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Adds Reader.timeseries #1400

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Adds Reader.timeseries #1400

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richardjgowers
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Fixes partially #1383

Changes made in this Pull Request:

  • added deprecation warnings to all core.Timeseries classes
  • added timeseries method to ProtoReader

PR Checklist

  • Tests?
  • Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?

@richardjgowers richardjgowers added this to the 0.16.x milestone Jun 15, 2017
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So Encore uses DCDReader.timeseries (which isn't actually a Timeseries (as in the class)) but instead just a handy method for iterating and grabbing coordinates. I've put a implementation of this into ProtoReader so that all readers get a basic version of it

@kain88-de kain88-de mentioned this pull request Jun 15, 2017
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orbeckst
orbeckst requested changes Jun 16, 2017
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The deprecations should be merged with #1403 (I can do that); the new trajectory.timeseries functionality is a new feature and has to go in 0.17.0.

package/MDAnalysis/coordinates/base.py
@@ -1461,6 +1461,60 @@ def __repr__(self):
natoms=self.n_atoms
))

def timeseries(self, asel=None, start=None, stop=None, step=None,
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This is a new feature for trajectory readers. It cannot go into a patch release. It has to be in 0.17.0.

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Ok, I'll bump this into 0.17 then

package/MDAnalysis/coordinates/DCD.py
@@ -578,6 +579,7 @@ def timeseries(self, asel=None, start=None, stop=None, step=None, skip=None,
# XXX needs to be implemented
return self._read_timeseries(atom_numbers, start, stop, step, format)

@deprecate(message="This method will be removed in 0.17")
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All the deprecations can go in now.

I somehow missed your PR and did the reST deprecations in PR #1403

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@richardjgowers I cherry-picked your first two commits onto #1403

@richardjgowers richardjgowers modified the milestones: 0.17.0, 0.16.x Jun 16, 2017
@richardjgowers richardjgowers changed the title Issue 1383 timeseries deprecation Adds Reader.timeseries Jun 16, 2017
kain88-de
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package/CHANGELOG
@@ -17,6 +17,9 @@ mm/dd/yy

* 0.16.2

Deprecations
* deprecated core.Timeseries module (Issue #1383)
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this needs to be moved up the timeline or removed right?

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Yeah it's leftover from when this also did the deprecation

package/MDAnalysis/coordinates/base.py
# do we need copy in this case?
coordinates[i] = ts.positions[atom_numbers].copy()

return coordinates
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This is not implementing the format keyword argument. I guess you can copy the code I use in libdcd for this. There are also a lot of tests for it right now.

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And yeah, I'll have to deal with that in this PR too

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@orbeckst orbeckst Jul 4, 2017 •
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And we wanted to change the format kwarg to order.... #1400 (comment)

@kain88-de kain88-de mentioned this pull request Jun 25, 2017
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kain88-de
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package/MDAnalysis/coordinates/base.py
step : int (optional)
Step size for reading; the default ``None`` is equivalent to 1 and means to
read every frame.
format : str (optional)
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btw I'm for naming this option order format is confusing with the buildin

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See #1063 where this was already mooted.

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See #1453 for the issue.

@kain88-de kain88-de mentioned this pull request Jul 25, 2017
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@richardjgowers richardjgowers modified the milestones: 0.17.0, 1.0 Jan 25, 2018
@richardjgowers richardjgowers mentioned this pull request Sep 25, 2018
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@orbeckst orbeckst added the close? Evaluate if issue/PR is stale and can be closed. label Sep 28, 2018
orbeckst added a commit that referenced this pull request Jun 5, 2019
@orbeckst
timeseries for all readers (from PR #1400)
1913f73 
- updated format -> order kwarg
- updated docs
- note: general reader.timeseries only supports order="FAC" at the moment
- CHANGELOG
@orbeckst orbeckst mentioned this pull request Jun 5, 2019
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@richardjgowers richardjgowers mentioned this pull request Mar 4, 2020
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@hmacdope hmacdope mentioned this pull request Oct 26, 2022
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@RMeli RMeli deleted the issue-1383-timeseries_deprecation branch December 23, 2023 21:57
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