upgrade to Julia v0.7/1.0

.travis.yml

@@ -1,6 +1,7 @@
 language: julia
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
   - nightly
 notifications:
     email: false

REQUIRE

@@ -1 +1 @@
-julia 0.6
+julia 0.7

src/OBOParse.jl

@@ -1,5 +1,3 @@
-__precompile__()
-
 module OBOParse
 
 export
@@ -14,6 +12,8 @@ export
     parents, children,
     descendants, ancestors, relationship
 
+using Printf: @printf, @sprintf
+
 include("term.jl")
 include("typedef.jl")
 include("parser.jl")

src/ontology.jl

@@ -41,21 +41,21 @@ Base.length(ontology::Ontology) = length(ontology.terms)
 parents(ontology::Ontology, term::Term, rel::Symbol = :is_a) = ontology[relationship(term, rel)]
 children(ontology::Ontology, term::Term, rel::Symbol = :is_a) = ontology[rev_relationship(term, rel)]
 
-const VecOrTuple{T} = Union{Vector{T}, Tuple{Vararg{T}}}
+const VecOrTuple{T} = Union{Vector{T}, Tuple{Vararg{T}}} where T
 
 # return the set of all nodes of the ontology DAG that could be visited from `term`
 # node when traveling along `rels` edges using `rev` direction
-function transitive_closure{T}(ontology::Ontology, term::Term,
-                               rels::VecOrTuple{Symbol},
-                               rev::Type{Val{T}} = Val{false})
+function transitive_closure(ontology::Ontology, term::Term,
+                            rels::VecOrTuple{Symbol},
+                            rev::Bool = false)
     # TODO: check if transitive & non-cyclical before doing so?
     res = Set{TermId}()
     frontier_ids = Set{TermId}((term.id,))
     while true
         new_ids = Set{TermId}()
         for f_id in frontier_ids, rel in rels
             f_term = ontology[f_id]
-            f_rel_ids = T ? rev_relationship(f_term, rel) : relationship(f_term, rel)
+            f_rel_ids = rev ? rev_relationship(f_term, rel) : relationship(f_term, rel)
             union!(new_ids, f_rel_ids)
         end
         frontier_ids = setdiff!(new_ids, res)
@@ -65,9 +65,9 @@ function transitive_closure{T}(ontology::Ontology, term::Term,
     return res
 end
 
-descendants(ontology::Ontology, term::Term, rels::VecOrTuple{Symbol}) = ontology[transitive_closure(ontology, term, rels, Val{true})]
+descendants(ontology::Ontology, term::Term, rels::VecOrTuple{Symbol}) = ontology[transitive_closure(ontology, term, rels, true)]
 descendants(ontology::Ontology, term::Term, rel::Symbol = :is_a) = descendants(ontology, term, (rel,))
-ancestors(ontology::Ontology, term::Term, rels::VecOrTuple{Symbol}) = ontology[transitive_closure(ontology, term, rels, Val{false})]
+ancestors(ontology::Ontology, term::Term, rels::VecOrTuple{Symbol}) = ontology[transitive_closure(ontology, term, rels, false)]
 ancestors(ontology::Ontology, term::Term, rel::Symbol = :is_a) = ancestors(ontology, term, (rel,))
 
 function satisfies(ontology::Ontology, term1::Term, rel::Symbol, term2::Term)

src/parser.jl

@@ -22,22 +22,22 @@ struct OBOParseException <: Exception
 end
 
 function find_first_nonescaped(s, ch)
-    i = searchindex(s, ch)
-    while i > 0
+    i = findfirst(isequal(ch), s)
+    while i !== nothing
         numescapes = 0
         @inbounds for j in i-1:-1:1
             (s[j] == '\\') || break
             numescapes += 1
         end
         iseven(numescapes) && return i # this is not escaped
-        i = searchindex(s, ch, i+1)
+        i = findnext(isequal(ch), s, i+1)
     end
     return i
 end
 
 function removecomments(line)
-    i = find_first_nonescaped(line, "!")
-    return i > 0 ? line[1:i-1] : line
+    i = find_first_nonescaped(line, '!')
+    return i !== nothing ? line[1:i-1] : line
 end
 
 const id_tag = "id"
@@ -84,18 +84,20 @@ end
 
 function tagvalue(line)
     # TODO: what an ad hoc parser!
-    i = searchindex(line, ": ")
-    if i == 0
+    i = findfirst(": ", line)
+    if i === nothing
         # empty tag value
-        endswith(line, ":") && (return line, "", true)
-
-        # empty strings are dummy
-        return "", "", false
+        if endswith(line, ":")
+            return line, "", true
+        else
+            # empty strings are dummy
+            return "", "", false
+        end
     end
 
-    j = searchindex(line, " !")
-    tag = line[1:i-1]
-    value = j==0 ? line[i+2:end] : line[i+2:j-1]
+    j = findfirst(" !", line)
+    tag = line[1:first(i)-1]
+    value = j === nothing ? line[first(i)+2:end] : line[first(i)+2:first(j)-1]
 
     return tag, value, true
 end

src/term.jl

@@ -46,8 +46,14 @@ end
 
 
 Base.isless(term1::Term, term2::Term) = isless(term1.id, term2.id)
-Base.show(io::IO, term::Term) = @printf io "Term(\"%s\", \"%s\")" term.id term.name
-Base.showcompact(io::IO, term::Term) = print(io, term.id)
+
+function Base.show(io::IO, term::Term)
+    if get(io, :compact, false)
+        @printf io "Term(\"%s\", \"%s\")" term.id term.name
+    else
+        print(io, term.id)
+    end
+end
 
 isobsolete(term::Term) = term.obsolete
 

test/runtests.jl

@@ -1,5 +1,5 @@
 using OBOParse
-using Base.Test
+using Test
 
 const testdir = dirname(@__FILE__)