Merge pull request #55 from joegilkes/iobuffer_read

Add support for reading from IOBuffers

src/atoms.jl

@@ -289,9 +289,9 @@ AtomsBase.species(s::Atoms, i::_IDX) =
 
 # --------- FileIO compatible interface (hence not exported)
 
-load(file::Union{String,IOStream}, frame; kwargs...) = Atoms(read_frame(file, frame; kwargs...))
+load(file::Union{String,IOStream,IOBuffer}, frame; kwargs...) = Atoms(read_frame(file, frame; kwargs...))
 
-function load(file::Union{String,IOStream}; kwargs...)
+function load(file::Union{String,IOStream,IOBuffer}; kwargs...)
     seq = Atoms.(read_frames(file; kwargs...))
     if length(seq) == 1
         return seq[1]

src/fileio.jl

@@ -33,6 +33,18 @@ function cfopen(f::Function, filename::String, mode::String="r")
     end
 end
 
+function cfopen(f::Function, iob::IOBuffer, mode::String="r")
+    @static if Sys.iswindows()
+        throw(ErrorException("Reading frames from IOBuffers is not supported on Windows."))
+    end
+    fp = ccall(:fmemopen, Ptr{Cvoid}, (Ptr{Cvoid}, Cint, Cstring), pointer(iob.data, iob.ptr), iob.size, mode)
+    try
+        f(fp)
+    finally
+        cfclose(fp)
+    end
+end
+
 struct DictEntry
     key::Ptr{Cchar}
     data::Ptr{Cvoid}
@@ -258,7 +270,9 @@ end
     read_frame(file)
 
 Read a single frame from the ExtXYZ file `file`, which can be a file pointer,
-open IO stream or a string filename.
+an open IO stream, a string filename or an IOBuffer.
+
+Reading from IOBuffers is currently not supported on Windows.
 """
 function read_frame(fp::Ptr{Cvoid}; verbose=false)
     nat, info, arrays = try
@@ -291,8 +305,8 @@ function read_frame(fp::Ptr{Cvoid}; verbose=false)
     return dict
 end
 
-read_frame(file::Union{String,IOStream}, index; kwargs...) = only(read_frames(file, index; kwargs...))
-read_frame(file::Union{String,IOStream}; kwargs...) = read_frame(file, 1; kwargs...)
+read_frame(file::Union{String,IOStream,IOBuffer}, index; kwargs...) = only(read_frames(file, index; kwargs...))
+read_frame(file::Union{String,IOStream,IOBuffer}; kwargs...) = read_frame(file, 1; kwargs...)
 
 """
     iread_frames(file[, range])
@@ -327,33 +341,35 @@ function iread_frames(fp::Ptr{Cvoid}, range; close_fp=false, kwargs...)
     end
 end
 
-function iread_frames(file::Union{String,IOStream}, range; kwargs...)
+function iread_frames(file::Union{String,IOStream,IOBuffer}, range; kwargs...)
     fp = cfopen(file, "r")
     fp == C_NULL && error("file $file cannot be opened for reading")
     iread_frames(fp, range; close_fp=true, kwargs...)
 end
 
-iread_frames(file::Union{String,IOStream}, index::Int; kwargs...) = iread_frames(file, [index]; kwargs...)
-iread_frames(file::Union{String,IOStream}; kwargs...) = iread_frames(file, Iterators.countfrom(1); kwargs...)
+iread_frames(file::Union{String,IOStream,IOBuffer}, index::Int; kwargs...) = iread_frames(file, [index]; kwargs...)
+iread_frames(file::Union{String,IOStream,IOBuffer}; kwargs...) = iread_frames(file, Iterators.countfrom(1); kwargs...)
 
 """
     read_frames(file[, range])
 
-Read a sequence of frames from the ExtXYZ `file`, which can be specified by a file pointer, filename or IOStream.
+Read a sequence of frames from the ExtXYZ `file`, which can be specified by a file pointer, filename, IOStream or IOBuffer.
 
 `range` can be a single integer, range object or integer array of frame indices.
+
+Reading from IOBuffers is currently not supported on Windows.
 """
 read_frames(fp::Ptr{Cvoid}, range; kwargs...) = collect(iread_frames(fp, range; kwargs...))
 
-function read_frames(file::Union{String,IOStream}, range; kwargs...)
+function read_frames(file::Union{String,IOStream,IOBuffer}, range; kwargs...)
     cfopen(file) do fp
         fp == C_NULL && error("file $file cannot be opened for reading")
         read_frames(fp, range; kwargs...)
     end
 end
 
-read_frames(file::Union{String,IOStream}, index::Int; kwargs...) = read_frames(file, [index]; kwargs...)
-read_frames(file::Union{String,IOStream}; kwargs...) = read_frames(file, Iterators.countfrom(1); kwargs...)
+read_frames(file::Union{String,IOStream,IOBuffer}, index::Int; kwargs...) = read_frames(file, [index]; kwargs...)
+read_frames(file::Union{String,IOStream,IOBuffer}; kwargs...) = read_frames(file, Iterators.countfrom(1); kwargs...)
 
 function write_frame_dicts(fp::Ptr{Cvoid}, nat, info, arrays; verbose=false)
     nat = Cint(nat)

test/dict.jl

@@ -64,6 +64,14 @@ Si        13.00000000      14.00000000      $(frame+1).00000000          0
             close(f)
 
             @test all(seq1 .== seq3)
+
+            iob = IOBuffer(read(infile, String))
+            @static if Sys.iswindows()
+                @test_throws "not supported on Windows" read_frames(iob)
+            else
+                seq4 = read_frames(iob)
+                @test all(seq1 .== seq4)
+            end
         end
 
         @testset "convert" begin