Temporary dependency fix

Gets around Diversity dependency problems

Julia v1.0, new linked list tree, improved interface

v0.4.0

• Improved trait plotting
• New linked list tree, node and branch type
• Improved, more consistent and faster interface
• trait-based dispatch to use faster code paths
• New interface to allow an easier changeover of tree, node and branch types
• Defaults to polytomies
• Can now evolve discrete and continuous traits on the tree
• Compatible with Unitful to allow time-based branch lengths, and traits based on physical units
• Only compatible with Julia v1.0+

Enable plotting

Other minor fixes, but mostly to enable a first go at plotting.

NB Due to a regression in Julia v1.0.3, testing only works with v1.0.2, v1.1.0-rc1 and nightly, but this is also true (retrospectively) of the last release.

Fully functioning on 1.0.

Now that RCall works with Julia 1.0, so does Phylo's Julia->R interface.

Now working for Julia v0.6-v1.0!

Fixed all of the deprecations, so Phylo will now run on Julia 0.6, 0.7 and 1.0! Some workarounds for the time being to allow it to work despite some dependency problems.

Parse nexus files, allow polytomies, more 0.7 updates

• Allow polytomies
• Allow TreeSets containing multiple trees
• Add in parsenexus() to parse nexus tree files with one or more trees
• Switch Void to Nothing and add Compat for Julia 0.6

More fixes for 0.7 compatibility

• Remove use of Nullable, replace with Union{T, Void}
• Add in package manager for 0.7

Update to Julia v0.6, drop backward compatibility

Various fixes to handle deprecations in Julia v0.6 and nightly, dropping backward compatibility with v0.5.

Bugfixes and new ancestor and descendant info

• show() now working for trees again
• Now provides implementation of getparent(), getancestors(), getchildren(), getdescendants()
• update docs

Bugfixes and improved R interface

• @rput and @rget now work with new RCall RClass interface
• Can generate random ultrametric trees (using Ultrametric)
• Can translate and generate BinaryTrees of any kind where data types have default constructors, not just NamedTrees
• various bugfixes in interfaces