Move msmtools.flux.ReactiveFlux to pyemma.msm.models

[marscher]

see #416

In a follow up we should then remove the ReactiveFlux class from msmtools?

[marscher]

The tests passed on Travis. About to merge.

[franknoe]

I think that makes sense. Do we need to do it for 2.2, or can we
postpone this?

Am 17/05/16 um 21:21 schrieb Martin K. Scherer:

see #416 #416

In a follow up we should then remove the ReactiveFlux class from msmtools?

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    You can view, comment on, or merge this pull request online at:

#807

    Commit Summary

• [msm] moved msmtools.flux.ReactiveFlux to pyemma.msm.models

• fix test

• reactiveflux became a model

  File Changes
  

• M pyemma/msm/init.py
  https://github.com/markovmodel/PyEMMA/pull/807/files#diff-0 (5)

• M pyemma/msm/api.py
  https://github.com/markovmodel/PyEMMA/pull/807/files#diff-1 (99)

• M pyemma/msm/models/init.py
  https://github.com/markovmodel/PyEMMA/pull/807/files#diff-2 (1)

• A pyemma/msm/models/reactive_flux.py
  https://github.com/markovmodel/PyEMMA/pull/807/files#diff-3 (378)

• A pyemma/msm/tests/test_reactive_flux.py
  https://github.com/markovmodel/PyEMMA/pull/807/files#diff-4 (203)

  Patch Links:
  

• https://github.com/markovmodel/PyEMMA/pull/807.patch

• https://github.com/markovmodel/PyEMMA/pull/807.diff

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#807

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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]

some failures, but I don't understood what's wrong here.

[franknoe]

sorry, I had closed by mistake

[marscher]

The failures are caused because I've pushed the branch to origin instead to my fork, so travis opened up another special build for that, but in the meantime (while this job was running), I deleted the branch.

[coveralls]

Coverage increased (+0.1%) to 86.432% when pulling 56954f4 on marscher:move_msmtools_flux_to_pyemma into f18b417 on markovmodel:devel.

[franknoe]

BTW, I guess that also means that we will remove ReactiveFlux from msmtools in a future version? We should deprecate it then.

[marscher]

Yes, we should not have this "duplicate" for a long time.