remove pyemma.msm.$(msmtools subpackages)

[marscher]

Due to experience in the workshop it is confusing to users, if high-level objects and low-level API mix up in autocomplete (they've chosen to use the low level api, because the naming of desired quantities are more promising).

[marscher]

Or at least we should trigger a warning, if these functions are used

[franknoe]

I think that's a good point. PyEMMA has evolved from these low-level
functions, but now that we have a systematic object structure we might
consider msmtools to be completely separate. People can still use them
via import msmtools. It would certainly lead to more well-defined
packages. Let's discuss this after MolKin.

Am 03/09/15 um 14:05 schrieb Martin K. Scherer:

Due to experience in the workshop it is confusing to users, if
high-level objects and low-level API mix up in autocomplete (they've
chosen to use the low level api, because the naming of desired
quantities are more promising).

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#550.

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Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354
Web: research.franknoe.de

Mail: Arnimallee 6, 14195 Berlin, Germany

[franknoe]

Just to be clear: You want to remove these imports in msm.__init__ - correct?

from msmtools import analysis, estimation, generation, dtraj, flux

[marscher]

Exactly - this should go to the next minor release, since it changes the api.

[franknoe]

I agree

[marscher]

We haven't deprecated these packages yet. So removing them now will break the code of your users without a prior warning. So we should post-pone this to eg. 2.2

[franknoe]

yes

Am 22/03/16 um 12:54 schrieb Martin K. Scherer:

We haven't deprecated these packages yet. So removing them now will
break the code of your users without a prior warning. So we should
post-pone this to eg. 2.2

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Prof. Dr. Frank Noe
Head of Computational Molecular Biology group
Freie Universitaet Berlin

Phone: (+49) (0)30 838 75354
Web: research.franknoe.de

Mail: Arnimallee 6, 14195 Berlin, Germany