Merge pull request #5 from galenlynch/femtoCleaner

Deprecations for 0.7 and 1.0

Author: galenlynch

.travis.yml

@@ -7,6 +7,7 @@ os:
 julia:
   - 0.6
   - 0.7
+  - 1.0
   - nightly
 
 matrix:

README.md

@@ -23,7 +23,7 @@ For documentation on the use of `metadata`, please see the latest docs below.
 - [**LATEST**][docs-latest-url] — *in-development version of the documentation.*
 
 ## Project Status
-This package is tested against Julia `0.6`, `0.7`, and nightlies on Linux, OS X, and Windows.
+This package is tested against Julia `0.6`, `0.7`, `1.0`, and nightlies on Linux, OS X, and Windows.
 
 This package only supports reading from continuous files at the moment, with no immediate
 plans to support spike data.

REQUIRE

@@ -1,2 +1,3 @@
 julia 0.6
-LightXML 0.3
+LightXML 0.3 0.9
+Compat 1.0 2

appveyor.yml

@@ -5,6 +5,8 @@ environment:
   - 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/x86/0.7/julia-0.7-latest-win32.exe"
   - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/0.7/julia-0.7-latest-win64.exe"
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x86/1.0/julia-1.0-latest-win32.exe"
+  - JULIA_URL: "https://julialang-s3.julialang.org/bin/winnt/x64/1.0/julia-1.0-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"
 

src/OpenEphysLoader.jl

@@ -6,12 +6,15 @@ Provides array interfaces to file contents, without loading the entire file into
 """
 module OpenEphysLoader
 # Module to interact with Open Ephys files
-using LightXML
+using Compat, LightXML
+
+@static if VERSION >= v"0.7.0-DEV.2575"
+    using Dates
+end
+
 import Base: show,
-    showcompact,
     showerror,
     size,
-    linearindexing,
     getindex,
     setindex!,
     length

src/continuous.jl

@@ -47,9 +47,9 @@ mutable struct DataBlock <: BlockBuffer
 end
 function DataBlock()
     head = BlockHeader()
-    body = Vector{UInt8}(CONT_REC_BODY_SIZE)
-    data = Vector{CONT_REC_SAMP_BITTYPE}(CONT_REC_N_SAMP)
-    tail =  Vector{UInt8}(CONT_REC_TAIL_SIZE)
+    body = @compat Vector{UInt8}(undef, CONT_REC_BODY_SIZE)
+    data = @compat Vector{CONT_REC_SAMP_BITTYPE}(undef, CONT_REC_N_SAMP)
+    tail =  @compat Vector{UInt8}(undef, CONT_REC_TAIL_SIZE)
     DataBlock(head, body, data, tail)
 end
 
@@ -311,7 +311,7 @@ function convert_block!(block::DataBlock)
             unsafe_store!(ptr, ntoh(unsafe_load(ptr, idx)), idx)
         end
     end
-    unsafe_copy!(pointer(block.data), ptr, CONT_REC_N_SAMP)
+    @compat unsafe_copyto!(pointer(block.data), ptr, CONT_REC_N_SAMP)
     return block.data
 end
 

src/metadata.jl

@@ -309,7 +309,7 @@ function OERecordingMeta(settings::OESettings{S, T}, rec_e::LightXML.XMLElement)
         throw(CorruptedException("Could not find PROCESSOR elements"))
     end
     nproc = length(proc_es)
-    rec_procs = Vector{T}(nproc)
+    @compat rec_procs = Vector{T}(undef, nproc)
 
     for (i, proc_e) in enumerate(proc_es)
         id = find_matching_proc(settings.recording_chain, proc_e)
@@ -367,7 +367,7 @@ function OEExperMeta(settings::OESettings{S, T}, exper_e::LightXML.XMLElement) w
         throw(CorruptedException("Could not find RECORDING elements"))
     end
     nrec = length(rec_es)
-    recordings = Vector{OERecordingMeta{T}}(nrec)
+    @compat recordings = Vector{OERecordingMeta{T}}(undef, nrec)
     for (i, rec_e) in enumerate(rec_es)
         recordings[i] = OERecordingMeta(settings, rec_e)
     end
@@ -424,7 +424,7 @@ function channel_arr(proc_e::LightXML.XMLElement, ::Type{T} = String) where {T<:
     end
     nchan = length(channel_vec)
     chan_rec = fill(false, nchan)
-    chnos = Array{Int}(nchan)
+    @compat chnos = Array{Int}(undef, nchan)
     for (i, chan_e) in enumerate(channel_vec)
         sel_e = required_find_element(chan_e, "SELECTIONSTATE")
         record_attr = attribute(sel_e, "record", required=true)
@@ -441,7 +441,7 @@ function channel_arr(proc_e::LightXML.XMLElement, ::Type{T} = String) where {T<:
     # Channel info
     ch_info_e = required_find_element(proc_e, "CHANNEL_INFO")
     chinfo_children = collect(child_elements(ch_info_e))
-    channels = Array{OEChannel{T}}(nrec)
+    @compat channels = Array{OEChannel{T}}(undef, nrec)
     recno = 1
     for (i, chan_e) in enumerate(chinfo_children)
         if chan_rec[i]
@@ -451,7 +451,7 @@ function channel_arr(proc_e::LightXML.XMLElement, ::Type{T} = String) where {T<:
             chname = attribute(chan_e, "name", required = true)
             bitvolt_attr = attribute(chan_e, "gain", required = true)
             bitvolts = parse(Float64, bitvolt_attr)
-            channels[recno] = OEChannel{String}(chname,
+            @compat channels[recno] = OEChannel{String}(chname,
                                                 info_chno,
                                                 bitvolts,
                                                 Vector{Int}(),
@@ -517,7 +517,7 @@ function recordings_are_consistent(rec_es::Vector{LightXML.XMLElement})
     chan_xml = XmlNode("CHANNEL", XmlNode[], ["name", "filename"])
     proc_xml = XmlNode("PROCESSOR", [chan_xml], ["id"])
     nrec = length(rec_es)
-    attr_sets = Vector{Set{String}}(nrec)
+    @compat attr_sets = Vector{Set{String}}(undef, nrec)
     for (i, rec_e) in enumerate(rec_es)
         attr_sets[i] = Set(recurse_xml_attr(rec_e, proc_xml))
     end
@@ -585,7 +585,7 @@ end
 ### Helper Functions ###
 function required_find_element(e::LightXML.XMLElement, name::AbstractString)
     maybe_e = find_element(e, name)
-    isa(maybe_e, Void) && throw(CorruptedException("Could not find $name element"))
+    @compat isa(maybe_e, Nothing) && throw(CorruptedException("Could not find $name element"))
     return maybe_e
 end
 
@@ -614,10 +614,10 @@ end
 show(io::IO, a::SignalNode) = show(io, a.content)
 
 showfields(io::IO, a::Any) = showfields(IOContext(io, :depth => 0), a)
-function showfields(io::IOContext, a::Any)
+function showfields(io::IOContext, a::T) where T
     depth = get(io, :depth, 0)
     pad = "  " ^ depth
-    fields = fieldnames(a)
+    fields = fieldnames(T)
     depth > 0 && print(io, '\n')
     next_io = IOContext(IOContext(io, :typeinfo => Any), :depth => depth + 1)
     for field in fields

src/original.jl

@@ -161,7 +161,7 @@ function OriginalHeader(io::IOStream)
     length(head) == HEADER_N_BYTES || throw(CorruptedException("Header is malformed"))
     headstr = transcode(String, head)
     isvalid(headstr) || throw(CorruptedException("Header is malformed"))
-    substrs =  split(headstr, ';', keep = false)
+    substrs =  Compat.split(headstr, ';', keepempty = false)
     resize!(substrs, N_HEADER_LINE)
     return OriginalHeader(
         map(parseline, zip(HEADER_MATTYPES, HEADER_TARGET_TYPES, substrs))...
@@ -170,15 +170,19 @@ end
 
 "Parse a line of Matlab source code"
 function parseline end
-parseline(::Type{M}, ::Type{T}, str::AbstractString) where {T, M<:MATLABdata} = parseto(T, matread(M, str))::T
+function parseline(
+    ::Type{M}, ::Type{T}, str::AbstractString
+) where {T, M<:MATLABdata}
+    parseto(T, matread(M, str))
+end
 parseline(tup::Tuple) = parseline(tup...)
 
 "Convert a string to the desired type"
 function parseto end
-parseto(::Type{T}, str::AbstractString) where {T<:Number} = parse(str)::T
+parseto(::Type{T}, str::AbstractString) where T = parse(T, str)
 function parseto(::Type{DateTime}, str::AbstractString)
     m = match(HEADER_DATE_REGEX, str)
-    isa(m, Void) && throw(CorruptedException("Time created is improperly formatted"))
+    isa(m, @compat(Nothing)) && throw(CorruptedException("Time created is improperly formatted"))
     d = DateTime(m.captures[1], HEADER_DATEFORMAT)
     local hr, mn, sc
     try
@@ -203,32 +207,34 @@ function parseto(::Type{DateTime}, str::AbstractString)
 end
 parseto(::Type{VersionNumber}, str::AbstractString) = VersionNumber(str)
 parseto(::Type{String}, str::AbstractString) = String(str)
-parseto(::Type{T}, str::T) where {T<:AbstractString} = str
+parseto(::Type{T}, str::T) where T<:AbstractString = str
 
 "read a Matlab source line"
 function matread(::Type{T}, str::S) where {T<:MATLABdata, S<:AbstractString}
     regex = rx(T)
     goodread = false
     local m
-    if ismatch(regex, str)
+    if @compat occursin(regex, str)
         m = match(rx(T), str)
         isempty(m.captures) && throw(CorruptedException("Cannot parse header"))
     end
-    return S(m.captures[1])
+    return string(m.captures[1])
 end
 
 ### Matlab regular expressions ###
 rx(::Type{MATstr}) = r" = '(.*)'$"
 rx(::Type{MATint}) = r" = (\d*)$"
 rx(::Type{MATfloat}) = r" = ([-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)$"
 
-function show(io::IO, a::OriginalHeader)
-    fields = fieldnames(a)
+function show(io::IO, a::O) where O<:OriginalHeader
+    fields = fieldnames(O)
     for field in fields
-        println(io, "$field: $(getfield(a, field))")
+        println(io, field, ": ", getfield(a, field))
     end
 end
-showcompact(io::IO, header::OriginalHeader) = show(io, "channel: $(header.channel)")
+function showcompact(io::IO, header::OriginalHeader)
+    show(IOContext(io, :compact => true), "channel: $(header.channel)")
+end
 function show(io::IO, headers::Vector{OriginalHeader})
     for header in headers
         println(io, showcompact(header))

test/continuous.jl

@@ -1,5 +1,19 @@
+__precompile__()
 module TestContinuous
-using OpenEphysLoader, Main.TestUtilities, Main.TestOriginal, Base.Test
+using Compat, OpenEphysLoader
+using Main.TestUtilities, Main.TestOriginal
+
+@static if VERSION < v"0.7.0-DEV.2005"
+    using Base.Test
+else
+    using Test
+end
+
+@static if VERSION >= v"0.7.0-DEV.2575"
+    using Random
+end
+
+
 # Helper functions to test OpenEphysLoader's handling of
 # continuous files
 
@@ -72,7 +86,7 @@ end
 
 function block_idxes(blockno::Integer)
     nblocksamp = OpenEphysLoader.CONT_REC_N_SAMP
-    return (blockno - 1) * nblocksamp + (1:nblocksamp)
+    return (blockno - 1) * nblocksamp .+ (1:nblocksamp)
 end
 
 function to_block_contents(D::Vector, blockno::Integer, startsamp::Integer)
@@ -252,7 +266,7 @@ function write_continuous(
             io,
             view(
                 padded,
-                offset + (1:OpenEphysLoader.CONT_REC_N_SAMP)
+                offset .+ (1:OpenEphysLoader.CONT_REC_N_SAMP)
             ),
             tblock,
             recno
@@ -336,9 +350,9 @@ function time_conversion(
     startsamp::Integer,
     nsamp::Integer
 ) where T<:AbstractFloat
-    timepoints = (time_conversion(Int, startsamp, nsamp) - 1) / 30000
+    timepoints = (time_conversion(Int, startsamp, nsamp) .- 1) / 30000
     converted_times = similar(timepoints, T)
-    copy!(converted_times, timepoints)
+    @compat copyto!(converted_times, timepoints)
     return converted_times
 end
 

test/metadata.jl

@@ -1,5 +1,18 @@
+__precompile__()
 module TestMetadata
-using OpenEphysLoader, Main.TestUtilities, Base.Test
+using Compat, OpenEphysLoader
+using Main.TestUtilities
+
+@static if VERSION < v"0.7.0-DEV.2005"
+    using Base.Test
+else
+    using Test
+end
+
+@static if VERSION >= v"0.7.0-DEV.2575"
+    using Dates
+    using Random
+end
 
 test_dir = joinpath(dirname(@__FILE__), "data")
 
@@ -31,7 +44,7 @@ test_dir = joinpath(dirname(@__FILE__), "data")
         true, # dsp_offset
         0 # dsp_cutoff
     )
-    const BITVOLTS = 0.19499999284744263
+    BITVOLTS = 0.19499999284744263
     channel_1_ans = (
         "CH1",
         0,
@@ -71,10 +84,10 @@ test_dir = joinpath(dirname(@__FILE__), "data")
     test_fields(expermeta, expermeta_ans..., recordings = false, settings = false)
     @test ! isempty(expermeta.recordings)
     test_fields(expermeta.recordings[1], recording_ans..., recording_processors = false)
-    @test (show(DevNull, settings.recording_chain); true) # Test that this does not error
-    @test (show(DevNull, settings); true)
-    @test (show(DevNull, expermeta.recordings[1]); true)
-    @test (show(DevNull, expermeta); true)
+    @test @compat (show(devnull, settings.recording_chain); true) # Test that this does not error
+    @test @compat (show(devnull, settings); true)
+    @test @compat (show(devnull, expermeta.recordings[1]); true)
+    @test @compat (show(devnull, expermeta); true)
 
     #plug in settings
     @test_throws CorruptedException metadata(

test/original.jl

@@ -1,5 +1,16 @@
+__precompile__()
 module TestOriginal
-using OpenEphysLoader, Main.TestUtilities, Base.Test
+using Compat, OpenEphysLoader
+using Main.TestUtilities
+
+@static if VERSION < v"0.7.0-DEV.2005"
+    using Base.Test
+else
+    using Test
+end
+@static if VERSION >= v"0.7.0-DEV.2575"
+    using Dates
+end
 
 export write_fheader_fun,
     verify_header
@@ -29,7 +40,7 @@ function write_fheader_fun(
     @assert isfile(headerpath) "Could not load header file"
     open(headerpath, "r") do readio
         @assert stat(readio).size >= nbytes "Header not long enough"
-        head = readstring(readio)
+        head = read(readio, String)
     end
     trunchead = head[1:nbytes]
     return io::IOStream -> write(io, trunchead)
@@ -55,11 +66,11 @@ end
     filecontext(write_fheader_fun()) do io
         header = OriginalHeader(io)
         verify_header(header)
-        @test (show(DevNull, header); true) # test that it does not error
-        @test (showcompact(DevNull, header); true)
+        @test (show(@compat(devnull), header); true) # test that it does not error
+        @test (OpenEphysLoader.showcompact(@compat(devnull), header); true)
     end
 
-    @test (showerror(DevNull, CorruptedException("test")); true)
+    @test (showerror(@compat(devnull), CorruptedException("test")); true)
 
     # truncated header
     filecontext(write_fheader_fun(512)) do io

test/runtests.jl

@@ -1,4 +1,9 @@
-using Base.Test
+@static if VERSION < v"0.7.0-DEV.2005"
+    using Base.Test
+else
+    using Test
+end
+
 @testset "OpenEphysLoader.jl" begin
     include("util.jl")
     include("original.jl")