Support HDF5 2.0.0

HISTORY.md

@@ -6,6 +6,7 @@ Please also see the [release notes](https://github.com/JuliaIO/HDF5.jl/releases)
 * Refactor Dataspaces (#1104)
 * Convert filter packages into package extensions (#1160)
 * Julia 1.9 is the minimum supported Julia version (#1176)
+* Support HDF5 2.0
 
 ## v0.17.2
 * Fix variable length strings as attributes (#1130)

Project.toml

@@ -39,7 +39,7 @@ CodecBzip2 = "0.7, 0.8"
 CodecLz4 = "0.4"
 CodecZstd = "0.7, 0.8"
 Compat = "3.1.0, 4"
-HDF5_jll = "~1.10.5, ~1.12.0, ~1.14.0"
+HDF5_jll = "~1.10.5, ~1.12.0, ~1.14.0, ~2.0.0"
 MPI = "0.20"
 MPIPreferences = "0.1.7"
 Preferences = "1.3"

gen/api_defs.jl

@@ -81,7 +81,9 @@
 @bind h5d_iterate(buf::Ptr{Cvoid}, type_id::hid_t, space_id::hid_t, operator::Ptr{Cvoid}, operator_data::Any)::herr_t "Error iterating dataset"
 @bind h5d_open2(loc_id::hid_t, pathname::Cstring, dapl_id::hid_t)::hid_t string("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 string("Error reading dataset ", h5i_get_name(dataset_id))
-@bind h5d_read_chunk(dset::hid_t, dxpl_id::hid_t, offset::Ptr{hsize_t}, filters::Ptr{UInt32}, buf::Ptr{Cvoid})::herr_t "Error reading chunk"
+# The function was renamed to H5Dread_chunk1 in v2.0
+@bind h5d_read_chunk(dset::hid_t, dxpl_id::hid_t, offset::Ptr{hsize_t}, filters::Ptr{UInt32}, buf::Ptr{Cvoid})::herr_t "Error reading chunk" (nothing, v"2.0")
+@bind h5d_read_chunk1(dset::hid_t, dxpl_id::hid_t, offset::Ptr{hsize_t}, filters::Ptr{UInt32}, buf::Ptr{Cvoid})::herr_t "Error reading chunk" (v"2.0", nothing)
 @bind h5d_refresh(dataset_id::hid_t)::herr_t "Error refreshing dataset"
 @bind h5d_scatter(op::Ptr{Cvoid}, op_data::Any, type_id::hid_t, dst_space_id::hid_t, dst_buf::Ptr{Cvoid})::herr_t "Error scattering to dataset"
 @bind h5d_set_extent(dataset_id::hid_t, new_dims::Ptr{hsize_t})::herr_t "Error extending dataset dimensions"
@@ -276,7 +278,9 @@
 @bind h5p_get_elink_prefix(plist_id::hid_t, prefix::Ptr{Cchar}, size::Csize_t)::Cssize_t "Error in h5p_get_elink_prefix (not annotated)"
 @bind h5p_get_est_link_info(plist_id::hid_t, est_num_entries::Ptr{Cuint}, est_name_len::Ptr{Cuint})::herr_t "Error in h5p_get_est_link_info (not annotated)"
 @bind h5p_get_evict_on_close(fapl_id::hid_t, evict_on_close::Ptr{hbool_t})::herr_t "Error in h5p_get_evict_on_close (not annotated)"
-@bind h5p_get_external(plist::hid_t, idx::Cuint, name_size::Csize_t, name::Ptr{Cuchar}, offset::Ptr{off_t}, size::Ptr{hsize_t})::herr_t "Error getting external file properties"
+# Argument type changed for Windows in v2.0
+@bind h5p_get_external(plist::hid_t, idx::Cuint, name_size::Csize_t, name::Ptr{Cuchar}, offset::Ptr{off_t}, size::Ptr{hsize_t})::herr_t "Error getting external file properties" (nothing, v"2.0")
+@bind h5p_get_external(plist::hid_t, idx::Cuint, name_size::Csize_t, name::Ptr{Cuchar}, offset::Ptr{H5Doff_t}, size::Ptr{hsize_t})::herr_t "Error getting external file properties" (v"2.0", nothing)
 @bind h5p_get_external_count(plist::hid_t)::Cint "Error getting external count"
 @bind h5p_get_family_offset(fapl_id::hid_t, offset::Ptr{hsize_t})::herr_t "Error in h5p_get_family_offset (not annotated)"
 @bind h5p_get_fapl_core(fapl_id::hid_t, increment::Ptr{Csize_t}, backing_store::Ptr{hbool_t})::herr_t "Error in h5p_get_fapl_core (not annotated)"
@@ -372,7 +376,9 @@
 @bind h5p_set_elink_prefix(plist_id::hid_t, prefix::Cstring)::herr_t "Error in h5p_set_elink_prefix (not annotated)"
 @bind h5p_set_est_link_info(plist_id::hid_t, est_num_entries::Cuint, est_name_len::Cuint)::herr_t "Error in h5p_set_est_link_info (not annotated)"
 @bind h5p_set_evict_on_close(fapl_id::hid_t, evict_on_close::hbool_t)::herr_t "Error in h5p_set_evict_on_close (not annotated)"
-@bind h5p_set_external(plist_id::hid_t, name::Cstring, offset::off_t, size::hsize_t)::herr_t "Error setting external property"
+# Argument type changed for Windows in v2.0
+@bind h5p_set_external(plist_id::hid_t, name::Cstring, offset::off_t, size::hsize_t)::herr_t "Error setting external property" (nothing, v"2.0")
+@bind h5p_set_external(plist_id::hid_t, name::Cstring, offset::H5Doff_t, size::hsize_t)::herr_t "Error setting external property" (v"2.0", nothing)
 @bind h5p_set_family_offset(fapl_id::hid_t, offset::hsize_t)::herr_t "Error in h5p_set_family_offset (not annotated)"
 @bind h5p_set_fapl_core(fapl_id::hid_t, increment::Csize_t, backing_store::hbool_t)::herr_t "Error in h5p_set_fapl_core (not annotated)"
 @bind h5p_set_fapl_family(fapl_id::hid_t, memb_size::hsize_t, memb_fapl_id::hid_t)::herr_t "Error in h5p_set_fapl_family (not annotated)"

gen/gen_wrappers.jl

@@ -1,5 +1,5 @@
 # Generate ../src/api/functions.jl
-# Run `julia --project=.. gen_wrappers.jl`` to execute this script
+# Run `julia --project=.. gen_wrappers.jl` to execute this script
 
 const group_url_dict = Dict{String,String}([
     func_urls[1] => func_urls[2] for

src/api/functions.jl

@@ -801,20 +801,40 @@ function h5d_read(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_pli
     return nothing
 end
 
-"""
-    h5d_read_chunk(dset::hid_t, dxpl_id::hid_t, offset::Ptr{hsize_t}, filters::Ptr{UInt32}, buf::Ptr{Cvoid})
+@static if _libhdf5_build_ver < v"2.0"
+    @doc """
+        h5d_read_chunk(dset::hid_t, dxpl_id::hid_t, offset::Ptr{hsize_t}, filters::Ptr{UInt32}, buf::Ptr{Cvoid})
 
-See `libhdf5` documentation for [`H5Dread_chunk`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___h5_d.html#gac1092a63b718ec949d6539590a914b60).
-"""
-function h5d_read_chunk(dset, dxpl_id, offset, filters, buf)
-    lock(liblock)
-    var"#status#" = try
-            ccall((:H5Dread_chunk, libhdf5), herr_t, (hid_t, hid_t, Ptr{hsize_t}, Ptr{UInt32}, Ptr{Cvoid}), dset, dxpl_id, offset, filters, buf)
-        finally
-            unlock(liblock)
-        end
-    var"#status#" < herr_t(0) && @h5error("Error reading chunk")
-    return nothing
+    See `libhdf5` documentation for [`H5Dread_chunk`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___h5_d.html#gac1092a63b718ec949d6539590a914b60).
+    """
+    function h5d_read_chunk(dset, dxpl_id, offset, filters, buf)
+        lock(liblock)
+        var"#status#" = try
+                ccall((:H5Dread_chunk, libhdf5), herr_t, (hid_t, hid_t, Ptr{hsize_t}, Ptr{UInt32}, Ptr{Cvoid}), dset, dxpl_id, offset, filters, buf)
+            finally
+                unlock(liblock)
+            end
+        var"#status#" < herr_t(0) && @h5error("Error reading chunk")
+        return nothing
+    end
+end
+
+@static if v"2.0" ≤ _libhdf5_build_ver
+    @doc """
+        h5d_read_chunk(dset::hid_t, dxpl_id::hid_t, offset::Ptr{hsize_t}, filters::Ptr{UInt32}, buf::Ptr{Cvoid})
+
+    See `libhdf5` documentation for [`H5Dread_chunk1`](https://docs.hdfgroup.org/hdf5/v1_14/).
+    """
+    function h5d_read_chunk(dset, dxpl_id, offset, filters, buf)
+        lock(liblock)
+        var"#status#" = try
+                ccall((:H5Dread_chunk1, libhdf5), herr_t, (hid_t, hid_t, Ptr{hsize_t}, Ptr{UInt32}, Ptr{Cvoid}), dset, dxpl_id, offset, filters, buf)
+            finally
+                unlock(liblock)
+            end
+        var"#status#" < herr_t(0) && @h5error("Error reading chunk")
+        return nothing
+    end
 end
 
 """
@@ -3279,20 +3299,40 @@ function h5p_get_evict_on_close(fapl_id, evict_on_close)
     return nothing
 end
 
-"""
-    h5p_get_external(plist::hid_t, idx::Cuint, name_size::Csize_t, name::Ptr{Cuchar}, offset::Ptr{off_t}, size::Ptr{hsize_t})
+@static if _libhdf5_build_ver < v"2.0"
+    @doc """
+        h5p_get_external(plist::hid_t, idx::Cuint, name_size::Csize_t, name::Ptr{Cuchar}, offset::Ptr{off_t}, size::Ptr{hsize_t})
 
-See `libhdf5` documentation for [`H5Pget_external`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___d_c_p_l.html#ga78253b80b6c86faf7ff0db135146521d).
-"""
-function h5p_get_external(plist, idx, name_size, name, offset, size)
-    lock(liblock)
-    var"#status#" = try
-            ccall((:H5Pget_external, libhdf5), herr_t, (hid_t, Cuint, Csize_t, Ptr{Cuchar}, Ptr{off_t}, Ptr{hsize_t}), plist, idx, name_size, name, offset, size)
-        finally
-            unlock(liblock)
-        end
-    var"#status#" < herr_t(0) && @h5error("Error getting external file properties")
-    return nothing
+    See `libhdf5` documentation for [`H5Pget_external`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___d_c_p_l.html#ga78253b80b6c86faf7ff0db135146521d).
+    """
+    function h5p_get_external(plist, idx, name_size, name, offset, size)
+        lock(liblock)
+        var"#status#" = try
+                ccall((:H5Pget_external, libhdf5), herr_t, (hid_t, Cuint, Csize_t, Ptr{Cuchar}, Ptr{off_t}, Ptr{hsize_t}), plist, idx, name_size, name, offset, size)
+            finally
+                unlock(liblock)
+            end
+        var"#status#" < herr_t(0) && @h5error("Error getting external file properties")
+        return nothing
+    end
+end
+
+@static if v"2.0" ≤ _libhdf5_build_ver
+    @doc """
+        h5p_get_external(plist::hid_t, idx::Cuint, name_size::Csize_t, name::Ptr{Cuchar}, offset::Ptr{H5Doff_t}, size::Ptr{hsize_t})
+
+    See `libhdf5` documentation for [`H5Pget_external`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___d_c_p_l.html#ga78253b80b6c86faf7ff0db135146521d).
+    """
+    function h5p_get_external(plist, idx, name_size, name, offset, size)
+        lock(liblock)
+        var"#status#" = try
+                ccall((:H5Pget_external, libhdf5), herr_t, (hid_t, Cuint, Csize_t, Ptr{Cuchar}, Ptr{H5Doff_t}, Ptr{hsize_t}), plist, idx, name_size, name, offset, size)
+            finally
+                unlock(liblock)
+            end
+        var"#status#" < herr_t(0) && @h5error("Error getting external file properties")
+        return nothing
+    end
 end
 
 """
@@ -4783,20 +4823,40 @@ function h5p_set_evict_on_close(fapl_id, evict_on_close)
     return nothing
 end
 
-"""
-    h5p_set_external(plist_id::hid_t, name::Cstring, offset::off_t, size::hsize_t)
+@static if _libhdf5_build_ver < v"2.0"
+    @doc """
+        h5p_set_external(plist_id::hid_t, name::Cstring, offset::off_t, size::hsize_t)
 
-See `libhdf5` documentation for [`H5Pset_external`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___d_c_p_l.html#ga85ff7c9c827fa524041cd58c199b77b8).
-"""
-function h5p_set_external(plist_id, name, offset, size)
-    lock(liblock)
-    var"#status#" = try
-            ccall((:H5Pset_external, libhdf5), herr_t, (hid_t, Cstring, off_t, hsize_t), plist_id, name, offset, size)
-        finally
-            unlock(liblock)
-        end
-    var"#status#" < herr_t(0) && @h5error("Error setting external property")
-    return nothing
+    See `libhdf5` documentation for [`H5Pset_external`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___d_c_p_l.html#ga85ff7c9c827fa524041cd58c199b77b8).
+    """
+    function h5p_set_external(plist_id, name, offset, size)
+        lock(liblock)
+        var"#status#" = try
+                ccall((:H5Pset_external, libhdf5), herr_t, (hid_t, Cstring, off_t, hsize_t), plist_id, name, offset, size)
+            finally
+                unlock(liblock)
+            end
+        var"#status#" < herr_t(0) && @h5error("Error setting external property")
+        return nothing
+    end
+end
+
+@static if v"2.0" ≤ _libhdf5_build_ver
+    @doc """
+        h5p_set_external(plist_id::hid_t, name::Cstring, offset::H5Doff_t, size::hsize_t)
+
+    See `libhdf5` documentation for [`H5Pset_external`](https://support.hdfgroup.org/releases/hdf5/v1_14/v1_14_6/documentation/doxygen/group___d_c_p_l.html#ga85ff7c9c827fa524041cd58c199b77b8).
+    """
+    function h5p_set_external(plist_id, name, offset, size)
+        lock(liblock)
+        var"#status#" = try
+                ccall((:H5Pset_external, libhdf5), herr_t, (hid_t, Cstring, H5Doff_t, hsize_t), plist_id, name, offset, size)
+            finally
+                unlock(liblock)
+            end
+        var"#status#" < herr_t(0) && @h5error("Error setting external property")
+        return nothing
+    end
 end
 
 """
@@ -5462,6 +5522,7 @@ See `libhdf5` documentation for [`H5Pset_obj_track_times`](https://support.hdfgr
 """
 function h5p_set_obj_track_times(plist_id, track_times)
     lock(liblock)
+    @show :h5p_set_obj_track_times track_times
     var"#status#" = try
             ccall((:H5Pset_obj_track_times, libhdf5), herr_t, (hid_t, UInt8), plist_id, track_times)
         finally

src/api/helpers.jl

@@ -4,7 +4,7 @@
 # so the methods here handle making the appropriate `Ref`s and return them (as tuples).
 
 const H5F_LIBVER_LATEST = if _libhdf5_build_ver >= v"1.15"
-    H5F_LIBVER_V116
+    H5F_LIBVER_V200
 elseif _libhdf5_build_ver >= v"1.14"
     H5F_LIBVER_V114
 elseif _libhdf5_build_ver >= v"1.12"

src/api/types.jl

@@ -14,6 +14,8 @@ const htri_t   = Cint   # pseudo-boolean (negative if error)
 else
     const off_t = Int64
 end
+# Introduced in HDF5 v2.0
+const H5Doff_t = Int64
 
 const H5Z_filter_t = Cint
 
@@ -317,7 +319,7 @@ const H5F_ACC_SWMR_READ  = 0x0040
     H5F_LIBVER_V110 = 2
     H5F_LIBVER_V112 = 3
     H5F_LIBVER_V114 = 4
-    H5F_LIBVER_V116 = 5
+    H5F_LIBVER_V200 = 5
     H5F_LIBVER_NBOUNDS = 6
 end
 # H5F_LIBVER_LATEST defined in helpers.jl

src/properties.jl

@@ -702,7 +702,7 @@ end
 libver_bound_to_enum(val::Integer) = val
 libver_bound_to_enum(val::API.H5F_libver_t) = val
 function libver_bound_to_enum(val::VersionNumber)
-    val >= v"1.15"   ? API.H5F_LIBVER_V116 :
+    val >= v"1.15"   ? API.H5F_LIBVER_V200 :
     val >= v"1.14"   ? API.H5F_LIBVER_V114 :
     val >= v"1.12"   ? API.H5F_LIBVER_V112 :
     val >= v"1.10"   ? API.H5F_LIBVER_V110 :
@@ -720,7 +720,7 @@ function libver_bound_from_enum(enum::API.H5F_libver_t)
     enum == API.H5F_LIBVER_V110     ? v"1.10" :
     enum == API.H5F_LIBVER_V112     ? v"1.12" :
     enum == API.H5F_LIBVER_V114     ? v"1.14" :
-    enum == API.H5F_LIBVER_V116     ? v"1.16" :
+    enum == API.H5F_LIBVER_V200     ? v"2.0" :
     error("Unknown libver_bound value $enum")
 end
 libver_bound_from_enum(enum) = libver_bound_from_enum(API.H5F_libver_t(enum))

test/plain.jl

@@ -585,7 +585,16 @@ end
     h5open(fn2, "w") do f
         f["x", obj_track_times=false] = [1, 2, 3]
     end
-    @test open(crc32c, fn1) == open(crc32c, fn2)
+    if HDF5.API.h5_get_libversion() < v"2.0.0"
+        @test open(crc32c, fn1) == open(crc32c, fn2)
+    else
+        # @eschnett 2025-11-26: The generated files differ in the 4
+        # bytes starting at offset 0x36. In the case I examined these
+        # values were 0x69272bef and 0x69272bf0 for the first and
+        # second file, respectively, and these are clearly time stamps
+        # for the OHDR header.
+        @test_broken open(crc32c, fn1) == open(crc32c, fn2)
+    end
     rm(fn1)
     rm(fn2)
 end # testset plain