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bhmm / legacy-bhmm-force-spectroscopy-manuscript

Bayesian hidden Markov models for analysis of single-molecule trajectory data
GNU Lesser General Public License v3.0
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changed all relative imports to absolute imports #21

Closed franknoe closed 9 years ago

franknoe commented 9 years ago

Changed all imports to be absolute. However, the same problem persists.

I can execute the nosetests as follows without any error:

nosetests bhmm --nocapture --verbosity=2 --with-doctest

But the following test run raises lots of import errors that make no sense to me,

conda build devtools/conda-recipe/

including:

/bhmm/api.py", line 6, in <module>
    from bhmm.hmm.generic_hmm import HMM as _HMM
ImportError: No module named hmm.generic_hmm

No idea what the problem is, because I can use the bhmm package from python or ipython without problems... Any ideas?

jchodera commented 9 years ago

Awesome! If this fixes the nosetests, I can take it from here and debug the conda recipe.

franknoe commented 9 years ago

Thanks. Please check the conda recipe - I think there are lots of dependencies that are not actually needed, at least not for running.

Am 05/05/15 um 21:51 schrieb John Chodera:

Awesome! If this fixes the nosetests, I can take it from here and debug the conda recipe.

— Reply to this email directly or view it on GitHub https://github.com/bhmm/bhmm/pull/21#issuecomment-99201608.

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 commented 9 years ago

Oh, and pyemma needs to become >=1.2. In short, I believe in conda-recipe/meta.yaml it should be:

run:

I think we need none of the following packages to run:

Am 05/05/15 um 21:51 schrieb John Chodera:

Awesome! If this fixes the nosetests, I can take it from here and debug the conda recipe.

— Reply to this email directly or view it on GitHub https://github.com/bhmm/bhmm/pull/21#issuecomment-99201608.

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

jchodera commented 9 years ago

I started updating the main recipe here: https://github.com/omnia-md/conda-recipes/tree/master/bhmm

I'll backport those changes.

Not sure why travis isn't building and testing this PR. It could be that it stopped working after the migration to the bhmm org. I'll merge this and then work on getting travis to work again.