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DCD-Cython #1372

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Jul 8, 2017
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671f1b4
new Cython-based DCD file handling code
kain88-de Jun 30, 2016
9e40e7a
implement frame reading
kain88-de Oct 1, 2016
f4d7740
TST: Added first draft of testing module for new Cython-based DCD fil…
tylerjereddy Oct 21, 2016
a2ccb3d
initial work on DCD writing
tylerjereddy Jan 10, 2017
ab0f981
ENH: restored DCD-related import checking in MDAnalysis/coordinates/_…
tylerjereddy Jan 14, 2017
c749a13
exception handling in DCD
tylerjereddy Jan 14, 2017
6182da5
ENH: added py3 compatibility for block_import.
tylerjereddy Jan 14, 2017
09ff489
compile _dcdmodule again
kain88-de Jan 16, 2017
1475c99
ENH: New DCD reading code now appears to handle unit cell information…
tylerjereddy Jan 29, 2017
5df264e
ENH: Fixed an IOError message in libdcd.pyx that referred to TRR file…
tylerjereddy Jan 30, 2017
c783f2d
DCD writing
tylerjereddy Jan 30, 2017
a93d37c
DCD unit test improvements
tylerjereddy Feb 13, 2017
0020b3e
ENH: Added proper DCDFile remarks / header string handling -- all uni…
tylerjereddy Mar 9, 2017
ced318b
DCDFile variables that are testing-only / implementation details are …
tylerjereddy Mar 16, 2017
04de2c0
Replaced a standard library assertion with a numpy assertion in the l…
tylerjereddy Mar 16, 2017
7bcec26
DCDFile now allows overwriting, based on feedback in PR#1155.
tylerjereddy Mar 16, 2017
d3573e1
current_frame variable is now updated in write method of DCDFile.
tylerjereddy Mar 16, 2017
fdb7685
Removed spurious header writing; fixed an issue in write() method of …
tylerjereddy Apr 20, 2017
6c7a691
Patched issue with frame iteration in test_coord_match -- all unit te…
tylerjereddy Apr 21, 2017
6092980
Attempted formatting fixes in test_libdcd.py.
tylerjereddy Apr 21, 2017
0d43e4f
added DCD regression tests against data from old DCDReader
tylerjereddy Apr 21, 2017
f247e7b
DCD unit cell data handling and tests
tylerjereddy May 9, 2017
021665d
test_header_remarks has been adjusted to perform a direct string comp…
tylerjereddy May 11, 2017
0d60576
Simplified code in test_iteration() unit test based on PR comments.
tylerjereddy May 11, 2017
6d7e8b6
DCDWriteTestRandom now pins down the random seed for testing robustness.
tylerjereddy May 11, 2017
9091ac9
fixes in libdcd
kain88-de May 22, 2017
b26de04
Refactor libdcd test
kain88-de May 23, 2017
c8d50d2
Added new property-based unit test, test_written_remarks_property(), …
tylerjereddy May 26, 2017
d14ffb5
fix write_file function
kain88-de May 28, 2017
24656c3
add write dtype handling
kain88-de May 28, 2017
e4382e3
check tell in iteration
kain88-de May 28, 2017
2596974
use sensible warnings when only a header is written
kain88-de May 28, 2017
7632871
remove double definition
kain88-de May 28, 2017
f919d79
restucture libdcd test order
kain88-de May 28, 2017
23272c5
deactivate correl tests for now
kain88-de May 28, 2017
e2e8e84
start work on new dcd reader
kain88-de May 28, 2017
d446fcd
fix unicode name in open
kain88-de May 28, 2017
5fb3878
improve dt unit handling
kain88-de May 28, 2017
e06b0ff
Fix unitcell handling
kain88-de May 28, 2017
54abc2d
fix failing tests
kain88-de May 29, 2017
473f1c5
enable new style reader/writer tests
kain88-de May 30, 2017
71668a9
fix up docs
kain88-de May 30, 2017
9e75910
remove old C dcd reader
kain88-de May 30, 2017
e64127f
remove duplicate tests
kain88-de May 30, 2017
1888130
add header property
kain88-de May 30, 2017
911bff5
remove old module from setup.py
kain88-de May 30, 2017
4ea19bb
move unitcell handling from libdcd to DCDReader
kain88-de May 30, 2017
95a5808
add hypothesis to travis tests
kain88-de Jun 1, 2017
ccbf0ba
DCD header improvements
kain88-de May 30, 2017
b409b20
general clean up
kain88-de Jun 1, 2017
fcfbf5d
reactivate hypothesis tests
tylerjereddy Jun 1, 2017
e651f59
use timeseries
kain88-de Jun 1, 2017
64098d8
fix ndims DCD reader error
kain88-de Jun 2, 2017
65ea67b
fix timeseries
kain88-de Jun 2, 2017
f189510
have readframes with start,stop,step
kain88-de Jun 2, 2017
979c8dd
fix linter problems
kain88-de Jun 2, 2017
8ba9f19
remove dcd from timestep API test
kain88-de Jun 2, 2017
4c308c7
fix unitcell initialization
kain88-de Jun 2, 2017
4d0a44f
support ordered readframes
kain88-de Jun 2, 2017
51ba896
allow subset reading in readframes
kain88-de Jun 2, 2017
9a07c00
speed up
kain88-de Jun 2, 2017
66d42a2
add docs
kain88-de Jun 2, 2017
2c754d4
copy timestep
kain88-de Jun 4, 2017
9b1d607
fixed known failure in transition
kain88-de Jun 4, 2017
f0170be
update changelog
kain88-de Jun 4, 2017
eb1c001
DCD test improvements
tylerjereddy Jun 14, 2017
d3c437d
update libdcd and DCDReader docs
kain88-de Jun 15, 2017
f9492ee
yapify DCD
kain88-de Jun 15, 2017
9f79004
fix error in DCD Reader and remove confusing comment
kain88-de Jun 15, 2017
19316df
fix test for dcd
kain88-de Jun 15, 2017
11bef65
test_libdcd test_seek_over_max() now appropriately checks for EOFErro…
tylerjereddy Jun 15, 2017
3d5e2d7
reorder tests
kain88-de Jun 16, 2017
3bc9c02
add readframes tests
kain88-de Jun 16, 2017
64093cb
fix backwards step in readframes
kain88-de Jun 16, 2017
82de16a
add new timeseries tests to test_dcd
kain88-de Jun 16, 2017
8ed06ce
Convert test_libdcd.py to pytest
kain88-de Jun 25, 2017
ae52229
delete old files
kain88-de Jun 25, 2017
36105ae
fixup CHANGELOG & setup.py with rebase cleaning
kain88-de Jun 25, 2017
49f3e54
fix DCD writer errors
kain88-de Jun 25, 2017
76290ee
add random unit cell test to test_dcd
kain88-de Jun 25, 2017
ad64253
prefer to use format over string interpolation
kain88-de Jun 25, 2017
8ca3fd3
add information about charm bitfield
kain88-de Jun 25, 2017
7420bd3
uniformly use xyz to refer to coordinates in libdcd
kain88-de Jun 25, 2017
134199e
fixup DCD sphinx error
kain88-de Jun 25, 2017
717346a
add Exception names to libdcd docs
kain88-de Jun 25, 2017
366290e
remove unnecessary check
kain88-de Jun 25, 2017
bd9c425
reach 100% coverage of DCD.py
kain88-de Jun 25, 2017
ce6573b
add libdcd to rst docs
kain88-de Jun 26, 2017
ceb7313
push test loop into pytest parametrize
kain88-de Jun 26, 2017
0097099
update libdcd
kain88-de Jul 3, 2017
015f15a
use assert_array_equal
kain88-de Jul 3, 2017
619526c
avoid copy in dcd writer
kain88-de Jul 3, 2017
2d2ce49
modify changelog
kain88-de Jul 4, 2017
23e3d28
refactor libdcd header API
kain88-de Jul 4, 2017
6f2001f
don't change dt when using nsavc for writing
kain88-de Jul 4, 2017
32efca9
improve docs for libdcd and DCD
kain88-de Jul 3, 2017
25bfb7c
improve unitcell decoding
kain88-de Jul 7, 2017
6423abb
update test_libdcd with pytest style guides
kain88-de Jul 7, 2017
9bec7bd
use pytest style for test_dcd
kain88-de Jul 7, 2017
8cbac38
update license header
kain88-de Jul 7, 2017
42c7105
install hypothesis for tests with setup.py
orbeckst Jul 8, 2017
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4 changes: 2 additions & 2 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ env:
- MAIN_CMD="pytest ${PYTEST_LIST} ${PYTEST_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST} ${NOSE_FLAGS}"
- SETUP_CMD=""
- BUILD_CMD="pip install -v package/ && pip install testsuite/"
- CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scipy griddataformats pytest-cov pytest-xdist"
- CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy griddataformats seaborn coveralls clustalw=2.1 pytest-cov pytest-xdist"
- CONDA_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib scipy griddataformats pytest-cov pytest-xdist hypothesis"
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did we end up using hypothesis tests?

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yes

- CONDA_ALL_DEPENDENCIES="mmtf-python nose=1.3.7 mock six biopython networkx cython joblib nose-timer matplotlib netcdf4 scikit-learn scipy griddataformats seaborn coveralls clustalw=2.1 pytest-cov pytest-xdist hypothesis"
# Install griddataformats from PIP so that scipy is only installed in the full build (#1147)
- PIP_DEPENDENCIES='pytest-raises'
- CONDA_CHANNELS='biobuilds conda-forge'
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4 changes: 3 additions & 1 deletion package/CHANGELOG
Original file line number Diff line number Diff line change
Expand Up @@ -13,11 +13,13 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
mm/dd/17 richardjgowers, rathann, orbeckst, tylerjereddy, mtiberti
mm/dd/17 richardjgowers, rathann, orbeckst, tylerjereddy, mtiberti, kain88-de

* 0.17.0

Enhancements
* add low level lib.formats.libdcd module for reading/writing DCD (PR #1372)
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Perhaps say "replaced old DCD handling code with ..."

* replace old DCD reader with a Python 3 ready DCD reader (Issue #659)

Deprecations

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784 changes: 273 additions & 511 deletions package/MDAnalysis/coordinates/DCD.py

Large diffs are not rendered by default.

195 changes: 0 additions & 195 deletions package/MDAnalysis/coordinates/include/correl.h

This file was deleted.

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