Merge pull request #40 from PierreBarrat/fix_failing_docs

Fix failing docs
PierreBarrat · Feb 22, 2024 · 794a305 · 794a305
2 parents 0f60e93 + 09c4d38
commit 794a305
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Showing 5 changed files with 11 additions and 5 deletions.
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+TreeKnit = "03f602be-98a1-4bb2-9504-fbd3406624a7"
 TreeTools = "62f0eae3-8c0e-4032-a621-7756092209e5"
 
 [compat]

diff --git a/docs/make.jl b/docs/make.jl
@@ -3,6 +3,7 @@ using Documenter
 
 Documenter.makedocs(;
 	source = "src",
+    warnonly = [:missing_docs,],
 	clean = true,
 	doctest = true,
 	modules = Module[TreeKnit],

diff --git a/src/main.jl b/src/main.jl
@@ -142,12 +142,14 @@ function run_treeknit!(trees::AbstractVector{<:Tree}, oa::OptArgs; naive=false)
 
     oa.pre_resolve && resolve!(trees...)
 
+    # function used for inferring the MCCs
+    # for every pair of trees (i,j), will be called as
+    # `f(oa, trees[i], trees[j]; output = :mccs)`
     f = if naive
-		TreeKnit.naive_mccs
+		(oa, t1, t2; kwargs...) -> TreeKnit.naive_mccs(t1, t2)
 	else
 		TreeKnit.runopt
 	end
-
     return if oa.parallel == true
         run_parallel_treeknit!(trees, oa; infer_mccs_function=f)
     else
@@ -157,7 +159,9 @@ end
 
 run_treeknit!(trees; kwargs...) = run_treeknit!(trees, OptArgs(length(trees); kwargs...))
 
-run_treeknit!(t1::Tree, t2::Tree; kwargs...) = run_treeknit!([t1,t2], OptArgs(;kwargs...))
+function run_treeknit!(t1::Tree, t2::Tree; naive=false, kwargs...)
+    return run_treeknit!([t1,t2], OptArgs(;kwargs...); naive)
+end
 run_treeknit!(t1::Tree, t2::Tree, oa::OptArgs) = run_treeknit!([t1,t2], oa)
 
 run_treeknit(trees, oa::OptArgs) = run_treeknit!(map(copy, trees), oa)

diff --git a/src/mcc_base.jl b/src/mcc_base.jl
@@ -23,7 +23,7 @@ function naive_mccs(treelist)
     checklist = Dict(k=>false for k in keys(tref.lleaves))
 
     # Explore one leaf at a time
-    mc_clades = []
+    mc_clades = Vector{String}[]
     for (cl,v) in checklist
         if !v # If leave not already visited
             # Root of current maximal clade, in all trees

diff --git a/src/objects.jl b/src/objects.jl
@@ -56,7 +56,7 @@ end
 """
 	function OptArgs(K::Int; method=:none, kwargs...)
 
-OptArgs constructor will default to :better_trees method if K>2, :better_MCCs if K==2.
+OptArgs constructor will default to `:better_trees` method if `K>2`, `:better_MCCs` if `K==2`.
 """
 function OptArgs(K::Int; method=:none, kwargs...)
 	kwargs_dict = Dict(kwargs)