5abac3fec2
[WIP] working write dset of strings, but with memory leak [text]
2021-06-09 18:10:59 +02:00
57b2b63902
add C preprocessor directive for memory reclaim call
2021-06-09 13:52:54 +02:00
5c4782eb03
fix Fortran interface
2021-06-08 16:11:38 +02:00
842b0efaa8
use strncat instead of strcat
2021-06-08 14:59:03 +02:00
2e210bc212
bring back the max_str_len argument for read_ functions [hdf5]
2021-06-08 14:50:59 +02:00
57a83d7cf2
cleaning front end
2021-06-08 14:50:17 +02:00
36e85039d5
make file names consistent with the C test
2021-06-08 14:39:04 +02:00
f2c5a3a51b
add max_str_len argument to read/write a single string
2021-06-08 10:45:43 +02:00
231fe479e7
inline with master branch
2021-06-07 11:01:37 +02:00
1ce1872916
fix missing things after merge
2021-06-04 18:42:35 +02:00
ea9ffaea43
Fix fortran tests
2021-06-04 18:14:45 +02:00
d57f2004ba
Merge branch 'master' into add-strings
2021-06-04 18:09:26 +02:00
31bf17c66a
Merge branch 'master' into evgeny
2021-06-04 17:30:51 +02:00
34478e366a
resolve front end
2021-06-04 17:28:56 +02:00
1bfc8d0c6c
fix typos
2021-06-04 17:02:14 +02:00
5b1cf03aaf
[WIP] add has/read/write functions for string attributes [front,hdf5]
2021-06-04 15:33:50 +02:00
4549276e86
Add trexio_set_one_based in fortran interface
2021-06-04 15:00:13 +02:00
77f2858548
Add index in files
2021-06-04 14:43:27 +02:00
3ce9c57376
safer strncpy in the front end
2021-06-04 09:18:59 +02:00
4fceb6624d
fix error handling in write_group_dset
2021-06-03 17:33:31 +02:00
52e636f610
fix error handling in read_group_dset
2021-06-03 17:32:50 +02:00
40e9aa9234
introduce max_str_len parameter
2021-06-03 16:13:11 +02:00
ed1393f5de
Merge branch 'automake' of github.com:TREX-CoE/trexio into automake
2021-06-03 13:56:49 +02:00
75af136d4f
Moved sparse documentation in src/templates_front/templator_front.org
2021-06-03 13:56:45 +02:00
aa4251b943
read_group_dset can operate on char* directly instead of char**
2021-06-03 13:41:43 +02:00
d2bc25ef03
less allocations in the front end
2021-06-03 13:39:02 +02:00
40bfc581ee
use newline char as a delimeter
2021-06-03 10:26:19 +02:00
5043d058bd
Merge branch 'automake' of github.com:TREX-CoE/trexio into automake
2021-06-03 09:57:57 +02:00
a5ae1d239b
Improve HDF5 in configure
2021-06-03 01:25:20 +02:00
693f8d3846
fix file reopening for writing new variables
2021-06-02 20:19:39 +02:00
7a9d078859
remove append mode
2021-06-02 14:40:23 +02:00
0b5136f14c
add error handling for an attempt to overwrite something
2021-06-02 14:23:58 +02:00
8aa4721758
Documentation
2021-06-02 11:19:03 +02:00
196224c63b
use newline character as a delimeter for array of strings
2021-06-01 18:12:15 +02:00
0f444074c9
better error handling [front]
2021-06-01 16:45:13 +02:00
6979c84c38
parse char* strings and convert them to char** for back ends
2021-06-01 14:58:16 +02:00
f45fee6cbf
explicit types for strings [HDF5]
2021-06-01 10:41:00 +02:00
753c767ce2
first working prototype for string datasets [HDF5]
2021-05-31 16:42:11 +02:00
edfe8817d1
[WIP] temporarily disable calls to text back end
2021-05-31 16:40:25 +02:00
b5a6987758
first prototype of read/write string datasets
2021-05-31 13:26:52 +02:00
c18b75a11d
explicit string type in front end templates
2021-05-28 17:53:26 +02:00
8b580fee4a
Automake done. Need to improve tests
2021-05-28 13:36:39 +02:00
42f81b2cc6
prepare templates and files for datasets with strings [all]
2021-05-27 15:14:01 +02:00
70531b0ff6
more general group_dset_h5_dtype variable in the templates [hdf5]
2021-05-27 13:59:45 +02:00
1575c1f4d0
add functions for has/read/write_dset_str [front]
2021-05-27 13:58:35 +02:00
Evgeny Posenitskiy
29d927675e
Major refactoring of the generator script ( #47 )
...
* minor cleaning
* create functions for dictionary parsers in the external file
* remove files_exclude since post-processing does the job
* no need to have group_group_dset when propagatin dsets
* oneliner for paths to templates
* add dset_per_group dict
* add function to iteratively populate string based on triggers list
* added recursive replacer for numbers
* add recursive replaces for datasets
* add function for text groups [iterative+recursive upd]
* do not define triggers in the master script
* transition to helper dictionaries
* cleaning
* comment main code blocks
* rearrange parameters
* add documentation strings to the functions
* minor cleaning and changes
* adapt build_trexio script
* add consisteny check for dimensioning variables
2021-05-26 19:11:46 +02:00
1d5c452071
Not bugs found with scan-build
2021-05-19 22:02:40 +02:00
0cc24bd21e
error handling for trexio_text_deinit function
2021-05-19 15:03:15 +02:00
q-posev
f77a5af4e0
fix a typo
2021-05-18 12:07:37 +02:00
q-posev
047153b7c1
remove NULL pointer check for file_name in text
2021-05-18 11:43:05 +02:00
q-posev
d97c111284
fix the default precision of int datasets
2021-05-18 11:42:26 +02:00
692f45ed7f
Correct rank in Fortran interface
2021-05-08 00:35:53 +02:00
cd8332a3e5
Added notes for sparse data structures
2021-05-07 00:02:12 +02:00
87bb6fcb6e
Better error messages
2021-05-06 19:56:42 +02:00
7302f02b9c
Improved error messages
2021-05-06 19:54:37 +02:00
181fe988f3
Fixed append problem
2021-05-06 19:40:27 +02:00
1cfa313d07
Error messages
2021-05-06 18:25:51 +02:00
q-posev
6e54e89d24
inttypes macros for rdm
2021-05-06 18:17:41 +02:00
20d551a70b
include inttypes to fix portability issues in text back end
2021-05-06 18:08:28 +02:00
57655a8344
add error message for an attempt to overwrite dimensioning variables
2021-05-06 17:44:31 +02:00
db5544e810
Improved error codes
2021-05-06 15:09:50 +02:00
5e3c085fb7
discard patch for rdm
2021-05-06 09:38:28 +02:00
d3b35ae453
discard portability patch
2021-05-06 09:35:48 +02:00
q-posev
48d300674a
portability patch for mac
2021-05-06 09:19:05 +02:00
c7349ef2ef
datarootdir in src/Makefile.in
2021-05-05 13:46:40 +02:00
f272d27863
pkgconfig
2021-05-05 12:17:15 +02:00
f7dea1fd1c
Fixed configure and install
2021-05-05 11:37:48 +02:00
9c2b240418
more portable HDF5 back end
2021-05-04 20:22:58 +02:00
5f4f94646f
replace ULLONG with UINT64
2021-05-04 14:16:12 +02:00
daf3fdeb8b
Fixed warning about strlen in strncpy
2021-05-04 10:03:32 +02:00
03f58a649e
fixed make install and introduced uninstall targets
2021-05-03 15:15:49 +02:00
q-posev
a9c506dd15
fix distcheck rule
2021-04-30 20:10:06 +02:00
q-posev
be8386f770
rm libtrexio after creating a copy in the lib directory
2021-04-30 19:58:38 +02:00
4578fb1a2b
adapt rules for new structure of the root directory
2021-04-30 19:04:43 +02:00
51660199c2
create tests directory
2021-04-30 15:50:41 +02:00
1e9581e2d2
move tests to the corresponding directory
2021-04-30 15:50:05 +02:00
caee3576b7
move generator to tools directory
2021-04-30 14:22:32 +02:00
203e9027a6
fix paths
2021-04-30 14:12:23 +02:00
faa936cc54
move build_trexio script to tools directory
2021-04-30 13:50:51 +02:00
Evgeny Posenitskiy
818d66d4d3
Autoconfig with optional HDF5 compilation ( #42 )
...
Makefile.in:
* recursive build;
* advanced make targets;
* major support for autoconf and minor for package managers.
configure.ac:
* optional HDF5 compilation [default: --with-hdf5];
* add -fPIC to CFLAGS if missing.
2021-04-28 15:30:18 +02:00
08a28c9ae4
Using pkg-config for hdf5 in Makefile
2021-04-26 22:46:43 +02:00
728d7bb3ad
Fixed test : coord(3,12)
2021-04-20 01:34:11 +02:00
Evgeny Posenitskiy
8defdaa0c0
org-mode to html conversion for the documentation website ( #41 )
...
* working static html doc website generated from org-mode files
* fix build_doc script
* add gitignore
* add gitignore
* clean html garbage
* documented hdf5
* documented text back end
2021-04-09 16:45:44 +02:00
7e55933fea
make consistent hierarchy in org-mode files
2021-04-08 11:40:50 +02:00
b656917323
consistent naming init/deinit instead init/finalize in back ends
2021-04-08 11:31:51 +02:00
b8c9bfa2df
renamed build_trex script
2021-04-08 11:25:42 +02:00
Evgeny Posenitskiy
c43259176d
Add 32-bit funcs and document front end ( #39 )
...
* 32-bit functions
* adapt tests since the default write/read_num is now 32-bit
* minor cleaning in the generator
* add test for _32 functionality
* rm stdint-based types from test
* documentation
* rm trailing whitespaces in emacs
* change TREXIO_INVALID_BACK_END
* update gitignore
2021-04-07 17:37:04 +02:00
4e47e497d5
Table to generate error codes and string_of_error function
2021-04-01 22:48:04 +02:00
0419a8c87b
Improved Makefile
2021-04-01 22:45:42 +02:00
200473ad16
generate full library + dummy fix for group names
2021-03-30 21:42:42 +02:00
42df2253eb
better error handling
2021-03-30 16:03:34 +02:00
7d24442984
FIX: truncated precision of floats [text]
2021-03-30 15:44:26 +02:00
5fb1418f9b
BUG: truncated precision for doubles [text]
2021-03-30 14:20:46 +02:00
53d51a7902
add tests for has_ functionality
2021-03-30 11:56:04 +02:00
0d0bed0585
forgot text templator
2021-03-30 11:51:05 +02:00
068beacb07
working has_ functions [all]
2021-03-30 11:50:02 +02:00
679c462d63
enhanced fortran interface
2021-03-29 14:34:41 +02:00
Evgeny Posenitskiy
18c6fb845f
Smart deallocation of dsets upon failure in read_group [text] ( #35 )
...
* fix FC variable
* smart deallocation of dsets + some cleaning in templator [text]
2021-03-29 13:27:54 +02:00
5fc0371276
Compliant with CERT
2021-03-29 00:37:56 +02:00
086a34d5b1
const
2021-03-29 00:34:56 +02:00
3f2261ea9b
Undefined num_id in HDF5
2021-03-29 00:34:03 +02:00
9edeb7825e
strncat
2021-03-28 22:41:49 +02:00
56389752de
const
2021-03-28 22:38:32 +02:00
4e68a808a0
scope and shadowed variable
2021-03-28 22:14:24 +02:00
35daf9db05
Redundant assignments
2021-03-28 22:10:56 +02:00
e10285efee
Format strings
2021-03-28 22:01:56 +02:00
f1e02350ac
Format unsigned
2021-03-28 16:35:32 +02:00
966efc66c1
Fixed: duplicate rc == EOF
2021-03-28 16:32:42 +02:00
000aad336c
Fixed: file not const when write
2021-03-28 16:31:15 +02:00
83fa39ee30
Fixed unsigned int < 0
2021-03-28 16:24:35 +02:00
700803528f
Format for unsigned long + overflows in struct
2021-03-28 16:22:14 +02:00
f8dae45c10
Changed i++ into ++i in loops
2021-03-28 15:48:27 +02:00
ea61a24291
Fixed: uint can't be <0
2021-03-28 15:45:18 +02:00
6cb7f4e074
Fixed: rc was not checked for multiple dims
2021-03-28 15:43:49 +02:00
10483b882c
Add cppcheck in Makefile
2021-03-28 15:24:13 +02:00
1b0a60f2fe
use strncpy instead of strcpy to avoid possible buffer overflows
2021-03-28 11:18:50 +02:00
c56bc49ddd
Fixed resource leak (fclose)
2021-03-27 19:40:27 +01:00
ebb5ff62d3
better make for tests
2021-03-25 11:42:13 +01:00
aa160d9bea
make build scripts consistent
2021-03-25 11:41:13 +01:00
91fdbf20df
better test [fortran]
2021-03-24 17:22:58 +01:00
81810669ab
link module when compiling fortran test
2021-03-24 17:14:23 +01:00
f8a28a037d
more fortran-ic trexio_open
2021-03-24 17:13:53 +01:00
c0b6f95e52
more fortran-ic test
2021-03-24 16:06:04 +01:00
f7c78e73d2
more fortran-ic interface + flexible dtypes for dsets
2021-03-24 16:05:38 +01:00
8d3b35736c
working read_dset + structured test file [fortran]
2021-03-24 11:14:47 +01:00
4bdd6ea8f3
adapt for fortran interface
2021-03-23 18:19:35 +01:00
cf26966b70
working write_dset [fortran]
2021-03-23 18:12:53 +01:00
0a28b5e5a5
working read_num [fortran]
2021-03-23 16:34:13 +01:00
d680120efe
working write_num [fortran]
2021-03-23 14:57:11 +01:00
ac44fc29a6
add test, works for h5 but failt for txt
2021-03-22 16:40:45 +01:00
baa50bdbe2
adapt for fortran
2021-03-22 16:15:37 +01:00
7f3dc0879c
wip: write nums
2021-03-22 16:15:07 +01:00
4cf1d966d0
better fix
2021-03-19 09:12:10 +01:00
22a87a6a55
fix the bash script
2021-03-18 21:13:13 +01:00
696d867725
minor cleaning in the generator
2021-03-18 21:12:28 +01:00
e322a6e42d
add gitignore for src
2021-03-18 21:11:56 +01:00
c0f2bd3106
remove old files
2021-03-18 20:54:03 +01:00
241ae3a74a
Little changes in the bash script
2021-03-18 17:30:48 +01:00
71bb61dd5b
fix memory leak
2021-03-17 17:02:58 +01:00
8a02ea07e2
fix for dset_dtype calloc and fscanf/fprintf
2021-03-17 15:49:43 +01:00
6e7b9a370d
to test for nucleus
2021-03-17 14:50:02 +01:00
fcfe91d498
working and compiling for nucleus
2021-03-17 14:33:32 +01:00
c3321b04fd
add a bash script to be converted into make later
2021-03-16 19:52:33 +01:00
cc02849689
fixed to compile
2021-03-16 19:05:05 +01:00
aa67877948
generator for text backend before test
2021-03-16 18:34:07 +01:00
0da57b6b6c
adapt recent changes in master text backend
2021-03-15 14:13:38 +01:00
44f615857b
add shell scripts to compile populated files
2021-03-13 20:21:32 +01:00
6a2533be3b
Merge branch 'master' of github.com:TREX-CoE/trexio into generator-1
2021-03-13 20:16:42 +01:00
455168efc6
Fixed
2021-03-13 00:56:16 +01:00
e6a211127c
Improved checks in text backend
2021-03-13 00:19:39 +01:00
945c0c2a7d
Added MALLOC and FREE macros
2021-03-12 16:18:11 +01:00
4c40b33d1b
Merge branch 'master' of github.com:TREX-CoE/trexio into generator-1
2021-03-12 15:00:49 +01:00
798c1a1d99
works for charges
2021-03-12 14:05:31 +01:00
cbddfa6010
works for nucleus_coord; text backend adapted
2021-03-12 11:56:03 +01:00
adf44a7ca7
modify frontend
2021-03-12 11:55:02 +01:00
fcb0fa0330
Merge branch 'master' of github.com:TREX-CoE/trexio into generator-1
2021-03-11 09:14:39 +01:00
76fe1b9783
TODO: templator for text backend
2021-03-10 16:56:45 +01:00
9244e6f0c0
fix templators
2021-03-10 16:55:21 +01:00
f29f3d4263
added templator for frontend
2021-03-10 14:51:15 +01:00
c0b319a751
adapt generator for frontend
2021-03-10 14:50:51 +01:00
8f295d4d12
better path-ing and some cleaning
2021-03-10 11:54:23 +01:00
ca234fb569
dimension in write_dset populated properply + error handling
2021-03-10 11:48:43 +01:00
fba6c88973
proper path-ing using os.path
2021-03-10 10:27:44 +01:00
ba0f14a6cc
TODO: properly populate dimensions in write_dset
2021-03-09 16:31:12 +01:00
50841e1937
wip: generate read/write_dset functions
2021-03-09 15:48:32 +01:00
ebc7aa5d40
dummy generator for auxiliary files
2021-03-09 11:58:47 +01:00
9b54f71f4a
initial generator
2021-03-05 16:50:44 +01:00
30927be21d
initial templator
2021-03-05 16:50:26 +01:00
3110a35562
new read/write for numerical attributes
2021-03-05 15:49:05 +01:00
Evgeny Posenitskiy
b964b73bbe
removed bracket
2021-03-04 20:43:44 +01:00
Evgeny Posenitskiy
e624be1435
Merge branch 'master' into change_h5rw_datasets
2021-03-04 20:21:08 +01:00
1df9cd7177
uint32 rank and better error handling
2021-03-04 19:39:06 +01:00
05d55028c4
add error codes for invalid returns
2021-03-04 19:36:32 +01:00
db1f1d6980
fix leaking memory
2021-03-04 18:53:13 +01:00
e52cfbafea
dummy write and smart read
2021-03-04 15:02:23 +01:00
aee737fa23
provide dimensions and decouple dataset read/write from parent group
2021-03-04 14:03:34 +01:00
88d2808200
missing mode in rdm
2021-03-04 14:00:56 +01:00
a3e2a3920d
modify the test to fail when appending on non-existing file
2021-03-04 09:41:27 +01:00
9494f02e37
append on non-existing file should fail
2021-03-04 09:41:00 +01:00
3ac1f8f135
Locking asked from the front to the back
2021-03-03 19:20:01 +01:00
d2efb67a9d
stupid but working implementation of read/write_dset decoupled from read_group
2021-03-03 15:59:30 +01:00
a9a00e8bec
make consistent with _hdf5.org file
2021-03-03 13:33:15 +01:00
b8c569f9a3
add test to read/append non-existing files
2021-03-03 13:19:47 +01:00
c370434dcf
add append mode to front end
2021-03-03 11:50:04 +01:00
ccf03370f7
add test for append in h5
2021-03-03 11:49:42 +01:00
886a3d2162
working append mode for hdf5
2021-03-03 11:49:21 +01:00
997bc92f52
Forgot org files
2021-03-03 10:09:50 +01:00
d4b2ff5c6e
Rewrote text back end
2021-03-03 02:28:00 +01:00
49a73b6d75
Renamed trio in trexio
2021-03-02 13:57:01 +01:00
a0172e26c1
consecutive testing for hdf5
2021-03-02 11:41:25 +01:00
cbb936564e
added write_h5 test
2021-03-02 11:27:09 +01:00
Evgeny Posenitskiy
2b228915ac
Merge branch 'master' into hdf5-backend
2021-03-02 11:03:15 +01:00
9cf8d26110
hdf5 backend working
2021-03-02 10:55:13 +01:00
472dd5fd91
add test to read nucleus_coord from hdf5
2021-02-23 18:20:14 +01:00
92f6a8fa81
replaced some ints with unsigned ints
2021-02-23 18:18:20 +01:00
29b4e4d313
WIP: hdf5: read_nucleus_coord works
2021-02-23 18:17:14 +01:00
ac9e1aa410
change int64 to uint64
2021-02-22 11:40:13 +01:00
258266004b
TODO in org file
2021-02-22 10:56:16 +01:00
0c60cf78d9
Example works with no memory leaks
2021-02-20 18:16:10 +01:00
43bbcfcdbf
Library compiles
2021-02-20 17:12:38 +01:00
