Restructure for Oligo Searcher Base Classes

[priyappillai]

• Create base Searcher classes (OligoSearcher, OligoSearcherMinimizeNumber, OligoSearcherMaximizeActivity, and GuideSearcher) to make GuideSearcherMinimizeGuides, GuideSearcherMaximizeActivity, and PrimerSearcherMinimizePrimers. Simplify some of the code underlying these classes
• Change guide_is_suitable_fn (previously used for specificity check) to is_suitable_fns - a list of suitability functions-and make the check_gc_content a part of this list
• Rename guide.py in utils to oligo.py - adjust design.py, alignment.py, coverage_analysis.py, alignment_query.py, target_search.py, & pick_test_targets.py accordingly
• Move construct_guide from alignment.py to Guide/Primer searchers; rename to construct_oligo. Keep as unique for both as, while they are the same right now, I expect to change the Primer construct_oligo in the future
• Add sequence complementarity functions to oligo.py
• Make the default compression function return the input so that compress does not need to be an input to compute_memoized
• Change blacklist to ignore

[codecov[bot]]

Codecov Report

Merging #57 (729b54e) into dev (0fe09eb) will increase coverage by 0.26%. The diff coverage is 93.62%.

@@            Coverage Diff             @@
##              dev      #57      +/-   ##
==========================================
+ Coverage   84.81%   85.08%   +0.26%     
==========================================
  Files          48       50       +2     
  Lines        7545     7755     +210     
==========================================
+ Hits         6399     6598     +199     
- Misses       1146     1157      +11     

Impacted Files	Coverage Δ
adapt/utils/lsh.py	98.02% <ø> (ø)
adapt/utils/mutate.py	92.30% <ø> (ø)
adapt/utils/year_cover.py	94.59% <ø> (ø)
adapt/utils/seq_io.py	31.86% <22.22%> (ø)
adapt/target_search.py	77.85% <84.21%> (+0.07%)	:arrow_up:
bin/design.py	64.28% <87.50%> (+0.06%)	:arrow_up:
adapt/utils/search.py	89.18% <89.18%> (ø)
adapt/alignment.py	95.34% <93.47%> (-0.44%)	:arrow_down:
adapt/guide_search.py	74.46% <96.29%> (-10.68%)	:arrow_down:
adapt/tests/test_guide_search.py	99.30% <98.42%> (-0.04%)	:arrow_down:
... and 12 more

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