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DCD-Cython #1372
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DCD-Cython #1372
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671f1b4
new Cython-based DCD file handling code
kain88-de 9e40e7a
implement frame reading
kain88-de f4d7740
TST: Added first draft of testing module for new Cython-based DCD fil…
tylerjereddy a2ccb3d
initial work on DCD writing
tylerjereddy ab0f981
ENH: restored DCD-related import checking in MDAnalysis/coordinates/_…
tylerjereddy c749a13
exception handling in DCD
tylerjereddy 6182da5
ENH: added py3 compatibility for block_import.
tylerjereddy 09ff489
compile _dcdmodule again
kain88-de 1475c99
ENH: New DCD reading code now appears to handle unit cell information…
tylerjereddy 5df264e
ENH: Fixed an IOError message in libdcd.pyx that referred to TRR file…
tylerjereddy c783f2d
DCD writing
tylerjereddy a93d37c
DCD unit test improvements
tylerjereddy 0020b3e
ENH: Added proper DCDFile remarks / header string handling -- all uni…
tylerjereddy ced318b
DCDFile variables that are testing-only / implementation details are …
tylerjereddy 04de2c0
Replaced a standard library assertion with a numpy assertion in the l…
tylerjereddy 7bcec26
DCDFile now allows overwriting, based on feedback in PR#1155.
tylerjereddy d3573e1
current_frame variable is now updated in write method of DCDFile.
tylerjereddy fdb7685
Removed spurious header writing; fixed an issue in write() method of …
tylerjereddy 6c7a691
Patched issue with frame iteration in test_coord_match -- all unit te…
tylerjereddy 6092980
Attempted formatting fixes in test_libdcd.py.
tylerjereddy 0d43e4f
added DCD regression tests against data from old DCDReader
tylerjereddy f247e7b
DCD unit cell data handling and tests
tylerjereddy 021665d
test_header_remarks has been adjusted to perform a direct string comp…
tylerjereddy 0d60576
Simplified code in test_iteration() unit test based on PR comments.
tylerjereddy 6d7e8b6
DCDWriteTestRandom now pins down the random seed for testing robustness.
tylerjereddy 9091ac9
fixes in libdcd
kain88-de b26de04
Refactor libdcd test
kain88-de c8d50d2
Added new property-based unit test, test_written_remarks_property(), …
tylerjereddy d14ffb5
fix write_file function
kain88-de 24656c3
add write dtype handling
kain88-de e4382e3
check tell in iteration
kain88-de 2596974
use sensible warnings when only a header is written
kain88-de 7632871
remove double definition
kain88-de f919d79
restucture libdcd test order
kain88-de 23272c5
deactivate correl tests for now
kain88-de e2e8e84
start work on new dcd reader
kain88-de d446fcd
fix unicode name in open
kain88-de 5fb3878
improve dt unit handling
kain88-de e06b0ff
Fix unitcell handling
kain88-de 54abc2d
fix failing tests
kain88-de 473f1c5
enable new style reader/writer tests
kain88-de 71668a9
fix up docs
kain88-de 9e75910
remove old C dcd reader
kain88-de e64127f
remove duplicate tests
kain88-de 1888130
add header property
kain88-de 911bff5
remove old module from setup.py
kain88-de 4ea19bb
move unitcell handling from libdcd to DCDReader
kain88-de 95a5808
add hypothesis to travis tests
kain88-de ccbf0ba
DCD header improvements
kain88-de b409b20
general clean up
kain88-de fcfbf5d
reactivate hypothesis tests
tylerjereddy e651f59
use timeseries
kain88-de 64098d8
fix ndims DCD reader error
kain88-de 65ea67b
fix timeseries
kain88-de f189510
have readframes with start,stop,step
kain88-de 979c8dd
fix linter problems
kain88-de 8ba9f19
remove dcd from timestep API test
kain88-de 4c308c7
fix unitcell initialization
kain88-de 4d0a44f
support ordered readframes
kain88-de 51ba896
allow subset reading in readframes
kain88-de 9a07c00
speed up
kain88-de 66d42a2
add docs
kain88-de 2c754d4
copy timestep
kain88-de 9b1d607
fixed known failure in transition
kain88-de f0170be
update changelog
kain88-de eb1c001
DCD test improvements
tylerjereddy d3c437d
update libdcd and DCDReader docs
kain88-de f9492ee
yapify DCD
kain88-de 9f79004
fix error in DCD Reader and remove confusing comment
kain88-de 19316df
fix test for dcd
kain88-de 11bef65
test_libdcd test_seek_over_max() now appropriately checks for EOFErro…
tylerjereddy 3d5e2d7
reorder tests
kain88-de 3bc9c02
add readframes tests
kain88-de 64093cb
fix backwards step in readframes
kain88-de 82de16a
add new timeseries tests to test_dcd
kain88-de 8ed06ce
Convert test_libdcd.py to pytest
kain88-de ae52229
delete old files
kain88-de 36105ae
fixup CHANGELOG & setup.py with rebase cleaning
kain88-de 49f3e54
fix DCD writer errors
kain88-de 76290ee
add random unit cell test to test_dcd
kain88-de ad64253
prefer to use format over string interpolation
kain88-de 8ca3fd3
add information about charm bitfield
kain88-de 7420bd3
uniformly use xyz to refer to coordinates in libdcd
kain88-de 134199e
fixup DCD sphinx error
kain88-de 717346a
add Exception names to libdcd docs
kain88-de 366290e
remove unnecessary check
kain88-de bd9c425
reach 100% coverage of DCD.py
kain88-de ce6573b
add libdcd to rst docs
kain88-de ceb7313
push test loop into pytest parametrize
kain88-de 0097099
update libdcd
kain88-de 015f15a
use assert_array_equal
kain88-de 619526c
avoid copy in dcd writer
kain88-de 2d2ce49
modify changelog
kain88-de 23e3d28
refactor libdcd header API
kain88-de 6f2001f
don't change dt when using nsavc for writing
kain88-de 32efca9
improve docs for libdcd and DCD
kain88-de 25bfb7c
improve unitcell decoding
kain88-de 6423abb
update test_libdcd with pytest style guides
kain88-de 9bec7bd
use pytest style for test_dcd
kain88-de 8cbac38
update license header
kain88-de 42c7105
install hypothesis for tests with setup.py
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Original file line number | Diff line number | Diff line change |
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@@ -13,11 +13,13 @@ The rules for this file: | |
* release numbers follow "Semantic Versioning" http://semver.org | ||
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------------------------------------------------------------------------------ | ||
mm/dd/17 richardjgowers, rathann, orbeckst, tylerjereddy, mtiberti | ||
mm/dd/17 richardjgowers, rathann, orbeckst, tylerjereddy, mtiberti, kain88-de | ||
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* 0.17.0 | ||
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Enhancements | ||
* add low level lib.formats.libdcd module for reading/writing DCD (PR #1372) | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Perhaps say "replaced old DCD handling code with ..." |
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* replace old DCD reader with a Python 3 ready DCD reader (Issue #659) | ||
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Deprecations | ||
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did we end up using hypothesis tests?
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yes