Readd effective counts

[marscher]

This commit was actually added by @franknoe just before @trendelkampschroer and me pulled out the msm subpackage.

Note that the tests will fail until we have the new dtrajs package.

[franknoe]

huh, but this was the first commit in dev_release_1.3, so how could that have been missed? Didn't you extract msmtools from the dev_release_1.3 branch?

[marscher]

yes we did this on an up to date dev_release branch. I do not know why this had happened.

[marscher]

I've double checked all subpackages of msm, if they are up2date with dev_release branch right now and only this function was missing.

[franknoe]

Before deleting something, can we make sure that we don't miss anything
here? The effective count stuff consists of multiple commits, starting from

markovmodel/PyEMMA@b279765

to

markovmodel/PyEMMA@ed6779e

and then another correction happened in

markovmodel/PyEMMA@a8bb502

Am 14/07/15 um 16:35 schrieb Martin K. Scherer:

yes we did this on an up to date dev_release branch. I do not know why
this had happened.

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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]

note that this function uses pyemma.util.statistics, which is currently
not included in msmtools

Am 14/07/15 um 16:36 schrieb Martin K. Scherer:

I've double checked all subpackages of msm, if they are up2date with
dev_release branch right now and only this function was missing.

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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

[marscher]

good point. Will the statistics module be contained in the new util git repo?

[marscher]

Am 14.07.2015 um 16:40 schrieb Frank Noe:

Before deleting something, can we make sure that we don't miss anything
here?
I've copied over the latest state from dev_release, so all those fixed
are contained.

[franknoe]

I don't know yet. Copy it into msmtools.util for now.

Am 14/07/15 um 16:43 schrieb Martin K. Scherer:

good point. Will the statistics module be contained in the new util git
repo?

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#20 (comment).

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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]

If we create a base module, let's first only put pyemma._base in there
and things in pyemma.util we're sure that we need to keep in a general
repo. I have the impression that some pyemma.util things are not really
used anymore.

Am 14/07/15 um 16:43 schrieb Martin K. Scherer:

good point. Will the statistics module be contained in the new util git
repo?

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#20 (comment).

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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

[marscher]

Am 14.07.2015 um 16:47 schrieb Frank Noe:

If we create a base module, let's first only put pyemma._base in there
and things in pyemma.util we're sure that we need to keep in a general
repo. I have the impression that some pyemma.util things are not really
used anymore.
Despite deprecated code it also contains code, which we do not want to
share (eg the logging and config modules).

[franknoe]

Am 14/07/15 um 16:48 schrieb Martin K. Scherer:

Am 14.07.2015 um 16:47 schrieb Frank Noe:

If we create a base module, let's first only put pyemma._base in there
and things in pyemma.util we're sure that we need to keep in a general
repo. I have the impression that some pyemma.util things are not really
used anymore.
Despite
"except for"
deprecated code it also contains code, which we do not want to
share (eg the logging and config modules).
Logging is actually used in _base.estimator

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#20 (comment).

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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

[marscher]

The logging initialization also depends on the pyemma config file. I do not see how to easily untangle this.

[marscher]

but I'm getting off topic right now. I will copy over the statistics module right now.