Add a thermodynamic primer mode to design.py

[priyappillai]

Create TmPredictor to see how far the predicted melting temperatures of PCR primers are from an ideal melting temperature and PrimerSearcherMaximizeActivity to optimize based on this predictor (and other similar ones in the future). These are ultimately used to design PCR primers with design.py with the option --primer-thermo. Eventually, as we add more objective function options, --primer-thermo could take in a string to specify which objective.

[codecov[bot]]

Codecov Report

Merging #67 (17ba749) into dev (0d91b39) will increase coverage by 0.09%. The diff coverage is 90.36%.

@@            Coverage Diff             @@
##              dev      #67      +/-   ##
==========================================
+ Coverage   87.28%   87.37%   +0.09%     
==========================================
  Files          56       56              
  Lines        9552     9765     +213     
==========================================
+ Hits         8337     8532     +195     
- Misses       1215     1233      +18     

Impacted Files	Coverage Δ
adapt/guide_search.py	75.00% <ø> (ø)
bin/tests/test_analyze_coverage.py	94.95% <ø> (ø)
adapt/utils/thermo.py	80.92% <61.53%> (-1.66%)	:arrow_down:
adapt/utils/search.py	87.48% <63.63%> (-1.27%)	:arrow_down:
adapt/utils/predict_activity.py	90.27% <87.23%> (-1.11%)	:arrow_down:
adapt/target_search.py	78.76% <91.04%> (+1.16%)	:arrow_up:
adapt/alignment.py	95.53% <100.00%> (ø)
adapt/primer_search.py	96.29% <100.00%> (+1.05%)	:arrow_up:
adapt/tests/test_guide_search.py	98.64% <100.00%> (+<0.01%)	:arrow_up:
adapt/tests/test_primer_search.py	100.00% <100.00%> (ø)
... and 8 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 0d91b39...17ba749. Read the comment docs.