fixup! force AlignedMapping elements to be 2-dimensional

Author: ilia-kats

src/hdf5_io.jl

@@ -277,19 +277,6 @@ end
 write_impl(parent::Union{HDF5.File, HDF5.Group}, name::AbstractString, data::SubArray; kwargs...) =
     write_impl(parent, name, copy(data); kwargs...)
 
-function write_impl(
-    parent::Union{HDF5.File, HDF5.Group},
-    name::AbstractString,
-    data::Union{BitArray, AbstractArray{Bool}},
-    ;
-    extensible::Bool=false,
-    compress::UInt8=0x9,
-    kwargs...,
-)
-    dtype = _datatype(Bool)
-    write_impl_array(parent, name, Array{UInt8}(data), dtype, size(data), compress)
-end
-
 function write_impl(
     parent::Union{HDF5.File, HDF5.Group},
     name::AbstractString,
@@ -346,6 +333,18 @@ function write_impl(
     write_impl_array(parentgrp, name, data, dtype, dims, compress)
 end
 
+function write_impl_array(
+    parent::Union{HDF5.File, HDF5.Group},
+    name::AbstractString,
+    data::Union{BitArray, AbstractArray{Bool}},
+    dtype::HDF5.Datatype,
+    dims::Union{Tuple{Vararg{<:Integer}}, Tuple{Tuple{Vararg{<:Integer, N}}, Tuple{Vararg{<:Integer, N}}}},
+    compress::UInt8,
+) where N
+    dtype = _datatype(Bool)
+    write_impl_array(parent, name, Array{UInt8}(data), dtype, dims, compress)
+end
+
 function write_impl_array(
     parent::Union{HDF5.File, HDF5.Group},
     name::AbstractString,

test/mudata.jl

@@ -82,10 +82,10 @@ end
     @test sort(names(md.var)) ==
           ["ad1:testcol", "ad2:testcol", "ad3:ad3col", "commoncol", "mutestcol", "testcol"]
     @test !any(ismissing.(md.var.commoncol))
-    @test sum(ismissing.(md.var.mutestcol[md.varm["ad1"]])) ==
-          sum(ismissing.(md.var.mutestcol[md.varm["ad2"]])) ==
+    @test sum(ismissing.(md.var.mutestcol[reshape(md.varm["ad1"], :)])) ==
+          sum(ismissing.(md.var.mutestcol[reshape(md.varm["ad2"], :)])) ==
           0
-    @test all(ismissing.(md.var.mutestcol[md.varm["ad3"]]))
+    @test all(ismissing.(md.var.mutestcol[reshape(md.varm["ad3"], :)]))
 end
 
 function test_row_slice(md, i1, n, d, j=:)
@@ -100,8 +100,8 @@ function test_row_slice(md, i1, n, d, j=:)
     ad1_names = filter(in(md["ad1"].obs_names), md.obs_names[i1])
     ad2_names = filter(in(md["ad2"].obs_names), md.obs_names[i1])
 
-    ad1_idx = filter(>(0x0), md.obsmap["ad1"][i1])
-    ad2_idx = filter(>(0x0), md.obsmap["ad2"][i1])
+    ad1_idx = filter(>(0x0), reshape(md.obsmap["ad1"], :)[i1])
+    ad2_idx = filter(>(0x0), reshape(md.obsmap["ad2"], :)[i1])
 
     ad1, ad2 = parent(md["ad1"])[ad1_idx, j], parent(md["ad2"])[ad2_idx, j]