Code

DCD-Cython#1372

Code

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kain88-de merged 101 commits intodevelopMDAnalysis/mdanalysis:developfrom dcd-cython-rebaseMDAnalysis/mdanalysis:dcd-cython-rebaseCopy head branch name to clipboardJul 8, 2017

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Commits on Jul 8, 2017

• new Cython-based DCD file handling code

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• implement frame reading

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• TST: Added first draft of testing module for new Cython-based DCD file handling interface.

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• initial work on DCD writing

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• ENH: restored DCD-related import checking in MDAnalysis/coordinates/__init__.py after upstream python 3 fixes.

  

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• exception handling in DCD

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• ENH: added py3 compatibility for block_import.

  

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• compile _dcdmodule again

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• ENH: New DCD reading code now appears to handle unit cell information properly. All tests in test_libdcd.py pass in python 2.7 and 3.5.

  

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• ENH: Fixed an IOError message in libdcd.pyx that referred to TRR files instead of DCD files.

  

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• DCD writing

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• DCD unit test improvements

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• ENH: Added proper DCDFile remarks / header string handling -- all unit tests now pass in python 2.7 & 3.5

  

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• DCDFile variables that are testing-only / implementation details are now prefixed with an underscore in response to comments in PR#1155.

  

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• Replaced a standard library assertion with a numpy assertion in the libdcd test suite, based on reviewer feedback in PR#1155.

  

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• DCDFile now allows overwriting, based on feedback in PR#1155.

  

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• current_frame variable is now updated in write method of DCDFile.

  

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• Removed spurious header writing; fixed an issue in write() method of DCDFile such that single-frame NAMD DCD trajectory writing exactly reproduces the coordinates from the input file.

  

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• Patched issue with frame iteration in test_coord_match -- all unit tests now pass.

  

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• Attempted formatting fixes in test_libdcd.py.

  

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• added DCD regression tests against data from old DCDReader

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• DCD unit cell data handling and tests

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• test_header_remarks has been adjusted to perform a direct string comparison, as requested in PR comments.

  

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• Simplified code in test_iteration() unit test based on PR comments.

  

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• DCDWriteTestRandom now pins down the random seed for testing robustness.

  

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• fixes in libdcd

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• Refactor libdcd test

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• Added new property-based unit test, test_written_remarks_property(), which reveals that DCDFile is not able to handle writing when an empty REMARKS string is provided.

  

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• fix write_file function

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• add write dtype handling

  

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  24656c3

• check tell in iteration

  

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  e4382e3

• use sensible warnings when only a header is written

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• remove double definition

  

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• restucture libdcd test order

  

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• deactivate correl tests for now

  

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• start work on new dcd reader

  

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• fix unicode name in open

  

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  d446fcd

• improve dt unit handling

  

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  5fb3878

• Fix unitcell handling

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  e06b0ff

• fix failing tests

  

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  54abc2d

• enable new style reader/writer tests

  

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• fix up docs

  

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  71668a9

• remove old C dcd reader

  

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• remove duplicate tests

  

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• add header property

  

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• remove old module from setup.py

  

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  911bff5

• move unitcell handling from libdcd to DCDReader

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  4ea19bb

• add hypothesis to travis tests

  

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• DCD header improvements

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  ccbf0ba

• general clean up

  

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• reactivate hypothesis tests

  

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• use timeseries

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  e651f59

• fix ndims DCD reader error

  

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• fix timeseries

  

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• have readframes with start,stop,step

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• fix linter problems

  

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• remove dcd from timestep API test

  

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• fix unitcell initialization

  

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• support ordered readframes

  

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• allow subset reading in readframes

  

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• speed up

  

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• add docs

  

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• copy timestep

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  2c754d4

• fixed known failure in transition

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  9b1d607

• update changelog

  

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  f0170be

• DCD test improvements

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• update libdcd and DCDReader docs

  

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• yapify DCD

  

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  f9492ee

• fix error in DCD Reader and remove confusing comment

  

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  9f79004

• fix test for dcd

  

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• test_libdcd test_seek_over_max() now appropriately checks for EOFError instead of IOError.

  

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• reorder tests

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• add readframes tests

  

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  3bc9c02

• fix backwards step in readframes

  

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• add new timeseries tests to test_dcd

  

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• Convert test_libdcd.py to pytest

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• delete old files

  

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• fixup CHANGELOG & setup.py with rebase cleaning

  

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• fix DCD writer errors

  

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• add random unit cell test to test_dcd

  

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• prefer to use format over string interpolation

  

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• add information about charm bitfield

  

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• uniformly use xyz to refer to coordinates in libdcd

  

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• fixup DCD sphinx error

  

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• add Exception names to libdcd docs

  

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• remove unnecessary check

  

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• reach 100% coverage of DCD.py

  

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• add libdcd to rst docs

  

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• push test loop into pytest parametrize

  

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• update libdcd

  

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• use assert_array_equal

  

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• avoid copy in dcd writer

  

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• modify changelog

  

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  2d2ce49

• refactor libdcd header API

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• don't change dt when using nsavc for writing

  

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  6f2001f

• improve docs for libdcd and DCD

  

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  32efca9

• improve unitcell decoding

  

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• update test_libdcd with pytest style guides

  

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• use pytest style for test_dcd

  

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• update license header

  

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• install hypothesis for tests with setup.py

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