Instead of counting, just set a very high max n
Init the GraphRef during KmerGraphinit
Fix: use class attrs for now instead of config
Read K from config if not supplied
Read K from config if not supplied
Remove the assert len(lines) == gr.n check since we now use max_n
Remove the assert len(lines) == gr.n check since we now use max_n
Check datrie and Py3.7 support
Install datrie via its github repo instead of PyPI
Separate tox rule for [snakemake]
Separate tox rule for [snakemake]
Separate tox rule for [snakemake]
Initial draft of Snakefile
Fix Snakefile
Debug why Snakemake isnt called in tox
Fix log call in KmerGraph
Delete KmerGraph work and solely use Snakemake to drive dataset generation
Use protocol=4 for pickle to bypass the hardcoded 4GB pickle limit (PEP3154)
Use Snakemake config to set node_labels csv
Use Snakemake config to set node_labels csv
Use Snakemake config to set node_labels csv
Check what GraphRef.close() is writing files out as
Try using numpy.loadtxt() instead of parsing
Switch Snakefile to use dill instead of celery
Load previous files via pickle for now
Fixed: wasnt dill, but the config was using MICs from test
Fixed: wasnt dill, but the config was using MICs from test
Add dill to requirements
Dont init the numpy arrays until subgraphs are created
Dont init the numpy arrays until subgraphs are created
Init node arrays on first call instead of via append()
Still dump the GraphRef instance in Snakefile
Dump the appended GraphRef to a different file
Add a sanity check before saving NumPy arrays
Snakemake is calling append with the required subgraphs, but not sure why the arrays are zero
Snakemake is calling append with the required subgraphs, but not sure why the arrays are zero
Use outputs/graphref_final.pkl
Call snakemake clean between tests
deleted: prairiedog/kmer_graph.py

Codecov Report

Merging #37 into master will decrease coverage by 1.76%. The diff coverage is 84.9%.

@@            Coverage Diff             @@
##           master      #37      +/-   ##
==========================================
- Coverage   93.46%   91.69%   -1.77%     
==========================================
  Files          11       10       -1     
  Lines         367      337      -30     
==========================================
- Hits          343      309      -34     
- Misses         24       28       +4

Impacted Files	Coverage Δ
prairiedog/prairiedog.py	`66.66% <0%> (-8.34%)`	:arrow_down:
prairiedog/kmers.py	`94.28% <100%> (+0.08%)`	:arrow_up:
prairiedog/subgraph_ref.py	`100% <100%> (ø)`	:arrow_up:
prairiedog/graph_ref.py	`94.01% <83.33%> (-5.99%)`	:arrow_down:

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 c52edea...eff38f8. Read the comment docs.

superphy / prairiedog

Switch to Snakemake as task runner (#36) #37

Codecov Report