Added outline of Jonathan's code to repo, not in working condition
Jonathan's mutual information feature similarity scorer is now functioning without crashing, but tests are not yet written and it doesn't use real frequencies.
Similarity score is now similar to Python implementation, results look good, but tests still fail
Merge remote-tracking branch 'upstream/master'
Added IC feature scorer and incomplete, broken test cases
Updated tests slightly, but they all still fail. Attempted to improve Ontology mocking but failed and deleted most of the attempt.
Merge branch 'master' into HEAD
[misc] Updated the code to work with the current master branch, applied codestyle, used proper logging initialization
Merged in changes from remote upstream
Fixed static checking errors from merge due to updated Phenotips interfaces
[misc] Updated code to work with the latest phenotips snapshot
Edited MutualInformationPatientSimilarity scoring to look only at set of ancestors, and not weighted counts of each node
Merged in changes from upstream remote
Merge branch 'master' of https://github.com/phenotips/patient-network
Merge branch 'master' into feature-mic
Merged master
Updated mutual information patient similarity to use harmonic mean of scores, to just use direct ancestor overlap (rather than weighted by count), and tightened conditional IC bound (untested).
Reformatted code to pass style checker
Fixed naming style error
Merge branch 'master' of https://github.com/phenotips/patient-network