This is a major update, incorporating a complete rewrite and upgrade of the GP class and many of the other core library components. It is not backwards compatible with previous versions of the library and it has removed some pieces of the GP class, but it should improve flexibility going forward. A number of documentation additions have also been made to improve presentation and help users understand what is going on.
Specific improvements that have been made:
* Refactor of the GP class to externalize fitting. A GaussianProcess object now more closely represents the mathematical definition in that routines for estimation/fitting have been externalized. MCMC sampling for estimation has been removed for the moment in this process, though I anticipate being able to add it back in the future.
* Addition of mean functions. Mean functions can be added using a string formula in a similar manner to R. This optionally uses the patsy library for creating models (and in the future, design matrices), though patsy is not required to use the base mean function implementation.
* Basic support for prior distributions on hyperparameters has been added. This should be improved in future releases.
* Predictions can now include/exclude the nugget from the variance as desired.
* Documentation improvements and examples have been added.
* Numerous other bugfixes.