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NEWS.md

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NEWS

  • v0.5.4
    • Use ResearchSoftwareMetadata package
  • v0.5.3
    • Add in metadata and crosswalk
  • v0.5.2
    • Bugfix in displaying node names
    • Link fix
    • Improve testing
    • Standardise formatting
  • v0.5.1
    • Allow export of trees to nexus and newick format
      • Overload Base.write() and Base.parse()
    • Generalise use of collections where possible
    • Improve testing
  • v0.5.0
    • Add recursive tree, node and branch types
    • Improve testing
    • Note, this is a breaking change because the RootedTree type is now an alias for RecursiveTree, not LinkTree for efficiency
  • v0.4.24
    • Fix workflows
  • v0.4.23
    • Fix type warnings
  • v0.4.22
    • Bug fixes
    • update to use Graphs.jl
    • update workflows
  • v0.4.21
    • Fixes to plotting and updated docs
  • v0.4.20
    • Fixes to plotting
  • v0.4.19
    • compatibility update
  • v0.4.7 to v0.4.18
    • fixed automation on new releases
    • documentation updates
  • v0.4.6
    • add sort function, sort! can be reversed
  • v0.4.5
    • Update compat issues
  • v0.4.4
    • Update Documenter and DataFrames versions
    • Require Julia v1
    • Calculate MRCA using mrca()
  • v0.4.3
    • Fix missing problem in show for branches
  • v0.4.2
    • Permanent dependency fix!
  • v0.4.1
    • Fixing dependencies to allow Diversity.jl to install
  • 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+
  • v0.3.3
    • Final version compatible with Julia v0.6
    • Enable plotting
  • v0.3.2
    • RCall interface now up and running with Julia v1.0.
  • v0.3.1
    • Working with Julia v0.7 and v1.0!
  • v0.3
    • 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
  • v0.2.1
    • Remove use of Nullable, replace with Union{T, Void}
    • Add in package manager for 0.7
  • v0.2.0
    • Add in parsenewick() to parse newick trees using Tokenize
    • Rename iterator and filter functions to nodeiter(), branchnamefilter(), etc and use function first ordering to allow do block.
    • Major bugfixes and addition of extensive testing of code.
  • v0.1.3
    • show() now working for trees again
    • Now provides implementation of getparent(), getancestors(), getchildren(), getdescendants()
    • update docs
  • v0.1.2
    • @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
  • v0.1.1
    • R <-> Julia interface
    • OrderedDict means tips remain in order originally presented
  • v0.1.0
    • Initial release