Release/v3.0.0

[creisle]

v3.0.0

Breaking Changes

• Uses snakemake instead of internal scheduler code
• Use JSON config instead of large number of command-line arguments
• Use nested translations to allow polycistronic transcripts in annotations file
• Do not use # to start header line in mavis tab files

New Features

• Add conversion tool for upgrading v3 annotations files and converting gtf/gff3 files

[creisle]

having issues with the merge, will re-open when I have them working

[codecov[bot]]

Codecov Report

Merging #314 (c2221fe) into master (e4c67a5) will increase coverage by 4.99%. The diff coverage is 88.60%.

@@            Coverage Diff             @@
##           master     #314      +/-   ##
==========================================
+ Coverage   81.44%   86.44%   +4.99%     
==========================================
  Files          57       54       -3     
  Lines       10328     9281    -1047     
  Branches        0     2397    +2397     
==========================================
- Hits         8412     8023     -389     
+ Misses       1916      778    -1138     
- Partials        0      480     +480     

Flag	Coverage Δ
unittests	86.44% <88.60%> (+4.99%)	:arrow_up:

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

Impacted Files	Coverage Δ
src/mavis/__init__.py	100.00% <ø> (ø)
src/mavis/cluster/__init__.py	100.00% <ø> (ø)
src/mavis/convert/cnvnator.py	100.00% <ø> (ø)
src/mavis/convert/starfusion.py	100.00% <ø> (ø)
src/mavis/convert/transabyss.py	81.57% <ø> (ø)
src/mavis/error.py	100.00% <ø> (ø)
src/mavis/illustrate/util.py	84.65% <ø> (ø)
src/mavis/validate/main.py	90.47% <ø> (ø)
src/tools/convert_annotations_format.py	78.90% <ø> (ø)
src/mavis/summary/summary.py	54.92% <50.00%> (ø)
... and 79 more

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