Docs

[franknoe]

Commenting http://pythonhosted.org//pytram

• Installation guide: make more verbose, start with nonexpert option (pypi) as preferred option. Git install for experts at the end
• API http://pythonhosted.org//pytram/api.html
  I find "_me" and "mathematical expression" a bit weird in terms of nomenclature. Maybe '_from_matrix'? or '_ma' for matrix data? I suggest to think of a clearer name, refactor and deprecate the old one.
• The documentation
  b_K_i : numpy.ndarray( shape=(T,M), dtype=numpy.float64 )
  reduced bias energies at the T thermodynamic and M discrete Markov states
  is perhaps sufficient for an expert, but you need to be more verbose and add examples for everybody else.
• ipython notebook examples should be linked to this site.
• tramdata
  I could not find out what that is and how you construct a tramdata object.

[ppxasjsm]

First point is updated.
I think the "mathematical expression" actually came from a discussion Chris and I had with you a while ago, when you originally suggested, that the API functions should be able to work on numpy arrays directly. Not everything is necessarily a matrix, but I guess we can think of a better name. I am not particularly good with coming up with those though.

b_K_i, doc, well we attempt to give an explanation in the docs for this, but it isn't perfect yet. The doc strings can of course also be extended, but this hasn't been a priority yet. In the end, the inexperience user should only be able to write a b_K_i file which is explained in the doc (in an improved way in the future). The ipython notebooks that give examples also show how to construct these files.

Yes we should link the ipython notebooks.

Indeed the Tramdata object is still missing from the Docs. I'll try an incorporate this.