[estimation] Bug fix. i) Sampler with reversible stationary vector ne…

[trendelkampschroer]

…eds only check undirected connectivity of count matrix. ii) is_positive checks >=1e-15 instead of >= 1e-8. iii) Use sgamma instead of gengamma to generate Gamma-distributed random variates, possibly avoiding underflow/overflow due to small/large scaling factor beta.

[franknoe]

Thank you very much. Can you please also run the PyEMMA unit tests when using this implementation, to make sure that there are no secondary effects?

[trendelkampschroer]

For the latest version of PyEMMA devel I get two errors realted to estimate_hidden_markov_model and timescales_hmsm.

I also get an import error for the name _get_indices_phi.

But these things don't seem to be related to the sampler, is that correct?

[marscher]

Latest version of pyemma needs mdtraj-1.5 and bhmm-0.5.2, please upgrade.

[trendelkampschroer]

mdtraj is already version 1.5.1 on my machine, when I do easy_install --user bhmm==0.5.2 I get the following error

Processing bhmm-0.5.2.tar.gz Writing /tmp/easy_install-nO7Fki/bhmm-0.5.2/setup.cfg Running bhmm-0.5.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-nO7Fki/bhmm-0.5.2/egg-dist-tmp-d4D4l2 error: Setup script exited with error: unknown file type '.pyx' (from './bhmm/hidden/impl_c/hidden.pyx')

[marscher]

please try pip install bhmm --user

[marscher]

upgrade setuptools first: pip install setuptools -U --user; pip install bhmm --user

[marscher]

The check if setuptools has a sufficient version seems not to work as expected.

[trendelkampschroer]

I've got bhmm-0.5.2. successfully installed, and the HMM-related errors are gone now.

Strangely I still get

ImportError: cannot import name _get_indices_phi

with a mdtraj version of 1.5.1

[marscher]

update your pyemma git/install to at least 2.0.2

[franknoe]

Then you don't have PyEMMA 2.0.2.

Am 13/11/15 um 16:30 schrieb Benjamin Trendelkamp-Schroer:

I've got bhmm-0.5.2. successfully installed, and the HMM-related errors are gone now.

Strangely I still get

ImportError: cannot import name _get_indices_phi

with a mdtraj version of 1.5.1

— Reply to this email directly or view it on GitHub https://github.com/markovmodel/msmtools/pull/62#issuecomment-156464103.

---

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

[trendelkampschroer]

I have PyEMMA latest git devel. I can successfully import pyemma in ipython, the error occurs only if I run nosetests/pyemma. Maybe we can have a look at it together next week.

[marscher]

I suppose nose imports pyemma from the wrong location then. If you invoke nose in your git working copy, it should use the right version.

[trendelkampschroer]

I have all tests on PyEMMA latest devel running successfully. Can someone please merge this pull-request.

[franknoe]

Thank you!