Update docs and exports

EcoJulia · Nov 25, 2023 · f54027e · f54027e
1 parent 6cc60e0
commit f54027e
Show file tree

Hide file tree

Showing 5 changed files with 56 additions and 41 deletions.
diff --git a/docs/src/man/attributes.md b/docs/src/man/attributes.md
@@ -1,25 +1,5 @@
 # Getting tree attributes
 
-## Phylo module and type docs
-
-```@docs
-Phylo
-BinaryTree
-NamedBinaryTree
-BinaryNode
-Node
-NamedTree
-PolytomousTree
-NamedPolytomousTree
-LinkTree
-LinkBranch
-LinkNode
-RootedTree
-ManyRootTree
-UnrootedTree
-TreeSet
-```
-
 ## Methods on TreeSets
 
 ```@docs
@@ -67,8 +47,10 @@ getbranchname
 hasbranch
 getbranch
 getbranches
+gettreeinfo
 validate!
 branchdims
+treetype
 ```
 
 ## Methods on Nodes
@@ -115,3 +97,12 @@ setrootheight!
 getbranchdata
 setbranchdata!
 ```
+
+## Iterators
+
+```@docs
+nodeiter
+nodenameiter
+branchiter
+branchnameiter
+```
diff --git a/docs/src/man/treetypes.md b/docs/src/man/treetypes.md
@@ -1,30 +1,48 @@
 # Data types
 
-### Tree sets
+## Tree sets
+
+## Tree types
 
-### Tree types
 This package offers a number of different types of tree, each
 optimised for a specific usage
 
-### Node types
-
-
-### Branch types
-
-
 ```@docs
+LinkTree
+TreeSet
 BinaryTree
-NamedBinaryTree
-BinaryNode
-Node
 NamedTree
 PolytomousTree
 NamedPolytomousTree
-LinkTree
-LinkBranch
+```
+
+## Node types
+
+```@docs
 LinkNode
-RootedTree
-ManyRootTree
-UnrootedTree
-TreeSet
-```
+BinaryNode
+Node
+```
+
+## Branch types
+
+```@docs
+LinkBranch
+Branch
+```
+
+## Random tree generator types
+
+```@docs
+Ultrametric
+Nonultrametric
+```
+
+## Iterator types
+
+```@docs
+NodeIterator
+NodeNameIterator
+BranchIterator
+BranchNameIterator
+```
diff --git a/src/Phylo.jl b/src/Phylo.jl
@@ -98,8 +98,9 @@ export treetype, roottype, nodetype, nodedatatype, nodenametype
 export branchtype, branchdatatype, branchnametype
 export createbranch!, deletebranch!
 export createnode!, createnodes!, deletenode!
-export getnodenames, getnodename, hasnode, getnode, getnodes
-export getbranchnames, getbranchname, hasbranch, getbranch, getbranches
+export getnodenames, getnodename, hasnode, getnode, getnodes, nnodes
+export getleafnames, getleaves, nleaves, getinternalnodes, ninternal
+export getbranchnames, getbranchname, hasbranch, getbranch, getbranches, nbranches
 export hasrootheight, getrootheight, setrootheight!
 export getparent, getancestors #, hasparent # unimplemented
 export getchildren, getdescendants #, haschildren # unimplemented
@@ -118,7 +119,6 @@ export validate!, traversal, branchdims
 export isleaf, isroot, isinternal, isunattached
 export degree, indegree, outdegree, hasinbound, getconnections, getinbound, getoutbounds
 export hasoutboundspace, hasinboundspace
-export getleafnames, getleaves, nleaves, nnodes, ninternal, nbranches
 export getleafinfo, setleafinfo!, leafinfotype
 export getnodedata, setnodedata!
 export hasheight, getheight, setheight!

diff --git a/src/TreeSet.jl b/src/TreeSet.jl
@@ -1,3 +1,8 @@
+"""
+    TreeSet
+
+A collection of trees with the same tips.
+"""
 mutable struct TreeSet{LABEL, RT, NL, N, B, TREE <:
                        AbstractTree{OneTree, RT, NL, N, B}} <:
     AbstractTree{ManyTrees, RT, NL, N, B}

diff --git a/src/trim.jl b/src/trim.jl
@@ -4,6 +4,7 @@ using Phylo.API
 
 """
     getinternalnodes(t::AbstractTree)
+
 Function to retrieve only the internal nodes from a tree, `t`, which does not
 include tips or root.