open(verbose=) removed. Default action='r' (was 'rw' but not documented before)

Author: scivision

API.md

@@ -31,7 +31,7 @@ call h%open(filename, action, comp_lvl)
 !! Opens hdf5 file
 
 character(*), intent(in) :: filename
-character(*), intent(in), optional :: action  !< r, w, rw
+character(*), intent(in), optional :: action  !< 'r', 'r+', 'w', 'rw'  (default 'r')
 integer, intent(in), optional      :: comp_lvl  !< 0: no compression. 1-9: ZLIB compression, higher is more compressior
 ```
 

Examples.md

@@ -272,12 +272,12 @@ call h5f%write_group('/scope/')
 call h5f%close()
 ```
 
-## verbose / debug
+## debug
 
-set options debug and /or verbose for diagnostics
+for diagnostic prints:
 
 ```sh
-call h5f%open(..., verbose=.true., debug=.true.)
+call h5f%open(..., debug=.true.)
 ```
 
 ## Permissive syntax

codemeta.json

@@ -3,11 +3,11 @@
     "@type": "SoftwareSourceCode",
     "codeRepository": "https://github.com/geospace-code/h5fortran",
     "contIntegration": "https://github.com/geospace-code/h5fortran/actions",
-    "dateModified": "2022-07-13",
+    "dateModified": "2022-07-20",
     "downloadUrl": "https://github.com/geospace-code/h5fortran/releases",
     "issueTracker": "https://github.com/geospace-code/h5fortran/issues",
     "name": "h5fortran",
-    "version": "4.7.1",
+    "version": "4.8.0",
     "identifier": "10.5281/zenodo.3757269",
     "description": "Lightweight object-oriented HDF5 Fortran interface",
     "applicationCategory": "file I/O",

src/interface.f90

@@ -21,7 +21,6 @@ module h5fortran
 character(:), allocatable :: filename
 integer(HID_T) :: file_id
 
-logical :: verbose=.true.
 logical :: debug=.false.
 logical :: fletcher32 = .false.
 logical :: shuffle = .false.
@@ -307,7 +306,7 @@ module subroutine h5write_6d(self, dname, A, chunk_size, istart, iend, stride, c
 logical, intent(in), optional :: compact
 end subroutine
 
-module subroutine h5write_7d(self,dname,A, chunk_size, istart, iend, stride, compact, dset_dims)
+module subroutine h5write_7d(self, dname, A, chunk_size, istart, iend, stride, compact, dset_dims)
 class(hdf5_file), intent(in) :: self
 character(*), intent(in) :: dname
 class(*), intent(in) :: A(:,:,:,:,:,:,:)
@@ -577,20 +576,21 @@ module function id2name(id)
 character(:), allocatable :: id2name
 end function
 
-module subroutine h5open(self, filename, action, comp_lvl, shuffle, fletcher32, verbose, debug)
+module subroutine h5open(self, filename, action, comp_lvl, shuffle, fletcher32, debug)
 !! open/create file
 !!
 !! PARAMETERS:
 !! ----------
 !! filename
 !! action: "r", "w", "rw"
+
 class(hdf5_file), intent(inout) :: self
 character(*), intent(in) :: filename
 character(*), intent(in), optional :: action !< r, r+, rw, w, a
 integer, intent(in), optional :: comp_lvl  !< 0: no compression. 1-9: ZLIB compression, higher is more compressior
 logical, intent(in), optional :: shuffle
 logical, intent(in), optional :: fletcher32
-logical, intent(in), optional :: verbose, debug
+logical, intent(in), optional :: debug
 end subroutine
 
 module subroutine h5close(self, close_hdf5_interface)

src/utils.f90

@@ -26,7 +26,7 @@
 character(2048) :: name
 
 call h5iget_name_f(id, name, len(name, SIZE_T), L, ierr)
-if(ierr /= 0) error stop "h5fortran:id2name:h5iget_name"
+if(ierr /= 0) error stop "ERROR:h5fortran:id2name:h5iget_name"
 
 id2name = name(:L)
 
@@ -37,21 +37,23 @@
 
 character(:), allocatable :: laction
 integer :: ier
+integer(HID_T) :: fapl !< file access property list
+integer :: file_mode
 
 if(self%is_open()) then
   write(stderr,*) 'h5fortran:open: file handle already open: '//self%filename
   return
 endif
 
-laction = 'rw'
-if(present(action)) laction = action
+laction = 'r'
+if (present(action)) laction = action
 
 self%filename = filename
 
-if (present(comp_lvl) .and. laction /= "r") self%comp_lvl = comp_lvl
-if (present(verbose)) self%verbose = verbose
-if (present(debug)) self%debug = debug
+if(present(debug)) self%debug = debug
 
+!> compression parameter
+if(present(comp_lvl) .and. laction /= "r") self%comp_lvl = comp_lvl
 if(self%comp_lvl > 0) then
   self%shuffle = .true.
   self%fletcher32 = .true.
@@ -72,33 +74,42 @@
 call h5open_f(ier)
 if (ier /= 0) error stop 'ERROR:h5fortran:open: HDF5 library initialize'
 
-if(self%verbose) then
+if(self%debug) then
   call h5eset_auto_f(1, ier)
 else
   call h5eset_auto_f(0, ier)
 endif
 if (ier /= 0) error stop 'ERROR:h5fortran:open: HDF5 library set traceback'
 
+fapl = H5P_DEFAULT_F
+
 select case(laction)
 case('r')
-  if(.not. is_hdf5(filename)) error stop "ERROR:h5fortran:open: file does not exist: "//filename
-  call h5fopen_f(filename, H5F_ACC_RDONLY_F, self%file_id,ier)
+  file_mode = H5F_ACC_RDONLY_F
 case('r+')
-  if(.not. is_hdf5(filename)) error stop "ERROR:h5fortran:open: file does not exist: "//filename
-  call h5fopen_f(filename, H5F_ACC_RDWR_F, self%file_id, ier)
+  file_mode = H5F_ACC_RDWR_F
 case('rw', 'a')
   if(is_hdf5(filename)) then
-    call h5fopen_f(filename, H5F_ACC_RDWR_F, self%file_id, ier)
+    file_mode = H5F_ACC_RDWR_F
   else
-    call h5fcreate_f(filename, H5F_ACC_TRUNC_F, self%file_id, ier)
+    file_mode = H5F_ACC_TRUNC_F
   endif
 case ('w')
-  call h5fcreate_f(filename, H5F_ACC_TRUNC_F, self%file_id, ier)
+  file_mode = H5F_ACC_TRUNC_F
 case default
-  error stop 'ERROR:h5fortran:open: Unsupported action: ' // laction
+  error stop 'ERROR:h5fortran:open Unsupported action ' // laction // ' for ' // filename
 end select
 
-if (ier /= 0) error stop "ERROR:h5fortran:open: HDF5 file open failed: "//filename
+if (file_mode == H5F_ACC_RDONLY_F .or. file_mode == H5F_ACC_RDWR_F) then
+  if(.not. is_hdf5(filename)) error stop "ERROR:h5fortran:open: not an HDF5 file: "//filename
+  call H5Fopen_f(filename, file_mode, self%file_id, ier, access_prp=fapl)
+  if (ier /= 0) error stop "ERROR:h5fortran:open:H5Fopen: " // filename
+elseif(file_mode == H5F_ACC_TRUNC_F) then
+  call H5Fcreate_f(filename, file_mode, self%file_id, ier, access_prp=fapl)
+  if (ier /= 0) error stop "ERROR:h5fortran:open:H5Fcreate: " // filename
+else
+  error stop "ERROR:h5fortran:open: Unsupported file mode: " // filename
+endif
 
 end procedure h5open
 
@@ -298,15 +309,15 @@
 
 !> check for matching rank, else bad reads can occur--doesn't always crash without this check
 call h5ltget_dataset_ndims_f(self%file_id, dname, drank, ierr)
-if (ierr/=0) error stop 'ERROR:h5fortran:rank_check: get_dataset_ndim ' // dname // ' read ' // self%filename
+if (ierr/=0) error stop 'ERROR:h5fortran:rank_check:get_dataset_ndims: ' // dname // ' in ' // self%filename
 
 if (drank == mrank) return
 
 if (present(vector_scalar) .and. drank == 1 .and. mrank == 0) then
   !! check if vector of length 1
   call h5ltget_dataset_info_f(self%file_id, dname, dims=ddims, &
     type_class=type_class, type_size=type_size, errcode=ierr)
-  if (ierr/=0) error stop 'ERROR:h5fortran:rank_check: get_dataset_info ' // dname // ' read ' // self%filename
+  if (ierr/=0) error stop 'ERROR:h5fortran:rank_check:get_dataset_info ' // dname // ' in ' // self%filename
   if (ddims(1) == 1) then
     vector_scalar = .true.
     return

src/write_scalar.f90

@@ -13,7 +13,7 @@
 integer(HSIZE_T) :: dims(0)
 integer :: ier, L
 
-if(.not.self%is_open()) error stop 'h5fortran:write: file handle is not open'
+if(.not.self%is_open()) error stop 'ERROR:h5fortran:write: file handle is not open'
 
 select type (A)
 type is (real(real32))
@@ -32,7 +32,7 @@
   L = len(A)  !< workaround for GCC 8.3.0 bug
   call hdf_create(self, dname, H5T_NATIVE_CHARACTER, dims, dims, file_space_id, dset_id, dtype_id, charlen=L)
   call h5dwrite_f(dset_id, dtype_id, A, dims, ier)
-  if (ier /= 0) error stop 'h5fortran:write:string: could not write ' // dname // ' to ' // self%filename
+  if (ier /= 0) error stop 'ERROR:h5fortran:write:string: could not write ' // dname // ' to ' // self%filename
   call h5tclose_f(dtype_id, ier)
 class default
   error stop "ERROR:h5fortran:write: unsupported type for " // dname

src/writer.inc

@@ -27,7 +27,7 @@ type is (character(*))
   charlen = len(A)
   dtype = H5T_NATIVE_CHARACTER
 class default
-  error stop "unknown variable type for " // dname
+  error stop "ERROR:h5fortran:writer:unknown variable type for " // dname
 end select
 
 call hdf_create(self, dname, dtype, mem_dims, dims_dset, file_space_id, dset_id, &

test/CMakeLists.txt

@@ -33,7 +33,6 @@ else()
 endif()
 set_tests_properties(${name} PROPERTIES
 FIXTURES_REQUIRED h5lib
-WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
 )
 
 if(${name} MATCHES ".*fail.*")
@@ -179,4 +178,7 @@ DISABLED $<NOT:$<BOOL:${h5ls}>>
 
 get_property(test_names DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY TESTS)
 
-set_tests_properties(${test_names} PROPERTIES TIMEOUT 60)
+set_tests_properties(${test_names} PROPERTIES
+TIMEOUT 60
+WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+)

test/test_array.f90

@@ -15,7 +15,7 @@ program array_test
 call test_write_slice('test_array.h5')
 print *, 'PASSED: slice write'
 
-call test_readwrite_array('test_group_array.f90', ng=69, nn=100, pn=5)
+call test_readwrite_array('test_group_array.h5', ng=69, nn=100, pn=5)
 print *,'PASSED: array write / read'
 
 
@@ -49,7 +49,7 @@ subroutine test_basic_array(filename)
 r1 = i1
 r2 = i2
 
-call h%open(filename, action='w', comp_lvl=1, verbose=.False.)
+call h%open(filename, action='w', comp_lvl=1)
 
 call h%write('/int32-1d', i1)
 call h%write('/test/group2/int32-2d', i2)
@@ -59,7 +59,7 @@ subroutine test_basic_array(filename)
 call h%close()
 
 !! read
-call h%open(filename, action='r', verbose=.false.)
+call h%open(filename, action='r')
 
 !> int32
 call h%read('/int32-1d', i1t)
@@ -146,7 +146,7 @@ subroutine test_write_slice(filename)
 integer(int32), dimension(4,4) :: i2t
 
 
-call h%open(filename, action='r+', verbose=.true., debug=.true.)
+call h%open(filename, action='r+', debug=.true.)
 
 call h%create('/int32a-1d', dtype=H5T_NATIVE_INTEGER, dset_dims=int([3], hsize_t))
 call h%write('/int32a-1d', [1,3], istart=[1], iend=[2])

test/test_fail_nonexist_variable.f90

@@ -7,7 +7,7 @@ program nonexistvar
 type(hdf5_file) :: h
 character(*), parameter :: filename = 'bad.h5'
 
-call h%open(filename, action='r', verbose=.false.)
+call h%open(filename, action='r')
 call h%read('/not-exist', u)
 call h%close()