diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 860e22a..bea5530 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -13,8 +13,9 @@ jobs: fail-fast: false matrix: version: - - '1.6' + - '1.9' - '1' + - 'nightly' os: - ubuntu-latest - macOS-latest diff --git a/.gitignore b/.gitignore index ddb6fb9..ea8a00e 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ *.jl.mem /deps/deps.jl /docs/build +Manifest.toml \ No newline at end of file diff --git a/Manifest.toml b/Manifest.toml deleted file mode 100644 index f92d48e..0000000 --- a/Manifest.toml +++ /dev/null @@ -1,105 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -[[ArgTools]] -uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" - -[[Artifacts]] -uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" - -[[Base64]] -uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" - -[[DataStructures]] -deps = ["InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "73eb18320fe3ba58790c8b8f6f89420f0a622773" -uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.17.11" - -[[Dates]] -deps = ["Printf"] -uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" - -[[Downloads]] -deps = ["ArgTools", "LibCURL", "NetworkOptions"] -uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" - -[[InteractiveUtils]] -deps = ["Markdown"] -uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" - -[[LibCURL]] -deps = ["LibCURL_jll", "MozillaCACerts_jll"] -uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" - -[[LibCURL_jll]] -deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] -uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" - -[[LibSSH2_jll]] -deps = ["Artifacts", "Libdl", "MbedTLS_jll"] -uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" - -[[Libdl]] -uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" - -[[Logging]] -uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" - -[[Markdown]] -deps = ["Base64"] -uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" - -[[MbedTLS_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" - -[[MozillaCACerts_jll]] -uuid = "14a3606d-f60d-562e-9121-12d972cd8159" - -[[NetworkOptions]] -uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" - -[[OrderedCollections]] -deps = ["Random", "Serialization", "Test"] -git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1" -uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.1.0" - -[[Printf]] -deps = ["Unicode"] -uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" - -[[Random]] -deps = ["Serialization"] -uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" - -[[Requires]] -deps = ["UUIDs"] -git-tree-sha1 = "d37400976e98018ee840e0ca4f9d20baa231dc6b" -uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.0.1" - -[[SHA]] -uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" - -[[Serialization]] -uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" - -[[Test]] -deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] -uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[[UUIDs]] -deps = ["Random", "SHA"] -uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" - -[[Unicode]] -uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" - -[[Zlib_jll]] -deps = ["Libdl"] -uuid = "83775a58-1f1d-513f-b197-d71354ab007a" - -[[nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" diff --git a/Project.toml b/Project.toml index 6790f76..72160db 100644 --- a/Project.toml +++ b/Project.toml @@ -1,16 +1,38 @@ name = "YAXArrayBase" uuid = "90b8fcef-0c2d-428d-9c56-5f86629e9d14" authors = ["Fabian Gans "] -version = "0.6.1" +version = "0.7.0" [deps] DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" -Requires = "ae029012-a4dd-5104-9daa-d747884805df" + [compat] -DataStructures = "0.17, 0.18" -Requires = "1" -julia = "1.6" +DataStructures = "0.17,0.18" +julia = "1.9" +ArchGDAL = "0.10" +AxisArrays = "0.4" +AxisKeys = "0.2" +DimensionalData = "0.24" +NetCDF = "0.11" +Zarr = "0.8" + +[extensions] +ArchGDALExt = "ArchGDAL" +AxisArraysExt = "AxisArrays" +AxisKeysExt = "AxisKeys" +DimensionalDataExt = "DimensionalData" +NamedDimsExt = "NamedDims" +NetCDFExt = "NetCDF" +ZarrExt = "Zarr" +[weakdeps] +ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" +AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9" +AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" +DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0" +NamedDims = "356022a1-0364-5f58-8944-0da4b18d706f" +NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9" +Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99" diff --git a/src/axisarrays/archgdal.jl b/ext/ArchGDALExt/ArchGDALExt.jl similarity index 82% rename from src/axisarrays/archgdal.jl rename to ext/ArchGDALExt/ArchGDALExt.jl index 1b2101d..6342d48 100644 --- a/src/axisarrays/archgdal.jl +++ b/ext/ArchGDALExt/ArchGDALExt.jl @@ -1,6 +1,11 @@ -import .ArchGDAL: RasterDataset, AbstractRasterBand, +module ArchGDALExt +import ArchGDAL: RasterDataset, AbstractRasterBand, getgeotransform, width, height, getname, getcolorinterp, getband, nraster, getdataset +using ArchGDAL: ArchGDAL as AG + import YAXArrayBase: dimname, dimnames, dimvals, iscontdim, getattributes, getdata, yaxcreate + +#include("archgdaldataset.jl") function dimname(a::RasterDataset, i) if i == 1 @@ -33,10 +38,10 @@ end iscontdim(a::RasterDataset, i) = i < 3 ? true : nraster(a)<8 function getattributes(a::RasterDataset) globatts = Dict{String,Any}( - "projection_PROJ4"=>ArchGDAL.toPROJ4(ArchGDAL.newspatialref(ArchGDAL.getproj(a))), - "projection_WKT"=>ArchGDAL.toWKT(ArchGDAL.newspatialref(ArchGDAL.getproj(a))), + "projection_PROJ4"=>AG.toPROJ4(AG.newspatialref(AG.getproj(a))), + "projection_WKT"=>AG.toWKT(AG.newspatialref(AG.getproj(a))), ) - bands = (getbandattributes(ArchGDAL.getband(a, i)) for i in 1:size(a, 3)) + bands = (getbandattributes(AG.getband(a, i)) for i in 1:size(a, 3)) allbands = mergewith(bands...) do a1,a2 isequal(a1,a2) ? a1 : missing end @@ -65,7 +70,7 @@ function dimvals(b::AbstractRasterBand, i) end iscontdim(a::AbstractRasterBand, i) = true function getattributes(a::AbstractRasterBand) - atts = getattributes(ArchGDAL.RasterDataset(ArchGDAL.getdataset(a))) + atts = getattributes(AG.RasterDataset(AG.getdataset(a))) bandatts = getbandattributes(a) merge(atts, bandatts) end @@ -84,4 +89,5 @@ function getbandattributes(a::AbstractRasterBand) insertattifnot!(atts, AG.getoffset(a), "add_offset", iszero) insertattifnot!(atts, AG.getscale(a), "scale_factor", x->isequal(x, one(x))) atts +end end \ No newline at end of file diff --git a/src/datasets/archgdal.jl b/ext/ArchGDALExt/archgdaldataset.jl similarity index 93% rename from src/datasets/archgdal.jl rename to ext/ArchGDALExt/archgdaldataset.jl index 9ec60e9..0ea4f1e 100644 --- a/src/datasets/archgdal.jl +++ b/ext/ArchGDALExt/archgdaldataset.jl @@ -1,9 +1,3 @@ -import .ArchGDAL: RasterDataset, AbstractRasterBand, - getgeotransform, width, height, getname, getcolorinterp, - getband, nraster, getdataset, ArchGDAL -using .ArchGDAL.DiskArrays: GridChunks, DiskArrays, eachchunk -const AG = ArchGDAL - struct GDALBand{T} <: AG.DiskArrays.AbstractDiskArray{T,2} filename::String band::Int @@ -221,8 +215,10 @@ allow_parallel_write(::GDALDataset) = false allow_missings(::Type{<:GDALDataset}) = false allow_missings(::GDALDataset) = false -backendlist[:gdal] = GDALDataset -push!(backendregex,r".tif$"=>GDALDataset) -push!(backendregex,r".gtif$"=>GDALDataset) -push!(backendregex,r".tiff$"=>GDALDataset) -push!(backendregex,r".gtiff$"=>GDALDataset) \ No newline at end of file +function __init__() + backendlist[:gdal] = GDALDataset + push!(backendregex,r".tif$"=>GDALDataset) + push!(backendregex,r".gtif$"=>GDALDataset) + push!(backendregex,r".tiff$"=>GDALDataset) + push!(backendregex,r".gtiff$"=>GDALDataset) +end \ No newline at end of file diff --git a/src/axisarrays/axisarrays.jl b/ext/AxisArraysExt.jl similarity index 73% rename from src/axisarrays/axisarrays.jl rename to ext/AxisArraysExt.jl index a6a5c31..7b908ec 100644 --- a/src/axisarrays/axisarrays.jl +++ b/ext/AxisArraysExt.jl @@ -1,5 +1,6 @@ -using .AxisArrays: AxisArrays, AxisArray - +module AxisArraysExt +using AxisArrays: AxisArrays, AxisArray +import YAXArrayBase: dimname, dimnames, dimvals, iscontdim, getattributes, getdata, yaxcreate dimname(a::AxisArray, i) = AxisArrays.axisnames(a)[i] dimnames(a::AxisArray) = AxisArrays.axisnames(a) dimvals(a::AxisArray, i) = AxisArrays.axisvalues(a)[i] @@ -11,3 +12,4 @@ function yaxcreate(::Type{<:AxisArray}, data, dnames, dvals, atts) end AxisArray(data; d...) end +end \ No newline at end of file diff --git a/src/axisarrays/axiskeys.jl b/ext/AxisKeysExt.jl similarity index 71% rename from src/axisarrays/axiskeys.jl rename to ext/AxisKeysExt.jl index d39437f..e30723a 100644 --- a/src/axisarrays/axiskeys.jl +++ b/ext/AxisKeysExt.jl @@ -1,5 +1,6 @@ -import .AxisKeys - +module AxisKeysExt +import AxisKeys +import YAXArrayBase: dimname, dimnames, dimvals, iscontdim, getattributes, getdata, yaxcreate dimnames(a::AxisKeys.KeyedArray) = AxisKeys.dimnames(a) dimvals(a::AxisKeys.KeyedArray,i) = AxisKeys.getproperty(a,AxisKeys.dimnames(a,i)) @@ -8,3 +9,4 @@ getdata(a::AxisKeys.KeyedArray) = parent(parent(a)) yaxcreate(::Type{<:AxisKeys.KeyedArray}, data, dnames, dvals, atts) = AxisKeys.KeyedArray(data; map(i->dnames[i]=>dvals[i],1:ndims(data))...) +end \ No newline at end of file diff --git a/src/axisarrays/dimensionaldata.jl b/ext/DimensionalDataExt.jl similarity index 71% rename from src/axisarrays/dimensionaldata.jl rename to ext/DimensionalDataExt.jl index 3e86b17..8472175 100644 --- a/src/axisarrays/dimensionaldata.jl +++ b/ext/DimensionalDataExt.jl @@ -1,5 +1,6 @@ -using .DimensionalData: DimArray, DimensionalData, data, Dim, metadata - +module DimensionalDataExt +using DimensionalData: DimArray, DimensionalData, data, Dim, metadata +import YAXArrayBase: dimname, dimnames, dimvals, iscontdim, getattributes, getdata, yaxcreate _dname(::DimensionalData.Dim{N}) where N = N _dname(d::DimensionalData.Dimension) = DimensionalData.name(d) dimname(x::DimArray, i) = _dname(DimensionalData.dims(x)[i]) @@ -17,3 +18,4 @@ function yaxcreate(::Type{<:DimArray},data,dnames,dvals,atts) end DimArray(data,d,metadata = atts) end +end \ No newline at end of file diff --git a/src/axisarrays/nameddims.jl b/ext/NamedDimsExt.jl similarity index 64% rename from src/axisarrays/nameddims.jl rename to ext/NamedDimsExt.jl index fd41a55..bc08181 100644 --- a/src/axisarrays/nameddims.jl +++ b/ext/NamedDimsExt.jl @@ -1,4 +1,6 @@ -using .NamedDims: NamedDimsArray +module NamedDimsExt +using NamedDims: NamedDimsArray +import YAXArrayBase: dimname, dimnames, dimvals, iscontdim, getattributes, getdata, yaxcreate dimname(a::NamedDimsArray{N},i) where N = N[i] dimnames(a::NamedDimsArray{N}) where N = N getdata(a::NamedDimsArray) = parent(a) @@ -6,3 +8,4 @@ function yaxcreate(::Type{<:NamedDimsArray},data, dnames, dvals, atts) n = ntuple(i->dnames[i],ndims(data)) NamedDimsArray(data,n) end +end diff --git a/src/datasets/netcdf.jl b/ext/NetCDFExt.jl similarity index 66% rename from src/datasets/netcdf.jl rename to ext/NetCDFExt.jl index 3611e83..fe78ab8 100644 --- a/src/datasets/netcdf.jl +++ b/ext/NetCDFExt.jl @@ -1,4 +1,6 @@ -using .NetCDF +module NetCDFExt +import YAXArrayBase: YAXArrayBase as YAB +using NetCDF """ NetCDFDataset @@ -43,37 +45,40 @@ function readblock!(v::NetCDFVariable, aout, r::AbstractUnitRange...) aout .= aouttemp end end -iscompressed(v::NetCDFVariable) = NetCDF.open(v->v.compress > 0, v.filename, v.varname) +YAB.iscompressed(v::NetCDFVariable) = NetCDF.open(v->v.compress > 0, v.filename, v.varname) Base.size(v::NetCDFVariable) = v.size -get_var_dims(ds::NetCDFDataset,name) = NetCDF.open(v->map(i->i.name,v[name].dim),ds.filename) -get_varnames(ds::NetCDFDataset) = NetCDF.open(v->collect(keys(v.vars)),ds.filename) -get_var_attrs(ds::NetCDFDataset, name) = NetCDF.open(v->v[name].atts,ds.filename) -get_global_attrs(ds::NetCDFDataset) = NetCDF.open(nc->nc.gatts, ds.filename) +YAB.get_var_dims(ds::NetCDFDataset,name) = NetCDF.open(v->map(i->i.name,v[name].dim),ds.filename) +YAB.get_varnames(ds::NetCDFDataset) = NetCDF.open(v->collect(keys(v.vars)),ds.filename) +YAB.get_var_attrs(ds::NetCDFDataset, name) = NetCDF.open(v->v[name].atts,ds.filename) +YAB.get_global_attrs(ds::NetCDFDataset) = NetCDF.open(nc->nc.gatts, ds.filename) function Base.getindex(ds::NetCDFDataset, i) s,et = NetCDF.open(j->(size(j),eltype(j)),ds.filename,i) NetCDFVariable{et,length(s)}(ds.filename, i, s) end Base.haskey(ds::NetCDFDataset,k) = NetCDF.open(nc->haskey(nc.vars,k),ds.filename) -function add_var(p::NetCDFDataset, T::Type, varname, s, dimnames, attr; +function YAB.add_var(p::NetCDFDataset, T::Type, varname, s, dimnames, attr; chunksize=s, compress = -1) dimsdescr = Iterators.flatten(zip(dimnames,s)) nccreate(p.filename, varname, dimsdescr..., atts = attr, t=T, chunksize=chunksize, compress=compress) NetCDFVariable{T,length(s)}(p.filename,varname,(s...,)) end -function create_empty(::Type{NetCDFDataset}, path, gatts=Dict()) +function YAB.create_empty(::Type{NetCDFDataset}, path, gatts=Dict()) NetCDF.create(_->nothing, path, NcVar[], gatts = gatts) NetCDFDataset(path) end -allow_parallel_write(::Type{<:NetCDFDataset}) = false -allow_parallel_write(::NetCDFDataset) = false +YAB.allow_parallel_write(::Type{<:NetCDFDataset}) = false +YAB.allow_parallel_write(::NetCDFDataset) = false -allow_missings(::Type{<:NetCDFDataset}) = false -allow_missings(::NetCDFDataset) = false +YAB.allow_missings(::Type{<:NetCDFDataset}) = false +YAB.allow_missings(::NetCDFDataset) = false -backendlist[:netcdf] = NetCDFDataset -push!(backendregex,r".nc$"=>NetCDFDataset) +function __init__() +YAB.backendlist[:netcdf] = NetCDFDataset +push!(YAB.backendregex,r".nc$"=>NetCDFDataset) +end +end \ No newline at end of file diff --git a/src/datasets/zarr.jl b/ext/ZarrExt.jl similarity index 50% rename from src/datasets/zarr.jl rename to ext/ZarrExt.jl index 44bb11d..b4fe210 100644 --- a/src/datasets/zarr.jl +++ b/ext/ZarrExt.jl @@ -1,14 +1,23 @@ -using .Zarr: ZArray, ZGroup, zgroup, zcreate, +module ZarrExt +using YAXArrayBase +using Zarr: ZArray, ZGroup, zgroup, zcreate, to_zarrtype, zopen, Compressor +import YAXArrayBase: YAXArrayBase as YAB +export ZarrDataset + +function __init__() +YAXArrayBase.backendlist[:zarr] = ZarrDataset +push!(YAXArrayBase.backendregex, r"(.zarr$)|(.zarr/$)"=>ZarrDataset) +end struct ZarrDataset g::ZGroup end ZarrDataset(g::String;mode="r") = ZarrDataset(zopen(g,mode,fill_as_missing=false)) -get_var_dims(ds::ZarrDataset,name) = reverse(ds[name].attrs["_ARRAY_DIMENSIONS"]) -get_varnames(ds::ZarrDataset) = collect(keys(ds.g.arrays)) -function get_var_attrs(ds::ZarrDataset, name) +YAB.get_var_dims(ds::ZarrDataset,name) = reverse(ds[name].attrs["_ARRAY_DIMENSIONS"]) +YAB.get_varnames(ds::ZarrDataset) = collect(keys(ds.g.arrays)) +function YAB.get_var_attrs(ds::ZarrDataset, name) #We add the fill value to the attributes to be consistent with NetCDF a = ds[name] if a.metadata.fill_value !== nothing @@ -17,7 +26,7 @@ function get_var_attrs(ds::ZarrDataset, name) ds[name].attrs end end -get_global_attrs(ds::ZarrDataset) = ds.g.attrs +YAB.get_global_attrs(ds::ZarrDataset) = ds.g.attrs Base.getindex(ds::ZarrDataset, i) = ds.g[i] Base.haskey(ds::ZarrDataset,k) = haskey(ds.g,k) @@ -26,16 +35,16 @@ Base.haskey(ds::ZarrDataset,k) = haskey(ds.g,k) # add_var(p,S, varname, s, dimnames, attr; fill_value = defaultfillval(S), fill_as_missing=true, kwargs...) # end -function add_var(p::ZarrDataset, T::Type, varname, s, dimnames, attr; +function YAB.add_var(p::ZarrDataset, T::Type, varname, s, dimnames, attr; chunksize=s, fill_as_missing=false, kwargs...) attr2 = merge(attr,Dict("_ARRAY_DIMENSIONS"=>reverse(collect(dimnames)))) - fv = get(attr,"_FillValue",get(attr,"missing_value",defaultfillval(T))) + fv = get(attr,"_FillValue",get(attr,"missing_value",YAB.defaultfillval(T))) za = zcreate(T, p.g, varname,s...;fill_value = fv,fill_as_missing,attrs=attr2,chunks=chunksize,kwargs...) za end #Special case for init with Arrays -function add_var(p::ZarrDataset, a::AbstractArray, varname, dimnames, attr; +function YAB.add_var(p::ZarrDataset, a::AbstractArray, varname, dimnames, attr; kwargs...) T = to_zarrtype(a) b = add_var(p,T,varname,size(a),dimnames,attr;kwargs...) @@ -43,12 +52,13 @@ function add_var(p::ZarrDataset, a::AbstractArray, varname, dimnames, attr; a end -create_empty(::Type{ZarrDataset}, path, gatts=Dict()) = ZarrDataset(zgroup(path, attrs=gatts)) +YAB.create_empty(::Type{ZarrDataset}, path, gatts=Dict()) = ZarrDataset(zgroup(path, attrs=gatts)) + + -backendlist[:zarr] = ZarrDataset -push!(backendregex, r"(.zarr$)|(.zarr/$)"=>ZarrDataset) +YAB.allow_parallel_write(::ZarrDataset) = true +YAB.allow_missings(::ZarrDataset) = false +YAB.to_dataset(g::ZGroup; kwargs...) = ZarrDataset(g) +YAB.iscompressed(a::ZArray{<:Any,<:Any,<:Compressor}) = true -allow_parallel_write(::ZarrDataset) = true -allow_missings(::ZarrDataset) = false -to_dataset(g::ZGroup; kwargs...) = ZarrDataset(g) -iscompressed(a::ZArray{<:Any,<:Any,<:Compressor}) = true \ No newline at end of file +end \ No newline at end of file diff --git a/src/YAXArrayBase.jl b/src/YAXArrayBase.jl index 8763272..2800dfc 100644 --- a/src/YAXArrayBase.jl +++ b/src/YAXArrayBase.jl @@ -1,6 +1,6 @@ module YAXArrayBase -using Requires: @require -using DataStructures: OrderedDict + + using DataStructures: OrderedDict include("datasets/datasetinterface.jl") include("axisarrays/axisinterface.jl") @@ -22,30 +22,6 @@ function __init__() ) backendregex = Pair[] - - @require NamedDims="356022a1-0364-5f58-8944-0da4b18d706f" include("axisarrays/nameddims.jl") - - @require DimensionalData="0703355e-b756-11e9-17c0-8b28908087d0" include("axisarrays/dimensionaldata.jl") - - @require AxisArrays="39de3d68-74b9-583c-8d2d-e117c070f3a9" include("axisarrays/axisarrays.jl") - - @require AxisIndices="f52c9ee2-1b1c-4fd8-8546-6350938c7f11" include("axisarrays/axisindices.jl") - - @require AxisKeys="94b1ba4f-4ee9-5380-92f1-94cde586c3c5" include("axisarrays/axiskeys.jl") - - @require ArchGDAL="c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" begin - include("axisarrays/archgdal.jl") - include("datasets/archgdal.jl") - end - - - @require Zarr="0a941bbe-ad1d-11e8-39d9-ab76183a1d99" include("datasets/zarr.jl") - - @require NetCDF="30363a11-5582-574a-97bb-aa9a979735b9" include("datasets/netcdf.jl") - - - - end diff --git a/src/axisarrays/axisindices.jl b/src/axisarrays/axisindices.jl deleted file mode 100644 index 611c980..0000000 --- a/src/axisarrays/axisindices.jl +++ /dev/null @@ -1,8 +0,0 @@ -using .AxisIndices: AbstractAxis,AxisIndicesArray - -valfromaxis(ax::AbstractAxis) = keys(ax) - -getdata(a::AxisIndices.AxisIndicesArray) = parent(a) - -yaxcreate(::Type{<:AxisIndices.AxisIndicesArray}, data, dnames, dvals, atts) = - AxisIndices.AxisIndicesArray(data, (dvals...,)) diff --git a/test/Manifest.toml b/test/Manifest.toml new file mode 100644 index 0000000..66632ff --- /dev/null +++ b/test/Manifest.toml @@ -0,0 +1,920 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.9.0-beta3" +manifest_format = "2.0" +project_hash = "c1a79f88c48222efe8ed4f14d068c743fdc84a5d" + 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+[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.2.0+0" + +[[deps.libgeotiff_jll]] +deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "Libtiff_jll", "PROJ_jll", "Pkg"] +git-tree-sha1 = "13dfba87a1fe301c4b40f991d0ec990bbee59bbe" +uuid = "06c338fa-64ff-565b-ac2f-249532af990e" +version = "100.700.100+0" + +[[deps.libpng_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" +version = "1.6.38+0" + +[[deps.libsodium_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e" +uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8" +version = "1.0.20+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" + +[[deps.snappy_jll]] +deps = ["Artifacts", "JLLWrappers", "LZO_jll", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "985c1da710b0e43f7c52f037441021dfd0e3be14" +uuid = "fe1e1685-f7be-5f59-ac9f-4ca204017dfd" +version = "1.1.9+1" diff --git a/test/Project.toml b/test/Project.toml index e83ca66..1f897c9 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -1,7 +1,6 @@ [deps] ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -AxisIndices = "f52c9ee2-1b1c-4fd8-8546-6350938c7f11" AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0" Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" @@ -9,4 +8,6 @@ NamedDims = "356022a1-0364-5f58-8944-0da4b18d706f" NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a" +TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe" Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99" diff --git a/test/arrays.jl b/test/arrays.jl index edb6c7b..9794713 100644 --- a/test/arrays.jl +++ b/test/arrays.jl @@ -1,25 +1,9 @@ -using YAXArrayBase, DimensionalData, AxisArrays, AxisIndices, Test +using TestItems -struct M -end -Base.ndims(::M) = 2 -YAXArrayBase.getdata(::M) = reshape(1:12,3,4) -YAXArrayBase.dimname(::M,i) = i==1 ? :x : :y -YAXArrayBase.dimvals(::M,i) = i==1 ? (0.5:1.0:2.5) : (1.5:0.5:3.0) -YAXArrayBase.getattributes(::M) = Dict{String,Any}("a1"=>5, "a2"=>"att") - -@testset "AxisIndices" begin - using AxisIndices: AxisIndices - d = yaxconvert(AxisIndices.AxisIndicesArray,M()) - @test d isa AxisIndices.AxisIndicesArray - @test getdata(d) == reshape(1:12,3,4) - @test YAXArrayBase.dimnames(d) == (:Dim_1, :Dim_2) - @test dimvals(d,1) == 0.5:1.0:2.5 - @test dimvals(d,2) == 1.5:0.5:3.0 -end -@testset "AxisKeys" begin +@testitem "AxisKeys" begin using AxisKeys: KeyedArray + include("mock.jl") d = yaxconvert(KeyedArray,M()) @test d isa KeyedArray @test getdata(d) == reshape(1:12,3,4) @@ -29,8 +13,9 @@ end end -@testset "AxisArrays" begin +@testitem "AxisArrays" begin using AxisArrays: AxisArrays + include("mock.jl") d = yaxconvert(AxisArrays.AxisArray,M()) @test d isa AxisArrays.AxisArray @test getdata(d) == reshape(1:12,3,4) @@ -39,7 +24,8 @@ end @test dimvals(d,2) == 1.5:0.5:3.0 end -@testset "NamedTuples" begin +@testitem "NamedTuples" begin + include("mock.jl") d = yaxconvert(NamedTuple,M()) @test d isa NamedTuple @test getdata(d) == reshape(1:12,3,4) @@ -48,16 +34,18 @@ end @test dimvals(d,2) == 1.5:0.5:3.0 end -@testset "NamedDims" begin +@testitem "NamedDims" begin using NamedDims: NamedDimsArray + include("mock.jl") d = yaxconvert(NamedDimsArray,M()) @test d isa NamedDimsArray @test getdata(d) == reshape(1:12,3,4) @test YAXArrayBase.dimnames(d) == (:x, :y) end -@testset "DimensionalData" begin +@testitem "DimensionalData" begin using DimensionalData + include("mock.jl") d = yaxconvert(DimArray,M()) @test d isa DimArray @test getdata(d) == reshape(1:12,3,4) @@ -67,8 +55,9 @@ end @test getattributes(d) == Dict{String,Any}("a1"=>5, "a2"=>"att") end -@testset "ArchGDAL" begin +@testitem "ArchGDAL" begin import Downloads + include("mock.jl") p = Downloads.download("https://download.osgeo.org/geotiff/samples/gdal_eg/cea.tif") using ArchGDAL AG=ArchGDAL diff --git a/test/datasets.jl b/test/datasets.jl index 82aac31..f315210 100644 --- a/test/datasets.jl +++ b/test/datasets.jl @@ -10,7 +10,7 @@ import Downloads # This is the path to the Artifacts.toml we will manipulate artifact_toml = joinpath(@__DIR__,"Artifacts.toml") ncar_hash = artifact_hash("ncar", artifact_toml) -if ncar_hash == nothing || !artifact_exists(ncar_hash) +if ncar_hash === nothing || !artifact_exists(ncar_hash) oldhash = ncar_hash ncar_hash = create_artifact() do artifact_dir Downloads.download("https://www.unidata.ucar.edu/software/netcdf/examples/sresa1b_ncar_ccsm3-example.nc",joinpath(artifact_dir,"ncar.nc")) @@ -76,9 +76,9 @@ v = get_var_handle(ds, "tas") end @testset "Writing NetCDF" begin - test_write(YAXArrayBase.NetCDFDataset) + test_write(YAXArrayBase.backendlist[:netcdf]) end @testset "Writing Zarr" begin - test_write(YAXArrayBase.ZarrDataset) + test_write(YAXArrayBase.backendlist[:zarr]) end diff --git a/test/mock.jl b/test/mock.jl new file mode 100644 index 0000000..004a56f --- /dev/null +++ b/test/mock.jl @@ -0,0 +1,7 @@ +struct M +end +Base.ndims(::M) = 2 +YAXArrayBase.getdata(::M) = reshape(1:12,3,4) +YAXArrayBase.dimname(::M,i) = i==1 ? :x : :y +YAXArrayBase.dimvals(::M,i) = i==1 ? (0.5:1.0:2.5) : (1.5:0.5:3.0) +YAXArrayBase.getattributes(::M) = Dict{String,Any}("a1"=>5, "a2"=>"att") \ No newline at end of file diff --git a/test/runtests.jl b/test/runtests.jl index e75b09c..274847d 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,9 +1,10 @@ using YAXArrayBase -using Test +using Test, TestItemRunner +@run_package_tests @testset "Datasets" begin -include("datasets.jl") + include("datasets.jl") end -@testset "Arrays" begin - include("arrays.jl") -end \ No newline at end of file +#@testset "Arrays" begin +# include("arrays.jl") +#end \ No newline at end of file