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@github-actions github-actions released this 10 Sep 22:27
v0.12.1
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cadnano export upgraded

Can now export to cadnano from design that uses multiple helix groups.

rotate domains

Added method Strand.rotate_domains allowing domains to be "rotated" on a strand. Think of it like adding a crossover between the 5' and 3' ends, and removing another crossover.

type hints

Beefed up type hints, in particular making type variables StrandLabel and DomainLabel for the types of strand labels and domain labels, allowing Design, Strand, and Domain to be parameterized by them, so that a static type checker such as mypy will catch errors such as

domain: Domain[str] = Domain(label=123)    # error
domain2: Domain[str] = Domain(label='123') # fine
domain2.label = 123                        # error

NOTE: this particular type hint no longer makes sense since labels are now assumed to be strings: https://github.com/UC-Davis-molecular-computing/scadnano-python-package/releases/tag/v0.18.0

Also got rid of all previous mypy type errors.

Commits

  • [41a7f70]: updated paper URL now that DNA 2020 paper is published (David Doty) #136
  • [304e120]: added rotate_domains method to Strand to "rotate" domains of strand (i.e., like adding a crossover between the 5' and 3' ends, and removing another crossover) (David Doty) #136
  • [b7e41d0]: Design.write_scadnano_file now warns if a Loopout is the first or last substrand on a Strand (still allowed in intermediate designs) (David Doty) #136
  • [903510d]: fixed all mypy warnings; closes #109 (David Doty) #136
  • [b2012e9]: fixed mypy warnings in origami_rectangle (David Doty) #136
  • [a3248bc]: made Design, Strand and Domain generic parameterized by StrandLabel and DomainLabel. Made strand label not indented in serialized JSON (David Doty) #136
  • [080bf6d]: added example with domains names (some mismatching) (David Doty) #136
  • [a2a6b07]: updated names example to have more kinds of mismatches (David Doty) #136
  • [27baee2]: annotated variable to quiet mypy (David Doty) #136
  • [c5bdb1c]: Update names_domains_strands.py (David Doty) #136
  • [9b54b1e]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) #133
  • [4d62212]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) #133
  • [399f905]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) #133
  • [6233075]: Export code supports helix groups and associated unittest. test_6_helix_bundle_honeycomb restored. (Cosmo) #133
  • [a274a98]: Forcing the add of test_6_helix_bundle_honeycomb.sc which was ignored (Cosmo) #133
  • [3753e36]: Correct type annotation (Cosmo) #133
  • [627d45b]: Correcting syntax error (Cosmo) #133
  • [db82d47]: bumped version (David Doty) #136
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