>> First, a thanks to the developers for all the work on what promises >> to >> be a very fun python library. > have you tried it? is it fun? ;) Only a bit, the fun is going to come from scripting in something other than matlab. :D
>> I took on the task of creating a MacPorts Portfile for pymvpa. Here's > cool! Michael has prepped the install for MacOS X but I guess portfile > should be more native, thus easier to install for mac users. It provides a nice level of package management and eliminates the need to track down some of the optional dependencies. >> -) removed references to svm_set_verbosity as this function was not >> in >> the 2.88 version of libsvm > hm... indeed - we relied too much on the patched (with those > svm_set_verbosity exposed in Python) Debian shipped version, which > we also provided under 3rd/libsvm and which should be built/installed > whenever you build/install pymvpa (using Makefile though). > > > Is there 'original' port of libsvm which should be preferable over > the patched one we ship? There's a libsvm package already in macports. The recommended way to build packages is against libraries installed by the ports system. So I was faced with patching the libsvm source or the pymvpa source. I went with pymvpa for expediencies sake since pushing a patch upstream to the libsvm maintainer would have taken a while to be approved. > And where does it actually fail? set_verbosity is available in API > since > 2.84, so if you use our svmc.i while building -- everything should be > smooth, or am I missing something? It's missing from the 2.88 source found here: http://www.csie.ntu.edu.tw/~cjlin/libsvm/ It fails during the build_ext of the libsvm wrapper module with: error: ‘svm_set_verbosity’ was not declared in this scope > For now I just added additional check in externals if actually used > svmc > (committed and pushed) has that function available, but since we are > building custom swig interface, I guess, there is no much use for > it... > >> -) Added mvpa.support to the setup.py module install list, it was >> missing and the first tutorial threw an error. > my bad -- I was the one who refactor to have mvpa.support but > forgotten > to add it to setup.py > > Fixed in my branch (yoh/master) and maint/0.4 > >> The port has the following variants (optional support): > >> -) pynifti >> -) scipy >> -) hcluster >> -) libsvm > > There is no yet > shogun * Added: I had to make the shogun port first ;) > > pywt * Added: Had to submit a pywavelet port > > matplotlib/pylab * Added matplotlib > > > available in ports? > >> As always, if any of the developers object to my submission I will >> remove it quickly. > > hm... why we should? ;) is it still released under expat (MIT) > license? ;-) are copyright holders statements preserved? then license > is not violated and we only would vote 'go ahead'! We would also > prefer > if you somehow point to the available sources of the project (if those > aren't natively provided with the port, pardon my ignorance on this > subject) The pymvpa site is noted in the info and description parts of the port. > > >> The port isn't live yet (usually takes a day or >> so), but if anyone can't wait I'll gladly email the ports for use >> in a >> local overlay. > After it is available, it would be great if you sent us a patch > against > doc/installation.txt where you would describe availability of > portfiles... or just sent a statement describing it so we could add > it into documentation. > > If you feel that you might provide numerous patches/improvements -- > don't hesitate to ask, and we will set you up with 'commit' rights, or > in git terms it better be, rights to push, since you are allowed to > commit locally whenever you like ;) > keep in touch Will do. I have one question, currently I'm pulling the source from the master branch. I assume this branch is fairly volatile. Above you mention "maint/0.4" branch. Would the "main/\d.\d" branches be maintenance branches? It's best to pull from versioned/point release branches or tags if possible. ==One last thing....promise :) === Whne runing through the tutorials to test my installation, I ran into an error in the Getting Started Tutorial. Specifically, when creating a NiftiDataset the examples pass the nifti extension which produces an error. Cross referencing with pynifti API, I discovered that the extension should be left off, e.g.: > dataset = NiftiDataset(samples='data/bold', labels=attr.labels, > chunks=attr.chunks, mask='data/mask') Cheers, -james _______________________________________________ Pkg-ExpPsy-PyMVPA mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/pkg-exppsy-pymvpa
