Update code to 1.9 extensions and dependencies

Project.toml

@@ -7,6 +7,7 @@ version = "0.4.24"
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 IterableTables = "1c8ee90f-4401-5389-894e-7a04a3dc0f4d"
@@ -20,17 +21,36 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Tokenize = "0796e94c-ce3b-5d07-9a54-7f471281c624"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
+[weakdeps]
+RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+
+[extensions]
+PhyloRCallExt = "RCall"
+
 [compat]
 AxisArrays = "0.4"
-DataFrames = "^1"
+DataFrames = "1"
 DataStructures = "0.17, 0.18"
+Distances = "0.10"
 Distributions = "0.24, 0.25"
-Graphs = "^1"
-IterableTables = "^1"
-Missings = "^1"
-RecipesBase = "^1"
-Requires = "^1"
+Graphs = "1"
+IterableTables = "1"
+Missings = "1"
+Printf = "1"
+Random = "1"
+RecipesBase = "1"
+Requires = "1"
 SimpleTraits = "0.9"
+Statistics = "1"
 Tokenize = "0.5"
-Unitful = "^1"
-julia = "^1"
+Unitful = "1"
+julia = "1"
+
+[extras]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+RCall = "6f49c342-dc21-5d91-9882-a32aef131414"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["DataFrames", "RCall", "Test"]

src/rcall.jl → ext/PhyloRCallExt.jl

@@ -1,7 +1,20 @@
+module PhyloRCallExt
+
+if isdefined(Base, :get_extension)
+    using RCall
+    using RCall: protect, unprotect, rcall_p, RClass, isObject, isS4
+    import RCall: rcopy
+    import RCall: rcopytype
+    import RCall: sexp
+else
+    using ..RCall
+    using ..RCall: protect, unprotect, rcall_p, RClass, isObject, isS4
+    import ..RCall: rcopy
+    import ..RCall: rcopytype
+    import ..RCall: sexp
+end
+
 using Phylo
-using .RCall
-using .RCall: protect, unprotect, rcall_p, RClass, isObject, isS4
-import .RCall: rcopy
 
 function rcopy(::Type{T}, rt::Ptr{VecSxp}) where T <: AbstractTree
     if !isObject(rt) || isS4(rt) || rcopy(String, rcall_p(:class, rt)) != "phylo"
@@ -31,12 +44,9 @@ function rcopy(::Type{T}, rt::Ptr{VecSxp}) where T <: AbstractTree
     return tree
 end
 
-import .RCall.rcopytype
 
 rcopytype(::Type{RClass{:phylo}}, s::Ptr{VecSxp}) = RootedTree
 
-import .RCall.sexp
-
 function sexp(tree::T) where T <: AbstractTree
     validate!(tree) || @warn "Tree does not internally validate"
     leafnames = getleafnames(tree)
@@ -70,3 +80,5 @@ function sexp(tree::T) where T <: AbstractTree
     unprotect(1)
     return sobj
 end
+
+end

src/Phylo.jl

@@ -189,12 +189,15 @@ export distance, distances, heighttoroot, heightstoroot
 # Path into package
 path(path...; dir::String = "test") = joinpath(@__DIR__, "..", dir, path...)
 
-using Requires
+# This symbol is only defined on Julia versions that support extensions
+if !isdefined(Base, :get_extension)
+    using Requires
+end
+
+@static if !isdefined(Base, :get_extension)
 function __init__()
-    @require RCall="6f49c342-dc21-5d91-9882-a32aef131414" begin
-        println("Creating Phylo RCall interface...")
-        include("rcall.jl")
-    end
+    @require RCall="6f49c342-dc21-5d91-9882-a32aef131414" include("../ext/PhyloRCallExt.jl")
+end
 end
 
 end # module

test/runtests.jl

@@ -1,24 +1,18 @@
+using Random
 using Test
+using Phylo
 
 # Identify files in test/ that are testing matching files in src/
 #  - src/Source.jl will be matched by test/test_Source.jl
-
-filebase = map(file -> replace(file, r"(.*).jl$" => s"\1"),
-                filter(file -> occursin(r".*\.jl$", file),
-                       readdir("../src")))
-testbase = map(file -> replace(file, r"test_(.*).jl$" => s"\1"),
-                filter(str -> occursin(r"^test_.*\.jl$", str), readdir()))
-
-println()
-@info "Running tests for files:"
-for t in testbase
-    println("    = $t.jl")
+filebase = String[]
+for (root, dirs, files) in walkdir("../src")
+    append!(filebase,
+            map(file -> replace(file, r"(.*).jl" => s"\1"),
+                filter(file -> occursin(r".*\.jl", file), files)))
 end
-println()
 
-@testset "* Testing $t.jl" for t in testbase
-    include("test_$t.jl")
-end
+testbase = map(file -> replace(file, r"test_(.*).jl" => s"\1"),
+               filter(str -> occursin(r"^test_.*\.jl$", str), readdir()))
 
 # Identify tests with no matching file
 superfluous = filter(f -> f ∉ filebase, testbase)
@@ -32,16 +26,84 @@ if length(superfluous) > 0
 end
 
 # Identify files with no matching test
-missing = filter(f -> f ∉ testbase, filebase)
-if length(missing) > 0
+notest = filter(f -> f ∉ testbase, filebase)
+if length(notest) > 0
     println()
     @info "Potentially missing tests:"
-    for f in missing
+    for f in notest
         println("    - $f.jl")
     end
     println()
 end
 
+# Identify files in test/ that are testing matching files in ext/
+#  - ext/SourceExt.jl will be matched by test/ext_SourceExt.jl
+filebase = String[]
+for (root, dirs, files) in walkdir("../ext")
+    append!(filebase,
+            map(file -> replace(file, r"(.*).jl" => s"\1"),
+                filter(file -> occursin(r".*\.jl", file), files)))
+end
+
+extbase = map(file -> replace(file, r"ext_(.*).jl" => s"\1"),
+              filter(str -> occursin(r"^ext_.*\.jl$", str), readdir()))
+
+# Identify tests with no matching file
+superfluous = filter(f -> f ∉ filebase, extbase)
+if length(superfluous) > 0
+    println()
+    @info "Potentially superfluous extension tests:"
+    for f in superfluous
+        println("    + $f.jl")
+    end
+    println()
+end
+
+# Identify files with no matching test
+notest = filter(f -> f ∉ extbase, filebase)
+if length(notest) > 0
+    println()
+    @info "Potentially missing extension tests:"
+    for f in notest
+        println("    - $f.jl")
+    end
+    println()
+end
+
+# Seed RNG to make tests reproducible
+Random.seed!(1234)
+
+@testset "Phylo.jl" begin
+    @test isfile(Phylo.path("runtests.jl"))
+    println()
+    @info "Running tests for files:"
+    for t in testbase
+        println("    = $t.jl")
+    end
+    println()
+
+    @info "Running tests..."
+    @testset for t in testbase
+        fn = "test_$t.jl"
+        println("    * Testing $t.jl ...")
+        include(fn)
+    end
+
+    println()
+    @info "Running tests for extensions:"
+    for t in extbase
+        println("    = $t.jl")
+    end
+    println()
+
+    @info "Running extension tests..."
+    @testset for t in extbase
+        fn = "ext_$t.jl"
+        println("    * Testing $t.jl extension...")
+        include(fn)
+    end
+end
+
 # Identify files that are cross-validating results against other packages
 # test/pkg_Package.jl should validate results against the Package package
 
@@ -50,13 +112,17 @@ pkgbase = map(file -> replace(file, r"pkg_(.*).jl$" => s"\1"),
                           readdir()))
 
 if length(pkgbase) > 0
-    @info "Running cross-validation against:"
-    for p in pkgbase
-        println("    = $p")
-    end
-    println()
+    @info "Cross validation packages:"
+    @testset begin
+        for p in pkgbase
+            println("    = $p")
+        end
+        println()
 
-    @testset " * Validating against $p" for p in pkgbase
-        include("pkg_$p.jl")
+        @testset for p in pkgbase
+            fn = "pkg_$p.jl"
+            println("    * Validating $p.jl ...")
+            include(fn)
+        end
     end
 end