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deprecate hydrogen bond analysis in water bridge analysis #2913

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Merged
orbeckst merged 30 commits into from
Feb 5, 2021
Merged

deprecate hydrogen bond analysis in water bridge analysis #2913

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2a1a092
depricate hydrogen bond analysis in water bridge
Aug 18, 2020
68584d9
PEP8
Aug 18, 2020
eeedf71
PEP8
Aug 18, 2020
b007a63
PEP8
Aug 18, 2020
267ef75
PEP8
Aug 18, 2020
306fde1
fix import
Aug 18, 2020
e521435
Update CHANGELOG
Aug 18, 2020
c33d2dc
DeprecationWarning
Aug 18, 2020
ce5c552
PEP8
Aug 18, 2020
54efe5e
Update package/CHANGELOG
xiki-tempula Sep 29, 2020
e17e742
Update package/MDAnalysis/analysis/hbonds/wbridge_analysis.py
xiki-tempula Sep 29, 2020
728f154
Update package/MDAnalysis/analysis/hydrogenbonds/__init__.py
xiki-tempula Sep 29, 2020
8658ab3
Update wbridge_analysis.py
xiki-tempula Sep 29, 2020
7fad43d
warning test
Sep 30, 2020
689035b
Merge branch 'develop' into develop
xiki-tempula Sep 30, 2020
05ef615
PEP8
Sep 30, 2020
1d88243
Merge branch 'develop' of https://github.com/xiki-tempula/mdanalysis …
Sep 30, 2020
d7305f7
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Sep 30, 2020
01f0297
warning
Sep 30, 2020
6c0f56b
PEP8
Sep 30, 2020
e852f7a
catch warning
Sep 30, 2020
946a367
arrange order
Sep 30, 2020
6f4517c
fix loading issue
Sep 30, 2020
11258e7
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
Oct 3, 2020
da262bf
remove the file
Oct 24, 2020
53a1913
fix test
Oct 24, 2020
fa1d187
Update wbridge_analysis.rst
Oct 24, 2020
2cb9e03
Merge branch 'develop' of https://github.com/MDAnalysis/mdanalysis in…
Jan 10, 2021
d7ce7e5
fix doc string waring
xiki-tempula Jan 27, 2021
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fix doc
xiki-tempula Jan 27, 2021
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1 change: 1 addition & 0 deletions package/CHANGELOG
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Expand Up @@ -156,6 +156,7 @@ Changes
`__call__` (Issue #2860, PR #2859)
* deprecated ``analysis.helanal`` module has been removed in favour of
``analysis.helix_analysis`` (PR #2929)
* Move water bridge analysis from hbonds to hydrogenbonds (Issue #2739 PR #2913)
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@IAlibay IAlibay Feb 5, 2021

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Technically new changes go to the top of the list, but I'm willing to let that go.

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@orbeckst orbeckst Feb 5, 2021

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I appreciate your attention to detail.

I merged the whole thing nevertheless, as this has been sitting for way too long.


Deprecations

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1 change: 0 additions & 1 deletion package/MDAnalysis/analysis/hbonds/__init__.py
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Expand Up @@ -29,4 +29,3 @@

from .hbond_analysis import HydrogenBondAnalysis
from .hbond_autocorrel import HydrogenBondAutoCorrel, find_hydrogen_donors
from .wbridge_analysis import WaterBridgeAnalysis
2 changes: 2 additions & 0 deletions package/MDAnalysis/analysis/hydrogenbonds/__init__.py
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Expand Up @@ -23,6 +23,8 @@

__all__ = [
'HydrogenBondAnalysis'
'WaterBridgeAnalysis'
]

from .hbond_analysis import HydrogenBondAnalysis
from .wbridge_analysis import WaterBridgeAnalysis
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