new version

CHANGELOG.md

@@ -1,3 +1,6 @@
+## 0.5.6
+ - Add Aqua tests and eliminate method ambiguities
+
 ## 0.5.5
  - Experimental support for writing to and reading from `IO` objects e.g. `jldopen(io, "r")`
 

Project.toml

@@ -1,6 +1,6 @@
 name = "JLD2"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.5.5"
+version = "0.5.6"
 
 [deps]
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
@@ -13,7 +13,7 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
 [compat]
 FileIO = "1.5"
-MacroTools = "0.5"
+MacroTools = "0.5.10"
 OrderedCollections = "1"
 PrecompileTools = "1"
 Requires = "1.3"

README.md

@@ -1,8 +1,11 @@
 # JLD2
 
-| **Documentation**   |  **Tests**     | **CodeCov**  | **Downloads** |
-|:--------:|:---------------:|:-------:|:---:|
-|[![](https://img.shields.io/badge/docs-online-blue.svg)](https://JuliaIO.github.io/JLD2.jl/dev)| [![CI](https://github.com/JuliaIO/JLD2.jl/actions/workflows/ci.yml/badge.svg)](https://github.com/JuliaIO/JLD2.jl/actions/workflows/ci.yml) | [![codecov.io](https://codecov.io/github/JuliaIO/JLD2.jl/coverage.svg?branch=master)](https://codecov.io/github/JuliaIO/JLD2.jl?branch=master) | [![JLD2 Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Fmonthly_downloads%2FJLD2&query=total_requests&suffix=%2Fmonth&label=Downloads)](http://juliapkgstats.com/pkg/JLD2) |
+[![](https://img.shields.io/badge/docs-online-blue.svg)](https://JuliaIO.github.io/JLD2.jl/dev)
+[![CI](https://github.com/JuliaIO/JLD2.jl/actions/workflows/ci.yml/badge.svg)](https://github.com/JuliaIO/JLD2.jl/actions/workflows/ci.yml)
+[![codecov.io](https://codecov.io/github/JuliaIO/JLD2.jl/coverage.svg?branch=master)](https://codecov.io/github/JuliaIO/JLD2.jl?branch=master)
+[![JLD2 Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Fmonthly_downloads%2FJLD2&query=total_requests&suffix=%2Fmonth&label=Downloads)](http://juliapkgstats.com/pkg/JLD2)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
+
 
 JLD2 saves and loads Julia data structures in a format comprising a subset of HDF5, without any dependency on the HDF5 C library. 
 JLD2 is able to read most HDF5 files created by other HDF5 implementations supporting HDF5 File Format Specification Version 3.0 (i.e. libhdf5 1.10 or later) and similarly those should be able to read the files that JLD2 produces. JLD2 provides read-only support for files created with the JLD package.

src/backwards_compatibility.jl

@@ -1,15 +1,15 @@
 # The following block allows reading Union types written prior to v0.2
 const LEGACY_H5TYPE_UNION = VariableLengthDatatype(H5TYPE_DATATYPE)
 
-function jlconvert(::ReadRepresentation{Union, Vlen{DataTypeODR()}}, f::JLDFile,
+function jlconvert(::MappedRepr{Union, Vlen{DataTypeODR}}, f::JLDFile,
                    ptr::Ptr, header_offset::RelOffset)
-    v = Union{jlconvert(ReadRepresentation{DataType,Vlen{DataTypeODR()}}(), f, ptr, NULL_REFERENCE)...}
+    v = Union{jlconvert(MappedRepr{DataType,Vlen{DataTypeODR}}(), f, ptr, NULL_REFERENCE)...}
     track_weakref!(f, header_offset, v)
     v
 end
 
 constructrr(::JLDFile, ::Type{T}, dt::VariableLengthDatatype, ::Vector{ReadAttribute}) where {T<:Union} =
-    dt == LEGACY_H5TYPE_UNION ? (ReadRepresentation{Union,Vlen{DataTypeODR()}}(), true) :
+    dt == LEGACY_H5TYPE_UNION ? (MappedRepr{Union,Vlen{DataTypeODR}}(), true) :
                          throw(UnsupportedFeatureException())
 
 # The following definition is needed to correctly load Strings written
@@ -18,7 +18,7 @@ function read_array(f::JLDFile, dataspace::ReadDataspace,
                     rr::FixedLengthString{String}, layout::DataLayout,
                     filters::FilterPipeline, header_offset::RelOffset,
                     attributes::Union{Vector{ReadAttribute},Nothing})
-    rrv = ReadRepresentation{UInt8,odr(UInt8)}()
+    rrv = SameRepr{UInt8}()
     v = read_array(f, dataspace, rrv, layout, filters, NULL_REFERENCE, attributes)
     String(v)
 end

src/committed_datatype_introspection.jl

@@ -41,7 +41,7 @@ function stringify_committed_datatype(f, cdt; showfields=false)
         else
             # These are normal julia types
             dtrr = jltype(f, dt.members[i])
-            fieldtype = string(typeof(dtrr).parameters[1])
+            fieldtype = string(julia_type(dtrr))
         end
         push!(field_strs, "$(dt.names[i])::$(fieldtype)")
     end
@@ -97,7 +97,7 @@ function typestring_from_refs(f::JLDFile, ptr::Ptr)
     # Test for a potential null pointer indicating an empty array
     isinit = jlunsafe_load(convert(Ptr{UInt32}, ptr)) != 0
     if isinit
-        refs = jlconvert(ReadRepresentation{RelOffset, Vlen{RelOffset}}(), f, ptr, NULL_REFERENCE)
+        refs = jlconvert(MappedRepr{RelOffset, Vlen{RelOffset}}(), f, ptr, NULL_REFERENCE)
         #println("datatypes at refs $(Int.(getproperty.(refs,:offset)))")
         params =  Any[let
             # If the reference is to a committed datatype, read the datatype
@@ -127,10 +127,10 @@ function jlconvert_string_wrap(rr, f, offset)
     end
 end
 
-function jlconvert_string(rr::ReadRepresentation{T,DataTypeODR()},
+function jlconvert_string(::MappedRepr{T,DataTypeODR},
                         f::JLDFile,
                         ptr::Ptr) where T
-    mypath = String(jlconvert(ReadRepresentation{UInt8,Vlen{UInt8}}(), f, ptr, NULL_REFERENCE))
+    mypath = String(jlconvert(MappedRepr{UInt8,Vlen{UInt8}}(), f, ptr, NULL_REFERENCE))
     params = typestring_from_refs(f, ptr+odr_sizeof(Vlen{UInt8}))
     if startswith(mypath, r"Core|Main")
         mypath = last(split(mypath, "."; limit=2))
@@ -143,7 +143,7 @@ function jlconvert_string(rr::ReadRepresentation{T,DataTypeODR()},
     end
 end
 
-function jlconvert_string(::ReadRepresentation{Union, UnionTypeODR()}, f::JLDFile,
+function jlconvert_string(::MappedRepr{Union, UnionTypeODR}, f::JLDFile,
     ptr::Ptr)#, header_offset::RelOffset)
     # Skip union type description in the beginning
     ptr += odr_sizeof(Vlen{String})

src/data/custom_serialization.jl

@@ -47,20 +47,20 @@ h5convert!(out::Pointers, odr::Type{CustomSerialization{T,RelOffset}},
 h5convert_uninitialized!(out::Pointers, odr::Type{CustomSerialization{T,ODR}}) where {T,ODR} =
     h5convert_uninitialized!(out, ODR)
 
-jlconvert_canbeuninitialized(::ReadRepresentation{T,CustomSerialization{S,ODR}}) where {T,S,ODR} =
-    jlconvert_canbeuninitialized(ReadRepresentation{S,ODR}())
-jlconvert_isinitialized(::ReadRepresentation{T,CustomSerialization{S,ODR}}, ptr::Ptr) where {T,S,ODR} =
-    jlconvert_isinitialized(ReadRepresentation{S,ODR}(), ptr)
+jlconvert_canbeuninitialized(::MappedRepr{T,CustomSerialization{S,ODR}}) where {T,S,ODR} =
+    jlconvert_canbeuninitialized(MappedRepr{S,ODR}())
+jlconvert_isinitialized(::MappedRepr{T,CustomSerialization{S,ODR}}, ptr::Ptr) where {T,S,ODR} =
+    jlconvert_isinitialized(MappedRepr{S,ODR}(), ptr)
 
-function jlconvert(::ReadRepresentation{T,CustomSerialization{S,RelOffset}},
+function jlconvert(::MappedRepr{T,CustomSerialization{S,RelOffset}},
         f::JLDFile, ptr::Ptr, header_offset::RelOffset) where {T,S}
     # Concerns objects whose custom serialization is itself only referenced by a RelOffset
     # This be important when the original object is mutable
     offset = jlunsafe_load(pconvert(Ptr{RelOffset}, ptr))
     return rconvert(T, load_dataset(f, offset))
 end
 
-function jlconvert(::ReadRepresentation{T,CustomSerialization{S,ODR}},
+function jlconvert(::MappedRepr{T,CustomSerialization{S,ODR}},
           f::JLDFile, ptr::Ptr, header_offset::RelOffset) where {T,S,ODR}
 
     if ismutabletype(T) && !(T <: Core.SimpleVector)
@@ -70,15 +70,15 @@ function jlconvert(::ReadRepresentation{T,CustomSerialization{S,ODR}},
         track_weakref!(f, header_offset, obj)
 
         # actually load the data
-        v = rconvert(T, jlconvert(ReadRepresentation{S,ODR}(), f, ptr, header_offset))::T
+        v = rconvert(T, jlconvert(ReadRepresentation(S,ODR), f, ptr, header_offset))::T
         # copy fields to initial struct
         for i in 0:nfields(obj)-1
             fieldval = ccall(:jl_get_nth_field, Any, (Any, Csize_t), v, i)
             ccall(:jl_set_nth_field, Nothing, (Any, Csize_t, Any), obj, i, fieldval)
         end
         return obj
     else
-        v = rconvert(T, jlconvert(ReadRepresentation{S,ODR}(), f, ptr, header_offset))::T
+        v = rconvert(T, jlconvert(ReadRepresentation(S,ODR), f, ptr, header_offset))::T
         track_weakref!(f, header_offset, v)
         return v
     end

src/data/number_types.jl

@@ -22,7 +22,7 @@ struct BENumber{T}
     x::T
 end
 
-jlconvert(::ReadRepresentation{T,BENumber{T}}, ::JLDFile, ptr::Ptr, ::RelOffset) where {T} =
+jlconvert(::MappedRepr{T,BENumber{T}}, ::JLDFile, ptr::Ptr, ::RelOffset) where {T} =
     bswap(jlunsafe_load(pconvert(Ptr{T}, ptr)))
 
 function jltype(f::JLDFile, dt::FixedPointDatatype)
@@ -33,29 +33,29 @@ function jltype(f::JLDFile, dt::FixedPointDatatype)
         throw(UnsupportedFeatureException())
     if endianness == 0
         if dt.size == 8
-            return signed ? ReadRepresentation{Int64,Int64}() : ReadRepresentation{UInt64,UInt64}()
+            return signed ? SameRepr{Int64}() : SameRepr{UInt64}()
         elseif dt.size == 1
-            return signed ? ReadRepresentation{Int8,Int8}() : ReadRepresentation{UInt8,UInt8}()
+            return signed ? SameRepr{Int8}() : SameRepr{UInt8}()
         elseif dt.size == 4
-            return signed ? ReadRepresentation{Int32,Int32}() : ReadRepresentation{UInt32,UInt32}()
+            return signed ? SameRepr{Int32}() : SameRepr{Int32}()
         elseif dt.size == 2
-            return signed ? ReadRepresentation{Int16,Int16}() : ReadRepresentation{UInt16,UInt16}()
+            return signed ? SameRepr{Int16}() : SameRepr{UInt16}()
         elseif dt.size == 16
-            return signed ? ReadRepresentation{Int128,Int128}() : ReadRepresentation{UInt128,UInt128}()
+            return signed ? SameRepr{Int128}() : SameRepr{UInt128}()
         else
             throw(UnsupportedFeatureException())
         end
     else
         if dt.size == 8
-            return signed ? ReadRepresentation{Int64,BENumber{Int64}}() : ReadRepresentation{UInt64,BENumber{UInt64}}()
+            return signed ? MappedRepr{Int64,BENumber{Int64}}() : MappedRepr{UInt64,BENumber{UInt64}}()
         elseif dt.size == 1
-            return signed ? ReadRepresentation{Int8,BENumber{Int8}}() : ReadRepresentation{UInt8,BENumber{UInt8}}()
+            return signed ? MappedRepr{Int8,BENumber{Int8}}() : MappedRepr{UInt8,BENumber{UInt8}}()
         elseif dt.size == 4
-            return signed ? ReadRepresentation{Int32,BENumber{Int32}}() : ReadRepresentation{UInt32,BENumber{UInt32}}()
+            return signed ? MappedRepr{Int32,BENumber{Int32}}() : MappedRepr{UInt32,BENumber{UInt32}}()
         elseif dt.size == 2
-            return signed ? ReadRepresentation{Int16,BENumber{Int16}}() : ReadRepresentation{UInt16,BENumber{UInt16}}()
+            return signed ? MappedRepr{Int16,BENumber{Int16}}() : MappedRepr{UInt16,BENumber{UInt16}}()
         elseif dt.size == 16
-            return signed ? ReadRepresentation{Int128,BENumber{Int128}}() : ReadRepresentation{UInt128,BENumber{UInt128}}()
+            return signed ? MappedRepr{Int128,BENumber{Int128}}() : MappedRepr{UInt128,BENumber{UInt128}}()
         else
             throw(UnsupportedFeatureException())
         end
@@ -64,7 +64,7 @@ end
 
 # Special handling for booleans as they are not considered <: Integer in HDF5
 h5fieldtype(::JLDFile, ::Type{Bool}, ::Type{Bool}, ::Initialized) =BitFieldDatatype(1)
-jltype(::JLDFile, ::BitFieldDatatype) = ReadRepresentation{Bool, Bool}()
+jltype(::JLDFile, ::BitFieldDatatype) = SameRepr{Bool}()
 
 h5fieldtype(::JLDFile, ::Type{Float16}, ::Type{Float16}, ::Initialized) =
     FloatingPointDatatype(UInt8(DT_FLOATING_POINT) + 0x3<<4, 0x20, 0x0f, 0x00, 2, 0, 16, 10, 5, 0, 10, 0x0000000f)
@@ -82,17 +82,17 @@ h5fieldtype(::JLDFile, ::Type{BENumber{Float64}}, ::Type{Float64}, ::Initialized
 
 function jltype(f::JLDFile, dt::FloatingPointDatatype)
     if dt == h5fieldtype(f, Float64, Float64, Val{true})
-        return ReadRepresentation{Float64,Float64}()
+        return SameRepr{Float64}()
     elseif dt == h5fieldtype(f, Float32, Float32, Val{true})
-        return ReadRepresentation{Float32,Float32}()
+        return SameRepr{Float32}()
     elseif dt == h5fieldtype(f, Float16, Float16, Val{true})
-        return ReadRepresentation{Float16,Float16}()
+        return SameRepr{Float16}()
     elseif dt == h5fieldtype(f, BENumber{Float64}, Float64, Val{true})
-        return ReadRepresentation{Float32,BENumber{Float32}}()
+        return MappedRepr{Float32,BENumber{Float32}}()
     elseif dt == h5fieldtype(f, BENumber{Float32}, Float32, Val{true})
-        return ReadRepresentation{Float32,BENumber{Float32}}()
+        return MappedRepr{Float32,BENumber{Float32}}()
     elseif dt == h5fieldtype(f, BENumber{Float16}, Float16, Val{true})
-        return ReadRepresentation{Float32,BENumber{Float32}}()
+        return MappedRepr{Float32,BENumber{Float32}}()
     else
         throw(UnsupportedFeatureException())
     end
@@ -108,5 +108,5 @@ h5type(f::JLDFile, writeas::PrimitiveTypeTypes, x) =
 # Used only for custom serialization
 constructrr(f::JLDFile, T::PrimitiveTypeTypes, dt::Union{FixedPointDatatype,FloatingPointDatatype},
             ::Vector{ReadAttribute}) =
-    dt == h5fieldtype(f, T, T, Val{true}) ? (ReadRepresentation{T,T}(), true) :
+    dt == h5fieldtype(f, T, T, Val{true}) ? (SameRepr{T}(), true) :
                                             throw(UnsupportedFeatureException())