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fedarko / strainFlye

Pipeline for analyzing (rare) mutations in metagenome-assembled genomes
BSD 3-Clause "New" or "Revised" License
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Speed up (using mamba) and fix the CI; better installation documentation #69

Closed fedarko closed 1 year ago

fedarko commented 1 year ago

Closes #68.

Switched to mamba and replaced the defaults channel in the environment YAML with nodefaults, since mixing defaults and conda-forge causes problems for mamba (https://mamba.readthedocs.io/en/latest/user_guide/troubleshooting.html#mixing-the-defaults-and-conda-forge-channels). This combination of changes fixed and sped up the build.

I also updated the dev documentation (to mention using mamba instead of conda) and updated the environment YAML's upper limit on Python from <= 3.7 to < 3.8 (I think this is a more accurate way of writing this out, plus it matches what I already had in the setup.py and bioconda recipe files...)

codecov-commenter commented 1 year ago

Codecov Report

Merging #69 (ee7f5fd) into main (09ba9d3) will not change coverage. Report is 3 commits behind head on main. The diff coverage is n/a.

@@           Coverage Diff           @@
##             main      #69   +/-   ##
=======================================
  Coverage   80.49%   80.49%           
=======================================
  Files          20       20           
  Lines        2466     2466           
  Branches      555      555           
=======================================
  Hits         1985     1985           
  Misses        455      455           
  Partials       26       26