Update old dependencies found with piprot

These packages have been kept back because of known problems:
tornado - newer versions can cause a UnicodeDecodeError
    (https://github.com/ccnmtl/dmt/pull/159#issuecomment-61340032)
ipython - newer versions require a version of GNU readline which can
    cause problems on Mac OS.
Merge branch 'nikolas-update-libs'