Merge pull request #3 from tlnagy/tn/1.0-fixes

update for Julia 1.0

.travis.yml

@@ -4,7 +4,7 @@ os:
   - linux
   - osx
 julia:
-  - 0.6
+  - 1.0
   - nightly
 notifications:
   email: false

README.md

@@ -10,8 +10,6 @@ Add FileIO.jl integration for FCS files
 ```julia
 julia> using FileIO
 
-julia> using FCSFiles
-
 julia> flowrun = load("example.fcs")
 FCS.FlowSample{Float32}
     Machine: LSRFortessa

REQUIRE

@@ -1,2 +1,2 @@
-julia 0.6
+julia 0.7
 FileIO

src/FCSFiles.jl

@@ -8,11 +8,7 @@ include("parse.jl")
 
 export FlowSample
 
-try
-    add_format(format"FCS", "FCS", [".fcs"])
-end
-
-function FileIO.load(f::File{format"FCS"})
+function load(f::File{format"FCS"})
     open(f) do io
         offsets = parse_header(io)
 

src/parse.jl

@@ -1,16 +1,20 @@
 function parse_header(io)
     seekstart(io)
-    version = String(read(io, UInt8, 6))
+    rawversion = Array{UInt8}(undef, 6)
+    read!(io, rawversion)
+    version = String(rawversion)
     if "$version" != "FCS3.0" && version != "FCS3.1"
         warn("$version files are not guaranteed to work")
     end
     seek(io, 10)
     # start, end positions of TEXT, DATA, and ANALYSIS sections
-    offsets = Array{Int64}(6)
+    offsets = Array{Int64}(undef, 6)
     for i in 1:6
         # offsets are encoded as ASCII strings
-        raw_str = String(read(io, UInt8, 8))
-        offsets[i] = parse(Int, strip(join(raw_str)))
+        raw_str = Array{UInt8}(undef, 8)
+        read!(io, raw_str)
+        offsets_str = String(raw_str)
+        offsets[i] = parse(Int, strip(join(offsets_str)))
     end
 
     # DATA offsets are larger than 99,999,999bytes
@@ -24,14 +28,16 @@ end
 function parse_text(io, start_text::Int, end_text::Int)
     seek(io, start_text)
     # TODO: Check for supplemental TEXT file
-    raw_text = String(read(io, UInt8, end_text - start_text + 1))
+    raw_btext = Array{UInt8}(undef, end_text - start_text + 1)
+    read!(io, raw_btext)
+    raw_text = String(raw_btext)
     delimiter = raw_text[1]
 
     text_mappings = Dict{String, String}()
     # initialize iterator
-    prev, state = next(raw_text, start(raw_text))
-    while !done(raw_text, state)
-        i, state = next(raw_text, state)
+    iter_result = iterate(raw_text)
+    while iter_result !== nothing
+        i, state = iter_result
 
         # found a new key, value pair
         if i == '$'
@@ -42,7 +48,7 @@ function parse_text(io, start_text::Int, end_text::Int)
             # FCS keywords are case insensitive so force them uppercase
             text_mappings["\$"*uppercase(key)] = value
         end
-        prev = i
+        iter_result = iterate(raw_text, state)
     end
     text_mappings
 end
@@ -56,7 +62,8 @@ function parse_data(io,
     # Add support for data types other than float
     (text_mappings["\$DATATYPE"] != "F") && error("Non float32 support not implemented yet. Please see github issues for this project.")
 
-    flat_data = read(io, Float32, (end_data - start_data + 1) ÷ 4)
+    flat_data = Array{Float32}(undef, (end_data - start_data + 1) ÷ 4)
+    read!(io, flat_data)
     endian_func = get_endian_func(text_mappings)
     map!(endian_func, flat_data, flat_data)
 

src/type.jl

@@ -1,4 +1,4 @@
-immutable FlowSample{T}
+struct FlowSample{T}
     data::Dict{String, Vector{T}}
     params::Dict{String, String}
 end
@@ -38,6 +38,5 @@ Base.haskey(f::FlowSample, x) = haskey(f.data, x)
 Base.getindex(f::FlowSample, key) = f.data[key]
 Base.keys(f::FlowSample) = keys(f.data)
 Base.values(f::FlowSample) = values(f.data)
-Base.start(iter::FlowSample) = start(iter.data)
-Base.next(iter::FlowSample, state) = next(iter.data, state)
-Base.done(iter::FlowSample, state) = done(iter.data, state)
+Base.iterate(iter::FlowSample) = Base.iterate(iter.data)
+Base.iterate(iter::FlowSample, state) = Base.iterate(iter.data, state)

src/utils.jl

@@ -29,8 +29,9 @@ and the state of the iterator.
 function grab_word(iter, state, delimiter::Char)
     word = Char[]
     prev = ' '
-    while !done(iter, state)
-        i, state = next(iter, state)
+    iter_result = iterate(iter, state)
+    while iter_result !== nothing
+        i, state = iter_result
 
         # only add character if the current and previous are both
         # delimiters (i.e. escaped) or neither are
@@ -40,6 +41,7 @@ function grab_word(iter, state, delimiter::Char)
         else
             break
         end
+        iter_result = iterate(iter, state)
     end
     join(word), state
 end
@@ -53,7 +55,7 @@ returned by `parse_text`
 """
 function verify_text(text_mappings::Dict{String, String})
     # get all parameterized keywords $P1N, $P2N, etc
-    is_param = [contains(keyword, "n") for keyword in required_keywords]
+    is_param = [occursin("n", keyword) for keyword in required_keywords]
 
     # verify that all non-parameterized keywords are present in the mapping
     for non_param in required_keywords[.~is_param]
@@ -69,7 +71,7 @@ function verify_text(text_mappings::Dict{String, String})
 
     for params in required_keywords[is_param]
         for i in 1:n_params
-            if !haskey(text_mappings, replace(params, "n", i))
+            if !haskey(text_mappings, replace(params, "n"=>i))
                 error("FCS file is corrupted. It is missing required keyword $non_param in its TEXT section")
             end
         end

test/runtests.jl

@@ -1,6 +1,6 @@
 using FCSFiles
 using FileIO
-using Base.Test
+using Test
 
 flowrun = load("testdata/BD-FACS-Aria-II.fcs")