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Ran 16 May 2016 02:29PM UTC

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Committed 16 May 2016 02:29PM UTC coverage: 86.026% (+0.06%) from 85.964%

Job # python=2.7 CONDA_PY=27 CONDA_NPY=19

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travis-ci

Committed by Martin K. Scherer

Commit Message

Save traj file handling (#803)

If a reader has to be constructed within coordinates.save_traj(s), we only pass the file names actually needed to extract frames from to the reader. This fixes #788 (index unneeded files).

Involved changes:
* [featurereader] added option to return plain mdtraj.Trajectory objects
* [fragmentedreader] added reader_by_filename property
* [coor/api] handle chunk_size argument correctly (0 evaluates to False).
* default chunksize 1000
* [patches] added setitem method for Trajectory objs
* [reader_utils] def chunksize=1000, added setitem method for empty_traj created objs.
* [fragreader] use setitem method for traj objects collected by underlying featurereaders
* [datasource] handle too large RA indices for stride
* added create_traj in test.util.

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markovmodel / PyEMMA / 1999 / 1
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markovmodel / PyEMMA / 1999 / 1
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