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JuliaIO · Jul 6, 2022 · 228e355 · 228e355
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Showing 49 changed files with 6,677 additions and 3,497 deletions.
diff --git a/src/HDF5.jl b/src/HDF5.jl
@@ -9,18 +9,42 @@ import Mmap
 
 ### PUBLIC API ###
 
-export
-@read, @write,
-h5open, h5read, h5write, h5rewrite, h5writeattr, h5readattr,
-create_attribute, open_attribute, read_attribute, write_attribute, delete_attribute, rename_attribute, attributes, attrs,
-create_dataset, open_dataset, read_dataset, write_dataset,
-create_group, open_group,
-copy_object, open_object, delete_object, move_link,
-create_datatype, commit_datatype, open_datatype,
-create_property,
-group_info, object_info,
-dataspace, datatype,
-Filters, Drivers
+export @read,
+    @write,
+    h5open,
+    h5read,
+    h5write,
+    h5rewrite,
+    h5writeattr,
+    h5readattr,
+    create_attribute,
+    open_attribute,
+    read_attribute,
+    write_attribute,
+    delete_attribute,
+    rename_attribute,
+    attributes,
+    attrs,
+    create_dataset,
+    open_dataset,
+    read_dataset,
+    write_dataset,
+    create_group,
+    open_group,
+    copy_object,
+    open_object,
+    delete_object,
+    move_link,
+    create_datatype,
+    commit_datatype,
+    open_datatype,
+    create_property,
+    group_info,
+    object_info,
+    dataspace,
+    datatype,
+    Filters,
+    Drivers
 
 ### The following require module scoping ###
 
@@ -100,7 +124,12 @@ function h5read(filename, name_type_pair::Pair{<:AbstractString,DataType}; pv...
     dat
 end
 
-function h5read(filename, name::AbstractString, indices::Tuple{Vararg{Union{AbstractRange{Int},Int,Colon}}}; pv...)
+function h5read(
+    filename,
+    name::AbstractString,
+    indices::Tuple{Vararg{Union{AbstractRange{Int},Int,Colon}}};
+    pv...,
+)
     local dat
     fapl = FileAccessProperties(; fclose_degree = :strong)
     pv = setproperties!(fapl; pv...)
@@ -115,8 +144,6 @@ function h5read(filename, name::AbstractString, indices::Tuple{Vararg{Union{Abst
     dat
 end
 
-
-
 function Base.getindex(parent::Union{File,Group}, path::AbstractString; pv...)
     haskey(parent, path) || throw(KeyError(path))
     # Faster than below if defaults are OK
@@ -139,7 +166,12 @@ end
 
 # Assign syntax: obj[path] = value
 # Create a dataset with properties: obj[path, prop = val, ...] = val
-function Base.setindex!(parent::Union{File,Group}, val, path::Union{AbstractString,Nothing}; pv...)
+function Base.setindex!(
+    parent::Union{File,Group},
+    val,
+    path::Union{AbstractString,Nothing};
+    pv...,
+)
     need_chunks = any(k in keys(chunked_props) for k in keys(pv))
     have_chunks = any(k == :chunk for k in keys(pv))
 
@@ -157,17 +189,12 @@ function Base.setindex!(parent::Union{File,Group}, val, path::Union{AbstractStri
     write(parent, path, val; pv...)
 end
 
-
-
 # end of high-level interface
 
-
 include("api_midlevel.jl")
 
-
 #API.h5s_get_simple_extent_ndims(space_id::API.hid_t) = API.h5s_get_simple_extent_ndims(space_id, C_NULL, C_NULL)
 
-
 # Functions that require special handling
 
 const libversion = API.h5_get_libversion()
@@ -180,7 +207,6 @@ get_create_properties(g::Group)     = GroupCreateProperties(API.h5g_get_create_p
 get_create_properties(f::File)      = FileCreateProperties(API.h5f_get_create_plist(f))
 get_create_properties(a::Attribute) = AttributeCreateProperties(API.h5a_get_create_plist(a))
 
-
 const HAS_PARALLEL = Ref(false)
 
 """
@@ -204,12 +230,16 @@ function __init__()
     ASCII_ATTRIBUTE_PROPERTIES.char_encoding = :ascii
     UTF8_ATTRIBUTE_PROPERTIES.char_encoding = :utf8
 
-    @require FileIO="5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" begin
-        @require OrderedCollections="bac558e1-5e72-5ebc-8fee-abe8a469f55d" include("fileio.jl")
+    @require FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" begin
+        @require OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" include(
+            "fileio.jl",
+        )
     end
-    @require H5Zblosc="c8ec2601-a99c-407f-b158-e79c03c2f5f7" begin
-        set_blosc!(p::Properties, val::Bool) = val && push!(Filters.FilterPipeline(p), H5Zblosc.BloscFilter())
-        set_blosc!(p::Properties, level::Integer) = push!(Filters.FilterPipeline(p), H5Zblosc.BloscFilter(level=level))
+    @require H5Zblosc = "c8ec2601-a99c-407f-b158-e79c03c2f5f7" begin
+        set_blosc!(p::Properties, val::Bool) =
+            val && push!(Filters.FilterPipeline(p), H5Zblosc.BloscFilter())
+        set_blosc!(p::Properties, level::Integer) =
+            push!(Filters.FilterPipeline(p), H5Zblosc.BloscFilter(level = level))
     end
 
     return nothing

diff --git a/src/api/api.jl b/src/api/api.jl
@@ -7,8 +7,10 @@ const depsfile = joinpath(@__DIR__, "..", "..", "deps", "deps.jl")
 if isfile(depsfile)
     include(depsfile)
 else
-    error("HDF5 is not properly installed. Please run Pkg.build(\"HDF5\") ",
-          "and restart Julia.")
+    error(
+        "HDF5 is not properly installed. Please run Pkg.build(\"HDF5\") ",
+        "and restart Julia.",
+    )
 end
 
 include("types.jl")

diff --git a/src/api/error.jl b/src/api/error.jl
@@ -55,14 +55,20 @@ function Base.showerror(io::IO, err::H5Error)
         errval = unsafe_load(errptr)
         print(io, "\n", lpad("[$n] ", 4 + ndigits(n_total)))
         if errval.func_name != C_NULL
-            printstyled(io, unsafe_string(errval.func_name); bold=true)
+            printstyled(io, unsafe_string(errval.func_name); bold = true)
             print(io, ": ")
         end
         major = h5e_get_msg(errval.maj_num)[2]
         minor = h5e_get_msg(errval.min_num)[2]
         print(io, major, "/", minor)
         if errval.desc != C_NULL
-            printstyled(io, "\n", " "^(4 + ndigits(n_total)), unsafe_string(errval.desc), color=:light_black)
+            printstyled(
+                io,
+                "\n",
+                " "^(4 + ndigits(n_total)),
+                unsafe_string(errval.desc),
+                color = :light_black,
+            )
         end
         if SHORT_ERROR[]
             if n_total > 1