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All deprecations on AtomGroup and friends getters and setters. #698

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merged 19 commits into from
Apr 10, 2016
Merged

All deprecations on AtomGroup and friends getters and setters. #698

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ec46505
All deprecations on AtomGroup and friends getters and setters.
dotsdl Feb 6, 2016
0223603
Added deprecations to Residue angle methods.
dotsdl Feb 7, 2016
2b74bb2
Using AtomGroups for translate and rotateby inputs no longer deprecated
dotsdl Mar 28, 2016
5221353
Added warnings for property access at the appropriate level.
dotsdl Mar 28, 2016
417f610
_FIFTEEN -> _SIXTEEN; Segment now has segid property
dotsdl Mar 29, 2016
5452165
Updated bond related deprecations
richardjgowers Mar 29, 2016
3e65e1f
Atom id now a synonym for atom number, unless serial present.
dotsdl Mar 29, 2016
abf29ce
Added kwarg support to atom_property decorator
richardjgowers Mar 29, 2016
bfc2849
Merge branch 'issue-599-deprecations' of github.com:MDAnalysis/mdanal…
dotsdl Mar 30, 2016
da6e888
Removed "id" from Atom slots.
dotsdl Mar 30, 2016
b399e18
Added deprecations for Residue, Segment plural residue, segment props…
dotsdl Apr 1, 2016
378a794
Fixed neglected changes to copy-pasted code for property setters
dotsdl Apr 1, 2016
895fc99
Removed deprecated use of Segment.id
richardjgowers Apr 2, 2016
a58adf4
removed usage of deprecated functions Universe init
richardjgowers Apr 2, 2016
492baea
Removed deprecations on anchor mechanisms.
dotsdl Apr 4, 2016
2116879
Merge branch 'issue-599-deprecations' of github.com:MDAnalysis/mdanal…
dotsdl Apr 4, 2016
87f646f
Added deprecations to changelog; fixed some omissions.
dotsdl Apr 4, 2016
ae44111
Merge branch 'develop' into issue-599-deprecations
dotsdl Apr 4, 2016
9920d9e
Merge remote-tracking branch 'upstream/develop' into issue-599-deprec…
dotsdl Apr 7, 2016
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19 changes: 18 additions & 1 deletion package/CHANGELOG
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ The rules for this file:

------------------------------------------------------------------------------
??/??/16 jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jdetle, jbarnoud,
dotsdl, richardjgowers
dotsdl, richardjgowers

* 0.15.0

Expand Down Expand Up @@ -47,6 +47,23 @@ Changes

* Generalized contact analysis class added. (Issue #702)

Deprecations (Issue #599)

* Deprecated all `get_*` and `set_*` methods of Groups.
* Deprecation warnings for accessing atom attributes from Residue,
ResidueGroup, Segment, SegmentGroup. Will not be present or will
give per-level results.
* Deprecation warnings for accessing plural residue attributes from
Residue or Segment (will disappear), or from SegmentGroup (will give
per-Segment results).
* Deprecation warnings for accessing plural segment attributes from Segment
(will disappear).
* Deprecated Atom number, pos, centroid, universe setter
* Deprecated AtomGroup serials, write_selection
* Deprecated Residue name, id
* Deprecated Segment id, name
* Deprecated as_Universe function; not needed

02/28/16 tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst
manuel.nuno.melo, Balasubra, Saxenauts, mattihappy

Expand Down
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