Abstract and Combinatorial Design Plasmid Selection

[doublergreer]

Abstract Translator

• driven by translate_abstract_to_plasmids
• includes functions to take an abstract design with specified parts and a library of plasmids (containing these parts) to a list of plasmids that will assemble together using the MoClo protocol
• this list can be used as an input to the original sbol2build code to generate a detailed assembly plan
• closes Support for abstract designs #15

Combinatorial Support

• designs with combinatorial derivations are accepted by translate_abstract_to_plasmids
• components in the design referenced by a combinatorial derivation will be assigned $n$ plasmids with the same MoClo fusion sites, where $n$ is the number of variable components in the combinatorial derivations
  • this means that for a combinatorial design with 3 normal components and 1 combinatorially derived component with 3 variations, translate_abstract_to_plasmids will return a list of 6 plasmids
  • running golden_gate_assembly_plan from the original sbol2build with this list of plasmids will enumerate to 3 different composites inside the master assembly plan
  • closes Add ability support combinatorial designs #14

Other Enhancements

• added ruff linter, see README for details on adding to pre-commit
• closes Add linter #17

[Gonza10V]

Looks good to me