Merge pull request #12 from ChevronETC/julia07

samtkaplan · web-flow · commit a99ac092bd85 · 2018-08-10T10:30:34.000-05:00
Updates for Julia 0.7
diff --git a/.travis.yml b/.travis.yml
@@ -3,8 +3,7 @@ os:
   - linux
   - osx
 julia:
-  - 0.5
-  - 0.6
+  - 0.7
   - nightly
 matrix:
   allow_failures:
diff --git a/REQUIRE b/REQUIRE
@@ -1,4 +1,4 @@
-julia 0.5
+julia 0.7
 
 LightXML
 Documenter
diff --git a/appveyor.yml b/appveyor.yml
@@ -1,7 +1,6 @@
 environment:
   matrix:
-    - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.5/julia-0.5-latest-win64.exe"
-    - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.6/julia-0.6-latest-win64.exe"
+    - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.7/julia-0.7-latest-win64.exe"
 
 branches:
   only:
diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl
@@ -1,4 +1,4 @@
-using TeaSeis, BenchmarkTools
+using TeaSeis, BenchmarkTools, Random
 
 const fs="."
 const N1,N2,N3,N4,N5=100,11,12,2,3
@@ -62,7 +62,7 @@ function makepartialframe()
     f = makefname()
     io = jsopen(f,"w",axis_lengths=[N1,N2,1])
     d,h = allocframe(io)
-    srand(0)
+    Random.seed!(0)
     rand!(d)
     alive = fill(false, N2)
     alive[randperm(N2)[1:div(N2,2)]] .= true
diff --git a/demo/demo.jl b/demo/demo.jl
@@ -32,7 +32,7 @@ trcs, hdrs = allocframe(io)
 for ifrm = 1:size(io,3)
     readframe!(io, trcs, hdrs, ifrm)
     data_read[:,:,ifrm] = trcs
-    write(STDOUT, "read frame, trcs and hdrs API $(get(prop(io,stockprop[:FRAME]),hdrs[:,1]))\n")
+    write(stdout, "read frame, trcs and hdrs API $(get(prop(io,stockprop[:FRAME]),hdrs[:,1]))\n")
 end
 
 # demonstrate that the extrema of the written and read data agree with each other:
diff --git a/docs/make.jl b/docs/make.jl
@@ -3,4 +3,4 @@ using Documenter, TeaSeis
 makedocs(
     modules = [TeaSeis]
 )
-cp("build/README.md", "../README.md", remove_destination=true)
+cp("build/README.md", "../README.md", force=true)
diff --git a/src/TeaSeis.jl b/src/TeaSeis.jl
@@ -1,8 +1,6 @@
-__precompile__()
-
 module TeaSeis
 
-using LightXML
+using Dates, LightXML
 
 import
 Base.==,
diff --git a/src/dataproperty.jl b/src/dataproperty.jl
@@ -1,10 +1,10 @@
-immutable DataProperty
+struct DataProperty
     label::String
     format::Type
     value::Any
 end
 
-function DataProperty{T<:Real}(label::String, formatstring::String, value::T)
+function DataProperty(label::String, formatstring::String, value::T) where T<:Real
     format = Int32
     if formatstring == "int"
         format = Int32
diff --git a/src/extent.jl b/src/extent.jl
@@ -1,4 +1,4 @@
-type Extent
+mutable struct Extent
     name::String
     path::String
     index::Int32
diff --git a/src/geometry.jl b/src/geometry.jl
@@ -1,4 +1,4 @@
-immutable Geometry
+struct Geometry
     u1::Int
     un::Int
     v1::Int
diff --git a/src/teaseisio.jl b/src/teaseisio.jl
diff --git a/src/tracecompressor.jl b/src/tracecompressor.jl
@@ -1,4 +1,4 @@
-type TraceCompressor{T}
+mutable struct TraceCompressor{T}
     nsamples::Int
     nwindows::Int
     windowln::Int
@@ -89,8 +89,8 @@ function unpackframe!(c::TraceCompressor{Int16}, frame32::Array{Float32,2}, buff
 end
 
 function allocframebuf(c::TraceCompressor{Int16}, ntraces::Int)
-    bufarray = Array{UInt8}(ntraces * tracelength(c))
-    IOBuffer(bufarray, true, true, length(bufarray))
+    bufarray = Array{UInt8}(undef, ntraces * tracelength(c))
+    IOBuffer(bufarray, read=true, write=true, maxsize=length(bufarray))
 end
 
 tracelength(c::TraceCompressor{Int16})   = iseven(c.nsamples) == true ? 4 * c.nwindows + 2 * c.nsamples : 4 * c.nwindows + 2 * (c.nsamples + 1)
diff --git a/src/traceproperty.jl b/src/traceproperty.jl
@@ -1,17 +1,18 @@
-immutable TracePropertyDef{T}
+struct TracePropertyDef{T}
     label::String
     description::String
     format::Type{T}
     elementcount::Int32
-end
-function TracePropertyDef{T<:Number}(label::String, description::String, format::Type{T}, elementcount::Int)
-    _format = format
-    if format == UInt8
-        _format = Array{UInt8,1}
-    elseif elementcount > 1
-        _format = Array{format,1}
+
+    function TracePropertyDef(label::AbstractString, description::AbstractString, format::DataType, elementcount::Integer)
+        _format = format
+        if format == UInt8
+            _format = Array{UInt8,1}
+        elseif elementcount > 1
+            _format = Array{format,1}
+        end
+        new{_format}(String(label), String(description), _format, Int32(elementcount))
     end
-    TracePropertyDef(label, description, _format, Int32(elementcount))
 end
 function TracePropertyDef(label::AbstractString)
     for propdef in stockprop
@@ -21,26 +22,25 @@ function TracePropertyDef(label::AbstractString)
     end
     return TracePropertyDef(label, "", Int32, 1)
 end
-TracePropertyDef{T<:Number}(label::AbstractString, description::AbstractString, format::Type{T}, elementcount::Int) = TracePropertyDef(String(label), String(description), format, elementcount)
 
-type TraceProperty{T}
+mutable struct TraceProperty{T}
     def::TracePropertyDef{T}
     byteoffset::Int32
 end
-TraceProperty{T}(def::TracePropertyDef{T}, byteoffset::Int64) = TraceProperty(def, Int32(byteoffset))
+TraceProperty(def::TracePropertyDef{T}, byteoffset::Int64) where {T} = TraceProperty(def, Int32(byteoffset))
 
-function TraceProperty(label::String, description::String, format::String, elementcount::Int32, byteoffset::Int32)
-    _format = Void
+function TraceProperty(label::AbstractString, description::AbstractString, format::AbstractString, elementcount::Int32, byteoffset::Int32)
+    _format = Nothing
     if format == "INTEGER"
-        _format = elementcount == 1 ? Int32 : Array{Int32,1}
+        _format = Int32
     elseif format == "LONG"
-        _format = elementcount == 1 ? Int64 : Array{Int64,1}
+        _format = Int64
     elseif format == "FLOAT"
-        _format = elementcount == 1 ? Float32 : Array{Float32,1}
+        _format = Float32
     elseif format == "DOUBLE"
-        _format = elementcount == 1 ? Float64 : Array{Float64,1}
+        _format = Float64
     elseif format == "BYTESTRING"
-        _format = Array{UInt8,1}
+        _format = UInt8
     else
         error("unrecognized format: $(format)")
     end
@@ -75,15 +75,15 @@ in(item::String, col::Array{TraceProperty,1}) = in(item, propdef(col))
 
 function proplabel(props::Array{TracePropertyDef,1})
     n = length(props)
-    labels = Array{String}(n)
+    labels = Array{String}(undef, n)
     for i = 1:n
         labels[i] = props[i].label
     end
     return labels
 end
 
-sizeof{T<:Number}(propdef::TracePropertyDef{T}) = sizeof(T)*propdef.elementcount
-sizeof{T<:Array}(propdef::TracePropertyDef{T}) = sizeof(eltype(T))*propdef.elementcount
+sizeof(propdef::TracePropertyDef{T}) where {T<:Number} = sizeof(T)*propdef.elementcount
+sizeof(propdef::TracePropertyDef{T}) where {T<:Array} = sizeof(eltype(T))*propdef.elementcount
 sizeof(prop::TraceProperty) = sizeof(prop.def)
 
 propdef(prop::TraceProperty) = prop.def
diff --git a/test/test_compat.jl b/test/test_compat.jl
@@ -1,4 +1,4 @@
-using TeaSeis, LightXML, Base.Test
+using TeaSeis, LightXML, Test
 
 @testset "Compat Test" for (pmlbls, jslbls, pdefs) in (
     (("DPTH_IND", "CHAN", "XLINE_NO", "ILINE_NO", "OFB_NO"),
diff --git a/test/test_geometry.jl b/test/test_geometry.jl
@@ -1,4 +1,4 @@
-using TeaSeis, Base.Test
+using TeaSeis, Test
 
 @testset "Geometry" begin
     g = Geometry(
diff --git a/test/test_teaseisio.jl b/test/test_teaseisio.jl
@@ -1,13 +1,4 @@
-using TeaSeis, Base.Test
-
-# macro for compatability with julia 0.5
-macro mytest_warn(msg, expr)
-    if VERSION >= v"0.6.0"
-        return :(@test_warn $msg $expr)
-    else
-        return :(nothing)
-    end
-end
+using TeaSeis, Test, Random
 
 ENV["JAVASEIS_DATA_HOME"] = ""
 ENV["PROMAX_DATA_HOME"] = ""
@@ -169,11 +160,11 @@ mkdir(rundir)
         end
     end
     close(io)
-    @mytest_warn "Corrupt" jsopen(joinpath(rundir,"data.js")) # see top of file for @mytest_warn macro (for compatability with julia 0.5)
+    @test_warn "" jsopen(joinpath(rundir,"data.js"))
     rm(jsopen(joinpath(rundir,"data.js")))
 
     @testset "lstrt=$(lstrt),lincrs=$(lincrs),sz=$(sz),second=$(second),T=$(T)" for lstrt in ([1,1,1,1,1], [10,20,30,40,50]), lincrs in ([1,1,1,1,1],[1,2,3,4,5]), sz in ([5,6,7], [5,6,7,8], [5,6,7,8,9]), second in (["."],["$(rundir)/second"]), T in (Float32, Int16)
-        write(STDOUT, "lstrt=$(lstrt),lincrs=$(lincrs),sz=$(sz),second=$(second),T=$(T)\n")
+        write(stdout, "lstrt=$(lstrt),lincrs=$(lincrs),sz=$(sz),second=$(second),T=$(T)\n")
         labls = ["SAMPLE", "TRACE", "FRAME", "VOLUME", "HYPRCUBE"]
         pdefs = [stockprop[:SAMPLE], stockprop[:TRACE], stockprop[:FRAME], stockprop[:VOLUME], stockprop[:HYPRCUBE]]
         unts  = [stockunit[:UNKNOWN], "unknown", "unknown", "unknown", "unknown"]
@@ -241,7 +232,7 @@ mkdir(rundir)
         @test filesize(joinpath(filename1, "TraceMap")) == prod(sz[3:end]) * sizeof(Int32)
         @test io.mapped == true
         iotrcmp = open(joinpath(filename1, "TraceMap"))
-        @test read(iotrcmp,Int32,prod(sz[3:end])) == zeros(Int32,prod(sz[3:end]))
+        @test read!(iotrcmp,Array{Int32}(undef,prod(sz[3:end]))) == zeros(Int32,prod(sz[3:end]))
         close(iotrcmp)
 
         #
@@ -317,13 +308,13 @@ mkdir(rundir)
             map(itrc->set!(prop(io,propVI32), hdrs, itrc, [itrc,idxs[1]]), 1:sz[2])
             map(itrc->set!(prop(io,propVI64), hdrs, itrc, [itrc,idxs[1]]), 1:sz[2])
             map(itrc->set!(prop(io,propSTR), hdrs, itrc, "TEST"         ), 1:sz[2])
-            writeframe(io, reshape(trcs[:,:,ind2sub(size(io)[3:end],i)...],sz[1],sz[2]), hdrs)
+            writeframe(io, reshape(trcs[:,:,CartesianIndices(size(io)[3:end])[i]],sz[1],sz[2]), hdrs)
             @test isempty(io) == false
         end
 
         # ensure TraceMap was correctly written
         iotrcmap = open(joinpath(filename1, "TraceMap"))
-        @test read(iotrcmap, Int32, length(io)) == sz[2]*ones(Int32,prod(sz[3:end]))
+        @test read!(iotrcmap, Array{Int32}(undef,length(io))) == sz[2]*ones(Int32,prod(sz[3:end]))
         close(iotrcmap)
 
         # ensure that the trace extents were written properly
@@ -337,7 +328,7 @@ mkdir(rundir)
 
             if T == Float32
                 ioext = open(io.trcextents[i].path)
-                trcstest = convert(Array{Float32,1}, read(ioext, T, div(io.trcextents[i].size, sizeof(T))))
+                trcstest = convert(Array{Float32,1}, read!(ioext, Array{T}(undef, div(io.trcextents[i].size, sizeof(T)))))
                 close(ioext)
                 strt = div(io.trcextents[i].start, sizeof(T)) + 1
                 stop = strt + div(io.trcextents[i].size, sizeof(T)) - 1
@@ -366,7 +357,7 @@ mkdir(rundir)
             @test typeof(hdrs) == Array{UInt8,2}
             @test size(trcstest) == (sz[1],sz[2])
             @test size(hdrs) == (headerlength(io),sz[2])
-            @test vec(trcstest) ≈ vec(trcs[:,:,ind2sub(size(io)[3:end],i)...])
+            @test vec(trcstest) ≈ vec(trcs[:,:,CartesianIndices(size(io)[3:end])[i]])
             for itrc = 1:sz[2]
                 @test get(prop(io,stockprop[:TRACE]), hdrs, itrc) == lstrt[2] + (itrc-1)*lincrs[2]
                 @test get(prop(io,stockprop[:FRAME]), hdrs, itrc) == idxs[1]
@@ -553,7 +544,7 @@ mkdir(rundir)
         sz_sparse[1] = sz[1]
 
         frmtrcs, hdrs = allocframe(io)
-        for idx in CartesianRange(ntuple(i->sz_sparse[2+i],n-2))
+        for idx in CartesianIndices(ntuple(i->sz_sparse[2+i],n-2))
             jtrc = 1
             for itrc = 1:sz[2]
                 if jtrc <= sz_sparse[2] && itrc == indexes[1][jtrc]
@@ -584,7 +575,7 @@ mkdir(rundir)
         # read test, explicit fold and headers, multiple extents
         #
         io = jsopen(filename1)
-        for idx in CartesianRange(ntuple(i->sz_sparse[2+i], n-2))
+        for idx in CartesianIndices(ntuple(i->sz_sparse[2+i], n-2))
             fld = readframe!(io, frmtrcs, hdrs, idx.I...)
             @test fld == sz_sparse[2]
             for jtrc = 1:sz_sparse[2]
diff --git a/test/test_tracecompressor.jl b/test/test_tracecompressor.jl
@@ -1,4 +1,4 @@
-using TeaSeis, Base.Test
+using TeaSeis, Test
 
 @testset "Compressor Tests" begin
     # packing a single trace

-Original file line number
+Diff line change
   - linux
   - osx
 julia:
 -  - 0.5
 -  - 0.6
 +  - 0.7
   - nightly
 matrix:
   allow_failures:
Original file line number	Diff line number	Diff line change
`@@ -3,4 +3,4 @@ using Documenter, TeaSeis`
`3`	`3`	`makedocs(`
`4`	`4`	`modules = [TeaSeis]`
`5`	`5`	`)`
`6`		`-cp("build/README.md", "../README.md", remove_destination=true)`
	`6`	`+cp("build/README.md", "../README.md", force=true)`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-type Extent`
	`1`	`+mutable struct Extent`
`2`	`2`	`name::String`
`3`	`3`	`path::String`
`4`	`4`	`index::Int32`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-immutable Geometry`
	`1`	`+struct Geometry`
`2`	`2`	`u1::Int`
`3`	`3`	`un::Int`
`4`	`4`	`v1::Int`