Support Dgraph Bulk Load

[kevinkle]

Additional Changes:

• Move lemongraph install into base test image
• Change Dockerfile entry into prariedog instead of Snakemake
• Drop support for Py3.5 due to pathlib inconsistencies
• Support and output directory and sample directory config in Snakefile
• Add a dgraph rule in Snakefile for running dgraph bulk
• Implement a custom run_dgraph_bulk() function
• Silence Dgraph output logs if in --debug not specified, or in CI
• Add prairiedog Click commands for running dgraph bulk and dgraph ratel
• Fix preloading of Kmer .rdf
• Additional support for DgraphBundled subprocess logs
• Support outputting Dgraph files to a specific directory
• Additional exception handling for DgraphBundled

[codecov[bot]]

Codecov Report

Merging #136 into develop will decrease coverage by 0.44%. The diff coverage is 68.02%.

@@             Coverage Diff             @@
##           develop     #136      +/-   ##
===========================================
- Coverage       79%   78.55%   -0.45%     
===========================================
  Files           18       19       +1     
  Lines         1067     1236     +169     
===========================================
+ Hits           843      971     +128     
- Misses         224      265      +41

Impacted Files	Coverage Δ
prairiedog/kmers.py	91.66% <100%> (+0.3%)	:arrow_up:
prairiedog/node.py	89.47% <100%> (ø)	:arrow_up:
prairiedog/lemon_graph.py	85.49% <100%> (-1.04%)	:arrow_down:
prairiedog/errors.py	40.9% <33.33%> (-5.25%)	:arrow_down:
prairiedog/cli.py	49.09% <43.33%> (-6.09%)	:arrow_down:
prairiedog/dgraph.py	85.95% <55.55%> (+4.35%)	:arrow_up:
prairiedog/dgraph_bundled.py	77.61% <67.74%> (-18.47%)	:arrow_down:
prairiedog/dgraph_bundled_helper.py	87.09% <87.09%> (ø)
prairiedog/__init__.py	91.66% <88.88%> (-8.34%)	:arrow_down:
... and 2 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 06af24b...6c90091. Read the comment docs.

[codecov[bot]]

Codecov Report

Merging #136 into develop will decrease coverage by 0.44%. The diff coverage is 68.02%.

@@             Coverage Diff             @@
##           develop     #136      +/-   ##
===========================================
- Coverage       79%   78.55%   -0.45%     
===========================================
  Files           18       19       +1     
  Lines         1067     1236     +169     
===========================================
+ Hits           843      971     +128     
- Misses         224      265      +41

Impacted Files	Coverage Δ
prairiedog/kmers.py	91.66% <100%> (+0.3%)	:arrow_up:
prairiedog/node.py	89.47% <100%> (ø)	:arrow_up:
prairiedog/lemon_graph.py	85.49% <100%> (-1.04%)	:arrow_down:
prairiedog/errors.py	40.9% <33.33%> (-5.25%)	:arrow_down:
prairiedog/cli.py	49.09% <43.33%> (-6.09%)	:arrow_down:
prairiedog/dgraph.py	85.95% <55.55%> (+4.35%)	:arrow_up:
prairiedog/dgraph_bundled.py	77.61% <67.74%> (-18.47%)	:arrow_down:
prairiedog/dgraph_bundled_helper.py	87.09% <87.09%> (ø)
prairiedog/__init__.py	91.66% <88.88%> (-8.34%)	:arrow_down:
... and 2 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 06af24b...6c90091. Read the comment docs.