Adds methods for iterating and visiting

API.md

@@ -265,6 +265,32 @@ class(*), intent(out) :: attrval(:)  !< character, real, integer
 call h%delete_attr(dname, attr)
 ```
 
+## Iterate over all datasets in a group
+
+```fortran
+call h%iterate(group, callback)
+
+character(*), intent(in) :: group
+subroutine callback(group_name, object_name, object_type)
+  character(len=*), intent(in) :: group_name
+  character(len=*), intent(in) :: object_name
+  character(len=*), intent(in) :: object_type
+end subroutine
+```
+
+## Visit recursively all datasets starting from a group
+
+```fortran
+call h%visit(group, callback)
+
+character(*), intent(in) :: group
+subroutine callback(group_name, object_name, object_type)
+  character(len=*), intent(in) :: group_name
+  character(len=*), intent(in) :: object_name
+  character(len=*), intent(in) :: object_type
+end subroutine
+```
+
 ## high level operations
 
 These are single-call operations that are slower than the object-oriented methods above.

README.md

@@ -167,7 +167,7 @@ On HPC, we suggest using the HDF5 library provided by the HPC system for best pe
 * variable length dataset writing
 
 We didn't use `type(c_ptr)` and `c_loc()` internally for datasets as we observed problems when the actual argument is sliced on read/write.
-The current h5fortran impementation (Fortran `select type` for H5Dwrite/H5Dread) does work with sliced actual arguments.
+The current h5fortran implementation (Fortran `select type` for H5Dwrite/H5Dread) does work with sliced actual arguments.
 
 HDF5 Fortran 2003
 [features](https://docs.hdfgroup.org/archive/support/HDF5/doc/fortran/NewFeatures_F2003.pdf)

fpm.toml

@@ -8,12 +8,6 @@ auto-tests = false
 auto-examples = false
 external-modules = ["hdf5", "h5lt"]
 
-# HDF5 >= 1.10.6
-# link = ["hdf5_hl_fortran", "hdf5_fortran", "hdf5_hl", "hdf5"]
-
-# HDF5 < 1.10.6, and distros that rename the old way such as Ubuntu 22.04
-link = ["hdf5hl_fortran", "hdf5_fortran", "hdf5_hl", "hdf5"]
-
 [install]
 library = true
 
@@ -77,6 +71,17 @@ main = "test_shape.f90"
 name = "string"
 main = "test_string.f90"
 
+[[test]]
+name = "visit"
+main = "test_visit.f90"
+
+[[test]]
+name = "iterate"
+main = "test_iterate.f90"
+
 [[test]]
 name = "version"
 main = "test_version.f90"
+
+[dependencies]
+hdf5 = '*'

src/CMakeLists.txt

@@ -1,12 +1,14 @@
 set(s ${CMAKE_CURRENT_SOURCE_DIR})
 
 target_sources(h5fortran PRIVATE
+${s}/interface.f90
 ${s}/utils.f90
 ${s}/read.f90 ${s}/read_scalar.f90 ${s}/read_ascii.f90 ${s}/reader.f90
 ${s}/write.f90 ${s}/write_scalar.f90 ${s}/writer.f90
 ${s}/reader_lt.f90 ${s}/writer_lt.f90
-${s}/interface.f90
 ${s}/attr.f90
 ${s}/attr_read.f90
 ${s}/attr_write.f90
+${s}/iterate.f90
+${s}/visit.f90
 )

src/interface.f90

@@ -56,6 +56,8 @@ module h5fortran
 procedure, public :: is_open
 procedure, public :: delete_attr => attr_delete
 procedure, public :: exist_attr => attr_exist
+procedure, public :: iterate => hdf_iterate
+procedure, public :: visit => hdf_visit
 !! procedures without mapping
 
 !> below are procedure that need generic mapping (type or rank agnostic)
@@ -638,6 +640,60 @@ module logical function attr_exist(self, obj_name, attr_name)
 character(*), intent(in) :: obj_name, attr_name
 end function
 
+module subroutine hdf_iterate(self, group_name, callback)
+ !! Opens the HDF5 file and the specified group, then iterates over
+ !! all members of the group. For each member the user‐provided
+ !! callback is invoked with:
+ !!
+ !!   self - the HDF5 file object
+ !!   group_name - name of the group
+ !!   object_name - name of the member object
+ !!   object_type - a short string indicating type ("group", "dataset",
+ !!                 "datatype", or "other")
+ class(hdf5_file), intent(in) :: self
+ character(len=*), intent(in) :: group_name
+  interface
+    subroutine user_callback_interface(group_name, object_name, object_type)
+      character(len=*), intent(in) :: group_name
+        !! The name of the group being traversed.
+      character(len=*), intent(in) :: object_name
+        !! The name of the object encountered.
+      character(len=*), intent(in) :: object_type
+        !!A short description such as "group", "dataset",
+        !!                            "datatype", or "other"
+    end subroutine
+  end interface
+
+ procedure(user_callback_interface) :: callback
+end subroutine
+
+module subroutine hdf_visit(self, group_name, callback)
+ !! Opens the HDF5 file and the specified group, then visits recursively
+ !! all members of the group. For each member the user‐provided
+ !! callback is invoked with:
+ !!
+ !!   self - the HDF5 file object
+ !!   group_name - name of the group
+ !!   object_name - name of the member object
+ !!   object_type - a short string indicating type ("group", "dataset",
+ !!                 "datatype", or "other")
+ class(hdf5_file), intent(in) :: self
+ character(len=*), intent(in) :: group_name
+  interface
+    subroutine user_callback_interface(group_name, object_name, object_type)
+      character(len=*), intent(in) :: group_name
+        !! The name of the group being traversed.
+      character(len=*), intent(in) :: object_name
+        !! The name of the object encountered.
+      character(len=*), intent(in) :: object_type
+        !!A short description such as "group", "dataset",
+        !!                            "datatype", or "other"
+    end subroutine
+  end interface
+
+ procedure(user_callback_interface) :: callback
+end subroutine
+
 end interface
 
 

src/iterate.f90

@@ -0,0 +1,112 @@
+submodule (h5fortran) iterate_smod
+  use h5fortran
+  use hdf5
+  implicit none
+
+  interface
+    subroutine user_callback_interface(group_name, object_name, object_type)
+      character(len=*), intent(in) :: group_name
+        !! The name of the group being traversed.
+      character(len=*), intent(in) :: object_name
+        !! The name of the object encountered.
+      character(len=*), intent(in) :: object_type
+        !!A short description such as "group", "dataset",
+        !!                            "datatype", or "other"
+    end subroutine
+  end interface
+
+  type :: iterate_data_t
+     procedure(user_callback_interface), nopass, pointer :: callback => null()
+  end type iterate_data_t
+
+contains
+
+  module procedure hdf_iterate
+    use, intrinsic :: iso_c_binding, only: c_funptr, C_NULL_PTR, c_int
+    implicit none
+    integer(hid_t) :: group_id
+    integer(c_int) :: status
+    integer(hsize_t) :: idx
+    type(c_funptr) :: funptr
+    type(c_ptr) :: op_data_ptr
+    integer(c_int) :: return_value
+
+    type(iterate_data_t) :: data
+
+    ! Fill the iteration data with the user’s group name and callback.
+    data % callback => callback
+
+    ! Open the group.
+    call H5Gopen_f(self%file_id, trim(group_name), group_id, status)
+    call estop(status, "hdf_iterate:H5Gopen_f", self%filename, "Error opening group: " // trim(group_name))
+
+    idx = 0
+    op_data_ptr = C_NULL_PTR
+    ! Get the C function pointer for our internal callback.
+    funptr = c_funloc(internal_iterate_callback)
+
+    ! Call H5Literate_f to iterate over the group.
+    call H5Literate_f(group_id, H5_INDEX_NAME_F, H5_ITER_NATIVE_F, idx, &
+                      funptr, op_data_ptr, return_value, status)
+    call estop(status, "hdf_iterate:H5Literate_f", self%filename, "Error during iteration of group: " // trim(group_name))
+
+    ! Close the group and file.
+    call H5Gclose_f(group_id, status)
+
+  contains
+
+    integer(c_int) function internal_iterate_callback(grp_id, name, info, op_data) bind(C)
+      !!  internal_iterate_callback:
+      !!
+      !!  This is the callback procedure that will be passed to H5Literate_f.
+      !!  It matches HDF5’s expected signature (using bind(C)) and is called
+      !!  for each object in the group.
+      !!
+      !!  It extracts the object name from the provided character array,
+      !!  calls H5Oget_info_by_name_f to determine the object type, and then
+      !!  calls the user's callback with the high-level parameters.
+      use ISO_C_BINDING, only: c_int, c_ptr, c_null_char
+      implicit none
+      integer(c_long), value        :: grp_id
+      character(kind=c_char, len=1) :: name(0:255)
+      type(h5l_info_t)              :: info
+      type(c_ptr)                   :: op_data
+
+      integer :: status, i, len
+      type(H5O_info_t) :: infobuf
+      character(len=256) :: name_string
+      character(:), allocatable :: object_type
+
+      ! Build a Fortran string from the character array.
+      do i = 0, 255
+        len = i
+        if (name(i) == c_null_char) exit
+        name_string(i+1:i+1) = name(i)(1:1)
+      end do
+
+      ! Retrieve object info using the object name.
+      call H5Oget_info_by_name_f(grp_id, name_string(1:len), infobuf, status)
+      if (status /= 0) then
+        internal_iterate_callback = status
+        return
+      end if
+
+      if(infobuf % type == H5O_TYPE_GROUP_F)then
+        object_type = "group"
+      else if(infobuf % type == H5O_TYPE_DATASET_F)then
+        object_type = "dataset"
+      else if(infobuf % type == H5O_TYPE_NAMED_DATATYPE_F)then
+        object_type = "datatype"
+      else
+        object_type = "other"
+      endif
+
+      ! Call the user’s callback procedure.
+      call data % callback(group_name, name_string(1:len), object_type)
+
+      internal_iterate_callback = 0  ! Indicate success.
+    end function internal_iterate_callback
+
+  end procedure hdf_iterate
+
+end submodule

src/utils.f90

@@ -311,8 +311,9 @@
   write(stderr,*) "ERROR:h5fortran:get_slice: memory size /= dataset size: check variable slice (index). " // &
     " Dset_dims:", ddims, "C Mem_dims:", c_mem_dims, "mem_dims:", mem_dims, "rank(mem_dims):", rank(mem_dims)
   error stop "ERROR:h5fortran:get_slice " // dset_name
-elseif(any(iend-1 > ddims)) then
-  write(stderr,*) "ERROR:h5fortran:get_slice: iend: ", iend, ' > dset_dims: ', ddims
+elseif(any(iend-istart > ddims)) then
+  write(stderr,*) "ERROR:h5fortran:get_slice: slice bigger than dataset: check variable slice (index). " // &
+    " Dset_dims:", ddims, "C Mem_dims:", c_mem_dims, "mem_dims:", mem_dims, "rank(mem_dims):", rank(mem_dims)
   error stop "ERROR:h5fortran:get_slice " // dset_name
 endif
 

src/visit.f90

@@ -0,0 +1,112 @@
+submodule (h5fortran) visit_smod
+  use h5fortran
+  use hdf5
+  implicit none
+
+  interface
+    subroutine user_callback_interface(group_name, object_name, object_type)
+      character(len=*), intent(in) :: group_name
+        !! The name of the group being traversed.
+      character(len=*), intent(in) :: object_name
+        !! The name of the object encountered.
+      character(len=*), intent(in) :: object_type
+        !!A short description such as "group", "dataset",
+        !!                            "datatype", or "other"
+    end subroutine
+  end interface
+
+  type :: visit_data_t
+     procedure(user_callback_interface), nopass, pointer :: callback => null()
+  end type visit_data_t
+
+contains
+
+  module procedure hdf_visit
+    use, intrinsic :: iso_c_binding, only: c_funptr, C_NULL_PTR, c_int
+    implicit none
+    integer(hid_t) :: group_id
+    integer(c_int) :: status
+    integer(hsize_t) :: idx
+    type(c_funptr) :: funptr
+    type(c_ptr) :: op_data_ptr
+    integer(c_int) :: return_value
+
+    type(visit_data_t) :: data
+
+    ! Fill the iteration data with the user’s group name and callback.
+    data % callback => callback
+
+    ! Open the group.
+    call H5Gopen_f(self%file_id, trim(group_name), group_id, status)
+    call estop(status, "hdf_visit:H5Gopen_f", self%filename, "Error opening group: " // trim(group_name))
+
+    idx = 0
+    op_data_ptr = C_NULL_PTR
+    ! Get the C function pointer for our internal callback.
+    funptr = c_funloc(internal_visit_callback)
+
+    ! Call H5Lvisit_f to visit over the group.
+    call H5Ovisit_f(group_id, H5_INDEX_NAME_F, H5_ITER_NATIVE_F, &
+                      funptr, op_data_ptr, return_value, status)
+    call estop(status, "hdf_visit:H5Lvisit_f", self%filename, "Error during iteration of group: " // trim(group_name))
+
+    ! Close the group and file.
+    call H5Gclose_f(group_id, status)
+
+  contains
+
+    integer(c_int) function internal_visit_callback(grp_id, name, info, op_data) bind(C)
+      !!  internal_visit_callback:
+      !!
+      !!  This is the callback procedure that will be passed to H5Lvisit_f.
+      !!  It matches HDF5’s expected signature (using bind(C)) and is called
+      !!  for each object in the group.
+      !!
+      !!  It extracts the object name from the provided character array,
+      !!  calls H5Oget_info_by_name_f to determine the object type, and then
+      !!  calls the user's callback with the high-level parameters.
+      use ISO_C_BINDING, only: c_int, c_ptr, c_null_char
+      implicit none
+      integer(c_long), value        :: grp_id
+      character(kind=c_char, len=1) :: name(0:255)
+      type(h5l_info_t)              :: info
+      type(c_ptr)                   :: op_data
+
+      integer :: status, i, len
+      type(H5O_info_t) :: infobuf
+      character(len=256) :: name_string
+      character(:), allocatable :: object_type
+
+      ! Build a Fortran string from the character array.
+      do i = 0, 255
+        len = i
+        if (name(i) == c_null_char) exit
+        name_string(i+1:i+1) = name(i)(1:1)
+      end do
+
+      ! Retrieve object info using the object name.
+      call H5Oget_info_by_name_f(grp_id, name_string(1:len), infobuf, status)
+      if (status /= 0) then
+        internal_visit_callback = status
+        return
+      end if
+
+      if(infobuf % type == H5O_TYPE_GROUP_F)then
+        object_type = "group"
+      else if(infobuf % type == H5O_TYPE_DATASET_F)then
+        object_type = "dataset"
+      else if(infobuf % type == H5O_TYPE_NAMED_DATATYPE_F)then
+        object_type = "datatype"
+      else
+        object_type = "other"
+      endif
+
+      ! Call the user’s callback procedure.
+      call data % callback(group_name, name_string(1:len), object_type)
+
+      internal_visit_callback = 0  ! Indicate success.
+    end function internal_visit_callback
+
+  end procedure hdf_visit
+
+end submodule