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Merge branch 'automake' of github.com:TREX-CoE/trexio into automake

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This commit is contained in:
Anthony Scemama 2021-06-03 13:56:49 +02:00
commit ed1393f5de
4 changed files with 73 additions and 76 deletions
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9
Makefile.am
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@ -31,7 +31,7 @@
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
ACLOCAL_AMFLAGS = -I m4
CLEANFILES =
CLEANFILES = trexio.mod
VERSION_MAJOR = @VERSION_MAJOR@
VERSION_MINOR = @VERSION_MINOR@
@ -81,13 +81,16 @@ tests_test_c_LDFLAGS = -no-install
test_trexio_f = $(srcdir)/tests/trexio_f.f90
tests_test_f_SOURCES = tests/test_f.f90 $(test_trexio_f)
tests_test_f_SOURCES = $(test_trexio_f) tests/test_f.f90
tests_test_f_LDADD = src/libtrexio.la
tests_test_f_LDFLAGS = -no-install
$(test_trexio_f): $(trexio_f)
$(test_trexio_f):
cp $(trexio_f) $(test_trexio_f)
clean-local:
-rm -rf -- test_write.dir/ test_write_f.dir/ test_write.h5
if TREXIO_DEVEL
CLEANFILES += $(SOURCES) $(trexio_f) $(trexio_h)

92
src/templates_front/templator_front.org
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@ -115,31 +115,32 @@ typedef int32_t trexio_exit_code;
** Error handling
#+NAME: table-exit-codes
| Macro | Code | Description |
|-----------------------------+------+---------------------------|
| ~TREXIO_FAILURE~ | -1 | 'Unknown failure' |
| ~TREXIO_SUCCESS~ | 0 | 'Success' |
| ~TREXIO_INVALID_ARG_1~ | 1 | 'Invalid argument 1' |
| ~TREXIO_INVALID_ARG_2~ | 2 | 'Invalid argument 2' |
| ~TREXIO_INVALID_ARG_3~ | 3 | 'Invalid argument 3' |
| ~TREXIO_INVALID_ARG_4~ | 4 | 'Invalid argument 4' |
| ~TREXIO_INVALID_ARG_5~ | 5 | 'Invalid argument 5' |
| ~TREXIO_END~ | 6 | 'End of file' |
| ~TREXIO_READONLY~ | 7 | 'Read-only file' |
| ~TREXIO_ERRNO~ | 8 | strerror(errno) |
| ~TREXIO_INVALID_ID~ | 9 | 'Invalid ID' |
| ~TREXIO_ALLOCATION_FAILED~ | 10 | 'Allocation failed' |
| ~TREXIO_HAS_NOT~ | 11 | 'Element absent' |
| ~TREXIO_INVALID_NUM~ | 12 | 'Invalid dimensions' |
| ~TREXIO_NUM_ALREADY_EXISTS~ | 13 | 'Variable already exists' |
| ~TREXIO_OPEN_ERROR~ | 14 | 'Error opening file' |
| ~TREXIO_LOCK_ERROR~ | 15 | 'Error locking file' |
| ~TREXIO_UNLOCK_ERROR~ | 16 | 'Error unlocking file' |
| ~TREXIO_FILE_ERROR~ | 17 | 'Invalid file handle' |
| ~TREXIO_GROUP_READ_ERROR~ | 18 | 'Error reading group' |
| ~TREXIO_GROUP_WRITE_ERROR~ | 19 | 'Error writing group' |
| ~TREXIO_ELEM_READ_ERROR~ | 20 | 'Error reading element' |
| ~TREXIO_ELEM_WRITE_ERROR~ | 21 | 'Error writing element' |
| Macro | Code | Description |
|------------------------------+------+----------------------------------------|
| ~TREXIO_FAILURE~ | -1 | 'Unknown failure' |
| ~TREXIO_SUCCESS~ | 0 | 'Success' |
| ~TREXIO_INVALID_ARG_1~ | 1 | 'Invalid argument 1' |
| ~TREXIO_INVALID_ARG_2~ | 2 | 'Invalid argument 2' |
| ~TREXIO_INVALID_ARG_3~ | 3 | 'Invalid argument 3' |
| ~TREXIO_INVALID_ARG_4~ | 4 | 'Invalid argument 4' |
| ~TREXIO_INVALID_ARG_5~ | 5 | 'Invalid argument 5' |
| ~TREXIO_END~ | 6 | 'End of file' |
| ~TREXIO_READONLY~ | 7 | 'Read-only file' |
| ~TREXIO_ERRNO~ | 8 | strerror(errno) |
| ~TREXIO_INVALID_ID~ | 9 | 'Invalid ID' |
| ~TREXIO_ALLOCATION_FAILED~ | 10 | 'Allocation failed' |
| ~TREXIO_HAS_NOT~ | 11 | 'Element absent' |
| ~TREXIO_INVALID_NUM~ | 12 | 'Invalid dimensions' |
| ~TREXIO_NUM_ALREADY_EXISTS~ | 13 | 'Dimensioning variable already exists' |
| ~TREXIO_DSET_ALREADY_EXISTS~ | 14 | 'Dataset already exists' |
| ~TREXIO_OPEN_ERROR~ | 15 | 'Error opening file' |
| ~TREXIO_LOCK_ERROR~ | 16 | 'Error locking file' |
| ~TREXIO_UNLOCK_ERROR~ | 17 | 'Error unlocking file' |
| ~TREXIO_FILE_ERROR~ | 18 | 'Invalid file handle' |
| ~TREXIO_GROUP_READ_ERROR~ | 19 | 'Error reading group' |
| ~TREXIO_GROUP_WRITE_ERROR~ | 20 | 'Error writing group' |
| ~TREXIO_ELEM_READ_ERROR~ | 21 | 'Error reading element' |
| ~TREXIO_ELEM_WRITE_ERROR~ | 22 | 'Error writing element' |
# We need to force Emacs not to indent the Python code:
# -*- org-src-preserve-indentation: t
@ -186,14 +187,15 @@ return '\n'.join(result)
#define TREXIO_HAS_NOT ((trexio_exit_code) 11)
#define TREXIO_INVALID_NUM ((trexio_exit_code) 12)
#define TREXIO_NUM_ALREADY_EXISTS ((trexio_exit_code) 13)
#define TREXIO_OPEN_ERROR ((trexio_exit_code) 14)
#define TREXIO_LOCK_ERROR ((trexio_exit_code) 15)
#define TREXIO_UNLOCK_ERROR ((trexio_exit_code) 16)
#define TREXIO_FILE_ERROR ((trexio_exit_code) 17)
#define TREXIO_GROUP_READ_ERROR ((trexio_exit_code) 18)
#define TREXIO_GROUP_WRITE_ERROR ((trexio_exit_code) 19)
#define TREXIO_ELEM_READ_ERROR ((trexio_exit_code) 20)
#define TREXIO_ELEM_WRITE_ERROR ((trexio_exit_code) 21)
#define TREXIO_DSET_ALREADY_EXISTS ((trexio_exit_code) 14)
#define TREXIO_OPEN_ERROR ((trexio_exit_code) 15)
#define TREXIO_LOCK_ERROR ((trexio_exit_code) 16)
#define TREXIO_UNLOCK_ERROR ((trexio_exit_code) 17)
#define TREXIO_FILE_ERROR ((trexio_exit_code) 18)
#define TREXIO_GROUP_READ_ERROR ((trexio_exit_code) 19)
#define TREXIO_GROUP_WRITE_ERROR ((trexio_exit_code) 20)
#define TREXIO_ELEM_READ_ERROR ((trexio_exit_code) 21)
#define TREXIO_ELEM_WRITE_ERROR ((trexio_exit_code) 22)
#+end_src
#+begin_src f90 :tangle prefix_fortran.f90 :exports none
@ -212,14 +214,15 @@ return '\n'.join(result)
integer(trexio_exit_code), parameter :: TREXIO_HAS_NOT = 11
integer(trexio_exit_code), parameter :: TREXIO_INVALID_NUM = 12
integer(trexio_exit_code), parameter :: TREXIO_NUM_ALREADY_EXISTS = 13
integer(trexio_exit_code), parameter :: TREXIO_OPEN_ERROR = 14
integer(trexio_exit_code), parameter :: TREXIO_LOCK_ERROR = 15
integer(trexio_exit_code), parameter :: TREXIO_UNLOCK_ERROR = 16
integer(trexio_exit_code), parameter :: TREXIO_FILE_ERROR = 17
integer(trexio_exit_code), parameter :: TREXIO_GROUP_READ_ERROR = 18
integer(trexio_exit_code), parameter :: TREXIO_GROUP_WRITE_ERROR = 19
integer(trexio_exit_code), parameter :: TREXIO_ELEM_READ_ERROR = 20
integer(trexio_exit_code), parameter :: TREXIO_ELEM_WRITE_ERROR = 21
integer(trexio_exit_code), parameter :: TREXIO_DSET_ALREADY_EXISTS = 14
integer(trexio_exit_code), parameter :: TREXIO_OPEN_ERROR = 15
integer(trexio_exit_code), parameter :: TREXIO_LOCK_ERROR = 16
integer(trexio_exit_code), parameter :: TREXIO_UNLOCK_ERROR = 17
integer(trexio_exit_code), parameter :: TREXIO_FILE_ERROR = 18
integer(trexio_exit_code), parameter :: TREXIO_GROUP_READ_ERROR = 19
integer(trexio_exit_code), parameter :: TREXIO_GROUP_WRITE_ERROR = 20
integer(trexio_exit_code), parameter :: TREXIO_ELEM_READ_ERROR = 21
integer(trexio_exit_code), parameter :: TREXIO_ELEM_WRITE_ERROR = 22
#+end_src
:end:
@ -448,7 +451,6 @@ struct trexio_back_end_s {
2) ~mode~ - character containing open mode (see below)
- ~'w'~ - (write) creates a new file as READWRITE (overwrite existing file)
- ~'r'~ - (read) opens existing file as READONLY
- ~'a'~ - (append) either opens file in READWRITE mode if it already exists or creates a new one
3) ~back_end~ - integer number (or the corresponding global parameter) specifying the back end
- ~TREXIO_HDF5~ - for HDF5 back end (integer alternative: 0)
- ~TREXIO_TEXT~ - for TEXT back end (integer alternative: 1)
@ -479,7 +481,7 @@ trexio_open(const char* file_name, const char mode,
if (back_end < 0) return NULL;
if (back_end >= TREXIO_INVALID_BACK_END) return NULL;
if (mode != 'r' && mode != 'w' && mode != 'a') return NULL;
if (mode != 'r' && mode != 'w') return NULL;
trexio_t* result = NULL;
void* result_tmp = NULL;
@ -844,6 +846,7 @@ trexio_write_$group_num$_64 (trexio_t* const file, const int64_t num)
{
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (num < 0 ) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_num$(file) == TREXIO_SUCCESS) return TREXIO_NUM_ALREADY_EXISTS;
trexio_exit_code rc = TREXIO_GROUP_WRITE_ERROR;
@ -907,6 +910,7 @@ trexio_write_$group_num$_32 (trexio_t* const file, const int32_t num)
if (file == NULL) return TREXIO_INVALID_ARG_1;
if (num < 0 ) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_num$(file) == TREXIO_SUCCESS) return TREXIO_NUM_ALREADY_EXISTS;
trexio_exit_code rc = TREXIO_GROUP_WRITE_ERROR;
@ -1130,6 +1134,7 @@ trexio_write_$group_dset$_64 (trexio_t* const file, const $group_dset_dtype_doub
if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
@ -1231,6 +1236,7 @@ trexio_write_$group_dset$_32 (trexio_t* const file, const $group_dset_dtype_sing
if (file == NULL) return TREXIO_INVALID_ARG_1;
if ($group_dset$ == NULL) return TREXIO_INVALID_ARG_2;
if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;

19
src/templates_hdf5/templator_hdf5.org
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@ -97,13 +97,9 @@ trexio_hdf5_init (trexio_t* const file)
// reading the existing file -> open as RDONLY
f->file_id = H5Fopen(file->file_name, H5F_ACC_RDONLY, H5P_DEFAULT);
break;
case 'a':
// appending the existing file -> open as RDWR
f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
break;
case 'w':
// writing the existing file -> overwrite it (_TRUNC) [_EXCL | H5F_ACC_DEBUG as an alternative]
f->file_id = H5Fcreate(file->file_name, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
// writing the existing file -> open as RDWRITE
f->file_id = H5Fopen(file->file_name, H5F_ACC_RDWR, H5P_DEFAULT);
break;
}
@ -111,8 +107,7 @@ trexio_hdf5_init (trexio_t* const file)
switch (file->mode) {
case 'r':
case 'a':
// reading or appending non-existing file -> error
// reading non-existing file -> error
return TREXIO_FAILURE;
case 'w':
// writing non-existing file -> create it
@ -124,13 +119,15 @@ trexio_hdf5_init (trexio_t* const file)
/* Create or open groups in the hdf5 file assuming that they exist if file exists */
switch (file->mode) {
// the switch for 'r'/'a' is reached only if file exists
case 'r':
case 'a':
f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
break;
case 'w':
f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (f_exists == 1) {
f->$group$_group = H5Gopen(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT);
} else {
f->$group$_group = H5Gcreate(f->file_id, $GROUP$_GROUP_NAME, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
break;
}
if (f->$group$_group <= 0L) return TREXIO_INVALID_ID;

29
tests/test.c
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@ -67,8 +67,6 @@ int test_write(const char* file_name, const back_end_t backend) {
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_coord(file,coord);
assert (rc == TREXIO_SUCCESS);
rc = trexio_write_nucleus_charge(file,charge);
assert (rc == TREXIO_SUCCESS);
// check if the written data exists in the file
rc = trexio_has_nucleus_num(file);
@ -76,27 +74,26 @@ int test_write(const char* file_name, const back_end_t backend) {
rc = trexio_has_nucleus_coord(file);
assert (rc == TREXIO_SUCCESS);
// should not work: try to overwrite the nucleus_num
// should not work: try to overwrite the num variable
rc = trexio_write_nucleus_num(file,25);
printf("Test error message: %s\n", trexio_string_of_error(rc));
assert (rc == TREXIO_NUM_ALREADY_EXISTS);
// should not work: try to overwrite the dset
coord[0] = 666.666;
rc = trexio_write_nucleus_coord(file,coord);
assert (rc == TREXIO_DSET_ALREADY_EXISTS);
// close current session
rc = trexio_close(file);
assert (rc == TREXIO_SUCCESS);
// open file again in 'append' mode
file = trexio_open(file_name, 'a', TREXIO_HDF5);
// open file again in 'write' mode
file = trexio_open(file_name, 'w', backend);
assert (file != NULL);
// read the nucleus_num from existing file
rc = trexio_read_nucleus_num(file,&num);
assert (rc == TREXIO_SUCCESS);
assert (num == 12);
// overwrite the nucleus_coord
coord[0] = 666.666;
rc = trexio_write_nucleus_coord(file,coord);
// write some missing blocks (e.g. if forgot last time)
rc = trexio_write_nucleus_charge(file,charge);
assert (rc == TREXIO_SUCCESS);
// close current session
@ -148,12 +145,6 @@ int test_read(const char* file_name, const back_end_t backend) {
file2 = trexio_open(file_name2, 'r', backend);
assert (file2 == NULL);
// append non-existing file, should fail and return NULL
trexio_t* file3 = NULL;
file3 = trexio_open(file_name2, 'a', backend);
assert (file3 == NULL);
/*================= END OF TEST =====================*/
free(coord);