Updates prepping for julia 0.7 (#28)

.travis.yml

@@ -16,8 +16,5 @@ notifications:
 #  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
 #  - julia -e 'Pkg.clone(pwd()); Pkg.build("Automa"); Pkg.test("Automa"; coverage=true)'
 after_success:
-  # push coverage results to Coveralls
-  # - julia -e 'cd(Pkg.dir("Automa")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
-  # push coverage results to Codecov
   - julia -e 'cd(Pkg.dir("Automa")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
   - julia -e 'cd(Pkg.dir("Automa")); Pkg.add("Documenter"); ENV["DOCUMENTER_DEBUG"] = "true"; include(joinpath("docs", "make.jl"))'

README.md

@@ -54,7 +54,7 @@ context = Automa.CodeGenContext()
     tokens = Tuple{Symbol,String}[]
     mark = 0
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     emit(kind) = push!(tokens, (kind, data[mark:p-1]))
     $(Automa.generate_exec_code(context, machine, actions))
     return tokens, cs == 0 ? :ok : cs < 0 ? :error : :incomplete

REQUIRE

@@ -1,3 +1,3 @@
 julia 0.6
 DataStructures 0.5.1
-Compat 0.41.0
+Compat 0.55

appveyor.yml

@@ -1,13 +1,10 @@
 environment:
   matrix:
-    - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/0.6/julia-0.5-latest-win32.exe"
-    - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.5-latest-win64.exe"
-    - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
-    - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
+     - Julia_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
+     - Julia_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
 
 matrix:
-  allow_failures:
-    - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x86/julia-latest-win32.exe"
+    allow_failures:
     - JULIA_URL: "https://julialangnightlies-s3.julialang.org/bin/winnt/x64/julia-latest-win64.exe"
 
 branches:

benchmark/runbenchmarks.jl

@@ -1,6 +1,7 @@
 import Automa
 import Automa.RegExp: @re_str
 using BenchmarkTools
+import Compat: lastindex
 
 srand(1234)
 data = String(vcat([push!(rand(b"ACGTacgt", 59), UInt8('\n')) for _ in 1:1000]...))
@@ -29,7 +30,7 @@ VISUALIZE && writesvg("case1", machine)
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end
@@ -39,7 +40,7 @@ println("Automa.jl:            ", @benchmark match(data))
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false, loopunroll=10)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end
@@ -61,7 +62,7 @@ VISUALIZE && writesvg("case2", machine)
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end
@@ -71,7 +72,7 @@ println("Automa.jl:            ", @benchmark match(data))
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false, loopunroll=10)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end
@@ -93,7 +94,7 @@ VISUALIZE && writesvg("case3", machine)
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end
@@ -103,7 +104,7 @@ println("Automa.jl:            ", @benchmark match(data))
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false, loopunroll=10)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end
@@ -125,7 +126,7 @@ VISUALIZE && writesvg("case4", machine)
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end
@@ -135,7 +136,7 @@ println("Automa.jl:            ", @benchmark match(data))
 context = Automa.CodeGenContext(generator=:goto, checkbounds=false, loopunroll=10)
 @eval function match(data)
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     $(Automa.generate_exec_code(context, machine))
     return cs == 0
 end

docs/make.jl

@@ -5,14 +5,19 @@ using Automa
 # run(`julia preconditions.jl`)
 
 makedocs(
-    format=:html,
-    sitename="Automa.jl",
-    modules=[Automa],
-    pages=["Home" => "index.md", "References" => "references.md"])
+    format = :html,
+    sitename = "Automa.jl",
+    modules = [Automa],
+    pages = [
+        "Home" => "index.md",
+        "References" => "references.md"
+    ]
+)
 
 deploydocs(
-    repo="github.com/BioJulia/Automa.jl.git",
-    julia="0.6",
-    target="build",
-    deps=nothing,
-    make=nothing)
+    repo = "github.com/BioJulia/Automa.jl.git",
+    julia = "0.6",
+    target = "build",
+    deps = nothing,
+    make = nothing
+)

docs/src/index.md

@@ -52,7 +52,7 @@ context = Automa.CodeGenContext()
     tokens = Tuple{Symbol,String}[]
     mark = 0
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     emit(kind) = push!(tokens, (kind, data[mark:p-1]))
     $(Automa.generate_exec_code(context, machine, actions))
     return tokens, cs == 0 ? :ok : cs < 0 ? :error : :incomplete
@@ -251,7 +251,7 @@ context = Automa.CodeGenContext()
     $(Automa.generate_init_code(context, machine))
 
     # set end and EOF positions of data buffer
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
 
     # generate code to execute FSM
     $(Automa.generate_exec_code(context, machine, actions))

example/fasta.jl

@@ -4,6 +4,7 @@
 import Automa
 import Automa.RegExp: @re_str
 const re = Automa.RegExp
+import Compat: lastindex
 
 # Create a machine of FASTA.
 fasta_machine = (function ()
@@ -63,7 +64,7 @@ context = Automa.CodeGenContext(generator=:goto, checkbounds=false)
 
     # Initialize variables used by the state machine.
     $(Automa.generate_init_code(context, fasta_machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
 
     # This is the main loop to iterate over the input data.
     $(Automa.generate_exec_code(context, fasta_machine, fasta_actions))

example/numbers.jl

@@ -4,6 +4,7 @@
 import Automa
 import Automa.RegExp: @re_str
 const re = Automa.RegExp
+import Compat: lastindex
 
 # Describe patterns in regular expression.
 oct      = re"0o[0-7]+"
@@ -43,7 +44,7 @@ context = Automa.CodeGenContext()
     tokens = Tuple{Symbol,String}[]
     mark = 0
     $(Automa.generate_init_code(context, machine))
-    p_end = p_eof = endof(data)
+    p_end = p_eof = lastindex(data)
     emit(kind) = push!(tokens, (kind, data[mark:p-1]))
     $(Automa.generate_exec_code(context, machine, actions))
     return tokens, cs == 0 ? :ok : cs < 0 ? :error : :incomplete

src/Automa.jl

@@ -3,6 +3,15 @@ __precompile__()
 module Automa
 
 import DataStructures: DefaultDict
+import Compat: Compat,
+    AbstractDict,
+    argmax,
+    lastindex,
+    uninitialized,
+    findfirst,
+    Nothing,
+    popfirst!,
+    objectid
 
 if VERSION > v"0.7-"
     using Printf: @sprintf

src/action.jl

@@ -23,7 +23,7 @@ function Base.:(==)(l1::ActionList, l2::ActionList)
     if length(l1) != length(l2)
         return false
     end
-    for i in 1:endof(l1.actions)
+    for i in 1:lastindex(l1.actions)
         if l1.actions[i].name != l2.actions[i].name
             return false
         end
@@ -39,8 +39,8 @@ function Base.hash(list::ActionList, h::UInt)
 end
 
 function Base.push!(list::ActionList, action::Action)
-    i = findfirst(a -> a.name == action.name, list.actions)
-    if i > 0
+    i = Compat.findfirst(a -> a.name == action.name, list.actions)
+    if i != nothing
         if action.order < list.actions[i].order
             list.actions[i] = action  # replace
         end

src/byteset.jl

@@ -135,10 +135,10 @@ function range_encode(set::ByteSet)
     labels = collect(set)
     labels′ = UnitRange{UInt8}[]
     while !isempty(labels)
-        lo = shift!(labels)
+        lo = popfirst!(labels)
         hi = lo
         while !isempty(labels) && first(labels) == hi + 1
-            hi = shift!(labels)
+            hi = popfirst!(labels)
         end
         push!(labels′, lo:hi)
     end

src/codegen.jl

@@ -143,7 +143,7 @@ function generate_exec_code(ctx::CodeGenContext, machine::Machine, actions=nothi
         actions = Dict{Symbol,Expr}()
     elseif actions == :debug
         actions = debug_actions(machine)
-    elseif isa(actions, Associative{Symbol,Expr})
+    elseif isa(actions, AbstractDict{Symbol,Expr})
         actions = Dict{Symbol,Expr}(collect(actions))
     else
         throw(ArgumentError("invalid actions argument"))
@@ -181,7 +181,7 @@ function generate_table_code(ctx::CodeGenContext, machine::Machine, actions::Dic
 end
 
 function generate_transition_table(machine::Machine)
-    trans_table = Matrix{Int}(256, length(machine.states))
+    trans_table = Matrix{Int}(uninitialized, 256, length(machine.states))
     for j in 1:size(trans_table, 2)
         trans_table[:,j] = -j
     end

src/dfa.jl

@@ -17,7 +17,7 @@ function DFANode(final::Bool, nodes::Set{NFANode})
 end
 
 function Base.show(io::IO, node::DFANode)
-    print(io, summary(node), "(<", length(node.edges), " edges", '@', object_id(node), ">)")
+    print(io, summary(node), "(<", length(node.edges), " edges", '@', objectid(node), ">)")
 end
 
 struct DFA
@@ -28,7 +28,7 @@ end
 function validate(dfa::DFA)
     is_non_deterministic(e1, e2) = !(isdisjoint(e1.labels, e2.labels) || conflicts(e1.precond, e2.precond))
     for s in traverse(dfa.start)
-        for i in 1:endof(s.edges), j in 1:i-1
+        for i in 1:lastindex(s.edges), j in 1:i-1
             ei = s.edges[i][1]
             ej = s.edges[j][1]
             if overlaps(ei, ej)
@@ -190,7 +190,8 @@ function remove_redundant_preconds(names::Vector{Symbol}, pvs::Vector{UInt64})
     left = length(names)
     for name in names
         sort!(pvs)
-        k = findfirst(pv -> bitat(pv, left), pvs)
+        fnd = findfirst(pv -> bitat(pv, left), pvs)
+        k = ifelse(fnd == nothing, 0, fnd) # TODO: See if there is a more elegant way of doing this.
         if (k - 1) * 2 == length(pvs)
             redundant = true
             for i in 1:k-1
@@ -205,13 +206,13 @@ function remove_redundant_preconds(names::Vector{Symbol}, pvs::Vector{UInt64})
         end
         if redundant
             left -= 1
-            for i in 1:endof(pvs)
+            for i in 1:lastindex(pvs)
                 # remove the redundant bit
                 pvs[i] = pvs[i] & mask(left)
             end
         else
             push!(newnames, name)
-            for i in 1:endof(pvs)
+            for i in 1:lastindex(pvs)
                 # circular left shift
                 pvs[i] = ((pvs[i] << 1) & mask(left)) | bitat(pvs[i], left)
             end

src/memory.jl

@@ -57,7 +57,7 @@ function Base.getindex(mem::SizedMemory, i::Integer)
     return unsafe_load(mem.ptr, i)
 end
 
-function Base.endof(mem::SizedMemory)
+function Compat.lastindex(mem::SizedMemory)
     return Int(mem.len)
 end
 

src/nfa.jl

@@ -10,7 +10,7 @@ function NFANode()
 end
 
 function Base.show(io::IO, node::NFANode)
-    print(io, summary(node), "(<", length(node.edges), " edges", '@', object_id(node), ">)")
+    print(io, summary(node), "(<", length(node.edges), " edges", '@', objectid(node), ">)")
 end
 
 struct NFA

src/precond.jl

@@ -46,7 +46,7 @@ end
 function Base.push!(precond::Precondition, kv::Pair{Symbol,Value})
     name, value = kv
     i = findfirst(n -> n == name, precond.names)
-    if i == 0
+    if i == nothing
         push!(precond.names, name)
         push!(precond.values, value)
     else
@@ -74,7 +74,7 @@ function Base.start(precond::Precondition)
 end
 
 function Base.done(precond::Precondition, i)
-    return i > endof(precond.names)
+    return i > lastindex(precond.names)
 end
 
 function Base.next(precond::Precondition, i)