Fixes for Julia 1.5 (#41)

* Fixes for Julia 1.5

* Remove some tests again

* Run a full PkgSkeleton update

* tweak codecov

* Fix some windows tests

* Be explicit about Int type in tests

.codecov.yml

@@ -0,0 +1 @@
+comment: false

.travis.yml

@@ -1,10 +1,9 @@
 language: julia
-codecov: true
 os:
     - osx
     - linux
 julia:
-    - 1.2
+    - 1
     - 1.3
     - nightly
 
@@ -23,5 +22,6 @@ jobs:
         - julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
         - julia --project=docs docs/make.jl
       after_success: skip
-#after_success:
-#- julia -e 'import Pkg; Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder()); Codecov.submit(Codecov.process_folder())'
+after_success:
+  - julia --project=test/coverage -e 'using Pkg; Pkg.instantiate()'
+  - julia --project=test/coverage test/coverage/coverage.jl

appveyor.yml

@@ -0,0 +1,42 @@
+environment:
+  matrix:
+  - julia_version: 1
+  - julia_version: nightly
+
+platform:
+  - x86 # 32-bit
+  - x64 # 64-bit
+
+# # Uncomment the following lines to allow failures on nightly julia
+# # (tests will run but not make your overall status red)
+# matrix:
+#   allow_failures:
+#   - julia_version: nightly
+
+branches:
+  only:
+    - master
+    - /release-.*/
+
+notifications:
+  - provider: Email
+    on_build_success: false
+    on_build_failure: false
+    on_build_status_changed: false
+
+install:
+  - ps: iex ((new-object net.webclient).DownloadString("https://raw.githubusercontent.com/JuliaCI/Appveyor.jl/version-1/bin/install.ps1"))
+
+build_script:
+  - echo "%JL_BUILD_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_BUILD_SCRIPT%"
+
+test_script:
+  - echo "%JL_TEST_SCRIPT%"
+  - C:\julia\bin\julia -e "%JL_TEST_SCRIPT%"
+
+# # Uncomment to support code coverage upload. Should only be enabled for packages
+# # which would have coverage gaps without running on Windows
+# on_success:
+#   - echo "%JL_CODECOV_SCRIPT%"
+#   - C:\julia\bin\julia -e "%JL_CODECOV_SCRIPT%"

docs/Project.toml

@@ -3,3 +3,4 @@ AWSCore = "4f1ea46c-232b-54a6-9b17-cc2d0f3e6598"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"

src/Storage/Storage.jl

@@ -66,7 +66,7 @@ function getsub end
 Deletes the given key from the store.
 """
 
-citostring(i::CartesianIndex) = join(reverse((i - one(i)).I), '.')
+citostring(i::CartesianIndex) = join(reverse((i - oneunit(i)).I), '.')
 
 Base.getindex(s::AbstractStore, i::CartesianIndex) = s[citostring(i)]
 Base.delete!(s::AbstractStore, i::CartesianIndex) = delete!(s, citostring(i))

src/Storage/http.jl

@@ -13,7 +13,7 @@ struct HTTPStore <: AbstractStore
 end
 
 function Base.getindex(s::HTTPStore, k::String)
-r = HTTP.request("GET",joinpath(s.url,k),status_exception = false)
+r = HTTP.request("GET",string(s.url,"/",k),status_exception = false)
 if r.status >= 300
     if r.status == 404
         nothing
@@ -24,7 +24,7 @@ else
     r.body
 end
 end
-getsub(s::HTTPStore,n) = HTTPStore(joinpath(s.url,n))
+getsub(s::HTTPStore,n) = HTTPStore(string(s.url,"/",n))
 zname(s::HTTPStore) = split(s.url,"/")[end]
 
 

src/Storage/s3store.jl

@@ -29,7 +29,7 @@ end
 
 function Base.getindex(s::S3Store, i::String)
   try
-    return S3.get_object(s.aws,Bucket=s.bucket,Key=joinpath(s.store,i))
+    return S3.get_object(s.aws,Bucket=s.bucket,Key=string(s.store,"/",i))
   catch e
     if error_is_ignorable(e)
       return nothing
@@ -38,7 +38,7 @@ function Base.getindex(s::S3Store, i::String)
     end
   end
 end
-getsub(s::S3Store, d::String) = S3Store(s.bucket, joinpath(s.store,d), s.listversion, s.aws)
+getsub(s::S3Store, d::String) = S3Store(s.bucket, string(s.store,"/",d), s.listversion, s.aws)
 
 function storagesize(s::S3Store)
   r = cloud_list_objects(s)
@@ -62,13 +62,13 @@ end
 
 function isinitialized(s::S3Store, i::String)
   try
-    S3.head_object(s.aws,Bucket=s.bucket,Key=joinpath(s.store,i))
+    S3.head_object(s.aws,Bucket=s.bucket,Key=string(s.store,"/",i))
     return true
   catch e
     if error_is_ignorable(e)
       return false
     else
-      println(joinpath(s.store,i))
+      println(string(s.store,"/",i))
       throw(e)
     end
   end

src/ZArray.jl

@@ -3,8 +3,8 @@ import FillArrays: Fill
 import OffsetArrays: OffsetArray
 import DiskArrays: AbstractDiskArray
 import DiskArrays
-getfillval(target::Type{T}, t::String) where {T <: Number} = parse(T, t)
-getfillval(target::Type{T}, t::Union{T,Nothing}) where {T} = t
+getfillval(::Type{T}, t::String) where {T <: Number} = parse(T, t)
+getfillval(::Type{T}, t::Union{T,Nothing}) where {T} = t
 
 struct SenMissArray{T,N,V} <: AbstractArray{Union{T,Missing},N}
   x::Array{T,N}
@@ -256,7 +256,7 @@ function zcreate(::Type{T},storage::AbstractStore,
     length(dims) == length(chunks) || throw(DimensionMismatch("Dims must have the same length as chunks"))
     N = length(dims)
     C = typeof(compressor)
-    T2 = fill_value == nothing ? T : Union{T,Missing}
+    T2 = fill_value === nothing ? T : Union{T,Missing}
     metadata = Metadata{T2, N, C}(
         2,
         dims,

src/metadata.jl

@@ -27,8 +27,8 @@ typestr(t::Type{<:Signed}) = string('<', 'i', sizeof(t))
 typestr(t::Type{<:Unsigned}) = string('<', 'u', sizeof(t))
 typestr(t::Type{Complex{T}} where T<:AbstractFloat) = string('<', 'c', sizeof(t))
 typestr(t::Type{<:AbstractFloat}) = string('<', 'f', sizeof(t))
-typestr(t::Type{MaxLengthString{N,UInt32}}) where {N,T} = string('<', 'U', N)
-typestr(t::Type{MaxLengthString{N,UInt8}}) where {N,T} = string('<', 'S', N)
+typestr(::Type{MaxLengthString{N,UInt32}}) where N = string('<', 'U', N)
+typestr(::Type{MaxLengthString{N,UInt8}}) where N = string('<', 'S', N)
 
 const typestr_regex = r"^([<|>])([tbiufcmMOSUV])(\d+)$"
 const typemap = Dict{Tuple{Char, Int}, DataType}(

test/coverage/Project.toml

@@ -0,0 +1,2 @@
+[deps]
+Coverage = "a2441757-f6aa-5fb2-8edb-039e3f45d037"

test/coverage/coverage-summary.jl

@@ -0,0 +1,12 @@
+####
+#### Coverage summary, printed as "(percentage) covered".
+####
+#### Useful for CI environments that just want a summary (eg a Gitlab setup).
+####
+
+using Coverage
+cd(joinpath(@__DIR__, "..", "..")) do
+    covered_lines, total_lines = get_summary(process_folder())
+    percentage = covered_lines / total_lines * 100
+    println("($(percentage)%) covered")
+end

test/coverage/coverage.jl

@@ -0,0 +1,9 @@
+# only push coverage from one bot
+get(ENV, "TRAVIS_OS_NAME", nothing)       == "linux" || exit(0)
+get(ENV, "TRAVIS_JULIA_VERSION", nothing) == "1.5"   || exit(0)
+
+using Coverage
+
+cd(joinpath(@__DIR__, "..", "..")) do
+    Codecov.submit(Codecov.process_folder())
+end

test/runtests.jl

@@ -9,8 +9,8 @@ using PyCall
 
 @testset "ZArray" begin
     @testset "fields" begin
-        z = zzeros(Int, 2, 3)
-        @test z isa ZArray{Int, 2, Zarr.BloscCompressor,
+        z = zzeros(Int64, 2, 3)
+        @test z isa ZArray{Int64, 2, Zarr.BloscCompressor,
             Zarr.DictStore}
 
         @test z.storage.name === "data"
@@ -31,11 +31,11 @@ using PyCall
     end
 
     @testset "methods" begin
-        z = zzeros(Int, 2, 3)
-        @test z isa ZArray{Int, 2, Zarr.BloscCompressor,
+        z = zzeros(Int64, 2, 3)
+        @test z isa ZArray{Int64, 2, Zarr.BloscCompressor,
             Zarr.DictStore}
 
-        @test eltype(z) === Int
+        @test eltype(z) === Int64
         @test ndims(z) === 2
         @test size(z) === (2, 3)
         @test size(z, 2) === 3
@@ -47,7 +47,7 @@ using PyCall
     @testset "NoCompressor DirectoryStore" begin
         mktempdir(@__DIR__) do dir
             name = "nocompressor"
-            z = zzeros(Int, 2, 3, path="$dir/$name",
+            z = zzeros(Int64, 2, 3, path="$dir/$name",
                 compressor=Zarr.NoCompressor())
 
             @test z.metadata.compressor === Zarr.NoCompressor()

test/storage.jl

@@ -56,7 +56,7 @@ end
   @test isdir(joinpath(p,"foo","bar"))
   @test isfile(joinpath(p,"foo","bar","0.0.0"))
   @test isfile(joinpath(p,"foo","bar",".zarray"))
-  @test Zarr.path(ds)==joinpath(p,"foo")
+  @test Zarr.path(ds)==replace(joinpath(p,"foo"),"\\"=>"/")
 end
 
 @testset "DictStore" begin
@@ -75,9 +75,6 @@ end
 import AWSCore: aws_config
 
 @testset "AWS S3 Storage" begin
-  # These tests work locally but not on Travis, not idea why, will skip them for now
-  # TODO fix
-  #if get(ENV,"TRAVIS","") != "true"
     bucket = "zarr-demo"
     store = "store/foo"
     region = "eu-west-2"
@@ -92,7 +89,6 @@ import AWSCore: aws_config
     @test eltype(S3Array) == Zarr.ASCIIChar
     @test storagesize(S3Array) == 69
     @test String(S3Array[:]) == "Hello from the cloud!"
-  #end
 end
 
 @testset "GCS S3 Storage" begin