Update TreeTime #1207
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Update TreeTime #1207
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seeding the default `np.random`-RNG. Since 0.10.0, TreeTime uses its own instance of `np.random.default_rng` and globally setting `np.random.seed` no longer has the desired effect. By passing the `seed` to TreeTime, we now set the state of the relevant RNG.
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #1207 +/- ##
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Coverage 68.81% 68.81%
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Files 64 64
Lines 6936 6936
Branches 1693 1692 -1
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Hits 4773 4773
Misses 1856 1856
Partials 307 307
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victorlin
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May 8, 2023
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I'll fix up the commits and merge. |
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This PR updates the required TreeTime version to 0.10.0 or later. This version of TT handles random number generator state differently, which requires slight changes how the
augur refineargument--seedis handled. Instead of setting the default numpy RNG, this argument is now passed to the TreeTime constructor.In addition, this PR adds a flag
--greedy-resolvetoaugur refine. This is the default atm. But adding the flag will enable changing the default in the future.