%open, %close is for file. %open_group,%close_group for groups

also add destructor for files

add auto-close test

Author: scivision

API.md

@@ -20,7 +20,7 @@ type(hdf5_file) :: h1, h2, h3
 ```
 
 ```fortran
-call h%initialize(filename,ierr, status,action,comp_lvl,verbose,debug)
+call h%open(filename,ierr, status,action,comp_lvl,verbose,debug)
 !! Opens hdf5 file
 
 character(*), intent(in) :: filename
@@ -32,7 +32,7 @@ logical, intent(in), optional      :: verbose, debug
 ```
 
 ```fortran
-call h%finalize(ierr, close_hdf5_interface)
+call h%close(ierr, close_hdf5_interface)
 !! This must be called on each HDF5 file to flush buffers to disk
 !! data loss can occur if program terminates before this procedure
 !!

Examples.md

@@ -10,7 +10,7 @@ type(hdf5_file) :: h5f
 * gzip compression may be applied for rank ≥ 2 arrays by setting `comp_lvl` to a value between 1 and 9.
   Shuffle filter is automatically applied for better compression
 * string attributes may be applied to any variable at time of writing or later.
-* h5f%initialize(..., `comp_lvl=1`) option enables GZIP compression., where comp_lvl is from 1 to 9. bigger comp_lvl gives more compression but isslower to write.
+* h5f%open(..., `comp_lvl=1`) option enables GZIP compression., where comp_lvl is from 1 to 9. bigger comp_lvl gives more compression but isslower to write.
 
 `integer, intent(out) :: ierr` is an optional parameter. It will be non-zero if error detected.
 This value should be checked, particularly for write operations to avoid missing error conditions.
@@ -19,11 +19,11 @@ If `ierr` is omitted, then h5fortran will raise `error stop` if an error occurs.
 ## Create new HDF5 file, with variable "value1"
 
 ```fortran
-call h5f%initialize('test.h5', status='new')
+call h5f%open('test.h5', status='new')
 
 call h5f%write('/value1', 123.)
 
-call h5f%finalize()
+call h5f%close()
 ```
 
 ## create soft links to actual variable
@@ -47,11 +47,11 @@ This flushes and closes ALL HDF5 files, even those that may be invoked directly
 call hdf5_close()
 ```
 
-Normally, you should be calling `%finalize()` on each file to flush to disk when done using a file.
-If `%finalize()` or hdf5_close is not called, data loss can result.
+Normally, you should be calling `%close()` on each file to flush to disk when done using a file.
+If `%close()` or hdf5_close is not called, data loss can result.
 
 ```fortran
-call h5f%finalize()
+call h5f%close()
 ```
 
 At any time during the program, the `%flush()` method can be called to request the operating system to write a file to disk.
@@ -123,12 +123,12 @@ If the full path is not specified, the system temporary directory will be used i
 Otherwise, the current working directory + filename will be used.
 
 ```sh
-call h5%initialize('orbits.h5', status='scratch')
+call h5%open('orbits.h5', status='scratch')
 
 ...
 
-call h5%finalize()
-!! scratch file deleted by %finalize
+call h5%close()
+!! scratch file deleted by %close
 ```
 
 ## Add/append variable "value1" to existing HDF5 file "test.h5"
@@ -137,23 +137,23 @@ call h5%finalize()
 * if file `test.h5` does not exist, create it and add a variable to it.
 
 ```fortran
-call h5f%initialize('test.h5', status='unknown',action='rw')
+call h5f%open('test.h5', status='unknown',action='rw')
 
 call h5f%write('/value1', 123.)
 
-call h5f%finalize(ierr)
+call h5f%close(ierr)
 ```
 
 ## Add gzip compressed 3-D array "value2" to existing HDF5 file "test.h5"
 
 ```fortran
 real :: val2(1000,1000,3) = 0.
 
-call h5f%initialize('test.h5', comp_lvl=1)
+call h5f%open('test.h5', comp_lvl=1)
 
 call h5f%write('/value2', val2)
 
-call h5f%finalize(ierr)
+call h5f%close(ierr)
 ```
 
 chunk_size may optionally be set in the `%write()` method for 2-d to 7-d arrays.
@@ -164,7 +164,7 @@ Currently, data is written contiguous or compact if not compressed and is only c
 
 ## check if a variable exists
 
-the logical method %exist() checks if a dataset (variable) exists in the initialized HDF5 file.
+the logical method %exist() checks if a dataset (variable) exists in the opened HDF5 file.
 
 ```fortran
 exists = h5f%exist("/foo")
@@ -181,7 +181,7 @@ exists = h5exist("my.h5", "/foo")
 `h5f%ndims` we didn't use `%rank` to avoid confusion with intrinsic "rank()"
 
 ```fortran
-call h5f%initialize('test.h5', status='old',action='r')
+call h5f%open('test.h5', status='old',action='r')
 
 integer :: drank
 integer(hsize_t), allocatable :: dims(:)
@@ -192,11 +192,10 @@ call h5f%shape('/foo',dims)
 if (drank /= size(dims)) error stop
 ```
 
-
 ## Read scalar, 3-D array of unknown size
 
 ```fortran
-call h5f%initialize('test.h5', status='old',action='r')
+call h5f%open('test.h5', status='old',action='r')
 
 integer(hsize_t), allocatable :: dims(:)
 real, allocatable :: A(:,:,:)
@@ -205,7 +204,7 @@ call h5f%shape('/foo',dims)
 allocate(A(dims(1), dims(2), dims(3)))
 call h5f%read('/foo', A)
 
-call h5f%finalize()
+call h5f%close()
 ```
 
 ## read slice (part of) a disk array
@@ -223,7 +222,7 @@ then do:
 ```fortran
 real, dimension(3,5,7) :: A
 
-call h5f%initialize('test.h5', status='old',action='r')
+call h5f%open('test.h5', status='old',action='r')
 
 call h5f%read('/foo', A, istart=[5, 1, 2], iend=[7, 5, 8])
 ```
@@ -243,18 +242,18 @@ then do:
 ```fortran
 real, dimension(5,7,1) :: A
 
-call h5f%initialize('test.h5', status='unknown')
+call h5f%open('test.h5', status='unknown')
 
 call h5f%create('/foo', H5T_NATIVE_REAL, [5,7,1])
 call h5f%write('/foo', A, istart=[3, 4, 8], iend=[7, 10, 8])
 ```
 
-Note the h5f%create() call to initialize the disk variable.
+Note the h5f%create() call to open the disk variable.
 This step is also needed with h5py in Python or Matlab HDF5 h5create() before h5write().
 
 ## is dataset compact, contiguous, or chunked
 
-Assume file handle h5f was already initialized, the logical status is inspected:
+Assume file handle h5f was already opened, the logical status is inspected:
 
 ```fortran
 is_compact = h5f%is_compact("/foo")
@@ -277,19 +276,19 @@ call h5f%chunks('/foo', chunk_size)
 ```fortran
 real :: val2(1000,1000,3) = 0.
 
-call h5f%initialize('test.h5')
+call h5f%open('test.h5')
 
 call h5f%write_group('/scope/')
 
-call h5f%finalize()
+call h5f%close()
 ```
 
 ## verbose / debug
 
 set options debug and /or verbose for diagnostics
 
 ```sh
-call h5f%initialize(..., verbose=.true., debug=.true.)
+call h5f%open(..., verbose=.true., debug=.true.)
 ```
 
 ## Permissive syntax

Examples/example2.f90

@@ -10,11 +10,11 @@ program example2
 
 filename = 'h5fortran_example2.h5'
 
-call h5f%initialize(filename, status='replace')
+call h5f%open(filename, status='replace')
 call h5f%write('/x', 123)
-call h5f%finalize()
+call h5f%close()
 
-call h5f%initialize(filename, status='old', action='r')
+call h5f%open(filename, status='old', action='r')
 call h5f%read('/x', i32)
 if (i32 /= 123) error stop 'incorrect value read'
 

Install.md

@@ -74,9 +74,9 @@ implicit none
 
 type(hdf5_file) :: h5f
 
-call h5f%initialize('h5fortran_example2.h5', status='replace')
+call h5f%open('h5fortran_example2.h5', status='replace')
 call h5f%write('/x', 123)
-call h5f%finalize()
+call h5f%close()
 
 
 end program

VERSION

@@ -1 +1 @@
-3.8.1
+4.0.0

src/attributes.f90

@@ -113,11 +113,11 @@
 type(hdf5_file) :: h
 integer :: ier
 
-call h%initialize(filename, ier, status='old')
+call h%open(filename, ier, status='old')
 
 call h%writeattr_char(dname, attr, attrval, ier)
 
-if (ier == 0) call h%finalize(ier)
+if (ier == 0) call h%close(ier)
 
 if (present(ierr)) ierr = ier
 if (check(ier, filename, dname)) then
@@ -133,11 +133,11 @@
 type(hdf5_file) :: h
 integer :: ier
 
-call h%initialize(filename, ier, status='old')
+call h%open(filename, ier, status='old')
 
 call h%writeattr_num(dname, attr, attrval, ier)
 
-if (ier == 0) call h%finalize(ier)
+if (ier == 0) call h%close(ier)
 
 if (present(ierr)) ierr = ier
 if (check(ier, filename, dname)) then
@@ -153,17 +153,14 @@
 type(hdf5_file) :: h
 integer :: ier
 
-call h%initialize(filename, ier, status='old')
+call h%open(filename, ier, status='old')
 
 call h%readattr_char(dname, attr, attrval, ier)
 
-if (ier == 0) call h%finalize(ier)
+if (ier == 0) call h%close(ier)
 
 if (present(ierr)) ierr = ier
-if (check(ier, filename, dname)) then
-  if (present(ierr)) return
-  error stop
-endif
+if (check(ier, filename, dname) .and. .not. present(ierr)) error stop
 
 end procedure readattr_char_lt
 
@@ -173,17 +170,14 @@
 type(hdf5_file) :: h
 integer :: ier
 
-call h%initialize(filename, ier, status='old')
+call h%open(filename, ier, status='old')
 
 call h%readattr_num(dname, attr, attrval, ier)
 
-if (ier == 0) call h%finalize(ier)
+if (ier == 0) call h%close(ier)
 
 if (present(ierr)) ierr = ier
-if (check(ier, filename, dname)) then
-  if (present(ierr)) return
-  error stop
-endif
+if (check(ier, filename, dname) .and. .not. present(ierr)) error stop
 
 end procedure readattr_num_lt
 

src/interface.f90

@@ -40,9 +40,11 @@ module h5fortran
 
 contains
 !> define methods (procedures) that don't need generic procedure
-procedure, public :: initialize => hdf_initialize, finalize => hdf_finalize, &
+procedure, public :: initialize => hdf_initialize, open => hdf_initialize, &
+  finalize => hdf_finalize, close => hdf_finalize, &
   write_group, create => hdf_create, &
-  open => hdf_open_group, close => hdf_close_group, flush => hdf_flush, &
+  open_group => hdf_open_group, close_group => hdf_close_group, &
+  flush => hdf_flush, &
   ndims => hdf_get_ndims, &
   shape => hdf_get_shape, layout => hdf_get_layout, chunks => hdf_get_chunk, &
   exist => hdf_check_exist, exists => hdf_check_exist, &
@@ -100,6 +102,9 @@ module h5fortran
 hdf_read_scalar, hdf_read_1d, hdf_read_2d, hdf_read_3d, hdf_read_4d, hdf_read_5d, hdf_read_6d, hdf_read_7d, &
 writeattr_char, writeattr_num, readattr_char, readattr_num
 
+!> flush file to disk and close file if user forgets to do so.
+final :: destructor
+
 end type hdf5_file
 
 
@@ -130,9 +135,9 @@ module h5fortran
 !> Submodules
 
 interface !< pathlib.f90
-module logical function std_unlink(filename)
+module subroutine std_unlink(filename)
 character(*), intent(in) :: filename
-end function std_unlink
+end subroutine std_unlink
 
 module logical function is_absolute_path(path)
 character(*), intent(in) :: path
@@ -1069,14 +1074,26 @@ subroutine hdf_finalize(self, ierr, close_hdf5_interface)
 self%lid = 0
 
 if(self%is_scratch) then
-  if (std_unlink(self%filename)) write(stderr,*) 'WARNING: could not delete scratch file: ' // self%filename
+  call std_unlink(self%filename)
 endif
 
 self%is_open = .false.
 
 end subroutine hdf_finalize
 
 
+subroutine destructor(self)
+!! Close file and handle if user forgets to do so
+
+type(hdf5_file), intent(inout) :: self
+
+print *, "auto-closing " // self%filename
+
+call self%close()
+
+end subroutine destructor
+
+
 subroutine hdf_flush(self, ierr)
 !! request operating system flush data to disk.
 !! The operating system can do this when it desires, which might be a while.

src/pathlib.in.f90

@@ -37,11 +37,15 @@
 module procedure std_unlink
 !! deletes file in Fortran standard manner.
 integer :: i, u
+logical :: exists
+
+inquire(file=filename, exist=exists)
+if(.not. exists) return
 
 open(newunit=u, file=filename, iostat=i)
 close(u, status='delete', iostat=i)
 
-inquire(file=filename, exist=std_unlink)
+if(i/=0) write(stderr,*) "failed to delete file ", filename
 
 end procedure std_unlink
 

src/read/reader_lt.in.f90

@@ -8,9 +8,9 @@
 
 type(hdf5_file) :: h
 
-call h%initialize(filename, status='old', action='r')
+call h%open(filename, status='old', action='r')
 h5exist = h%exist(dname)
-call h%finalize()
+call h%close()
 
 end procedure h5exist
 

src/read/reader_lt_template.in.f90

@@ -1,9 +1,9 @@
 type(hdf5_file) :: h
 integer :: ier
 
-call h%initialize(filename, ier, status='old', action='r')
+call h%open(filename, ier, status='old', action='r')
 if (ier == 0) call h%read(dname, value, ier)
-if (ier == 0) call h%finalize(ier)
+if (ier == 0) call h%close(ier)
 
 if (present(ierr)) ierr = ier
 if (check(ier, filename, dname) .and. .not.present(ierr)) error stop