aqua tests & reduction of ambiguities

JuliaIO · Oct 16, 2024 · f8b8190 · f8b8190
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diff --git a/README.md b/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.

diff --git a/src/data/specialcased_types.jl b/src/data/specialcased_types.jl
@@ -286,8 +286,8 @@ end
 # convert to an array instead.
 const NTUPLE_INLINE_THRESHOLD = 10
 
-function writeas(NT::Type{NTuple{N,T}}) where {N,T}
-    if N > NTUPLE_INLINE_THRESHOLD
+function writeas(NT::Type{Tuple{T, Vararg{T,N}}}) where {N,T}
+    if (N+1) > NTUPLE_INLINE_THRESHOLD
         return Vector{T}
     else
         return NT

diff --git a/src/io/io_wrappers.jl b/src/io/io_wrappers.jl
@@ -142,7 +142,7 @@ function _read(io::RWBuffer, T::DataType)
 end
 # needed explicitly for avoiding ambiguities
 Base.read(io::RWBuffer, T::Type{UInt8}) = _read(io, T)
-Base.read(io::RWBuffer, T::PlainType) = _read(io, T)
+#Base.read(io::RWBuffer, T::PlainType) = _read(io, T)
 Base.write(io::RWBuffer, x::UInt8) = _write(io, x)
 jlwrite(io::RWBuffer, x::String) = _write(io, x)
 

diff --git a/src/misc.jl b/src/misc.jl
@@ -198,7 +198,7 @@ function flag2uint(flag::UInt8)
 end
 
 
-jlread(io::IO, ::Type{NTuple{N,T}}) where {N,T} = ntuple(_->jlread(io, T), Val{N}())
+jlread(io::IO, ::Type{Tuple{T, Vararg{T,N}}}) where {N,T} = ntuple(_->jlread(io, T), Val{N+1}())
 jlread(io::IO, ::Type{Tuple{}}) = ()
 
 function write_nb_int(io::IO, sz::Integer, nb::Integer)

diff --git a/src/object_headers.jl b/src/object_headers.jl
@@ -22,7 +22,7 @@ struct Hmessage{IO}
     m::Message{IO}
 end
 
-function write_header_message(io, vtype::Val{HMT}, hflags=0x00, size=0; kwargs...) where HMT
+function write_header_message(io, vtype::Val{HMT}, hflags::Integer=0x00, size=0; kwargs...) where HMT
     kw = (; kwargs...)
     size = compute_size(vtype, hflags, size, kw)
     jlwrite(io, UInt8(HMT))

diff --git a/test/Project.toml b/test/Project.toml
@@ -1,4 +1,5 @@
 [deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 CodecBzip2 = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd"
 CodecLz4 = "5ba52731-8f18-5e0d-9241-30f10d1ec561"
@@ -10,4 +11,5 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -34,3 +34,20 @@ include("unpack_test.jl")
 include("dataset_api.jl")
 include("mmap_test.jl")
 include("wrapped_io.jl")
+
+using TestItemRunner
+
+@run_package_tests
+
+@testitem "Aqua Testing" begin
+    using Aqua
+    Aqua.test_all(JLD2;
+        ambiguities = (;
+            # Some jlconvert methods are ambiguous for pathological type combinations
+            broken=true,
+        ),
+        deps_compat = (;
+            ignore = [:Mmap,],
+        ),
+    )
+end