Aquatests

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 @@
  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 @@
  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 @@
  # 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 @@
  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 @@
  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 @@
  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 @@
  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 @@
 
 # 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 @@
 
 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 @@
 # 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())