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Biopython v1.78 compatibility #4

Merged
merged 8 commits into from
Sep 11, 2020
Merged

Biopython v1.78 compatibility #4

merged 8 commits into from
Sep 11, 2020

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veghp
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@veghp veghp commented Sep 8, 2020

  • Fixes license autodetection
  • Adds Biopython v1.78 compatibility
  • Removes StickyEndSeq.circularized() method that has a runtime error and is not needed
  • Otherwise code same as v2.0.1

All examples ran fine without errors.

The method returns an error, beacuse StickyEndSeq has
no `annotations` that can be set. All circularized() calls in the
codebase are made from StickyEndFragment or HomologousFragment.
Removed method StickyEndSeq.circularized() did not work,
therefore API is not considered to be changed.
@veghp
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veghp commented Sep 8, 2020

Re commit 44c6fda, method StickyEndSeq.circularized() does not work, because StickyEndSeq has no annotations that can be set.

I propose to remove method circularized() from StickyEndSeq because it's never accessed (all calls are from StickyEndFragment or HomologousFragment), and sequences (Seq) do not have topology, but records (SeqRecord) do.

See test: https://coveralls.io/builds/29649291/source?filename=dnacauldron%2FFragment%2FStickyEndFragment%2FStickyEndSeq.py#L42

@Zulko please let me know if I missed something.

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Coverage Status

Coverage increased (+0.01%) to 88.8% when pulling b61b7e7 on dev into 0892ace on master.

@veghp veghp merged commit 962822c into master Sep 11, 2020
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2 participants