The problem is that kernel is set to precomputed in the init, instead of the kernel function.

I agree with @GaelVaroquaux. kernel_function should be defined in init to make object clonable. The problem should be fixed there. Do you have a snippet that shows the problem?

@agramfort the sniplet is here #786.

I see two possiblities. The user has to specify kernel='precomputed', kernel_function=func (which I think is ugly)
or the kernel_function attribute is removed and kernel stores the function.

Lines 83-87 in svm/base.py are the problem. We could just remove them and replace the checks on whether the svm has a kernel_function by the check if the kernel is callable.

indeed and replace the hasattr(self, 'kernel_function') with callable('kernel')
try the fix and see if all tests pass.

I agree it is a hack, but the entire user defined kernel behavior is a hack (it breaks the input/output behavior of basically everything) and this just makes it work. I agree with the solution from @amueller to fix the underlying problem. My original fix wasn't as ambitious because it is harder to predict what behavior that will have.

give a try to: #789

@agramfort is working on a cleaner solution see
#789
for more info. Closing this.