Adds Reader.timeseries by richardjgowers · Pull Request #1400 · MDAnalysis/mdanalysis

richardjgowers · 2017-06-15T12:23:02Z

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 · 2017-06-15T12:25:30Z

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

orbeckst

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.

orbeckst · 2017-06-16T04:22:20Z

package/MDAnalysis/coordinates/base.py

            natoms=self.n_atoms
        ))

+    def timeseries(self, asel=None, start=None, stop=None, step=None,


This is a new feature for trajectory readers. It cannot go into a patch release. It has to be in 0.17.0.

Ok, I'll bump this into 0.17 then

orbeckst · 2017-06-16T04:23:31Z

package/MDAnalysis/coordinates/DCD.py

        # 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")


All the deprecations can go in now.

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

orbeckst · 2017-06-16T04:36:09Z

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

kain88-de · 2017-06-24T11:11:49Z

package/CHANGELOG

  * 0.16.2

+Deprecations
+  * deprecated core.Timeseries module (Issue #1383)


this needs to be moved up the timeline or removed right?

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

kain88-de · 2017-06-24T11:13:39Z

package/MDAnalysis/coordinates/base.py

+            # do we need copy in this case?
+            coordinates[i] = ts.positions[atom_numbers].copy()
+
+        return coordinates


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.

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

And we wanted to change the format kwarg to order.... #1400 (comment)

kain88-de · 2017-06-25T13:07:44Z

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)


btw I'm for naming this option order format is confusing with the buildin

See #1063 where this was already mooted.

See #1453 for the issue.

- updated format -> order kwarg - updated docs - note: general reader.timeseries only supports order="FAC" at the moment - CHANGELOG

richardjgowers added 3 commits June 13, 2017 09:16

Deprecated core.Timeseries module

58a27c5

Deprecated DCDReader.correl

589aad6

Addde timeseries to ReaderBase

74dd6bf

richardjgowers added the Work in progress label Jun 15, 2017

richardjgowers added this to the 0.16.x milestone Jun 15, 2017

Removed manual timeseries from Universe.transfer_to_memory

de3d934

kain88-de mentioned this pull request Jun 15, 2017

release 0.16.2 #1401

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11 tasks

orbeckst requested changes Jun 16, 2017

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richardjgowers modified the milestones: 0.17.0, 0.16.x Jun 16, 2017

richardjgowers changed the title ~~Issue 1383 timeseries deprecation~~ Adds Reader.timeseries Jun 16, 2017

kain88-de requested changes Jun 24, 2017

View reviewed changes

kain88-de mentioned this pull request Jun 25, 2017

DCD-Cython #1372

Merged

4 tasks

kain88-de reviewed Jun 25, 2017

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kain88-de mentioned this pull request Jul 25, 2017

[WIP] u.transfer_to_memory also transfers the box #1537

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4 tasks

richardjgowers modified the milestones: 0.17.0, 1.0 Jan 25, 2018

richardjgowers mentioned this pull request Sep 25, 2018

MemoryReader facelift #2080

Merged

4 tasks

orbeckst added the close? Evaluate if issue/PR is stale and can be closed. label Sep 28, 2018

richardjgowers closed this Oct 3, 2018

orbeckst added a commit that referenced this pull request Jun 5, 2019

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 mentioned this pull request Jun 5, 2019

timeseries() for all Readers #2271

Closed

4 tasks

richardjgowers mentioned this pull request Mar 4, 2020

Can only run encore convergence on DCDReader/MemoryReader trajectories #2578

Closed

hmacdope mentioned this pull request Oct 26, 2022

Revive having timeseries for all readers and /or having a transfer_to_memory function at the reader level. #3881

Closed

RMeli deleted the issue-1383-timeseries_deprecation branch December 23, 2023 21:57

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richardjgowers commented Jun 15, 2017

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orbeckst commented Jun 16, 2017

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orbeckst Jul 4, 2017 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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orbeckst Jul 4, 2017 •

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