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Add sampler.py with Pymbar #17
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Codecov Report
@@ Coverage Diff @@
## master #17 +/- ##
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+ Coverage 99.63% 99.65% +0.02%
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Files 5 6 +1
Lines 273 293 +20
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+ Hits 272 292 +20
Misses 1 1
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Unit tests have been added. Still need to add doc strings. |
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Looks like the test environment needs pymbar
. I will update the testing worklflow like we did in ulipolyBinder, planckton, msibi, etc :)
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LGTM! a couple minor comments
cmeutils/sampling.py
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"to be lowered. See is_equilibrated for more information." | ||
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def is_equilibrated(data, threshold_fraction=0.80, threshold_neff=100, nskip=1): |
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this threshold might be a bit high. In reproducibility study we found we needed to lower it from 0.75 to get reasonable run times.
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Maybe set 0.50 as a default?
This PR adds 2 functions:
Still to do: