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remove universe.as_Universe #2920

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orbeckst opened this issue Aug 27, 2020 · 2 comments · Fixed by #2922
Closed
2 of 3 tasks

remove universe.as_Universe #2920

orbeckst opened this issue Aug 27, 2020 · 2 comments · Fixed by #2922
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@orbeckst @IAlibay
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deprecation Deprecated functionality to give advance warning for API changes. Difficulty-easy remove-2.0 deprecated in 1.0 and to be removed in 2.0
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2.0

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@orbeckst
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orbeckst commented Aug 27, 2020 •
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universe.as_Universe is not really needed

mdanalysis/package/MDAnalysis/core/universe.py

Lines 1327 to 1328 in 45e56e8

# TODO: what is the point of this function???
def as_Universe(*args, **kwargs):
and can be removed.

EDIT: @IAlibay found in PR #2922 that LeafletFinder is also affected and will not anymore accept a filename as input

  • remove for 2.0.0
  • deprecate as_Universe in 1.0.1 (see PR Backport 1.0.1 #2798 )
  • deprecate filename argument for LeafletFinder in 1.0.1
@orbeckst orbeckst added Difficulty-easy deprecation Deprecated functionality to give advance warning for API changes. remove-2.0 deprecated in 1.0 and to be removed in 2.0 labels Aug 27, 2020
@orbeckst orbeckst added this to the 2.0 milestone Aug 27, 2020
orbeckst added a commit that referenced this issue Aug 27, 2020
@orbeckst
deprecate core.universe.as_Universe
41ab4d1 
- see #2920
- add deprecation note
- add test
- update CHANGELOG for 1.0.1
@IAlibay
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IAlibay commented Aug 27, 2020 •
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I think the only use case of as_Universe is LeafletFinder, which to be honest is strange behaviour for MDAnalysis as a whole (i.e. we don't usually pass paths to files to analysis classes). Unless there's any objections, I'd suggest just making LeafletFinder's universe argument accept solely Universes.

@IAlibay IAlibay mentioned this issue Aug 27, 2020
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orbeckst added a commit that referenced this issue Aug 27, 2020
@orbeckst
deprecate core.universe.as_Universe
d4dc9e7 
- see #2920
- add deprecation note
- add test
- update CHANGELOG for 1.0.1
orbeckst added a commit that referenced this issue Aug 27, 2020
@orbeckst
deprecate core.universe.as_Universe
370bd4e 
- see #2920
- add deprecation note to as_Universe
- add deprecation notice to LeafletFinder: filename instead of Universe will be removed
  (uses as_Universe so users will see the DeprecationWarning from as_Universe)
- add test
- update CHANGELOG for 1.0.1
@orbeckst orbeckst self-assigned this Aug 27, 2020
@orbeckst
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Thanks for looking into what is affected. I added a deprecation note to LeafletFinder to the backport.

orbeckst added a commit that referenced this issue Aug 27, 2020
@orbeckst
deprecate core.universe.as_Universe
b27a59f 
- see #2920
- add deprecation note to as_Universe
- add deprecation notice to LeafletFinder: filename instead of Universe will be removed
  (uses as_Universe so users will see the DeprecationWarning from as_Universe)
- add test
- update CHANGELOG for 1.0.1
lilyminium pushed a commit that referenced this issue Aug 27, 2020
@IAlibay
Remove as_Universe (Issue #2920) (#2922)
3e6b38c 
 - Removes `as_Universe` from MDAnalysis.core.universe
 - LeafletFinder no longer accepts paths to files as Universes
PicoCentauri pushed a commit to PicoCentauri/mdanalysis that referenced this issue Mar 30, 2021
@IAlibay @PicoCentauri
Remove as_Universe (Issue MDAnalysis#2920) (MDAnalysis#2922)
2462b93 
 - Removes `as_Universe` from MDAnalysis.core.universe
 - LeafletFinder no longer accepts paths to files as Universes
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@orbeckst orbeckst

@IAlibay IAlibay

Labels
deprecation Deprecated functionality to give advance warning for API changes. Difficulty-easy remove-2.0 deprecated in 1.0 and to be removed in 2.0
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Milestone
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Remove as_Universe (Issue #2920) IAlibay/mdanalysis
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@orbeckst @IAlibay