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Fix doctest for MDAnalysis.analysis.rms (#3925) #4009

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merged 5 commits into from
Jan 31, 2023
Merged

Fix doctest for MDAnalysis.analysis.rms (#3925) #4009

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eee3120
Fix doctest for MDAnalysis.analysis.rms (#3925)
chrispfae Jan 23, 2023
887914c
Assign Timestep to underscore.
chrispfae Jan 24, 2023
b2bc642
Add name to AUTHORS and CHANGELOG
chrispfae Jan 26, 2023
af8d7bf
try to get versionchanged entries to show up.
IAlibay Jan 30, 2023
ee502ef
Merge branch 'develop' into issue-3925-rms
IAlibay Jan 31, 2023
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2 changes: 2 additions & 0 deletions package/AUTHORS
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Expand Up @@ -202,6 +202,8 @@ Chronological list of authors
- Utsav Khatu
- Patricio Barletta
- Mikhail Glagolev
2023
- Christian Pfaendner


External code
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2 changes: 1 addition & 1 deletion package/CHANGELOG
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Expand Up @@ -13,7 +13,7 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo
??/??/?? IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae

* 2.5.0

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9 changes: 6 additions & 3 deletions package/MDAnalysis/analysis/rms.py
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Expand Up @@ -235,13 +235,16 @@ def rmsd(a, b, weights=None, center=False, superposition=False):

Example
-------
>>> u = Universe(PSF,DCD)
>>> import MDAnalysis as mda
>>> from MDAnalysis.analysis.rms import rmsd
>>> from MDAnalysis.tests.datafiles import PSF, DCD
>>> u = mda.Universe(PSF, DCD)
>>> bb = u.select_atoms('backbone')
>>> A = bb.positions.copy() # coordinates of first frame
>>> u.trajectory[-1] # forward to last frame
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>>> _ = u.trajectory[-1] # forward to last frame
>>> B = bb.positions.copy() # coordinates of last frame
>>> rmsd(A, B, center=True)
3.9482355416565049
6.838544558398293

.. versionchanged: 0.8.1
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Suggested change
.. versionchanged: 0.8.1
.. versionchanged: 0.8.1

This is a slightly separate issue, but it looks like the versionchanged entries are being ignored because doctest need a blank line and so do versionchanged entries. I'll self merge this fix and see if it fixes the problem.

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That didn't fix it, I'm going to go ahead and shift the versionchanged problem to a separate issue, it's an issue that predates this fix anyways.

*center* keyword added
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