Add Aqua testing and minimum compat testing (#157)

* test minimum compat entries * add aqua and fix type piracy/ambiguities * bump minimum compatible progressmeter version
tlnagy · Apr 2, 2024 · ee4852f · ee4852f · tlnagy · Apr 15, 2024
1 parent b7dbc88
commit ee4852f
Show file tree

Hide file tree

Showing 12 changed files with 37 additions and 17 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -31,6 +31,10 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
+      - uses: julia-actions/julia-downgrade-compat@v1 # downgrade packages to minimum compatible version on 1.6
+        if: ${{ matrix.version == '1.6' }}
+        with:
+          skip: Mmap, UUIDs, Test 
       - uses: actions/cache@v1
         env:
           cache-name: cache-artifacts

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "TiffImages"
 uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
 authors = ["Tamas Nagy <[email protected]>"]
-version = "1.0.0"
+version = "0.10.0"
 
 [deps]
 ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
@@ -26,8 +26,10 @@ FileIO = "1"
 FixedPointNumbers = "0.8"
 IndirectArrays = "0.5.1, 1"
 Inflate = "0.1.4"
+Mmap = "1"
 OffsetArrays = "1"
 PkgVersion = "0.1.1, 0.3"
-ProgressMeter = "1"
+ProgressMeter = "1.3.3"
 SIMD = "3.4.5"
+UUIDs = "1"
 julia = "1.6"
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@ _"Don't get into a tiff with your images"_
 
 | **Stable release** | **Documentation**                 | **Build Status**                                              |
 |:------------------------------------------------------|:-------------------------------------------------------------------------|:--------------------------------------------------------------|
-| ![](https://juliahub.com/docs/TiffImages/version.svg) | [![][docs-stable-img]][docs-stable-url][![][docs-dev-img]][docs-dev-url] | [![][status-img]][status-url] [![][ci-img]][ci-url] [![][codecov-img]][codecov-url] |
+| ![](https://juliahub.com/docs/TiffImages/version.svg) | [![][docs-stable-img]][docs-stable-url][![][docs-dev-img]][docs-dev-url] | [![][status-img]][status-url] [![][ci-img]][ci-url] [![][codecov-img]][codecov-url] [![][aqua-img]][aqua-url] |
 
 This package aims to be a fast, minimal, and correct TIFF reader and writer
 written in Julia.
@@ -45,3 +45,6 @@ Please see the documentation above for usage details and examples
 
 [status-img]: https://www.repostatus.org/badges/latest/active.svg
 [status-url]: https://www.repostatus.org/#active
+
+[aqua-img]: https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg
+[aqua-url]: https://github.com/JuliaTesting/Aqua.jl
diff --git a/src/compression.jl b/src/compression.jl
@@ -215,6 +215,6 @@ function Base.read!(tfs::TiffFileStrip{S}, arr::AbstractVector{UInt8}, ::Val{COM
     lzw_decode!(tfs, arr)
 end
 
-function Base.read!(T, A, ::Val{C}) where C
+function Base.read!(::Union{TiffFile, TiffFileStrip}, ::AbstractVector{UInt8}, ::Val{C}) where C
     error("Compression $C is not implemented. Please open an issue against TiffImages.jl.")
 end
diff --git a/src/files.jl b/src/files.jl
@@ -32,7 +32,7 @@ function Base.read(io::Stream, ::Type{TiffFile})
     bs = need_bswap(io)
     offset_size = offsetsize(io)
     first_offset_raw = read(io, offset_size)
-    first_offset = Int(bs ? bswap(first_offset_raw) : first_offset_raw)
+    first_offset = Int(bs ? _bswap(first_offset_raw) : first_offset_raw)
     TiffFile{offset_size, typeof(io)}(nothing, filepath, io, first_offset, bs)
 end
 
@@ -82,12 +82,12 @@ offset(file::TiffFile{O}) where {O} = O
 
 function Base.read(file::TiffFile{O}, ::Type{T}) where {O, T}
     value = read(file.io, T)
-    file.need_bswap ? bswap(value) : value
+    file.need_bswap ? _bswap(value) : value
 end
 
 function Base.read(file::TiffFile{O}, ::Type{String}) where O
     value = read(file.io, O)
-    file.need_bswap ? bswap(value) : value
+    file.need_bswap ? _bswap(value) : value
 end
 
 function Base.read!(file::TiffFile, arr::AbstractArray)
@@ -100,7 +100,7 @@ Base.write(file::TiffFile, arr::AbstractVector{Any}) = write(file.io.io, Array{U
 Base.seek(file::TiffFile, n::Integer) = seek(file.io, n)
 FileIO.stream(file::TiffFile) = stream(file.io)
 
-Base.bswap(x::Rational{T}) where {T} = Rational(bswap(x.num), bswap(x.den))
+_bswap(x::Rational{T}) where {T} = Rational(_bswap(x.num), _bswap(x.den))
 
 Base.IteratorSize(::TiffFile) = Base.SizeUnknown()
 Base.eltype(::TiffFile{O}) where {O} = IFD{O}
diff --git a/src/ifds.jl b/src/ifds.jl
@@ -193,10 +193,10 @@ Advances the iterator to the next IFD.
    IFD
 - `Int`: Offset of the next IFD
 """
-function Base.iterate(file::TiffFile, state::Tuple{Union{IFD{O}, Nothing}, Int}) where {O}
+function Base.iterate(file::TiffFile, state::Tuple{Union{<: IFD, Nothing}, Int})
     curr_ifd, next_ifd_offset = state
     # if current element doesn't exist, exit
-    (curr_ifd == nothing) && return nothing
+    (curr_ifd === nothing) && return nothing
     (next_ifd_offset <= 0) && return (curr_ifd, (nothing, 0))
 
     seek(file.io, next_ifd_offset)
@@ -618,7 +618,7 @@ const nice_n = filter(x -> !(max(nextpow(2, x), 8) - x in [0,1,2,3,5]), 1:31)
             # arrange bytes so that each TT-sized lane contains a single code (+ extra bits)
             $(sym("b", i)) = shufflevector($(sym("a", i)), shuffle)
             # shift out extra low-order bits
-            $(sym("c", i)) = bswap(reinterpret(Vec{$count, $TT}, $(sym("b", i)))) >> shift
+            $(sym("c", i)) = _bswap(reinterpret(Vec{$count, $TT}, $(sym("b", i)))) >> shift
             # mask out extra high-order bits
             $(sym("d", i)) = $(sym("c", i)) & mask
             in_ptr += $m

diff --git a/src/layout.jl b/src/layout.jl
@@ -48,7 +48,6 @@ end
 struct Palette{T} <: Colorant{T, 1}
     i::T
 end
-Base.reinterpret(::Type{Palette{T}}, arr::A) where {T, N, S, A <: AbstractArray{S, N}} = arr
 
 interpretation(p::PhotometricInterpretations) = interpretation(Val(p))
 interpretation(::Val{PHOTOMETRIC_RGB}) = RGB

diff --git a/src/load.jl b/src/load.jl
@@ -51,10 +51,10 @@ function load(tf::TiffFile; verbose=true, mmap = false, lazyio = false)
         @debug "bswap'ing data"
         if !homogeneous
             for sub in loaded
-                sub .= bswap.(sub)
+                sub .= _bswap.(sub)
             end
         else
-            loaded .= bswap.(loaded)
+            loaded .= _bswap.(loaded)
         end
     end
 

diff --git a/src/utils.jl b/src/utils.jl
@@ -108,7 +108,8 @@ const julian_to_tiff = Dict(
     Int64               => 0x0011,   # SLONG8
 )
 
-Base.bswap(c::Colorant{T, N}) where {T, N} = mapc(bswap, c)
+_bswap(a) = bswap(a)
+_bswap(c::Colorant{T, N}) where {T, N} = mapc(bswap, c)
 
 function getstream(fmt, io, name)
     # adapted from https://github.com/JuliaStats/RDatasets.jl/pull/119/

diff --git a/test/Aqua.jl b/test/Aqua.jl
@@ -0,0 +1,5 @@
+using Aqua
+
+@testset "Aqua.jl tests" begin
+    Aqua.test_all(TiffImages)
+end
diff --git a/test/Project.toml b/test/Project.toml
@@ -1,12 +1,16 @@
 [deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9"
 ColorTypes = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
 ColorVectorSpace = "c3611d14-8923-5661-9e6a-0046d554d3a4"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 FixedPointNumbers = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+SIMD = "fdea26ae-647d-5447-a871-4b548cad5224"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestImages = "5e47fb64-e119-507b-a336-dd2b206d9990"
-SIMD = "fdea26ae-647d-5447-a871-4b548cad5224"
+
+[compat]
+Aqua = "0.8"
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -8,6 +8,8 @@ using Statistics
 using Test
 using TiffImages
 
+include("Aqua.jl")
+
 DocMeta.setdocmeta!(TiffImages, :DocTestSetup, :(using TiffImages); recursive=true)
 doctest(TiffImages)
 
@@ -268,7 +270,7 @@ end
     m = sum(ref.data .- other.data) ./ length(ref)
     @test m.r < 0.001 && m.g < 0.001 && m.b < 0.001
 
-    @test other.ifds[1][TiffImages.BITSPERSAMPLE].data == UInt16[12,12,12]
+    @test ifds(other)[TiffImages.BITSPERSAMPLE].data == UInt16[12,12,12]
 
     other = TiffImages.load(get_example("shapes_lzw_14bps.tif"))
     m = sum(ref.data .- other.data) ./ length(ref)