subsample: Add helper function for setting --nthreads

[victorlin]

This will be useful in Snakemake workflows to prevent over/under-allocating threads.

Downstream PRs

• Set threads for augur subsample docs.nextstrain.org#267
• Set threads for augur subsample measles#109

Checklist

• Manually tested in rsv and measles
• Automated checks pass changes aren't covered by checks
• Check if you need to add a changelog message
• Check if you need to add tests
• Check if you need to update docs

[codecov]

Codecov Report

❌ Patch coverage is 16.66667% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 74.41%. Comparing base (a974866) to head (4af0d31).
⚠️ Report is 28 commits behind head on master.

Files with missing lines	Patch %	Lines
augur/subsample.py	16.66%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1963      +/-   ##
==========================================
- Coverage   74.45%   74.41%   -0.04%     
==========================================
  Files          82       82              
  Lines        9102     9108       +6     
  Branches     1855     1856       +1     
==========================================
+ Hits         6777     6778       +1     
- Misses       2020     2025       +5     
  Partials      305      305              

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[victorlin]

@jameshadfield do you think this would still be feasible with the augur proximity integration in #1962?

[jameshadfield]

Can we chat about this tomorrow?

I haven't yet implemented the --nthreads stuff yet, so proximity calculations just run with 1 thread. That's not good - the function is designed to parallalize really well, and without parallalization is unnecessarily slow.

[victorlin]

Sure!

[victorlin]

Closing per nextstrain/docs.nextstrain.org#267 (comment)