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mirror of https://github.com/TREX-CoE/trexio.git synced 2024-12-23 12:56:53 +01:00
Commit Graph

374 Commits

Author SHA1 Message Date
e06e0b3745 commented brute force patch for re-defining constants in the target language 2021-07-20 10:42:25 +02:00
9fa2bc2835 disable type casting in constant definitions to access them in the target language
required because SWIG cannot handle definitions with type casting
2021-07-20 10:39:05 +02:00
d527561440 add test of basic I/O for Python 2021-07-19 17:59:26 +02:00
79d374bdff [WIP] Python interface generated by SWIG 2021-07-19 17:58:50 +02:00
411334e2ee Merge branch 'master' into unit-testing 2021-06-22 14:46:39 +02:00
3bd730557c remove H5LDget_dset_dims to be compatible with HDF5 v.1.8.21 2021-06-22 12:21:25 +02:00
c8fd3ba045 remove redundant check of overwriting 2021-06-21 12:48:32 +02:00
07d2945333 rename TREXIO_NUM_ALREADY_EXISTS return code 2021-06-21 12:47:39 +02:00
ec0db01f0c Documentation in dist 2021-06-18 12:04:03 +02:00
q-posev
c9f639e0e8 fix compiler warning from MacOS 2021-06-17 20:20:46 +02:00
1a54b7fcf6 fix compiler warning for const pointers 2021-06-15 12:04:30 +02:00
ac45a937af Merge branch 'master' into add-strings 2021-06-15 11:49:42 +02:00
da188dbea0 add top-level read/write functions for single strings [fortran] 2021-06-15 11:26:03 +02:00
b92a15cce7 add top-level read/write functions for string arrays [fortran] 2021-06-15 10:20:01 +02:00
eadc2c63ac fix leaking memory [front] 2021-06-14 16:27:08 +02:00
5553e9110e add top-level read/write functions that accept arrays of strings directly 2021-06-14 15:40:26 +02:00
ae32a02652 pass max_str_len parameter also to read group_str 2021-06-14 14:36:19 +02:00
be66feec16 introduce _assert and _strarray2str helper subroutines for Fortran 2021-06-14 11:55:17 +02:00
535d7ed019 enable operation on string attributes [text] 2021-06-11 18:15:30 +02:00
a40804be2e fix leaking memory and avoid allocation of empty blocks 2021-06-11 14:46:24 +02:00
13b8d24108 [WIP] prepare new subloop triggers for the generator to properly read/free groups [text] 2021-06-10 16:35:38 +02:00
2b3e79054a [WIP] working pieces for read_dset_str [text] 2021-06-10 16:34:16 +02:00
bec752361c Index OK 2021-06-10 01:49:43 +02:00
1b504d92bf Merge branch 'master' into index 2021-06-10 00:32:20 +02:00
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