Resolve deprecation warnings for v0.7

.travis.yml

@@ -3,13 +3,16 @@ os:
     - linux
     - osx
 julia:
-    - 0.5
-    - 0.6
+    - 0.7
+    - 1.0
     - nightly
+addons:
+  apt:
+    packages:
+        - hdf5-tools
+before_script:
+    - if [ $TRAVIS_OS_NAME = osx ]; then brew install gcc; brew link --overwrite gcc; brew install hdf5; fi
 notifications:
     email: false
-script:
-    - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
-    - julia -e 'Pkg.clone(pwd()); Pkg.build("MAT"); Pkg.test("MAT"; coverage=true)'
 after_success:
     - julia -e 'cd(Pkg.dir("MAT")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'

REQUIRE

@@ -1,4 +1,4 @@
-julia 0.5
+julia 0.7-beta2
 HDF5
 BufferedStreams 0.2.0
 Libz

src/MAT.jl

@@ -22,11 +22,9 @@
 # OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
 # WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 
-VERSION >= v"0.4.0-dev+6521" && __precompile__()
-
 module MAT
 
-using HDF5, Compat
+using HDF5, Compat, SparseArrays
 
 include("MAT_HDF5.jl")
 include("MAT_v5.jl")
@@ -53,7 +51,7 @@ function matopen(filename::AbstractString, rd::Bool, wr::Bool, cr::Bool, tr::Boo
     rawfid = open(filename, "r")
 
     # Check for MAT v4 file
-    magic = read!(rawfid, Vector{UInt8}(4))
+    magic = read!(rawfid, Vector{UInt8}(undef, 4))
     for i = 1:length(magic)
         if magic[i] == 0
             close(rawfid)
@@ -76,7 +74,7 @@ function matopen(filename::AbstractString, rd::Bool, wr::Bool, cr::Bool, tr::Boo
     # Check for HDF5 file
     for offset = 512:512:fs-8
         seek(rawfid, offset)
-        if read!(rawfid, Vector{UInt8}(8)) == HDF5_HEADER
+        if read!(rawfid, Vector{UInt8}(undef, 8)) == HDF5_HEADER
             close(rawfid)
             return MAT_HDF5.matopen(filename, rd, wr, cr, tr, ff)
         end
@@ -143,7 +141,7 @@ end
 Write a dictionary containing variable names as keys and values as values
 to a Matlab file, opening and closing it automatically.
 """
-function matwrite{S, T}(filename::AbstractString, dict::Associative{S, T})
+function matwrite(filename::AbstractString, dict::AbstractDict{S, T}) where {S, T}
     file = matopen(filename, "w")
     try
         for (k, v) in dict

src/MAT_HDF5.jl

@@ -28,15 +28,15 @@
 
 module MAT_HDF5
 
-using HDF5
+using HDF5, SparseArrays
 
 import Base: read, write, close
 import HDF5: names, exists, HDF5ReferenceObj, HDF5BitsKind
 
 const HDF5Parent = Union{HDF5File, HDF5Group}
 const HDF5BitsOrBool = Union{HDF5BitsKind,Bool}
 
-type MatlabHDF5File <: HDF5.DataFile
+mutable struct MatlabHDF5File <: HDF5.DataFile
     plain::HDF5File
     toclose::Bool
     writeheader::Bool
@@ -45,7 +45,7 @@ type MatlabHDF5File <: HDF5.DataFile
     function MatlabHDF5File(plain, toclose::Bool=true, writeheader::Bool=false, refcounter::Int=0)
         f = new(plain, toclose, writeheader, refcounter)
         if toclose
-            finalizer(f, close)
+            finalizer(close, f)
         end
         f
     end
@@ -115,24 +115,24 @@ const sparse_attr_matlab = "MATLAB_sparse"
 const int_decode_attr_matlab = "MATLAB_int_decode"
 
 ### Reading
-function read_complex{T}(dtype::HDF5Datatype, dset::HDF5Dataset, ::Type{Array{T}})
+function read_complex(dtype::HDF5Datatype, dset::HDF5Dataset, ::Type{Array{T}}) where T
     if !check_datatype_complex(dtype)
         close(dtype)
         error("Unrecognized compound data type when reading ", name(dset))
     end
     memtype = build_datatype_complex(T)
     sz = size(dset)
-    dbuf = Array{T}(2, sz...)
+    dbuf = Array{T}(undef, 2, sz...)
     st = sizeof(T)
-    buf = reinterpret(UInt8, dbuf, (2 * st, sz...))
+    buf = reshape(reinterpret(UInt8, vec(dbuf)), (2 * st, sz...))
     HDF5.h5d_read(dset.id, memtype.id, HDF5.H5S_ALL, HDF5.H5S_ALL, HDF5.H5P_DEFAULT, buf)
 
     if T == Float32
-        d = reinterpret(Complex64, dbuf, sz)
+        d = reinterpret(ComplexF32, dbuf, sz)
     elseif T == Float64
-        d = reinterpret(Complex128, dbuf, sz)
+        d = collect(reshape(reinterpret(ComplexF64, vec(dbuf)), sz))
     else
-        d = slicedim(dbuf, 1, 1) + im * slicedim(dbuf, 1, 2)
+        d = copy(selectdim(dbuf, 1, 1)) + im * copy(selectdim(dbuf, 1, 2))
     end
     length(d) == 1 ? d[1] : d
 end
@@ -146,7 +146,7 @@ function m_read(dset::HDF5Dataset)
             return ""
         else
             T = mattype == "canonical empty" ? Union{} : str2eltype_matlab[mattype]
-            return Array{T}(dims...)
+            return Array{T}(undef, dims...)
         end
     end
 
@@ -155,7 +155,7 @@ function m_read(dset::HDF5Dataset)
     if mattype == "cell"
         # Cell arrays, represented as an array of refs
         refs = read(dset, Array{HDF5ReferenceObj})
-        out = Array{Any}(size(refs))
+        out = Array{Any}(undef, size(refs))
         f = file(dset)
         for i = 1:length(refs)
             dset = f[refs[i]]
@@ -290,12 +290,12 @@ elseif length(s) > 63
 end
 
 toarray(x::Array) = x
-toarray(x::Array{Bool}) = reinterpret(UInt8, x)
+toarray(x::Array{Bool}) = reinterpret.(UInt8, x)
 toarray(x::Bool) = UInt8[x]
 toarray(x) = [x]
 
 # Write the MATLAB type string for dset
-m_writetypeattr{T}(dset, ::Type{Complex{T}}) = m_writetypeattr(dset, T)
+m_writetypeattr(dset, ::Type{Complex{T}}) where T = m_writetypeattr(dset, T)
 function m_writetypeattr(dset, T)
     if !haskey(type2str_matlab, T)
         error("Type ", T, " is not (yet) supported")
@@ -324,7 +324,7 @@ function m_writeempty(parent::HDF5Parent, name::String, data::Array)
 end
 
 # Write an array to a dataset in a MATLAB file, returning the dataset
-function m_writearray{T<:HDF5BitsOrBool}(parent::HDF5Parent, name::String, adata::Array{T})
+function m_writearray(parent::HDF5Parent, name::String, adata::Array{T}) where {T<:HDF5BitsOrBool}
     dset, dtype = d_create(parent, name, adata)
     try
         HDF5.writearray(dset, dtype.id, adata)
@@ -336,14 +336,14 @@ function m_writearray{T<:HDF5BitsOrBool}(parent::HDF5Parent, name::String, adata
         close(dtype)
     end
 end
-function m_writearray{T<:HDF5BitsOrBool}(parent::HDF5Parent, name::String, adata::Array{Complex{T}})
+function m_writearray(parent::HDF5Parent, name::String, adata::Array{Complex{T}}) where {T<:HDF5BitsOrBool}
     dtype = build_datatype_complex(T)
     try
         stype = dataspace(adata)
         obj_id = HDF5.h5d_create(parent.id, name, dtype.id, stype.id)
         dset = HDF5Dataset(obj_id, file(parent))
         try
-            arr = reinterpret(T, adata, tuple(2, size(adata)...))
+            arr = collect(reshape(reinterpret(T, adata), tuple(2, size(adata)...)))
             HDF5.writearray(dset, dtype.id, arr)
         catch e
             close(dset)
@@ -358,7 +358,7 @@ function m_writearray{T<:HDF5BitsOrBool}(parent::HDF5Parent, name::String, adata
 end
 
 # Write a scalar or array
-function m_write{T<:HDF5BitsOrBool}(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, data::Union{T, Complex{T}, Array{T}, Array{Complex{T}}})
+function m_write(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, data::Union{T, Complex{T}, Array{T}, Array{Complex{T}}}) where {T<:HDF5BitsOrBool}
     if isempty(data)
         m_writeempty(parent, name, data)
         return
@@ -372,7 +372,7 @@ function m_write{T<:HDF5BitsOrBool}(mfile::MatlabHDF5File, parent::HDF5Parent, n
 end
 
 # Write sparse arrays
-function m_write{T}(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, data::SparseMatrixCSC{T})
+function m_write(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, data::SparseMatrixCSC{T}) where T
     g = g_create(parent, name)
     try
         m_writetypeattr(g, T)
@@ -425,7 +425,7 @@ function m_write(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, str::A
 end
 
 # Write cell arrays
-function m_write{T}(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, data::Array{T})
+function m_write(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, data::Array{T}) where T
     pathrefs = "/#refs#"
     fid = file(parent)
     local g
@@ -456,7 +456,7 @@ function m_write{T}(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, dat
             close(a)
         end
         # Write the items to the reference group
-        refs = Array{HDF5ReferenceObj}(size(data))
+        refs = Array{HDF5ReferenceObj}(undef, size(data))
         for i = 1:length(data)
             mfile.refcounter += 1
             itemname = string(mfile.refcounter)
@@ -482,7 +482,7 @@ end
 
 # Check that keys are valid for a struct, and convert them to an array of ASCIIStrings
 function check_struct_keys(k::Vector)
-    asckeys = Vector{String}(length(k))
+    asckeys = Vector{String}(undef, length(k))
     for i = 1:length(k)
         key = k[i]
         if !isa(key, AbstractString)
@@ -505,7 +505,7 @@ function m_write(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, k::Vec
 end
 
 # Write Associative as a struct
-m_write(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, s::Associative) =
+m_write(mfile::MatlabHDF5File, parent::HDF5Parent, name::String, s::AbstractDict) =
     m_write(mfile, parent, name, check_struct_keys(collect(keys(s))), collect(values(s)))
 
 # Write generic CompositeKind as a struct
@@ -532,7 +532,7 @@ end
 
 ## Type conversion operations ##
 
-type MatlabString; end
+struct MatlabString end
 
 const str2type_matlab = Dict(
     "canonical empty" => nothing,
@@ -590,9 +590,9 @@ function read(obj::HDF5Object, ::Type{MatlabString})
         data = reshape(data, sz[2:end])
     end
     if ndims(data) == 1
-        return convert(String, convert(Vector{Char}, data))
+        return String(convert(Vector{Char}, data))
     elseif ndims(data) == 2
-        return datap = String[rstrip(convert(String, convert(Vector{Char}, vec(data[i, :])))) for i = 1:size(data, 1)]
+        return datap = String[rstrip(String(convert(Vector{Char}, vec(data[i, :])))) for i = 1:size(data, 1)]
     else
         return data
     end
@@ -603,7 +603,7 @@ function read(obj::HDF5Object, ::Type{Bool})
 end
 function read(obj::HDF5Object, ::Type{Array{Bool}})
     tf = read(obj, Array{UInt8})
-    reinterpret(Bool, tf)
+    convert(Array{Bool}, reinterpret(Bool, tf))
 end
 
 ## Utilities for handling complex numbers