Major updates to database management, ftp, pbs, etc.

[grabear]

Fixes issues #134, #95

• Version bump to
• Added BaseBlastN and OrthoBlastN classes.
• Added BaseQsub and Qsub classes.
• Added Qwatch.
• Created the FullUtilities class.
• Added config folder which contains templates, static input files (karg and gpcr datasets), and scripts.
• Added BaseDatabaseManagement and DatabaseManagement classes.
• Added NcbiblastnCommandline class which is compatible with version 5 blast databases.
• Migrated from nose to pytest while still using unittests.
• Deprecated sge, mpi, and streamieo modules
• Moved qstat.py to pbs module.
• Added .coveragerc for eventual code coverage setup.
• Added readthedocs.yml for documentation.

[sdhutchins]

OMG, 550 commits lol

[sdhutchins]

[grabear]

I have done my best @sdhutchins!

[sdhutchins]

I have done my best @sdhutchins!

I just had to tease you! lol There's a lot here...

[sdhutchins]

@grabear something is suddenly broken with the blast stuff? Any ideas?

[sdhutchins]

Something changed with the taxonomy on NCBI's end that's causing the blast test to fail.

[grabear]

It might be ete3 as well. That's always weird. I'm going to check this out after lunch. Can't do much right now.

[sdhutchins]

It might be ete3 as well. That's always weird. I'm going to check this out after lunch. Can't do much right now.

No worries! Seems like something small.

[sdhutchins]

It might be ete3 as well. That's always weird. I'm going to check this out after lunch. Can't do much right now.

Seems someone else had the same issue as well. https://github.com/etetoolkit/ete/issues/469

I'll try a work around that just "kills" the blast to make the test pass.

[sdhutchins]

@grabear im going to add back code coverage this afternoon, and I think I we'll be good to go since that text failure isn't based on us.

[sdhutchins]

Once you review #167, we can go on and merge this!

I'm so happyyyyy! haha

[codecov[bot]]

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@64593b1). Click here to learn what that means. The diff coverage is n/a.

@@            Coverage Diff            @@
##             master     #155   +/-   ##
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  Coverage          ?   15.13%           
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  Files             ?       67           
  Lines             ?     4182           
  Branches          ?        0           
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  Hits              ?      633           
  Misses            ?     3549           
  Partials          ?        0           

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[grabear]