[msm-api] fixed links to classes. Use PEP8 formatting.
[sphinx] import pyemma from a relative path. Inserting in sys.path sometimes import from installed package
fix returns: -> returns
move submodule ipython to new location
[hmm] handle java exception and reraise as RuntimeError
[msm/analysis] Tolerance for assessment functions is now tol=1e-12
[msm/analysis] Unit test contains large transition matrix example to capture too restrictive tol parameter in is_transition_matrix. Fixes #23
Merge pull request #25 from trendelkampschroer/devel

Too high floating point tolerance in msm.analysis assessment functions
[hmm] convert lag time to int
[CI] install cython in appveyor environments.
[pystallone] handle different max heap sizes for 32 and 64 bit
try to import first
dbg
appveyor dpl on tag only
import jpype prior pyemma