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Cython xdrlib #441

Merged
merged 64 commits into from
Jan 17, 2016
Merged

Cython xdrlib #441

merged 64 commits into from
Jan 17, 2016

Commits on Jan 17, 2016

  1. Remove old XDR code 

    Refactoring this is not really worth it. I'll start the xdr
interface from scratch.
    @kain88-de
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  2. Add currentversion of xdrlib 

    This is the newest version accessible from the GROMACS
devs.
    @kain88-de
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  3. Readd original changes for seeking in XDR files 

    These are the changes that have been made my Manuel to enable seeking in
the xtc/trr files. The C modules compile besides of some changes I need
to make to the cython wrappers.

Signed-off-by: Max Linke <max_linke@gmx.de>
    @mnmelo @kain88-de
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  4. Fix memleak in xtc offset calculation 

    It was never returned how the the offsets array actually had become.
This means there was no way of taking back controll over a small part of
the allocated memory. Resulting in a memory leak. This new version also
returns the information about the actual size of the offsets array.
    @kain88-de
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  5. Add XTCfile object module 

    This adds a clean wrapper for xtc functions in the xdrlib of GROMACS.
The object acts similar to a normal file object in python. This should
be the a clean wrap and enable to use xtc files with little fuss inside
of mdanalysis. It currently is still somewhat slow. After fixes edges
with the API and integrating it into a Reader class I'll have a look
into optimizing it.
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  6. Add test for new XTCFile object 

    This adds a comprehensive set of tests for the new XTCFile class.
It tests most error conditions that are easy to generate and comes
with it's own set of small test files. Even though I'm doing some IO
everything runs very fast because the files involved are small.
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  7. Add TRRFile module 

    This is a copy of the xtc module enabling to use trr files.
    @kain88-de
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  8. Add tests for trr module

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  9. Readd XTC-Reader/Writer class 

    This is now a 'simple' wrapper around the xtcfile object.
That simplifies the code quite a lot and it looks like we have a proper
seperation of responsibilities in the code
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  10. Readd the TRR-Reader/Writer classes 

    Basically it is the same as the XTC module. Just small
changes for the TRR format.
    @kain88-de
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  11. Add new tests for XTC and TRR reader/writer 

    Delete also old TimeStep tests since that object doesn't exists
anymore in the code.
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  12. Add C_ptr to ndarray wrapper 

    I need a way to convert pointers to numpy arrays in cython that is
portable across numpy versions and python versions. This file should to
exactly that. It will help me to treat the xdrlib correctly. The
wrapper
is a bit more complex then just setting the OWN_DATA flag in a newly
created array to allow us a fine controll over the used deallocator.
Then numpy can change it's allocater in the future and this will still
work.
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  13. deactivate some tests 

    deactivate persistence test
deactivate timestep tests
deactivate atom_group velocity source test
   what was this testing anyway???
    @kain88-de
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  14. remove libxdrfile2 tests

    @kain88-de
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  15. Unify xtc/trr file wrappers 

    Use a common base class for the two. This reduces duplicated code.

Check BOX tolerance to 2 decimal places xdrlib

Upto 2 decimal places accuracy is enough for box vectors.
Well it's exactly the value I need to have the tests pass.
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  16. test common xdrlib functions in a base class

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  17. Create XDR base class and adopt XTC/TRR

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  18. Make n_frames a property

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  19. Don't look into offsets when seeking to frame 0 

    Looking into the offsets array would trigger a calculation of the
offsets. This modifocation allows to still use lazy loading in the
XTCReader and still inspect the second frame to calculate a dt.
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  20. Avoid offset calculation in XDRBaseReader init

    @kain88-de
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  21. Persistently save offsets

    @kain88-de
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  22. PEP8-fy test_persistence.py

    @kain88-de
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  23. Fix offsets path algorithm 

    The algorithm could only deal with relative paths. This
works also for absolute paths
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  24. better warning message 

    the new system doesn't abort the offset loading. It just
reloads them directly with construction then.
    @kain88-de
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  25. get most persistence tests to pass

    @kain88-de
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  26. remove lazy loading persistence offset tests 

    The new XDR-classes don't support lazy loading for the
offsets anymore.
    @kain88-de
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  27. Refactor from tempfile to tempdir 

    This ensures cleaning up for us and we don't have to do those unlink
things.
    @kain88-de
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  28. remove cruft from persistence tests

    @kain88-de
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  29. Only try a savez 

    It can fail when the directory is read-only or when something
else happens to the directory. In that case just fail silently
    @kain88-de
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  30. Deactivate mismatch tests 

    Since I can't possibly test for them right now they have to be
deactivated.
    @kain88-de
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  31. Move xdr persistence test to xdr tests

    @kain88-de
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  32. merge xdr test files

    @kain88-de
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  33. Get 100% coverage in XDR.py 

    This will only test that the code path is run. Not that the does
anything correct.
    @kain88-de
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  34. Fix small things in XDR.py

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  35. improve xdrlib doc strings

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  36. Reactivate timestep tests

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  37. clean up test_timestep_api

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  38. clean up test_xdr.py

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  39. completely remove test_vel_src. 

    The code has been removed.
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  40. Add licence info the each file

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  41. Combine xdrlib tests

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  42. Remove unused variable

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  43. Add smal docstring to XTC and TRR reader

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  44. Forget offsets when xdrfile is closed. 

    This ensures that offsets are recalculated if another file is opened
with the same xdrfile instance.
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  45. Use better precision interface for xtc writing 

    This new interface is more intuitive.
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  46. Offer precision keyword in XTCWriter 

    The old class supported this so I should do this here as well
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  47. Use old gromacs precision in xdrlib 

    This is to better deal with the precision return value here.
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  48. convert to xdrlib precision for XTC saving 

    Use a more sensible precision definition inside of MDAnalysis.
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  49. Fix type in doc-string

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  50. Add information how test.xtc/trr was created 

    This also includes information how to read the content of the files
in ascii without using MDAnalysis
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  51. Add test to write non default xtc precision

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  52. use float type for precision

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  53. test precision setting in xtcwriter.

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  54. deactivate unused tests

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  55. Add XTC sub selection test

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  56. XDR fix spelling error

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  57. really test offset mismatch

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  58. Various QC fixes in XDR.py

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  59. Fix test Error 

    Base test classes in test files seem to be needed to start with an
underscore otherwise nose picks them up and tries to lets their tests
run.
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  60. Fix Doc strings

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  61. Fix up doc strings

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  62. Fix up doc strings

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  63. ignore *.npz files created during testing

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  64. Add changelog info

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