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Standardising formatting #92

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merged 7 commits into from
Jan 6, 2024
Merged

Standardising formatting #92

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4505524
Standardising formatting
richardreeve Jan 5, 2024
b9aad00
Typo in show for RecursiveNodes and docs cleaning
richardreeve Jan 5, 2024
16b8344
Fix validation and its testing
richardreeve Jan 5, 2024
0fda604
Fix TreeSet leaves and testing
richardreeve Jan 5, 2024
7235ac7
Test TreeSet leaf info
richardreeve Jan 5, 2024
1233eb2
Improve createnodes! testing
richardreeve Jan 5, 2024
511483e
Fix getsiblings and test
richardreeve Jan 6, 2024
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26 changes: 12 additions & 14 deletions docs/make.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -2,22 +2,20 @@ using Documenter
using Phylo

makedocs(modules = [Phylo, Phylo.API],
sitename = "Phylo.jl",
sitename = "Phylo.jl",
pages = ["Home" => "index.md",
"Tutorial / Quick start" => "tutorial.md",
"Manual" => Any[
"Phylogeny data types" => "man/treetypes.md",
"Creating and writing phylogenies" => "man/io.md",
"Manipulating and building phylogenies" => "man/manipulating.md",
"Traversal and iterators" => "man/traversal.md",
"Getting phylogeny attributes" => "man/attributes.md",
"Modelling traits" => "man/modelling.md",
"Plotting" => "man/plotting.md"
],
"List of functions" => "functionlist.md",
"API" => "api.md"];
"Tutorial / Quick start" => "tutorial.md",
"Manual" => Any["Phylogeny data types" => "man/treetypes.md",
"Creating and writing phylogenies" => "man/io.md",
"Manipulating and building phylogenies" => "man/manipulating.md",
"Traversal and iterators" => "man/traversal.md",
"Getting phylogeny attributes" => "man/attributes.md",
"Modelling traits" => "man/modelling.md",
"Plotting" => "man/plotting.md"],
"List of functions" => "functionlist.md",
"API" => "api.md"];
format = Documenter.HTML(size_threshold_ignore = ["man/plotting.md",
"man/io.md"]))
"man/io.md"]))

deploydocs(repo = "github.com/EcoJulia/Phylo.jl.git",
devbranch = "dev",
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13 changes: 7 additions & 6 deletions ext/PhyloRCallExt.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -16,8 +16,9 @@ end

using Phylo

function rcopy(::Type{T}, rt::Ptr{VecSxp}) where T <: AbstractTree
if !isObject(rt) || isS4(rt) || rcopy(String, rcall_p(:class, rt)) != "phylo"
function rcopy(::Type{T}, rt::Ptr{VecSxp}) where {T <: AbstractTree}
if !isObject(rt) || isS4(rt) ||
rcopy(String, rcall_p(:class, rt)) != "phylo"
error("Object is not of S3 phylo class, aborting")
end

Expand All @@ -44,17 +45,17 @@ function rcopy(::Type{T}, rt::Ptr{VecSxp}) where T <: AbstractTree
return tree
end


rcopytype(::Type{RClass{:phylo}}, s::Ptr{VecSxp}) = RootedTree

function sexp(tree::T) where T <: AbstractTree
function sexp(tree::T) where {T <: AbstractTree}
validate!(tree) || @warn "Tree does not internally validate"
leafnames = getleafnames(tree)
root = getnodename.(tree, getroots(tree))
if (length(root) != 1)
error("Can't currently translate tree with > 1 roots")
end
nontips = [getnodename(tree, node) for node in traversal(tree, preorder)
nontips = [getnodename(tree, node)
for node in traversal(tree, preorder)
if isinternal(tree, node)]
tor = Dict{Symbol, Any}()
tor[:Nnode] = length(nontips) + length(root)
Expand All @@ -69,7 +70,7 @@ function sexp(tree::T) where T <: AbstractTree
for branch in bi
lengths[index] = getlength(tree, branch)
edges[index, :] = indexin([getnodename(tree, src(tree, branch)),
getnodename(tree, dst(tree, branch))], nodes)
getnodename(tree, dst(tree, branch))], nodes)
index += 1
end
tor[:edge] = edges
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