Release/v3.1.1

[calchoo]

Improvements

• Update mavis summary

Bugfixes

• Fix ref alt calculation
• Fix tests so tests can run again on github

[codecov]

Codecov Report

Patch coverage: 95.23% and project coverage change: -0.55 ⚠️

Comparison is base (dbbd9a3) 87.49% compared to head (fb4b645) 86.94%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #349      +/-   ##
==========================================
- Coverage   87.49%   86.94%   -0.55%     
==========================================
  Files          57       57              
  Lines       10314     9390     -924     
  Branches     2802     2355     -447     
==========================================
- Hits         9024     8164     -860     
+ Misses        790      751      -39     
+ Partials      500      475      -25     

Flag	Coverage Δ
unittests	86.94% <95.23%> (-0.53%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/mavis/annotate/variant.py	88.72% <ø> (ø)
src/mavis/convert/__init__.py	87.76% <ø> (ø)
src/mavis/convert/transabyss.py	81.57% <ø> (-4.96%)	⬇️
src/mavis/summary/main.py	77.30% <ø> (-2.17%)	⬇️
src/mavis/validate/assemble.py	90.28% <ø> (ø)
src/mavis/validate/gather.py	83.88% <ø> (ø)
src/tools/convert_annotations_format.py	78.90% <ø> (-4.79%)	⬇️
src/mavis/pairing/pairing.py	89.86% <75.00%> (-2.96%)	⬇️
src/mavis/summary/summary.py	70.00% <93.02%> (+1.57%)	⬆️
src/mavis/annotate/file_io.py	77.06% <100.00%> (-3.42%)	⬇️
... and 9 more

... and 6 files with indirect coverage changes

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