[msm/estimation] Implemented new feature for count_matrix function. The shape of the returned matrix is always (nstates, nstates) with nstates the number of states observed at lagtime=1. The implementation has a new optional nstates keyword. This keyword allows to specify the total number of states, nstates, in the model. If the specified number, nstates, is smaller than the number of states observed at lagtime=1 an error is raised. The leyword is potentially useful for analysing e.g umbrella sampling data. If most of the umbrellas never visit states with a high state index, but a set of compatible count-matrices (with same shape) is required, e.g. for TRAM analysis, the user can set the nstate keyword and obtain a set of compatible matrices. The unit tests have been extended to cover the keyword. The default value of some test-cases had to change in order to acompany the new convention
Merge pull request #28 from trendelkampschroer/merge_cmatrix

[msm/estimation] nstates feature for count_matrix function. See discussion #24
Revert "[coordinates] Be gone from this 'devel' branch"

This reverts commit 3915f14d766890dff9f22a83b70618d84b9b3483.
[coordinates] fix some sphinx warnings; pep8 formatting