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[deprecation] Bio.pairwise2 is deprecated in favor of Bio.Align.PairwiseAligner #3950

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IAlibay opened this issue Dec 7, 2022 · 2 comments · Fixed by #3951
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[deprecation] Bio.pairwise2 is deprecated in favor of Bio.Align.PairwiseAligner #3950

IAlibay opened this issue Dec 7, 2022 · 2 comments · Fixed by #3951
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Component-Analysis deprecation Deprecated functionality to give advance warning for API changes.
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2.4.0

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@IAlibay
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IAlibay commented Dec 7, 2022 •
edited by orbeckst
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We're currently getting warnings about the above, we should amend align.py as necessary.

EDIT: Based on discussion on PR #3951 we'll deprecate and remove in 3.0.
@IAlibay IAlibay added this to the 2.4.0 milestone Dec 7, 2022
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IAlibay commented Dec 7, 2022

I'm adding this to the 2.4.0 milestone since we're getting these warnings everywhere.

@orbeckst orbeckst self-assigned this Dec 7, 2022
orbeckst added a commit that referenced this issue Dec 7, 2022
@orbeckst
replaced deprecated Bio.pairwise2 with Bio.Align.PairwiseAligner
1564039 
- fix #3950
- engineered return tuple as namedtuple to functionally match
  the originally returned pairwise2.Alignment; we only documented
  a tuple as return type anyway
- update CHANGELOG
@orbeckst orbeckst mentioned this issue Dec 7, 2022
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@orbeckst orbeckst added deprecation Deprecated functionality to give advance warning for API changes. Component-Analysis labels Dec 8, 2022
@orbeckst orbeckst mentioned this issue Dec 8, 2022
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orbeckst commented Dec 8, 2022

I created MDAnalysis/UserGuide#244 to document the functionality without the need for sequence_alignment().

@orbeckst orbeckst mentioned this issue Dec 8, 2022
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orbeckst added a commit that referenced this issue Dec 8, 2022
@orbeckst @IAlibay
deprecate sequence_alignment() and replace deprecated Bio.pairwise2 w…
a05a524 
…ith Bio.Align.PairwiseAligner (#3951)

* deprecate align.sequence_alignment for removal in 3.0
  - add deprecation
  - test for deprecation warning
  - combined tests for sequence_alignment in a class for easier removal
  - update CHANGELOG
* replaced deprecated Bio.pairwise2 with Bio.Align.PairwiseAligner
  - fix #3950
  - engineered return tuple as namedtuple to functionally match
    the originally returned pairwise2.Alignment; we only documented
    a tuple as return type anyway
* use biopython >= 1.80 feature for updated alig.sequence_alignment()
* additional docs for sequence_alignment()
  (The docs show how one should write code if/when we deprecated this function.)
* update CHANGELOG

Co-authored-by: Irfan Alibay <[email protected]>
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Component-Analysis deprecation Deprecated functionality to give advance warning for API changes.
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2.4.0
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@orbeckst @IAlibay