Save graph after benchmark
Decrease log levels for Kmer parsing
Benchmark with 0.01% of available genomes first
0.001%
Use underscores instead of : for filenames
Fix kmer count when creating graph
Start doing some munging for the format we need
About to integrate GraphRef as a component to KmerGraph
Restructure code to suit the DiffPool format, will break a bunch of tests
Restructure code to suit the DiffPool format, will break a bunch of tests
Comment out GraphRef.append() to see what tests pass
Change tests to be based of subgraphs
Fix output folder creation
Check if the kmer_map is bugging out
Use a shutdown()
Fix node_id iteration
Fix node_id iteration
Unique count is slow
Use a set
Use a set
Contextmanage the ProcessPoolExecutor
Fix using add instead of update
Add a check against unique_kmer count
Add a check against unique_kmer count
Fix linting errors
Add a check against KmerGraph node ids
Fix actual NetworkX graph creation
Use shortened files for KmerGraph tests
Use shortened files for KmerGraph tests
Try to fix class method patching
Try to fix class method patching
Try to fix class method patching
Check that the # of unqiue kmers == # nodes
Check that the # of unqiue kmers == # nodes
Add the initial framework for creating graph indicators/labels and node labels/attributes
Add pandas as a req
Integrate coveralls
Setup default samples/
Fix syntax errors
Fix syntax errors
Fix import MIC data
Fix import MIC data
Was ignoring the mic df.pkl
Dont try to label a test file
Fix cli test
Fix cli test
Fix flake8 error
Fix import
Check whats going on with codecov
Move codecov call to circleci instead of tox
Move codecov call to circleci instead of tox
Fix? pytest-cov
Fixes codecov
Cache both requirements.txt and requirements_dev.txt
Move GRef and SubgraphRef to their own files
Add a check against the KMERS_graph_indicator.txt file
Use shortened files for graph output tests
Check CSVs can be read
See if setting config.MIC_CSV directly works instead of patching
Fix KMERS_graph_indicator.txt output
Fix KMERS_graph_indicator.txt output
Test KMERS_node_labels.txt and KMERS_node_attributes.txt output
Fix dictionary write out
Fix dictionary write out
Check that we havent assigned some kmer id > 4^k
Switch to json lib to dump dictionaries
Switch to json lib to dump dictionaries
Back to file writing, json lib doesnt accept int as dict keys
Write out adj matrix
Write out adj matrix
Use abstract method

Codecov Report

:exclamation: No coverage uploaded for pull request base (master@e1a2cdd). Click here to learn what that means. The diff coverage is 97.36%.

@@            Coverage Diff            @@
##             master      #29   +/-   ##
=========================================
  Coverage          ?   94.45%           
=========================================
  Files             ?       11           
  Lines             ?      361           
  Branches          ?        0           
=========================================
  Hits              ?      341           
  Misses            ?       20           
  Partials          ?        0

Impacted Files	Coverage Δ
prairiedog/prairiedog.py	`100% <100%> (ø)`
prairiedog/gref.py	`100% <100%> (ø)`
prairiedog/kmers.py	`94.2% <100%> (ø)`
prairiedog/subgraph_ref.py	`100% <100%> (ø)`
prairiedog/kmer_graph.py	`94.82% <100%> (ø)`
prairiedog/config.py	`100% <100%> (ø)`
prairiedog/graph_ref.py	`100% <100%> (ø)`
prairiedog/networkx_graph.py	`87.09% <70%> (ø)`
prairiedog/graph.py	`72.41% <80%> (ø)`
prairiedog/cli.py	`94.11% <90.9%> (ø)`

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 e1a2cdd...e7f6208. Read the comment docs.

superphy / prairiedog

Creates all required files except the node_labels (#28) #29

Codecov Report