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Edinburgh-Genome-Foundry / DnaCauldron

:alembic: Simple cloning simulator (Golden Gate etc.) for single and combinatorial assemblies
https://edinburgh-genome-foundry.github.io/DnaCauldron/
MIT License
51 stars 11 forks source link

Biopython v1.78 compatibility #4

Closed veghp closed 4 years ago

veghp commented 4 years ago

All examples ran fine without errors.

veghp commented 4 years ago

Re commit https://github.com/Edinburgh-Genome-Foundry/DnaCauldron/pull/4/commits/44c6fda31640c255907bb51c424c3ef168071382, 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.

coveralls commented 4 years ago

Coverage Status

Coverage increased (+0.01%) to 88.8% when pulling b61b7e78de673616c31bdce0e3b1eb9ae099f6a1 on dev into 0892ace4bc58c6f8e6224d5d3e4cc26101086798 on master.