v0.5.2 (#598)

* remove warning that is no longer relevant (#595)

* only warn for anon functions (#597)

* only warn for anon functions

* compat for v1.6

* can't test for warning if warning is removed

* improve test

* bump version

CHANGELOG.md

@@ -1,3 +1,7 @@
+## 0.5.2
+ - Remove left-over warning
+ - Restrict warning for storing `Function` objects to `anonymous` functions.
+
 ## 0.5.1
  - Bugfix and added test for bug introduced in v0.5.0
 

Project.toml

@@ -1,6 +1,6 @@
 name = "JLD2"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.5.1"
+version = "0.5.2"
 
 [deps]
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"

src/data/reconstructing_datatypes.jl

@@ -592,9 +592,8 @@ function reconstruct_odr(f::JLDFile, dt::CompoundDatatype,
         i = findfirst(==(Symbol(k)), dt.names)
         if typeref != NULL_REFERENCE
             dtrr = jltype(f, f.datatype_locations[typeref])
-            odr_sizeof(dtrr) != 0 && @warn "Field $k has non-zero size in file, this should not happen"
         elseif !isnothing(i)
-            offset = dt.offsets[i]
+            offset == dt.offsets[i] || throw(InternalError("Field offsets were incorrectly mapped."))
             dtrr = jltype(f, dt.members[i])
         else
             throw(InternalError("Field $k not found in datatype"))

src/data/writing_datatypes.jl

@@ -219,7 +219,6 @@ end
     if f.disable_commit
         throw(ArgumentError("Attempted to commit DataType $readas but committing is disabled."))
     end
-    io = f.io
 
     # This needs to be written this way or type inference gets unhappy...
     # Also needs to happen here so that we write the DataType type
@@ -229,7 +228,7 @@ end
 
     offset = f.end_of_data
 
-    seek(io, offset)
+    seek(f.io, offset)
     id = length(f.datatypes)+1
     h5o = h5offset(f, offset)
     cdt = CommittedDatatype(h5o, id)
@@ -383,15 +382,15 @@ const H5TYPE_DATATYPE = CompoundDatatype(
 )
 
 function h5fieldtype(f::JLDFile, ::Type{T}, readas::Type, ::Initialized) where T<:DataType
+    if f.disable_commit
+        throw(ArgumentError("Attempted to commit DataType $readas but committing is disabled."))
+    end
     if !(readas <: DataType) || (T isa Type{Type{T}} where T)
         @lookup_committed f readas
         return commit(f, H5TYPE_DATATYPE, DataType, readas)
     end
 
     @lookup_committed f DataType
-    if f.disable_commit
-        throw(ArgumentError("Attempted to commit DataType $readas but committing is disabled."))
-    end
     io = f.io
     offset = f.end_of_data
 
@@ -446,6 +445,11 @@ end
 
 function h5convert!(out::Pointers, ::DataTypeODR, f::JLDFile, T::DataType, wsession::JLDWriteSession)
     t = typename(T)
+    if T <: Function && isgensym(nameof(T.instance))
+        @warn LazyString("Attempting to store ", T, ".\n",
+                         "JLD2 only stores functions by name.\n",
+                         " This may not be useful for anonymous functions.")
+    end
     store_vlen!(out, UInt8, f, unsafe_wrap(Vector{UInt8}, t), f.datatype_wsession)
     if isempty(T.parameters)
         h5convert_uninitialized!(out+odr_sizeof(Vlen{UInt8}), Vlen{UInt8})
@@ -627,9 +631,6 @@ end
 # fieldodr, but actually encoding the data for things that odr stores
 # as references
 @nospecializeinfer function odr(@nospecialize(T::Type))
-    if T <: Function
-        @warn LazyString("Attempting to store ", T, ".\n Function types cannot be propertly stored in JLD2 files.\n Loading may yield unexpected results.")
-    end
     if !hasdata(T)
         # A pointer singleton or ghost. We need to write something, but we'll
         # just write a single byte.

src/julia_compat.jl

@@ -28,4 +28,10 @@ end
     end
 else
     using Base: @nospecializeinfer
+end
+
+@static if VERSION < v"1.7.0"
+    isgensym(s::Symbol) = '#' in string(s)
+else
+    using Base: isgensym
 end

test/loadsave.jl

@@ -745,44 +745,47 @@ end
 end
 
 @testset "Disable committing datatypes" begin
-    cd(mktempdir()) do
-        jldopen("test.jld2", "w") do f
-            f.disable_commit = true
+    fn = joinpath(mktempdir(), "disable_committing_datatypes.jld2")
+    jldopen(fn, "w") do f
+        f.disable_commit = true
 
-            @test_throws ArgumentError f["1"] = Dict(1=>2)
-            @test_throws ArgumentError f["2"] = Vector{Float64}
-            @test_throws ArgumentError f["3"] = (1,2,3)
-            # this could eventually be allowed
-            @test_throws ArgumentError f["4"] = (; a=1, b=2)
-        end
+        @test_throws ArgumentError f["1"] = Dict(1=>2)
+        @test_throws ArgumentError f["2"] = Vector{Float64}
+        @test_throws ArgumentError f["3"] = (1,2,3)
+        @test_throws ArgumentError f["4"] = :asymbol
+        # No throw
+        f["5"] = "a string"
+        # this could eventually be allowed
+        @test_throws ArgumentError f["4"] = (; a=1, b=2)
     end
 end
 
 
 @testset "Missing Types in Tuples" begin
-    cd(mktempdir()) do
-        eval(:(module ModuleWithFunction
-            fun(x) = x+1
-        end))
-        if VERSION ≥ v"1.7"
-            @test_warn(
-                contains("Function types cannot"),
-                eval(:(save_object("test.jld2", (1, ModuleWithFunction.fun, 2))))
-            )
-        else
-            eval(:(save_object("test.jld2", (1, ModuleWithFunction.fun, 2))))
-        end
-        obj = load_object("test.jld2")
-        @test length(obj) == 3
-        @test obj[1] == 1
-        @test obj[2] == eval(:(ModuleWithFunction.fun))
-        @test obj[3] == 2
-
-        eval(:(module ModuleWithFunction end))
-        obj = load_object("test.jld2")
-        @test length(obj) == 3
-        @test obj[1] == 1
-        @test JLD2.isreconstructed(obj[2])
-        @test obj[3] == 2
+    fn = joinpath(mktempdir(), "missing_types_in_tuple.jld2")
+    eval(:(module ModuleWithFunction
+        fun(x) = x+1
+    end))
+    eval(:(save_object($fn, (1, ModuleWithFunction.fun, 2))))
+    obj = load_object(fn)
+    @test length(obj) == 3
+    @test obj[1] == 1
+    @test obj[2] == eval(:(ModuleWithFunction.fun))
+    @test obj[3] == 2
+
+    eval(:(module ModuleWithFunction end))
+    obj = load_object(fn)
+    @test length(obj) == 3
+    @test obj[1] == 1
+    @test JLD2.isreconstructed(obj[2])
+    @test obj[3] == 2
+
+end
+
+if VERSION ≥ v"1.7"
+    @testset "Storing an anonymous function" begin
+        fn = joinpath(mktempdir(), "storing_anon_function.jld2")
+        f = x -> x+1
+        @test_warn contains("Attempting to store") save_object(fn, f)
     end
 end