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Improve libdcd cython #3888

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merged 42 commits into from
Nov 29, 2022
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1e7f5b1
add annotate_cython setup.cfg option
hmacdope Oct 26, 2022
ff6677e
improve some of the DCD
hmacdope Oct 26, 2022
c1b6147
continue adding types
hmacdope Oct 26, 2022
b8074fc
add types and fix is_periodic
hmacdope Oct 26, 2022
c8ba7d7
change whence dict
hmacdope Oct 26, 2022
5c25473
further improve dcd
hmacdope Oct 26, 2022
8a3b558
continue to improve reading
hmacdope Oct 26, 2022
41d6cca
incremental improvements
hmacdope Oct 26, 2022
64092cc
rever cython range
hmacdope Oct 27, 2022
4519bbd
revert n_frames check
hmacdope Oct 27, 2022
d9276ab
add note to DCD for query
hmacdope Oct 27, 2022
9a4f0cf
move DCD reader to no copy API and update tests accordingly
hmacdope Oct 28, 2022
fb40390
update chanelog
hmacdope Oct 28, 2022
8e82299
small changes
hmacdope Oct 28, 2022
adb30bf
suggestions from code review
hmacdope Oct 29, 2022
0e3761b
Merge branch 'develop' into improve_dcd_cython
orbeckst Oct 31, 2022
73fbb39
add module level directives
hmacdope Nov 1, 2022
72acd3b
try contiguous
hmacdope Nov 1, 2022
749da5e
Revert "try contiguous"
hmacdope Nov 1, 2022
5832c77
Merge remote-tracking branch 'upstream/develop' into improve_dcd_cython
hmacdope Nov 6, 2022
cd79359
update changelog
hmacdope Nov 6, 2022
def0c14
experimental pxdify
hmacdope Nov 6, 2022
873a9be
pxdify libdcd
hmacdope Nov 7, 2022
be3b51a
Merge remote-tracking branch 'upstream/develop' into improve_dcd_cython
hmacdope Nov 12, 2022
43bbf3e
fix bad changelog merge
hmacdope Nov 15, 2022
5d646b8
fix bad changelog merge2
hmacdope Nov 15, 2022
e9584e3
deprecate DCD
hmacdope Nov 15, 2022
23f2912
fix docs and tests
hmacdope Nov 15, 2022
070be37
fix changelog
hmacdope Nov 22, 2022
edc613f
apply oliver suggestions
hmacdope Nov 22, 2022
ec1f44a
add temporary buffer to DCD reader
hmacdope Nov 22, 2022
8d36ba0
Merge remote-tracking branch 'upstream/develop' into improve_dcd_cython
hmacdope Nov 22, 2022
8c8bd13
add DCD to public libmdanalysis API
hmacdope Nov 22, 2022
51eec87
fix up changeleog
hmacdope Nov 23, 2022
8dad311
fix libdma import
hmacdope Nov 23, 2022
5ef937a
fix up changeleog again
hmacdope Nov 23, 2022
d565b22
go back to compiling as C
hmacdope Nov 23, 2022
283372f
fix changelog c++
hmacdope Nov 23, 2022
d61ef01
remove c++
hmacdope Nov 23, 2022
c0a1d72
fix dcd imports
hmacdope Nov 23, 2022
24bf4b1
fix is_periodic
hmacdope Nov 23, 2022
64ad08a
make int cast explicit
hmacdope Nov 24, 2022
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fix docs and tests
  • Loading branch information
hmacdope committed Nov 15, 2022
commit 23f2912440d32da9d7fc1f2ffb7cc3df990c9c8f
11 changes: 10 additions & 1 deletion package/MDAnalysis/coordinates/DCD.py
Original file line number Diff line number Diff line change
@@ -96,6 +96,14 @@ class DCDReader(base.ReaderBase):
degrees then it is assumed it is a new-style CHARMM unitcell (at least
since c36b2) in which box vectors were recorded.

.. deprecated:: 2.4.0
DCDReader currently makes independent timesteps
by copying the :class:`Timestep` associated with the reader.
Other readers update the :class:`Timestep` inplace meaning all
references to the :class:`Timestep` contain the same data. The unique
independent :class:`Timestep` behaviour of the DCDReader is deprecated
will be changed in 3.0 to be the same as other readers

.. warning::
The DCD format is not well defined. Check your unit cell
dimensions carefully, especially when using triclinic boxes.
@@ -158,7 +166,7 @@ def __init__(self, filename, convert_units=True, dt=None, **kwargs):
self.ts.dt = dt
warnings.warn("DCDReader currently makes independent timesteps"
" by copying self.ts while other readers update"
" self.ts. This behaviour will be changed in"
" self.ts inplace. This behaviour will be changed in"
" 3.0 to be the same as other readers",
category=DeprecationWarning)

@@ -195,6 +203,7 @@ def _read_next_timestep(self, ts=None):
if self._frame == self.n_frames - 1:
raise IOError('trying to go over trajectory limit')
if ts is None:
#TODO remove copying the ts in 3.0
ts = self.ts.copy()
frame = self._file.read()
self._frame += 1
2 changes: 1 addition & 1 deletion testsuite/MDAnalysisTests/coordinates/base.py
Original file line number Diff line number Diff line change
@@ -451,7 +451,7 @@ def test_frame_collect_all_same(self, reader):
if isinstance(reader, mda.coordinates.memory.MemoryReader):
pytest.xfail("memoryreader allows independent coordinates")
if isinstance(reader, mda.coordinates.DCD.DCDReader):
pytest;.xfail("DCDReader allows independent coordinates."
pytest.xfail("DCDReader allows independent coordinates."
"This behaviour is deprecated and will be changed"
"in 3.0")
collected_ts = []