As described in https://discourse.julialang.org/t/ann-plans-for-removing-packages-that-do-not-yet-support-1-0-from-the-general-registry/ we are planning on removing packages that do not support 1.0 from the General registry. This package has been detected to not support 1.0 and is thus slated to be removed. The removal of packages from the registry will happen approximately a month after this issue is open.

To transition to the new Pkg system using Project.toml, see https://github.com/JuliaRegistries/Registrator.jl#transitioning-from-require-to-projecttoml.
To then tag a new version of the package, see https://github.com/JuliaRegistries/Registrator.jl#via-the-github-app.

If you believe this package has erroneously been detected as not supporting 1.0 or have any other questions, don't hesitate to discuss it here or in the thread linked at the top of this post.

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If you'd like for me to do this for you, comment TagBot fix on this issue.
I'll open a PR within a few hours, please be patient!

Hi Justin, thanks for these tools! We would like to use your types and functions to add analysis methods for discrete traits in PhyloNetworks. In your implementation of general rate matrices, when there is no analytical formulation of the transition probabilities, your P function performs a matrix exponential each time it's called:

function P(gtr::GTR, t::Float64)
  if t < 0.
    error("Time must be positive")
  end
  return expm(Q(gtr)*t)
end

The Q matrix has the same eigenvalues/vectors for all branches and for all tree topologies. So did you think about storing the eigen-decomposition of Q in some way, to use it repeatedly on different branches and when the tree topology changes, rather than re-calculating the decomposition each time for each branch? or did I miss something?

I'll tag @crsl4, @mkborregaard and @pbastide, who are interested in cross-compatibility between Julia packages for biology and evolution.