes and howtos. Is the scipy wiki an appropriate place for this? Eg, a link under "Topical Software" to "MatplotlibCookbook". As a cookbook, it could potentially create a lot of pages; presumably authors might want to upload images as well, so it might also consume more bandwidth and storage than typical wiki pages. I have no problem shopping for another place to host it, but I think the scipy site would be ideal if the scipy devs and enthought agree. Thanks! JDH

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File swig_num_gen.py, anyone?
by Fernando Perez July 28, 2005

July 28, 2005

Hi all, I need to wrap some C code and I want to allow it to use Numeric arrays. The swig_num.i file, which is in scipy's Lib/cluster/src directory, seems like a useful tool for this task. But if I try to use it, I get a swath of swig deprecation warnings, along with a few errors. I'd rather not fix that .i file by hand, b/c it carries at the top this warning: /************************************************************************/ /* swig_num.i -- typemaps for mapping C arrays to Python Numeric arrays */ /* */ /* This file is auto-generated by swig_num_gen.py. */ /* DO NOT EDIT THIS FILE DIRECTLY unless you want your changes */ /* clobbered by the next run of the generator. */ /************************************************************************/ Unfortunately the file swig_num_gen.py seems to have gone AWOL. Google doesn't find it, and not even a locate call directly at the scipy.org server (while ssh'd in) finds it, so it seems not even to be in the bowels of the CVS repo. Does anybody have an idea of where that file is? I'd rather work on fixing the code generator rather than the final .i file, especially because the zillion warnings are of only 2 kinds, and I'm pretty sure fixing each at the source would involve fixing only one pattern. Alternatively, if anybody has a good set of typemaps to use swig with Numeric which they can pass my way, I'll be very grateful. Cheers, f

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Load MATLAB 7 MAT-files in scipy
by Nils Wagner July 27, 2005

July 27, 2005

Hi all, AFAIK, it's not possible to load MATLAB 7 MAT-files in scipy. help (io.loadmat) results in Both v4 (Level 1.0) and v6 matfiles are supported. Version 7.0 files are not yet supported. I am curious about the current features of scipy regarding I/O of MAT-files generated by Matlab v4 and v6 How about sparse matrix support ? Any comment would be appreciated. Nils References http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=77…

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Re: [SciPy-dev] Another attempt at converting SciPy CVS to Subversion
by Bill Northcott July 27, 2005

July 27, 2005

As of 09:30 UTC 27th July cvs seems to be broken. Bill Northcott

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bulding with Fink on 10.4 with xcode-2.1
by ChrisK July 27, 2005

July 27, 2005

I was rebuilding scipy on Max OS X and had to do some slight patching. This is with fink on Max OS 10.4.2 using XCode 2.1 (w/gcc 4.0), for the scipy-py24 package. (for version 0.3.2) There were two files where 'static' was causing a compile error: scipy/Lib/interpolate/fitpack.pyf scipy/Lib/stats/ranlib_all.c and one file that did not setup HAVE_INVERSE_HYPERBOLIC properly, which was fixed by patching the build file: scipy/scipy_core/scipy_base/setup_scipy_base.py Thus the 4th compile worked. So I thought I would post this patch here in case someone could put them in upstream. I have also sent this to the fink site and maintainer. -- Chris --- scipy/Lib/interpolate/fitpack.pyf 2003-12-04 05:00:00.000000000 -0500 +++ scipy/Lib/interpolate/fitpack.pyf 2005-07-26 16:21:05.000000000 -0400 @@ -238,7 +238,7 @@ ! nx,tx,ny,ty,c,fp,ier = surfit_smth(x,y,z,[w,xb,xe,yb,ye,kx,ky,s,eps,lwrk2]) usercode ''' - static int calc_lwrk1(void) { + int calc_lwrk1(void) { int u = nxest-kx-1; int v = nyest-ky-1; int km = MAX(kx,ky)+1; @@ -250,7 +250,7 @@ else {b1=by;b2=by+u-kx;} return u*v*(2+b1+b2)+2*(u+v+km*(m+ne)+ne-kx-ky)+b2+1; } - static int calc_lwrk2(void) { + int calc_lwrk2(void) { int u = nxest-kx-1; int v = nyest-ky-1; int bx = kx*v+ky+1; @@ -305,7 +305,7 @@ ! tx,ty,c,fp,ier = surfit_lsq(x,y,z,tx,ty,[w,xb,xe,yb,ye,kx,ky,eps,lwrk2]) usercode ''' - static int calc_lwrk1(void) { + int calc_lwrk1(void) { int u = nxest-kx-1; int v = nyest-ky-1; int km = MAX(kx,ky)+1; @@ -317,7 +317,7 @@ else {b1=by;b2=by+u-kx;} return u*v*(2+b1+b2)+2*(u+v+km*(m+ne)+ne-kx-ky)+b2+1; } - static int calc_lwrk2(void) { + int calc_lwrk2(void) { int u = nxest-kx-1; int v = nyest-ky-1; int bx = kx*v+ky+1; --- scipy/Lib/stats/ranlib_all.c 2004-08-27 12:31:44.000000000 -0400 +++ scipy/Lib/stats/ranlib_all.c 2005-07-26 16:44:29.000000000 -0400 @@ -2146,7 +2146,7 @@ extern long Xm1,Xm2,Xa1,Xa2,Xcg1[],Xcg2[]; extern long Xqanti[]; */ -static void inrgcm(void); +void inrgcm(void); static long ignlgi,curntg,k,s1,s2,z; static long qqssd,qrgnin; /* @@ -2245,7 +2245,7 @@ *(Xcg2+g-1) = *(Xlg2+g-1); #undef numg } -static void inrgcm(void) +void inrgcm(void) /* ********************************************************************** void inrgcm(void) --- scipy/scipy_core/scipy_base/setup_scipy_base.py 2004-10-04 11:21:02.000000000 -0400 +++ scipy/scipy_core/scipy_base/setup_scipy_base.py 2005-07-26 17:03:57.000000000 -0400 @@ -33,6 +33,7 @@ sources = umath_c_sources) sources = [umath_c, os.path.join(local_path,'isnan.c')] define_macros = [] + define_macros.append(('HAVE_INVERSE_HYPERBOLIC',None)) if sys.byteorder == "little": define_macros.append(('USE_MCONF_LITE_LE',None)) else: --- scipy/scipy_core/scipy_distutils/gnufcompiler.py 2004-10-04 05:30:54.000000000 -0400 +++ scipy/scipy_core/scipy_distutils/gnufcompiler.py 2005-07-26 16:21:05.000000000 -0400 @@ -28,7 +28,7 @@ 'compiler_f77' : [fc_exe,"-Wall","-fno-second-underscore"], 'compiler_f90' : None, 'compiler_fix' : None, - 'linker_so' : [fc_exe], + 'linker_so' : ['gcc -bundle -flat_namespace -undefined suppress'], 'archiver' : ["ar", "-cr"], 'ranlib' : ["ranlib"], } @@ -53,7 +53,7 @@ # This is when Python is from Apple framework opt.extend(["-Wl,-framework","-Wl,Python"]) #else we are running in Fink python. - opt.extend(["-lcc_dynamic","-bundle"]) +# opt.extend(["-lcc_dynamic","-bundle"]) else: opt.append("-shared") if sys.platform[:5]=='sunos': @@ -95,6 +95,7 @@ opt.extend(['gcc',g2c]) else: opt.append(g2c) + opt.append('cc_dynamic') return opt def get_flags_debug(self):

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Bug in f2py
by Nils Wagner July 25, 2005

July 25, 2005

Hi all, python setup.py build results in Reading fortran codes... Reading file 'Lib/optimize/lbfgsb-0.9/lbfgsb.pyf' (format:free) Post-processing... Block: _lbfgsb Block: setulb "name 'x' is not defined" in evaluating 'len(x)' (available names: []) Traceback (most recent call last): File "setup.py", line 124, in ? setup_package(ignore_packages) File "setup.py", line 112, in setup_package url = "http://www.scipy.org", File "/home/nwagner/cvs/scipy/scipy_core/scipy_distutils/core.py", line 73, in setup return old_setup(**new_attr) File "/usr/lib/python2.4/distutils/core.py", line 149, in setup dist.run_commands() File "/usr/lib/python2.4/distutils/dist.py", line 946, in run_commands self.run_command(cmd) File "/usr/lib/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/usr/lib/python2.4/distutils/command/build.py", line 112, in run self.run_command(cmd_name) File "/usr/lib/python2.4/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/usr/lib/python2.4/distutils/dist.py", line 966, in run_command cmd_obj.run() File "/home/nwagner/cvs/scipy/scipy_core/scipy_distutils/command/build_src.py", line 129, in run self.build_sources() File "/home/nwagner/cvs/scipy/scipy_core/scipy_distutils/command/build_src.py", line 215, in build_sources self.build_extension_sources(ext) File "/home/nwagner/cvs/scipy/scipy_core/scipy_distutils/command/build_src.py", line 255, in build_extension_sources sources = self.f2py_sources(sources, ext) File "/home/nwagner/cvs/scipy/scipy_core/scipy_distutils/command/build_src.py", line 399, in f2py_sources f2py2e.run_main(f2py_options + ['--build-dir',target_dir,source]) File "/usr/lib/python2.4/site-packages/f2py2e/f2py2e.py", line 417, in run_main postlist=callcrackfortran(files,options) File "/usr/lib/python2.4/site-packages/f2py2e/f2py2e.py", line 356, in callcrackfortran postlist=crackfortran.crackfortran(files) File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 2521, in crackfortran postlist=postcrack(grouplist[0]) File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 1469, in postcrack g=postcrack(g,tab=tab+'\t') File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 1487, in postcrack block['body']=analyzebody(block,args,tab=tab) File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 1628, in analyzebody b=postcrack(b,as,tab=tab+'\t') File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 1487, in postcrack block['body']=analyzebody(block,args,tab=tab) File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 1628, in analyzebody b=postcrack(b,as,tab=tab+'\t') File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 1483, in postcrack block['vars']=analyzevars(block) File "/usr/lib/python2.4/site-packages/f2py2e/crackfortran.py", line 2140, in analyzevars length = _eval_length(vars[n]['charselector']['*'], NameError: global name '_eval_length' is not defined Nils

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