Release/v2.2.9

[creisle]

BugFixes

• Update links to old docs to use new RTD links
• Make sure column and settings files are generated when RTD builds the docs
• write logs when jobs fail running in local mode

Improvements

• TypeError: sequence item 0: expected str instance, NoneType found #234 add better error message for mavis not found on path

[codecov]

Codecov Report

Merging #235 (e7127e7) into master (74cc132) will increase coverage by 10.64%.
The diff coverage is 78.26%.

@@             Coverage Diff             @@
##           master     #235       +/-   ##
===========================================
+ Coverage   80.51%   91.16%   +10.64%     
===========================================
  Files          52       52               
  Lines        9126     9132        +6     
===========================================
+ Hits         7348     8325      +977     
+ Misses       1778      807      -971     

Flag	Coverage Δ
unittests	91.16% <78.26%> (+10.64%)	⬆️

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

Impacted Files	Coverage Δ
mavis/schedule/local.py	73.46% <66.66%> (+47.93%)	⬆️
mavis/schedule/pipeline.py	73.31% <90.90%> (+17.62%)	⬆️
mavis/annotate/fusion.py	96.02% <0.00%> (+0.33%)	⬆️
mavis/bam/cigar.py	98.14% <0.00%> (+0.61%)	⬆️
mavis/bam/cache.py	88.31% <0.00%> (+0.64%)	⬆️
mavis/schedule/job.py	78.26% <0.00%> (+0.72%)	⬆️
mavis/cluster/main.py	90.24% <0.00%> (+0.81%)	⬆️
mavis/annotate/genomic.py	93.12% <0.00%> (+1.03%)	⬆️
mavis/breakpoint.py	95.00% <0.00%> (+1.53%)	⬆️
mavis/illustrate/elements.py	96.37% <0.00%> (+1.69%)	⬆️
... and 18 more

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[creisle]

The error fix will now report this error

    'The mavis executable was not found on the current PATH. '
FileNotFoundError: The mavis executable was not found on the current PATH. This is required in order to run external scripts. Please add mavis to the PATH with PATH=$PATH:/path/to/mavis/bin

Instead of the less informative

  File "...pipeline.py", line 277, in write_submission_script
    fh.write(' \\\n\t'.join(commands) + '\n\n')
TypeError: sequence item 0: expected str instance, NoneType found

[mattdoug604]

Consider using textwrap.dedent() to keep the string inline with the rest of the code without adding any extra whitespace. I think it's a standard python library.

[creisle]

cool! I didn't know there was a function for that! I have similar strings in other parts of the code tho so I will make an issue so we can replace them all at once instead of just here. created #236