Staple Architecture with basic testing

[shanilpanara]

Summary

First 5 weeks of Masters Project - Coding Progress:

• StapleAlgorithm1 - an algorithm which generates some staples on a scaffold which we wouldn't really use in real life however it was made more complicated than necessary to develop the StapleBaseClass.
• StapleBaseClass - will add more to Staple architecture #27 for more indepth description of the architecture. But:
  • this is able to both extract relevant properties from any scaffold generated through the programme (given it is a LatticeRoute)
  • it sets up a multidimensional array (lattice) which stores information about each nucleotide
  • this lattice can be read to generate staples (using a StaplingAlgorithm) and written to (by `write_staples_to_array)
  • finally, we can read the lattice and convert every staple to an oxDNA strand, outputting this collection in a StapleContainer in which we can write methods to edit the collection of staples to generate multiple possible configurations

Further updates

• 17/02/21: Added a "check this even runs" test with more advanced pytest features

[codecov]

Codecov Report

Merging #32 (78da6ab) into predeploy (fb61f1f) will increase coverage by 4.23%.
The diff coverage is 100.00%.

@@              Coverage Diff              @@
##           predeploy      #32      +/-   ##
=============================================
+ Coverage      75.39%   79.62%   +4.23%     
=============================================
  Files             14       14              
  Lines           1345     1345              
=============================================
+ Hits            1014     1071      +57     
+ Misses           331      274      -57     

Impacted Files	Coverage Δ
drawNA/lattice/route.py	74.19% <100.00%> (+13.97%)	⬆️
drawNA/lattice/utils.py	71.87% <0.00%> (+3.12%)	⬆️
drawNA/lattice/_lattice.py	68.45% <0.00%> (+12.79%)	⬆️

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[shanilpanara]

@debeshmandal from looking at the build errors, it seems they are due to a softnanotools import error, how do I go about solving this?

[debeshmandal]

@debeshmandal from looking at the build errors, it seems they are due to a softnanotools import error, how do I go about solving this?

Just add softnanotools to the imports in the file .github/workflows/*.yml