v0.8.0

TreeTools v0.8.0

Diff since v0.7.5

Breaking: API cleanup

• Reduced namespace footprint: many functions demoted from export to public (node2tree, prunesubtree!, binarize!, ladderize!, check_tree, arecompatible, iscompatible, delete_branches!, print_tree_ascii, share_labels, divtime, distance_matrix)
• newick is now exported as the primary function to get a Newick string; write_newick(tree) is deprecated in its favour
• All @deprecate entries centralized in TreeTools.jl
• New deprecations: divtime → distance, POT/POTleaves → traversal(tree, :postorder), write_newick(tree) → newick(tree)
• Removed dead code: parse_bootstrap stub, __subtree_prune_regraft!

New features

• diameter: O(n) tree diameter function using a post-order recursive pass
• graftnode!: loop detection via a safe=true/false kwarg; previously grafting a node onto one of its own descendants would silently corrupt the tree

Bug fixes

• delete_null_branches!: was calling the TreeNode-level delete_branches! instead of the Tree-level one, leaving stale entries in lnodes — nodes appeared deleted from the structure but were still visible via nodes(tree)

Documentation

• Completed modifying_the_tree.md: delete, graft, insert, and rooting sections with doctests
• Added delete_null_branches! section with regression doctest
• Added diameter and distance_matrix to useful_functions.md

CI

• Minimum Julia version lowered from 1.12 to 1.11 (actual minimum based on stdlib compat entries)
• CI matrix now covers Julia 1.11, 1.12, and nightly (nightly allowed to fail)

Merged pull requests:

• Minor refactor (#56) (@PierreBarrat)

Closed issues:

• Upgrade ResumableFunctions to v1 (#52)

v0.7.5

TreeTools v0.7.5

Diff since v0.7.4

v0.7.4

TreeTools v0.7.4

Diff since v0.7.3

v0.7.3

TreeTools v0.7.3

Diff since v0.7.2

Merged pull requests:

• fix root_like_model! in the case of models with a polytomy at root (#55) (@PierreBarrat)

v0.7.2

TreeTools v0.7.2

Diff since v0.7.1

Merged pull requests:

• add ArgCheck to deps - remove most @Assert - require positive branch len (#53) (@PierreBarrat)
• created submodule - implemented basic birth_death - write tests (#54) (@PierreBarrat)

v0.7.1

TreeTools v0.7.1

Diff since v0.7.0

v0.7.0

TreeTools v0.7.0

Diff since v0.6.14

Merged pull requests:

• Rework traversal functions (#51) (@PierreBarrat)

v0.6.14

TreeTools v0.6.14

Diff since v0.6.13

v0.6.13

TreeTools v0.6.13

Diff since v0.6.12

v0.6.12

TreeTools v0.6.12

Diff since v0.6.11

Merged pull requests:

• add simple_shapes.jl (#50) (@PierreBarrat)