ImportError: No module named trajectory in mdtraj

[cxhernandez]

I'm trying to use msmbuilder.tpt but it seems that mdtraj.trajectory is still a dependency. I believe it should be changed to mdtraj.core.trajectory.

[rmcgibbo]

You're right. There are a couple places where MSMBuilder master isn't updated to mdtraj-0.8 yet. I think in CreateAtomIndices there are a couple lines that need to change too.

[kyleabeauchamp]

I fixed a related issue (in project.py) in #372.

[rmcgibbo]

@cxhernandez: do you have the traceback for this?

[rmcgibbo]

CreateAtomIndices is actually fine.

[cxhernandez]

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-1-91e0525542cd> in <module>()
----> 1 from msmbuilder import tpt
      2 import numpy as np
      3 import scipy.io as sio
      4 import networkx as nx
      5 from __future__ import print_function

/Users/cu3alibre/anaconda/lib/python2.7/site-packages/msmbuilder-2.8-py2.7-macosx-10.5-x86_64.egg/msmbuilder/__init__.py in <module>()
     47 __all__ = ["geometry", "metrics", "msm_analysis", "MSMLib", "clustering", "project", "reduce"]
     48 
---> 49 import clustering, geometry, metrics, msm_analysis, MSMLib, clustering, project, reduce
     50 from project import Project

/Users/cu3alibre/anaconda/lib/python2.7/site-packages/msmbuilder-2.8-py2.7-macosx-10.5-x86_64.egg/msmbuilder/project/__init__.py in <module>()
----> 1 from project import Project
      2 from builder import ProjectBuilder, FahProjectBuilder

/Users/cu3alibre/anaconda/lib/python2.7/site-packages/msmbuilder-2.8-py2.7-macosx-10.5-x86_64.egg/msmbuilder/project/project.py in <module>()
     33 import mdtraj as md
     34 from mdtraj import io
---> 35 from mdtraj.trajectory import HDF5TrajectoryFile
     36 import logging
     37 from msmbuilder.utils import keynat

ImportError: No module named trajectory

[cxhernandez]

project.py was the issue

[rmcgibbo]

Okay. @kyleabeauchamp fixed this in #372