Merge pull request #620 from JuliaIO/dev

Draft: new version

CHANGELOG.md

@@ -1,16 +1,20 @@
+## 0.5.10
+ - fix regression for `UInt32`
+ - **Deprecation**: Do not rely on JLD2 to load a compression library. This feature will be removed in a future release. Instead explicitly add `using` statements into your scripts.
+
 ## 0.5.9
  - fix regression for `Union{Bool,Nothing}` array elements (#617)
- - fix printing issue in `printtoc` 
+ - fix printing issue in `printtoc`
 
 ## 0.5.8
  - Stop using `Base.module_keys` as it is removed on nightly
 
 ## 0.5.7
  - Fix edge case for uninitialized Vlens
- 
+
 ## 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")`
 
@@ -27,7 +31,7 @@ that may get GC'ed while storing is in progress! (#603)
 
 ## 0.5.1
  - Bugfix and added test for bug introduced in v0.5.0
- 
+
 ## 0.5.0
  - Improved encoding of committed datatypes.
  This fixes longstanding issues but new files will not be loaded correctly with JLD2 versions prior to `v0.5.0`.
@@ -58,7 +62,7 @@ that may get GC'ed while storing is in progress! (#603)
  - fix `Upgrade` for Singleton types
 
 ## 0.4.50
- - Don't hide exception data during loading and saving (#569) 
+ - Don't hide exception data during loading and saving (#569)
 
 ## 0.4.49
  - update compat bounds
@@ -68,7 +72,7 @@ that may get GC'ed while storing is in progress! (#603)
  - fix behaviour for unnormalized strings
  - add missing method for load_attributes
  - clean up `using` statements
- 
+
 ## 0.4.47
  - fix loading structs with more than 256 fields (#558)
 
@@ -107,7 +111,7 @@ that may get GC'ed while storing is in progress! (#603)
  - restrict default Dict encoding to Base implementations
 
 ## 0.4.37
- - Update Dict encoding for latest julia 
+ - Update Dict encoding for latest julia
 
 ## 0.4.36
  - compat bound for TranscodingStreams.jl
@@ -129,22 +133,22 @@ that may get GC'ed while storing is in progress! (#603)
 ## 0.4.31
  - fix UInt32 truncation error for absurdly large array sizes
  - move test-files to a separate repo
- 
+
 ## 0.4.30
  -  allow loading compressed files during precompilation #446 (@marius311)
- 
+
 ## 0.4.29
  - added `Upgrade` feature
- 
+
 ## 0.4.28
  - compatibility to julia v1.9-dev (@eschnett)
- 
+
 ## 0.4.26
  - fix identity relations with custom serialization
 
 ## 0.4.25
  - remove leftover debug statement
- 
+
 ## 0.4.24
  - read-only support for `JLD.jl` files
  - read-only support for many HDF5 files. Most test files of HDF5.jl are covered
@@ -155,14 +159,14 @@ that may get GC'ed while storing is in progress! (#603)
 
 ## 0.4.23
  - Support for `const` fields in mutable structs
- 
+
 ## 0.4.22
  - Fix reconstruction of partially initialized structs
 
 ## 0.4.21
- - Add explicit type mapping 
+ - Add explicit type mapping
 
-## 0.4.20 
+## 0.4.20
  - TTFX improvements
  - Add a comment on jldsave (@BoundaryValueProblems)
 ## 0.4.19

Project.toml

@@ -1,6 +1,6 @@
 name = "JLD2"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.5.9"
+version = "0.5.10"
 
 [deps]
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"

src/compression.jl

@@ -33,35 +33,18 @@ end
 # Dynamic Package Loading Logic copied from FileIO
 const load_locker = Base.ReentrantLock()
 
-function _findmod(f::Symbol)
-    for (u,v) in Base.loaded_modules
-        (Symbol(v) == f) && return u
-    end
-    nothing
-end
-
-function topimport(modname)
-    @info "Attempting to dynamically load $modname"
-    @eval Base.__toplevel__  import $modname
-    u = _findmod(modname)
-    @eval $modname = Base.loaded_modules[$u]
-end
 
 function checked_import(pkg::Symbol)
     lock(load_locker) do
-        # kludge for test suite
-        if isdefined(Main, pkg)
-            m1 = getfield(Main, pkg)
-            isa(m1, Module) && return false, m1
+        for m in Base.loaded_modules_array()
+            (Symbol(m) == pkg) && return false, m
         end
-        if isdefined(JLD2, pkg)
-            m1 = getfield(JLD2, pkg)
-            isa(m1, Module) && return false, m1
+        @info "Attempting to dynamically load $pkg"
+        @eval Base.__toplevel__  import $pkg
+        for m in Base.loaded_modules_array()
+            (Symbol(m) == pkg) && return true, m
         end
-        m = _findmod(pkg)
-        (m === nothing) || return false, Base.loaded_modules[m]
-        topimport(pkg)
-        return true, Base.loaded_modules[_findmod(pkg)]
+        throw(InternalError("Module $pkg could not be loaded."))
     end
 end
 

src/data/number_types.jl

@@ -37,7 +37,7 @@ function jltype(f::JLDFile, dt::FixedPointDatatype)
         elseif dt.size == 1
             return signed ? SameRepr{Int8}() : SameRepr{UInt8}()
         elseif dt.size == 4
-            return signed ? SameRepr{Int32}() : SameRepr{Int32}()
+            return signed ? SameRepr{Int32}() : SameRepr{UInt32}()
         elseif dt.size == 2
             return signed ? SameRepr{Int16}() : SameRepr{UInt16}()
         elseif dt.size == 16

src/data/reconstructing_datatypes.jl

@@ -308,7 +308,7 @@ function _resolve_type(rr::MappedRepr{T,DataTypeODR},
                        hasparams::Bool,
                        params) where T
     parts = split(mypath, '.')
-    for mod in values(Base.loaded_modules)
+    for mod in Base.loaded_modules_array()
         resolution_attempt = _resolve_type_singlemodule(rr,
                                                         mod,
                                                         parts,

src/data/specialcased_types.jl

@@ -304,13 +304,15 @@ wconvert(::Type{String}, x::Module) = string(x)
 function rconvert(::Type{Module}, x::String)
     pkg = Symbol(x)
     # Try to find the module
-    # Start with the method used to find compression libraries
-    m =_findmod(pkg)
-    isnothing(m) || return Base.loaded_modules[m]
-    @info "Encountered reference to module $x, but it is not currently loaded."
+    for m in Base.loaded_modules_array()
+        (Symbol(m) == pkg) && return m
+    end
+    @warn "Encountered reference to module $x, but it is not currently loaded."
     return try
-        topimport(pkg)
-        Base.loaded_modules[_findmod(pkg)]
+        @eval Base.__toplevel__  import $pkg
+        for m in Base.loaded_modules_array()
+            (Symbol(m) == pkg) && return m
+        end
     catch
        @warn "Could not load module $x. Returning a dummy module"
        Module(Symbol(x*"_dummy"))

test/loadsave.jl

@@ -847,4 +847,21 @@ end
     loaded_data = load(fn, "data")
     @test !isassigned(loaded_data, 2)
     @test loaded_data[1] == :a
-end
+end
+
+@testset "Issue #619 - Number type turnaround" begin
+    fn = joinpath(mktempdir(), "number_type_turnaround.jld2")
+    types = [UInt8, Int8, UInt16, Int16, UInt32, Int32, UInt64, Int64, UInt128, Int128, Float16, Float32, Float64]
+    jldopen(fn, "w") do f
+        for t in types
+            f[string(t)] = typemax(t)
+        end
+    end
+    jldopen(fn) do f
+        for t in types
+            v = f[string(t)]
+            @test v isa t
+            @test v == typemax(t)
+        end
+    end
+end

test/modules.jl

@@ -21,7 +21,7 @@ S = BType(x)
 end
 
 @testset "name collisions" begin
-    mods = collect(values(Base.loaded_modules))
+    mods = Base.loaded_modules_array()
     # use whichever module would not be found first in a linear search
     M = findfirst(==(A), mods) < findfirst(==(B), mods) ? B : A
     x = M.SameNameType(42)

test/runtests.jl

@@ -1,5 +1,6 @@
 using JLD2, FileIO
 using Test
+using CodecZlib, CodecBzip2, CodecZstd, CodecLz4
 
 function better_success(cmd)
     fn1, _ = mktemp()