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Grab keys via callback iteration rather than many absolute calls #787

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Dec 28, 2020
Merged

Grab keys via callback iteration rather than many absolute calls #787

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04a9ccf
Grab keys via callback iteration rather than many absolute calls
jmert Dec 23, 2020
6065167
Automatically handle versioned libhdf5 naming
jmert Dec 24, 2020
73e62e4
Support libhdf5 version-specific bindings
jmert Dec 24, 2020
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2 changes: 2 additions & 0 deletions docs/src/api_bindings.md
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Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,7 @@ h5a_get_name(attr_id::hid_t, buf_size::Csize_t, buf::Ptr{UInt8})
h5a_get_name_by_idx(loc_id::hid_t, obj_name::Cstring, index_type::Cint, order::Cint, idx::hsize_t, name::Ptr{UInt8}, size::Csize_t, lapl_id::hid_t)
h5a_get_space(attr_id::hid_t)
h5a_get_type(attr_id::hid_t)
h5a_iterate(obj_id::hid_t, idx_type::Cint, order::Cint, n::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})
h5a_open(obj_id::hid_t, pathname::Ptr{UInt8}, aapl_id::hid_t)
h5a_read(attr_id::hid_t, mem_type_id::hid_t, buf::Ptr{Cvoid})
h5a_write(attr_hid::hid_t, mem_type_id::hid_t, buf::Ptr{Cvoid})
Expand Down Expand Up @@ -122,6 +123,7 @@ h5l_delete(obj_id::hid_t, pathname::Ptr{UInt8}, lapl_id::hid_t)
h5l_exists(loc_id::hid_t, pathname::Ptr{UInt8}, lapl_id::hid_t)
h5l_get_info(link_loc_id::hid_t, link_name::Ptr{UInt8}, link_buf::Ptr{H5L_info_t}, lapl_id::hid_t)
h5l_get_name_by_idx(loc_id::hid_t, group_name::Ptr{UInt8}, index_field::Cint, order::Cint, n::hsize_t, name::Ptr{UInt8}, size::Csize_t, lapl_id::hid_t)
h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})
```

## [`H5O`](https://portal.hdfgroup.org/display/HDF5/Objects) — Object Interface
Expand Down
44 changes: 25 additions & 19 deletions gen/api_defs.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,10 @@
#
# The C library names are automatically generated from the Julia function name by
# uppercasing the `h5?` and removing the first underscore ---
# e.g. `h5d_close` -> `H5Dclose`.
# For versioned bindings (such as `H5Dopen2`), the mapping between names is given
# explicitly in the `bind_exceptions` Dict in `bind_generator.jl`.
# e.g. `h5d_close` -> `H5Dclose`. Versioned function names (such as
# `h5d_open2` -> `H5Dopen2`) have the trailing number removed for the Julia function
# definition. Other arbitrary mappings may be added by adding an entry to the
# `bind_exceptions` Dict in `bind_generator.jl`.

###
### HDF5 General library functions
Expand All @@ -32,7 +33,7 @@
###

@bind h5a_close(id::hid_t)::herr_t "Error closing attribute"
@bind h5a_create(loc_id::hid_t, pathname::Ptr{UInt8}, type_id::hid_t, space_id::hid_t, acpl_id::hid_t, aapl_id::hid_t)::hid_t error("Error creating attribute ", h5a_get_name(loc_id), "/", pathname)
@bind h5a_create2(loc_id::hid_t, pathname::Ptr{UInt8}, type_id::hid_t, space_id::hid_t, acpl_id::hid_t, aapl_id::hid_t)::hid_t error("Error creating attribute ", h5a_get_name(loc_id), "/", pathname)
@bind h5a_create_by_name(loc_id::hid_t, obj_name::Ptr{UInt8}, attr_name::Ptr{UInt8}, type_id::hid_t, space_id::hid_t, acpl_id::hid_t, aapl_id::hid_t, lapl_id::hid_t)::hid_t error("Error creating attribute ", attr_name, " for object ", obj_name)
@bind h5a_delete(loc_id::hid_t, attr_name::Ptr{UInt8})::herr_t error("Error deleting attribute ", attr_name)
@bind h5a_delete_by_idx(loc_id::hid_t, obj_name::Ptr{UInt8}, idx_type::Cint, order::Cint, n::hsize_t, lapl_id::hid_t)::herr_t error("Error deleting attribute ", n, " from object ", obj_name)
Expand All @@ -44,6 +45,7 @@
@bind h5a_get_name_by_idx(loc_id::hid_t, obj_name::Cstring, index_type::Cint, order::Cint, idx::hsize_t, name::Ptr{UInt8}, size::Csize_t, lapl_id::hid_t)::Cssize_t "Error getting attribute name"
@bind h5a_get_space(attr_id::hid_t)::hid_t "Error getting attribute dataspace"
@bind h5a_get_type(attr_id::hid_t)::hid_t "Error getting attribute type"
@bind h5a_iterate2(obj_id::hid_t, idx_type::Cint, order::Cint, n::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})::herr_t error("Error iterating attributes in object ", h5i_get_name(obj_id))
@bind h5a_open(obj_id::hid_t, pathname::Ptr{UInt8}, aapl_id::hid_t)::hid_t error("Error opening attribute ", h5i_get_name(obj_id), "/", pathname)
@bind h5a_read(attr_id::hid_t, mem_type_id::hid_t, buf::Ptr{Cvoid})::herr_t error("Error reading attribute ", h5a_get_name(attr_id))
@bind h5a_write(attr_hid::hid_t, mem_type_id::hid_t, buf::Ptr{Cvoid})::herr_t "Error writing attribute data"
Expand All @@ -53,14 +55,14 @@
###

@bind h5d_close(dataset_id::hid_t)::herr_t "Error closing dataset"
@bind h5d_create(loc_id::hid_t, pathname::Ptr{UInt8}, dtype_id::hid_t, space_id::hid_t, lcpl_id::hid_t, dcpl_id::hid_t, dapl_id::hid_t)::hid_t error("Error creating dataset ", h5i_get_name(loc_id), "/", pathname)
@bind h5d_create2(loc_id::hid_t, pathname::Ptr{UInt8}, dtype_id::hid_t, space_id::hid_t, lcpl_id::hid_t, dcpl_id::hid_t, dapl_id::hid_t)::hid_t error("Error creating dataset ", h5i_get_name(loc_id), "/", pathname)
@bind h5d_flush(dataset_id::hid_t)::herr_t "Error flushing dataset"
@bind h5d_get_access_plist(dataset_id::hid_t)::hid_t "Error getting dataset access property list"
@bind h5d_get_create_plist(dataset_id::hid_t)::hid_t "Error getting dataset create property list"
@bind h5d_get_offset(dataset_id::hid_t)::haddr_t "Error getting offset"
@bind h5d_get_space(dataset_id::hid_t)::hid_t "Error getting dataspace"
@bind h5d_get_type(dataset_id::hid_t)::hid_t "Error getting dataspace type"
@bind h5d_open(loc_id::hid_t, pathname::Ptr{UInt8}, dapl_id::hid_t)::hid_t error("Error opening dataset ", h5i_get_name(loc_id), "/", pathname)
@bind h5d_open2(loc_id::hid_t, pathname::Ptr{UInt8}, dapl_id::hid_t)::hid_t error("Error opening dataset ", h5i_get_name(loc_id), "/", pathname)
@bind h5d_read(dataset_id::hid_t, mem_type_id::hid_t, mem_space_id::hid_t, file_space_id::hid_t, xfer_plist_id::hid_t, buf::Ptr{Cvoid})::herr_t error("Error reading dataset ", h5i_get_name(dataset_id))
@bind h5d_refresh(dataset_id::hid_t)::herr_t "Error refreshing dataset"
@bind h5d_set_extent(dataset_id::hid_t, new_dims::Ptr{hsize_t})::herr_t "Error extending dataset dimensions"
Expand All @@ -72,8 +74,8 @@
### Error Interface
###

@bind h5e_get_auto(estack_id::hid_t, func::Ref{Ptr{Cvoid}}, client_data::Ref{Ptr{Cvoid}})::herr_t "Error getting error reporting behavior"
@bind h5e_set_auto(estack_id::hid_t, func::Ptr{Cvoid}, client_data::Ptr{Cvoid})::herr_t "Error setting error reporting behavior"
@bind h5e_get_auto2(estack_id::hid_t, func::Ref{Ptr{Cvoid}}, client_data::Ref{Ptr{Cvoid}})::herr_t "Error getting error reporting behavior"
@bind h5e_set_auto2(estack_id::hid_t, func::Ptr{Cvoid}, client_data::Ptr{Cvoid})::herr_t "Error setting error reporting behavior"
@bind h5e_get_current_stack()::hid_t "Unable to return current error stack"

###
Expand All @@ -99,12 +101,12 @@
###

@bind h5g_close(group_id::hid_t)::herr_t "Error closing group"
@bind h5g_create(loc_id::hid_t, pathname::Ptr{UInt8}, lcpl_id::hid_t, gcpl_id::hid_t, gapl_id::hid_t)::hid_t error("Error creating group ", h5i_get_name(loc_id), "/", pathname)
@bind h5g_create2(loc_id::hid_t, pathname::Ptr{UInt8}, lcpl_id::hid_t, gcpl_id::hid_t, gapl_id::hid_t)::hid_t error("Error creating group ", h5i_get_name(loc_id), "/", pathname)
@bind h5g_get_create_plist(group_id::hid_t)::hid_t "Error getting group create property list"
@bind h5g_get_info(group_id::hid_t, buf::Ptr{H5G_info_t})::herr_t "Error getting group info"
@bind h5g_get_num_objs(loc_id::hid_t, num_obj::Ptr{hsize_t})::hid_t "Error getting group length"
@bind h5g_get_objname_by_idx(loc_id::hid_t, idx::hsize_t, pathname::Ptr{UInt8}, size::Csize_t)::Cssize_t error("Error getting group object name ", h5i_get_name(loc_id), "/", pathname)
@bind h5g_open(loc_id::hid_t, pathname::Ptr{UInt8}, gapl_id::hid_t)::hid_t error("Error opening group ", h5i_get_name(loc_id), "/", pathname)
@bind h5g_open2(loc_id::hid_t, pathname::Ptr{UInt8}, gapl_id::hid_t)::hid_t error("Error opening group ", h5i_get_name(loc_id), "/", pathname)

###
### Identifier Interface
Expand All @@ -129,14 +131,18 @@
@bind h5l_exists(loc_id::hid_t, pathname::Ptr{UInt8}, lapl_id::hid_t)::htri_t error("Cannot determine whether ", pathname, " exists")
@bind h5l_get_info(link_loc_id::hid_t, link_name::Ptr{UInt8}, link_buf::Ptr{H5L_info_t}, lapl_id::hid_t)::herr_t error("Error getting info for link ", link_name)
@bind h5l_get_name_by_idx(loc_id::hid_t, group_name::Ptr{UInt8}, index_field::Cint, order::Cint, n::hsize_t, name::Ptr{UInt8}, size::Csize_t, lapl_id::hid_t)::Cssize_t "Error getting object name"
# libhdf5 v1.10 provides the name H5Literate
# libhdf5 v1.12 provides the same under H5Literate1, and a newer interface on H5Literate2
@bind h5l_iterate(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})::herr_t error("Error iterating through links in group ", h5i_get_name(group_id)) (nothing, v"1.12")
@bind h5l_iterate1(group_id::hid_t, idx_type::Cint, order::Cint, idx::Ptr{hsize_t}, op::Ptr{Cvoid}, op_data::Ptr{Cvoid})::herr_t error("Error iterating through links in group ", h5i_get_name(group_id)) (v"1.12", nothing)

###
### Object Interface
###

@bind h5o_close(object_id::hid_t)::herr_t "Error closing object"
@bind h5o_copy(src_loc_id::hid_t, src_name::Ptr{UInt8}, dst_loc_id::hid_t, dst_name::Ptr{UInt8}, ocpypl_id::hid_t, lcpl_id::hid_t)::herr_t error("Error copying object ", h5i_get_name(src_loc_id), "/", src_name, " to ", h5i_get_name(dst_loc_id), "/", dst_name)
@bind h5o_get_info(object_id::hid_t, buf::Ptr{H5O_info_t})::herr_t "Error getting object info"
@bind h5o_get_info1(object_id::hid_t, buf::Ptr{H5O_info_t})::herr_t "Error getting object info"
@bind h5o_open(loc_id::hid_t, pathname::Ptr{UInt8}, lapl_id::hid_t)::hid_t error("Error opening object ", h5i_get_name(loc_id), "/", pathname)
@bind h5o_open_by_addr(loc_id::hid_t, addr::haddr_t)::hid_t error("Error opening object by address")
@bind h5o_open_by_idx(loc_id::hid_t, group_name::Ptr{UInt8}, index_type::Cint, order::Cint, n::hsize_t, lapl_id::hid_t)::hid_t error("Error opening object of index ", n)
Expand All @@ -158,7 +164,7 @@
@bind h5p_get_fapl_mpio32(fapl_id::hid_t, comm::Ptr{Hmpih32}, info::Ptr{Hmpih32})::herr_t "Error getting MPIO properties"
@bind h5p_get_fapl_mpio64(fapl_id::hid_t, comm::Ptr{Hmpih64}, info::Ptr{Hmpih64})::herr_t "Error getting MPIO properties"
@bind h5p_get_fclose_degree(fapl_id::hid_t, fc_degree::Ref{Cint})::herr_t "Error getting close degree"
@bind h5p_get_filter_by_id(plist_id::hid_t, filter_id::H5Z_filter_t, flags::Ref{Cuint}, cd_nelmts::Ref{Csize_t}, cd_values::Ptr{Cuint}, namelen::Csize_t, name::Ptr{UInt8}, filter_config::Ptr{Cuint})::herr_t "Error getting filter ID"
@bind h5p_get_filter_by_id2(plist_id::hid_t, filter_id::H5Z_filter_t, flags::Ref{Cuint}, cd_nelmts::Ref{Csize_t}, cd_values::Ptr{Cuint}, namelen::Csize_t, name::Ptr{UInt8}, filter_config::Ptr{Cuint})::herr_t "Error getting filter ID"
@bind h5p_get_layout(plist_id::hid_t)::Cint error("Error getting layout")
@bind h5p_get_libver_bounds(fapl_id::hid_t, low::Ref{Cint}, high::Ref{Cint})::herr_t "Error getting library version bounds"
@bind h5p_get_local_heap_size_hint(plist_id::hid_t, size_hint::Ref{Csize_t})::herr_t "Error getting local heap size hint"
Expand Down Expand Up @@ -191,16 +197,16 @@
###

@bind h5r_create(ref::Ptr{Cvoid}, loc_id::hid_t, pathname::Ptr{UInt8}, ref_type::Cint, space_id::hid_t)::herr_t error("Error creating reference to object ", h5i_get_name(loc_id), "/", pathname)
@bind h5r_dereference(obj_id::hid_t, oapl_id::hid_t, ref_type::Cint, ref::Ptr{Cvoid})::hid_t "Error dereferencing object"
@bind h5r_get_obj_type(loc_id::hid_t, ref_type::Cint, ref::Ptr{Cvoid}, obj_type::Ptr{Cint})::herr_t "Error getting object type"
@bind h5r_dereference2(obj_id::hid_t, oapl_id::hid_t, ref_type::Cint, ref::Ptr{Cvoid})::hid_t "Error dereferencing object"
@bind h5r_get_obj_type2(loc_id::hid_t, ref_type::Cint, ref::Ptr{Cvoid}, obj_type::Ptr{Cint})::herr_t "Error getting object type"
@bind h5r_get_region(loc_id::hid_t, ref_type::Cint, ref::Ptr{Cvoid})::hid_t "Error getting region from reference"

###
### Dataspace Interface
###

@bind h5s_close(space_id::hid_t)::herr_t "Error closing dataspace"
@bind h5s_combine_select(space1_id::hid_t, op::Cint, space2_id::hid_t)::hid_t "Error combining dataspaces"
@bind h5s_combine_select(space1_id::hid_t, op::Cint, space2_id::hid_t)::hid_t "Error combining dataspaces" (v"1.10.7", nothing)
@bind h5s_copy(space_id::hid_t)::hid_t "Error copying dataspace"
@bind h5s_create(class::Cint)::hid_t "Error creating dataspace"
@bind h5s_create_simple(rank::Cint, current_dims::Ptr{hsize_t}, maximum_dims::Ptr{hsize_t})::hid_t "Error creating simple dataspace"
Expand All @@ -220,15 +226,15 @@
### Datatype Interface
###

@bind h5t_array_create(basetype_id::hid_t, ndims::Cuint, sz::Ptr{hsize_t})::hid_t error("Error creating H5T_ARRAY of id ", basetype_id, " and size ", sz)
@bind h5t_array_create2(basetype_id::hid_t, ndims::Cuint, sz::Ptr{hsize_t})::hid_t error("Error creating H5T_ARRAY of id ", basetype_id, " and size ", sz)
@bind h5t_close(dtype_id::hid_t)::herr_t "Error closing datatype"
@bind h5t_committed(dtype_id::hid_t)::htri_t error("Error determining whether datatype is committed")
@bind h5t_commit(loc_id::hid_t, name::Ptr{UInt8}, dtype_id::hid_t, lcpl_id::hid_t, tcpl_id::hid_t, tapl_id::hid_t)::herr_t "Error committing type"
@bind h5t_commit2(loc_id::hid_t, name::Ptr{UInt8}, dtype_id::hid_t, lcpl_id::hid_t, tcpl_id::hid_t, tapl_id::hid_t)::herr_t "Error committing type"
@bind h5t_copy(dtype_id::hid_t)::hid_t "Error copying datatype"
@bind h5t_create(class_id::Cint, sz::Csize_t)::hid_t error("Error creating datatype of id ", class_id)
@bind h5t_enum_insert(dtype_id::hid_t, name::Cstring, value::Ptr{Cvoid})::herr_t error("Error adding ", name, " to enum datatype")
@bind h5t_equal(dtype_id1::hid_t, dtype_id2::hid_t)::htri_t "Error checking datatype equality"
@bind h5t_get_array_dims(dtype_id::hid_t, dims::Ptr{hsize_t})::Cint "Error getting dimensions of array"
@bind h5t_get_array_dims2(dtype_id::hid_t, dims::Ptr{hsize_t})::Cint "Error getting dimensions of array"
@bind h5t_get_array_ndims(dtype_id::hid_t)::Cint "Error getting ndims of array"
@bind h5t_get_class(dtype_id::hid_t)::Cint "Error getting class"
@bind h5t_get_cset(dtype_id::hid_t)::Cint "Error getting character set encoding"
Expand All @@ -247,7 +253,7 @@
@bind h5t_insert(dtype_id::hid_t, fieldname::Ptr{UInt8}, offset::Csize_t, field_id::hid_t)::herr_t error("Error adding field ", fieldname, " to compound datatype")
@bind h5t_is_variable_str(type_id::hid_t)::htri_t "Error determining whether string is of variable length"
@bind h5t_lock(type_id::hid_t)::herr_t "Error locking type"
@bind h5t_open(loc_id::hid_t, name::Ptr{UInt8}, tapl_id::hid_t)::hid_t error("Error opening type ", h5i_get_name(loc_id), "/", name)
@bind h5t_open2(loc_id::hid_t, name::Ptr{UInt8}, tapl_id::hid_t)::hid_t error("Error opening type ", h5i_get_name(loc_id), "/", name)
@bind h5t_set_cset(dtype_id::hid_t, cset::Cint)::herr_t "Error setting character set in datatype"
@bind h5t_set_ebias(dtype_id::hid_t, ebias::Csize_t)::herr_t "Error setting datatype floating point exponent bias"
@bind h5t_set_fields(dtype_id::hid_t, spos::Csize_t, epos::Csize_t, esize::Csize_t, mpos::Csize_t, msize::Csize_t)::herr_t "Error setting datatype floating point bit positions"
Expand Down
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