gave mcmc a class variable that stores the independent samples from calculate_covariance
now set random basis if cannot find eigen basis
random basis is ready for prime time
some changes to extraction_runner
keep re-setting trial until you get something that is not an exception
bug fix
mcmc_extractor will now store how many points were kept and how many total were considered
mcmc_extractor will now calculate how the mean and variance of data
mcmc_extractor keeps track of interesting statistics now
starting to write code to get good points out of APS output
wrote most of the subroutines
factored out random basis into its own set of functions in mcmc.cpp
that seems to work
commented out print statements in gaussian_process.cpp
removed 'refactoring' print statement from aps.cpp
removed statements printing results of gradient search to gradient_results.sav; I think those statements were creating a segmentation fault whenever gradient search aborted
rearranged some opening and closing of files in mcmc.cpp
print time_optimizing in timing file; I think that is where most of the overhead is coming from now
also, print the average amount of time per call through the whole process