Recent Releases of phylo.jl
phylo.jl - v0.5.2
Phylo v0.5.2
Merged pull requests: - Extensions (#90) (@richardreeve) - Node renaming (#91) (@richardreeve) - Standardising formatting (#92) (@richardreeve) - Minor fixes (#96) (@richardreeve)
Closed issues: - editing leaf names (#54) - How can I rename the leaf nodes of a ::RootedTree? (#70) - Support extended Newick? (#78) - How to cite Phylo.jl? (#83) - problem with outputnode function (#95)
- Julia
Published by github-actions[bot] almost 2 years ago
phylo.jl - v0.5.1
Phylo v0.5.1
Merged pull requests: - Allow export of trees (#88) (@richardreeve) - Vectors can be AbstractVectors (#89) (@richardreeve)
Closed issues:
- type signatures (#22)
- Test coverage (#50)
- Add function to save/write a tree in Newick format (#61)
- Extraneous linebreaks in show methods (#69)
- parsenexus() tree validation fails if '-' in TaxLabels (#75)
- Tree saving available? (#84)
- Julia
Published by github-actions[bot] over 2 years ago
phylo.jl - v0.5.0
Phylo v0.5.0
Breaking changes
- Add recursive tree, node and branch types, allowing type stability.
- Note, this is a breaking change because the RootedTree and UnrootedTree types are now an alias for RecursiveTree, not LinkTree for efficiency.
Other changes
- Improve testing, more type stability and validation
Merged pull requests: - Add fully recursive types, speed up parser, improve testing (#87) (@richardreeve)
- Julia
Published by github-actions[bot] over 2 years ago
phylo.jl - v0.4.22
Phylo v0.4.22
Closed issues: - enum for trait simulation only works in global scope (#68) - How to make colorbar disctrete? (#72) - Migrate from LightGraphs to Graphs (#77)
Merged pull requests: - Bug fixes (#80) (@richardreeve)
- Julia
Published by github-actions[bot] almost 3 years ago
phylo.jl - v0.4.21
Phylo v0.4.21
Merged pull requests: - fix plotting (#63) (@mkborregaard) - Add plotting docs (#64) (@mkborregaard) - Refactor docs (#65) (@mkborregaard) - patches rebase issues (#66) (@mkborregaard) - small doc fixes (#67) (@mkborregaard)
- Julia
Published by github-actions[bot] over 4 years ago
phylo.jl - v0.4.19
Phylo v0.4.19
Merged pull requests: - Typo in README.md url (#55) (@remi-garcia) - Fixing workflows (#56) (@richardreeve) - CompatHelper: bump compat for "DataFrames" to "1.0" (#57) (@github-actions[bot]) - CompatHelper: bump compat for "Missings" to "1.0" (#58) (@github-actions[bot]) - CompatHelper: bump compat for "Distributions" to "0.25" (#59) (@github-actions[bot])
- Julia
Published by github-actions[bot] almost 5 years ago
phylo.jl - v0.4.5
Phylo v0.4.5
Merged pull requests: - CompatHelper: bump compat for "RecipesBase" to "1.1" (#46) (@github-actions[bot]) - CompatHelper: bump compat for "DataFrames" to "0.22" (#47) (@github-actions[bot]) - CompatHelper: bump compat for "DataStructures" to "0.18" (#48) (@github-actions[bot]) - Compat (#49) (@richardreeve)
- Julia
Published by github-actions[bot] about 5 years ago
phylo.jl - Recreate docs for v0.4.4
Problem with docs construction when creating v0.4.4 - trying again
- Julia
Published by richardreeve about 5 years ago
phylo.jl - v0.4.4
Phylo v0.4.4
Closed issues: - Github workflows (#35) - DataFrames upper version (#36) - Use Documenter recent version (#37) - MRCA function? (#40)
Merged pull requests: - Maintenance work (#38) (@tpoisot) - Add common_ancestor function (#41) (@mkborregaard) - ignore manifest (#43) (@mkborregaard) - Github actions (#44) (@claireh93)
- Julia
Published by github-actions[bot] about 5 years ago
phylo.jl - v0.4.3
Phylo v0.4.3
Closed issues: - Newick format is general and permits multifurcations (#6) - design of Phylo (#14) - fix TypeError in case LinkBranch has no length information (#33)
Merged pull requests: - Fix #33 - non-missing expectation. (#34) (@richardreeve)
- Julia
Published by github-actions[bot] over 5 years ago
phylo.jl - Temporary dependency fix
Gets around Diversity dependency problems
- Julia
Published by richardreeve almost 6 years ago
phylo.jl - 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+
- Julia
Published by richardreeve almost 6 years ago
phylo.jl - 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.
- Julia
Published by richardreeve over 7 years ago
phylo.jl - Fully functioning on 1.0.
Now that RCall works with Julia 1.0, so does Phylo's Julia->R interface.
- Julia
Published by richardreeve over 7 years ago
phylo.jl - 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.
- Julia
Published by richardreeve over 7 years ago
phylo.jl - 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
- Julia
Published by richardreeve almost 8 years ago
phylo.jl - More fixes for 0.7 compatibility
- Remove use of Nullable, replace with Union{T, Void}
- Add in package manager for 0.7
- Julia
Published by richardreeve about 8 years ago
phylo.jl - 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.
- Julia
Published by richardreeve over 8 years ago
phylo.jl - Bugfixes and new ancestor and descendant info
- show() now working for trees again
- Now provides implementation of getparent(), getancestors(), getchildren(), getdescendants()
- update docs
- Julia
Published by richardreeve almost 9 years ago
phylo.jl - Bugfixes and improved R interface
@rputand@rgetnow work with newRCallRClassinterface- Can generate random ultrametric trees (using
Ultrametric) - Can translate and generate
BinaryTrees of any kind where data types have default constructors, not justNamedTrees - various bugfixes in interfaces
- Julia
Published by richardreeve almost 9 years ago
phylo.jl - Julia <-> R interface
- Julia <-> R
- OrderedDict to maintain order of tips
- update docs
- Julia
Published by richardreeve almost 9 years ago
phylo.jl - First release on METADATA
Release of phylogenetics package to use with Diversity package.
- Julia
Published by richardreeve almost 9 years ago