tweak and update format

Author: rafaqz

docs/make.jl

@@ -10,11 +10,7 @@ makedocs(;
         canonical="https://juliageo.github.io/ZarrDatasets.jl",
         assets=String[],
     ),
-    pages=[
-        "Home" => "index.md",
-    ],
+    pages=["Home" => "index.md"],
 )
 
-deploydocs(;
-    repo="github.com/JuliaGeo/ZarrDatasets.jl",
-)
+deploydocs(; repo="github.com/JuliaGeo/ZarrDatasets.jl")

src/ZarrDatasets.jl

@@ -1,10 +1,6 @@
 module ZarrDatasets
 
-import Base:
-    checkbounds,
-    getindex,
-    setindex!,
-    size
+import Base: checkbounds, getindex, setindex!, size
 
 import CommonDataModel:
     CFVariable,
@@ -26,12 +22,10 @@ import CommonDataModel:
     parentdataset,
     variable
 
-import DiskArrays:
-    eachchunk,
-    haschunks
+import DiskArrays: eachchunk, haschunks
 
 import CommonDataModel as CDM
-import JSON
+using JSON: JSON
 
 using DataStructures
 using Zarr

src/dataset.jl

@@ -1,9 +1,11 @@
 # Base interface
 
 Base.keys(ds::ZarrDataset) = keys(ds.zgroup.arrays)
-Base.haskey(ds::ZarrDataset, varname::SymbolOrString) = haskey(ds.zgroup.arrays, String(varname))
+function Base.haskey(ds::ZarrDataset, varname::SymbolOrString)
+    haskey(ds.zgroup.arrays, String(varname))
+end
 
-# CommonDataModel.jl interface
+# CommonDataModel.jl interface methods
 
 CDM.name(v::ZarrDataset) = Zarr.zname(v.zgroup)
 function CDM.variable(ds::ZarrDataset, varname::SymbolOrString)
@@ -43,7 +45,7 @@ end
 # groups
 function CDM.defGroup(ds::ZarrDataset, groupname::SymbolOrString; attrib=Dict())
     _attrib = Dict{String,Any}(attrib)
-    zg = zgroup(ds.zgroup, String(groupname), attrs=_attrib)
+    zg = zgroup(ds.zgroup, String(groupname); attrs=_attrib)
     dimensions = OrderedDict{Symbol,Int}()
     return ZarrDataset(ds, zg, dimensions, ds.iswritable, ds.maskingvalue)
 end
@@ -59,9 +61,12 @@ CDM.iswritable(ds::ZarrDataset) = ds.iswritable
 CDM.maskingvalue(ds::ZarrDataset) = ds.maskingvalue
 
 """
-    ZarrDataset(url::AbstractString, mode = "r"; kw...)
-    ZarrDataset(zg::Zarr.ZGroup; kw...)
-    ZarrDataset(f::Function, url::AbstractString, mode = "r"; kw...)
+    ds = ZarrDataset(url::AbstractString,mode = "r";
+                     _omitcode = [404,403],
+                     maskingvalue = missing)
+    ZarrDataset(zg::Zarr.ZGroup; _omitcode, maskingvalue)
+    ZarrDataset(f::Function,url::AbstractString,mode = "r";
+                     maskingvalue = missing)
 
 Open the zarr dataset at the url or path `url`. The mode can be `"r"` (read-only),
 `"w"` (write), or `"c"` (create). `ds` supports the API of the
@@ -108,51 +113,59 @@ zos1 = ZarrDataset(url) do ds
 end # implicit call to close(ds)
 ```
 """
-
-function ZarrDataset(url::AbstractString, mode = "r";
-                     parentdataset = nothing,
-                     _omitcode = [404,403],
-                     maskingvalue = missing,
-                     attrib = Dict(),
-                     )
-
+function ZarrDataset(
+    url::AbstractString,
+    mode="r";
+    parentdataset=nothing,
+    _omitcode=[404, 403],
+    maskingvalue=missing,
+    attrib=Dict(),
+)
     dimensions = OrderedDict{Symbol,Int}()
 
     zg = if mode in ("w", "r")
         zg = Zarr.zopen(url, mode)
     elseif mode == "c"
         store = Zarr.DirectoryStore(url)
-        zg = zgroup(store, "", attrs = Dict{String,Any}(attrib))
+        zg = zgroup(store, ""; attrs=Dict{String,Any}(attrib))
     else
         throw(ArgumentError("mode must be \"r\", \"w\" or \"c\", got $mode"))
     end
     ZarrDataset(zg; mode, parentdataset, _omitcode, maskingvalue, attrib)
 end
 
-function ZarrDataset(store::Zarr.AbstractStore, mode = "r";
-                     parentdataset = nothing,
-                     _omitcode = [404,403],
-                     maskingvalue = missing,
-                     attrib = Dict(),
-                     )
-    return ZarrDataset(zopen(store, mode); mode, parentdataset, _omitcode, maskingvalue, attrib)
+function ZarrDataset(
+    store::Zarr.AbstractStore,
+    mode="r";
+    parentdataset=nothing,
+    _omitcode=[404, 403],
+    maskingvalue=missing,
+    attrib=Dict(),
+)
+    return ZarrDataset(
+        zopen(store, mode); mode, parentdataset, _omitcode, maskingvalue, attrib
+    )
 end
-function ZarrDataset(zg::Zarr.ZGroup;
+
+function ZarrDataset(
+    zg::Zarr.ZGroup;
     mode="r",
     parentdataset=nothing,
     _omitcode=[404, 403],
     maskingvalue=missing,
     attrib=Dict(),
 )
     dimensions = ZarrDatasets.OrderedDict{Symbol,Int}()
+    iswritable = false
     if (zg.storage isa Zarr.HTTPStore) ||
-       (zg.storage isa Zarr.ConsolidatedStore{Zarr.HTTPStore})
+        (zg.storage isa Zarr.ConsolidatedStore{Zarr.HTTPStore})
         @debug "omit chunks on HTTP error" _omitcode
         Zarr.missing_chunk_return_code!(zg.storage, _omitcode)
     end
 
     for (varname, zarray) in zg.arrays
-        for (dimname, dimlen) in zip(reverse(zarray.attrs["_ARRAY_DIMENSIONS"]), size(zarray))
+        for (dimname, dimlen) in
+            zip(reverse(zarray.attrs["_ARRAY_DIMENSIONS"]), size(zarray))
             dn = Symbol(dimname)
             if haskey(dimensions, dn)
                 @assert dimensions[dn] == dimlen
@@ -162,11 +175,17 @@ function ZarrDataset(zg::Zarr.ZGroup;
         end
     end
 
-    return ZarrDataset(parentdataset, zg, dimensions, mode == "r" ? false : zg.writeable, maskingvalue)
-
+    return ZarrDataset(
+        parentdataset, zg, dimensions, mode == "r" ? false : zg.writeable, maskingvalue
+    )
 end
-ZarrDataset(fnames::AbstractArray{<:AbstractString,N}, args...; kwargs...) where {N} =
+
+function ZarrDataset(
+    fnames::AbstractArray{<:AbstractString,N}, args...; kwargs...
+) where {N}
     MFDataset(ZarrDataset, fnames, args...; kwargs...)
+end
+
 function ZarrDataset(f::Function, args...; kwargs...)
     ds = ZarrDataset(args...; kwargs...)
     try
@@ -176,6 +195,8 @@ function ZarrDataset(f::Function, args...; kwargs...)
     end
 end
 
+# Utility functions
+
 function _dim(ds::ZarrDataset, dimname::SymbolOrString)
     dimlen = get(ds.dimensions, Symbol(dimname), nothing)
 
@@ -188,4 +209,4 @@ function _dim(ds::ZarrDataset, dimname::SymbolOrString)
     end
 
     error("dimension $dimname is not defined")
-end
+end

src/types.jl

@@ -1,10 +1,21 @@
 
-struct ZarrVariable{T,N,TZA <: AbstractArray{T,N},TZG} <: CDM.AbstractVariable{T,N}
+"""
+    ZarrVariable <: CDM.AbstractVariable
+
+    ZarrVariable(zarray, parentdataset)
+
+A CommonDataModel.jl compatible zarr variable.
+
+Usually generated with `CommonDataModel.defvar(::ZarrDataset, args...; kw...)`
+"""
+struct ZarrVariable{T,N,TZA<:AbstractArray{T,N},TZG} <: CDM.AbstractVariable{T,N}
     zarray::TZA
     parentdataset::TZG
 end
 
-struct ZarrDataset{TDS <: Union{CDM.AbstractDataset,Nothing},Tmaskingvalue,TZ} <: CDM.AbstractDataset
+# Documented in dataset.jl
+struct ZarrDataset{TDS<:Union{CDM.AbstractDataset,Nothing},Tmaskingvalue,TZ} <:
+       CDM.AbstractDataset
     parentdataset::TDS
     zgroup::TZ
     dimensions::OrderedDict{Symbol,Int}

src/variable.jl

@@ -1,27 +1,41 @@
+# Base interface methods
 
-Base.getindex(v::ZarrVariable,ij::Union{Integer,Colon,AbstractVector{<:Integer}}...) = parent(v)[ij...]
-function Base.setindex!(v::ZarrVariable,data,ij::Union{Integer,Colon,AbstractVector{<:Integer}}...)
+function Base.getindex(
+    v::ZarrVariable, ij::Union{Integer,Colon,AbstractVector{<:Integer}}...
+)
+    parent(v)[ij...]
+end
+function Base.setindex!(
+    v::ZarrVariable, data, ij::Union{Integer,Colon,AbstractVector{<:Integer}}...
+)
     parent(v)[ij...] = data
 end
 Base.size(v::ZarrVariable) = size(parent(v))
 Base.parent(v::ZarrVariable) = v.zarray
 
+# DiskArrays.jl interface methods
 
-CDM.load!(v::ZarrVariable,buffer,ij...) = buffer .= view(parent(v),ij...)
+eachchunk(v::ZarrVariable) = eachchunk(parent(v))
+haschunks(v::ZarrVariable) = haschunks(parent(v))
+eachchunk(v::CFVariable{T,N,<:ZarrVariable}) where {T,N} = eachchunk(v.var)
+haschunks(v::CFVariable{T,N,<:ZarrVariable}) where {T,N} = haschunks(v.var)
+
+# CommonDataModel.jl interface methods
+
+CDM.load!(v::ZarrVariable, buffer, ij...) = buffer .= view(parent(v), ij...)
 CDM.name(v::ZarrVariable) = Zarr.zname(parent(v))
 CDM.dimnames(v::ZarrVariable) = Tuple(reverse(parent(v).attrs["_ARRAY_DIMENSIONS"]))
-
 CDM.dataset(v::ZarrVariable) = v.parentdataset
 
 function CDM.attribnames(v::ZarrVariable)
-    names = filter(!=("_ARRAY_DIMENSIONS"),keys(parent(v).attrs))
+    names = filter(!=("_ARRAY_DIMENSIONS"), keys(parent(v).attrs))
     if !isnothing(parent(v).metadata.fill_value) && !_iscoordvar(v)
-        push!(names,"_FillValue")
+        push!(names, "_FillValue")
     end
     return names
 end
 
-function CDM.attrib(v::ZarrVariable{T},name::SymbolOrString) where T
+function CDM.attrib(v::ZarrVariable{T}, name::SymbolOrString) where {T}
     if String(name) == "_FillValue" && !isnothing(parent(v).metadata.fill_value)
         return T(parent(v).metadata.fill_value)
     end
@@ -38,16 +52,9 @@ function CDM.defAttrib(v::ZarrVariable, name::SymbolOrString, value)
     io = IOBuffer()
 
     JSON.print(io, parent(v).attrs)
-    storage[parent(v).path,".zattrs"] = take!(io)
+    storage[parent(v).path, ".zattrs"] = take!(io)
 end
 
-
-# DiskArray methods
-eachchunk(v::ZarrVariable) = eachchunk(parent(v))
-haschunks(v::ZarrVariable) = haschunks(parent(v))
-eachchunk(v::CFVariable{T,N,<:ZarrVariable}) where {T,N} = eachchunk(v.var)
-haschunks(v::CFVariable{T,N,<:ZarrVariable}) where {T,N} = haschunks(v.var)
-
 """
     defVar(ds::ZarrDataset, name::SymbolOrString, vtype::DataType, dimensionnames; 
         chunksizes=nothing, attrib=Dict(), fillvalue=nothing)
@@ -62,8 +69,15 @@ does not necessarily indicate a missing value.
 
 See also `CommonDataModel.defVar` for more information.
 """
-function CDM.defVar(ds::ZarrDataset, name::SymbolOrString, vtype::DataType, dimensionnames; 
-    chunksizes=nothing, attrib=Dict(), fillvalue=nothing, kwargs...
+function CDM.defVar(
+    ds::ZarrDataset,
+    name::SymbolOrString,
+    vtype::DataType,
+    dimensionnames;
+    chunksizes=nothing,
+    attrib=Dict(),
+    fillvalue=nothing,
+    kwargs...,
 )
     @assert iswritable(ds)
 
@@ -83,15 +97,25 @@ function CDM.defVar(ds::ZarrDataset, name::SymbolOrString, vtype::DataType, dime
     end
 
     zarray = zcreate(
-        vtype, ds.zgroup, name, _size...;
+        vtype,
+        ds.zgroup,
+        name,
+        _size...;
         chunks=chunksizes,
         attrs=_attrib,
         fill_value=fillvalue,
-        kwargs...
+        kwargs...,
     )
 
-    # TODO zv is not used?
-    zv = ZarrVariable{vtype,ndims(zarray),typeof(zarray),typeof(ds)}(zarray, ds)
-
     return ds[name]
-end
+end
+
+# Utility functions
+
+function _iscoordvar(v)
+    dn = dimnames(v)
+    if length(dn) == 0
+        return false
+    end
+    return name(v) == first(dn)
+end

test/runtests.jl

@@ -9,4 +9,4 @@ using ZarrDatasets
     include("test_fillvalue.jl")
     include("test_preexisting.jl")
     include("test_aqua.jl")
-end
+end

test/test_aqua.jl

@@ -3,4 +3,4 @@ using ZarrDatasets
 
 Aqua.test_ambiguities(ZarrDatasets)
 # some internal ambiguities in DiskArray 0.3 probably fixed in 0.4
-Aqua.test_all(ZarrDatasets, ambiguities=false)
+Aqua.test_all(ZarrDatasets; ambiguities=false)