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v0.10.0: add auspice.json output, drop python 3.6

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@rneher rneher released this 07 May 09:16
· 69 commits to master since this release
  • the output directory now contains a json file that is compatible with auspice.us. Both time scaled phylogenies and ancestral inferences can now be visualized and explored using auspice. Available colorings are "Date", "genotype", "Branch support", and "Excluded". See PR #232 for details.
  • move most function related to IO of the command line wrappers into a separate file.
  • make TreeTime own its random number generator and add --rng-seed to control state in CLI. Any previous usage of numpy.random.seed will now be ignored in favor of --rng-seed. See PR #234
  • add flag --greedy-resolve (currently default) as inverse to --stochastic-resolve with the aim of switching the default behavior in the future.
    Add deprecation warning for greedy-resolve.
  • tighten conditions that trigger approximation of narrow distribution as a delta function in convolution using FFT PR #235.
  • Drop support for python 3.6.
  • Don't attempt to show figure when calling Phylo.draw to suppress matplotlib back-end warning.