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Cython xdrlib#441

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richardjgowers merged 64 commits intoMDAnalysis:developMDAnalysis/mdanalysis:developfrom kain88-de:cython-xdrlibkain88-de/mdanalysis:cython-xdrlibCopy head branch name to clipboardJan 17, 2016

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Commits on Jan 17, 2016

• Remove old XDR code

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• Add currentversion of xdrlib

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• Readd original changes for seeking in XDR files

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• Fix memleak in xtc offset calculation

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• Add XTCfile object module

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• Add test for new XTCFile object

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• Add TRRFile module

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• Add tests for trr module

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• Readd XTC-Reader/Writer class

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• Readd the TRR-Reader/Writer classes

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• Add new tests for XTC and TRR reader/writer

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• Add C_ptr to ndarray wrapper

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• deactivate some tests

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• remove libxdrfile2 tests

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• Unify xtc/trr file wrappers

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• test common xdrlib functions in a base class

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• Create XDR base class and adopt XTC/TRR

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• Make n_frames a property

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• Don't look into offsets when seeking to frame 0

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• Avoid offset calculation in XDRBaseReader init

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• Persistently save offsets

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• PEP8-fy test_persistence.py

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• Fix offsets path algorithm

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• better warning message

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• get most persistence tests to pass

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• remove lazy loading persistence offset tests

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• Refactor from tempfile to tempdir

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• remove cruft from persistence tests

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• Only try a savez

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• Deactivate mismatch tests

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• Move xdr persistence test to xdr tests

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• merge xdr test files

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• Get 100% coverage in XDR.py

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• Fix small things in XDR.py

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• improve xdrlib doc strings

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• Reactivate timestep tests

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• clean up test_timestep_api

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• clean up test_xdr.py

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• completely remove test_vel_src.

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• Add licence info the each file

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• Combine xdrlib tests

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• Remove unused variable

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• Add smal docstring to XTC and TRR reader

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• Forget offsets when xdrfile is closed.

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• Use better precision interface for xtc writing

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• Offer precision keyword in XTCWriter

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• Use old gromacs precision in xdrlib

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• convert to xdrlib precision for XTC saving

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• Fix type in doc-string

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• Add information how test.xtc/trr was created

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• Add test to write non default xtc precision

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• use float type for precision

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• test precision setting in xtcwriter.

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• deactivate unused tests

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• Add XTC sub selection test

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• XDR fix spelling error

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• really test offset mismatch

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• Various QC fixes in XDR.py

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• Fix test Error

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• Fix Doc strings

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• Fix up doc strings

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• Fix up doc strings

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• ignore *.npz files created during testing

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• Add changelog info

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