Remove unnecessary Compat requirements now we've dropped Julia 0.5 co…

…mpatibility.

README.md

@@ -17,7 +17,9 @@ julia> Pkg.add("Phylo")
 
 ## Project Status
 
-The package is tested against the current Julia `0.6` release, and `nightly` on Linux, OS X, and Windows.
+The package is tested against the current Julia `0.6` release, and
+`nightly` on Linux, OS X, and Windows. It is currently broken on
+nightly due to changes to Nullable handling, but this will be fixed soon...
 
 ## Contributing and Questions
 

REQUIRE

@@ -1,5 +1,4 @@
 julia 0.6
-Compat 0.33.0
 Distributions 0.12.2
 DataStructures 0.4.3
 Tokenize 0.1.0

src/API.jl

@@ -1,14 +1,12 @@
 using Phylo
-using Compat
 
 function _newlabel(ids::Vector{Label}) where Label <: Integer
     return isempty(ids) ? 1 : maximum(ids) + 1
 end
 
 function _newlabel(names::Vector{String}, prefix)
-    names = collect(Compat.Iterators.filter(n -> length(n) > length(prefix) &&
-                                            n[1:length(prefix)]==prefix,
-                                            names))
+    names = collect(Iterators.filter(n -> length(n) > length(prefix) &&
+                                     n[1:length(prefix)]==prefix, names))
     start = length(names) + 1
     name = prefix * "$start"
     while (name ∈ names)

src/Interface.jl

@@ -1,4 +1,3 @@
-using Compat
 using Phylo.API
 
 getnodes(tree::AbstractTree) = _getnodes(tree)

src/Iterators.jl

@@ -1,7 +1,6 @@
-using Compat
 using Phylo.API
 
-@compat abstract type AbstractTreeIterator{T <: AbstractTree} end
+abstract type AbstractTreeIterator{T <: AbstractTree} end
 
 function iteratorsize(::Type{AbstractTreeIterator})
     return Base.HasLength()
@@ -11,7 +10,7 @@ function iteratoreltype(::Type{AbstractTreeIterator})
     return Base.HasEltype()
 end
 
-@compat abstract type AbstractNodeIterator{T <: AbstractTree} <: AbstractTreeIterator{T} end
+abstract type AbstractNodeIterator{T <: AbstractTree} <: AbstractTreeIterator{T} end
 
 function start(ni::It) where It <: AbstractNodeIterator
     nodes = _getnodes(ni.tree)
@@ -44,7 +43,7 @@ function length(ni::It) where It <: AbstractNodeIterator
 end
 
 
-@compat abstract type AbstractBranchIterator{T <: AbstractTree} <: AbstractTreeIterator{T} end
+abstract type AbstractBranchIterator{T <: AbstractTree} <: AbstractTreeIterator{T} end
 
 function start(bi::It) where It <: AbstractBranchIterator
     branches = _getbranches(bi.tree)

src/Node.jl

@@ -1,7 +1,3 @@
-using Compat
-import Phylo.API: _hasinbound, _getinbound, _setinbound!, _deleteinbound!
-import Phylo.API: _outdegree, _hasoutboundspace, _getoutbounds, _addoutbound!, _deleteoutbound!
-
 """
     BinaryNode{T}(AbstractVector{T}, AbstractVector{T}) <: AbstractNode
 
@@ -26,31 +22,39 @@ mutable struct BinaryNode{T} <: AbstractNode
     end
 end
 
+import Phylo.API._hasinbound
 function _hasinbound(node::BinaryNode)
     return !isnull(node.inbound)
 end
 
+
+import Phylo.API._outdegree
 function _outdegree(node::BinaryNode)
     return (isnull(node.outbounds[1]) ? 0 : 1) +
         (isnull(node.outbounds[2]) ? 0 : 1)
 end
 
+
+import Phylo.API._hasoutboundspace
 function _hasoutboundspace(node::BinaryNode)
     return _outdegree(node) < 2
 end
 
+import Phylo.API._getinbound
 function _getinbound(node::BinaryNode)
     _hasinbound(node) ||
         error("Node has no inbound connection")
     return get(node.inbound)
 end
 
+import Phylo.API._setinbound!
 function _setinbound!(node::BinaryNode{T}, inbound::T) where T
     !_hasinbound(node) ||
         error("BinaryNode already has an inbound connection")
     node.inbound = inbound
 end
 
+import Phylo.API._deleteinbound!
 function _deleteinbound!(node::BinaryNode{T}, inbound::T) where T
     _hasinbound(node) ||
         error("Node has no inbound connection")
@@ -59,13 +63,15 @@ function _deleteinbound!(node::BinaryNode{T}, inbound::T) where T
     node.inbound = Nullable{T}()
 end
 
+import Phylo.API._getoutbounds
 function _getoutbounds(node::BinaryNode{T}) where T
     return isnull(node.outbounds[1]) ?
         (isnull(node.outbounds[2]) ? T[] : [get(node.outbounds[2])]) :
         (isnull(node.outbounds[2]) ? [get(node.outbounds[1])] :
          [get(node.outbounds[1]), get(node.outbounds[2])])
 end
 
+import Phylo.API._addoutbound!
 function _addoutbound!(node::BinaryNode{T}, outbound::T) where T
     isnull(node.outbounds[1]) ?
         node.outbounds = (Nullable(outbound), node.outbounds[2]) :
@@ -74,6 +80,7 @@ function _addoutbound!(node::BinaryNode{T}, outbound::T) where T
          error("BinaryNode already has two outbound connections"))
 end
 
+import Phylo.API._deleteoutbound!
 function _deleteoutbound!(node::BinaryNode{T}, outbound::T) where T
     !isnull(node.outbounds[1]) && get(node.outbounds[1]) == outbound ?
         node.outbounds = (node.outbounds[2], Nullable{T}()) :

src/Phylo.jl

@@ -13,14 +13,13 @@ a simple phylogenetics type.
 """
 module Phylo
 
-using Compat
 import Base: Pair, Tuple, show, showall, start, next, done,
     iteratorsize, iteratoreltype, eltype, length
 
-@compat abstract type AbstractNode end
-@compat abstract type AbstractBranch end
-@compat abstract type AbstractTree{NodeLabel, BranchLabel} end
-@compat abstract type AbstractInfo end
+abstract type AbstractNode end
+abstract type AbstractBranch end
+abstract type AbstractTree{NodeLabel, BranchLabel} end
+abstract type AbstractInfo end
 export AbstractNode, AbstractBranch, AbstractTree, AbstractInfo
 
 """

test/REQUIRE

@@ -1 +1,2 @@
 RCall 0.7.3
+Compat 0.33.0

test/test_Interface.jl

@@ -2,7 +2,6 @@ module TestInterface
 
 using Phylo
 using Compat.Test
-using Compat
 
 @testset "Build and tear down trees" begin
     @testset "For $TreeType" for TreeType in
@@ -31,9 +30,9 @@ using Compat
         pop!(innodes)
         branches =
             map(innodes) do node
-                itr = Compat.Iterators.filter(name ->
-                                              hasoutboundspace(tree, name) &&
-                                              name != node, allnodes)
+                itr = Iterators.filter(name ->
+                                       hasoutboundspace(tree, name) &&
+                                       name != node, allnodes)
                 addbranch!(tree, first(itr), node)
             end
         @test Set(branches) == Set(branchnameiter(tree))
@@ -56,7 +55,7 @@ using Compat
             outdegree(tree, species[1]) == 0 &&
             indegree(tree, species[1]) == 0
         @test_throws ErrorException getbranch(tree, b)
-        branches = collect(Compat.Iterators.filter(name -> name != b, branches))
+        branches = collect(Iterators.filter(name -> name != b, branches))
         @test Set(branches) == Set(branchnameiter(tree))
         b3 = getinbound(tree, species[2])
         source = src(tree, b3)