98e303ffe2
Merge branch 'master' of github.com:TREX-CoE/trexio
2022-01-07 11:22:44 +01:00
3f4b8e2c7e
cppcheck fixes
2022-01-07 11:21:12 +01:00
dbb6f78397
cppcheck fixes
2022-01-07 11:01:23 +01:00
3787226fd1
overlapping changes
2022-01-07 09:58:03 +01:00
1f7386c4ca
Missing break in front end
2022-01-07 08:57:45 +01:00
fc08ee68ef
Merge branch 'master' of github.com:TREX-CoE/trexio
2022-01-05 14:05:25 +01:00
Evgeny Posenitskiy
c687c80f92
Merge pull request #71 from TREX-CoE/add-sparse-datasets
...
Add Python API for sparse datasets
2022-01-05 13:57:32 +01:00
b65ec031dc
rename returned variable to n_int_read
2021-12-27 17:17:00 +01:00
4ef5386ae6
[cppcheck] fix some warnings
2021-12-27 16:29:26 +01:00
6ab5c67ebe
[pre-release] upgrade versions and produce wheels for CPython 3.10
2021-12-27 16:26:17 +01:00
31ffa574ab
finish top-level Python API for sparse data
2021-12-27 14:00:46 +01:00
722c546113
documentation for sparse arrays
...
+ add safe functions to Fortran API
2021-12-24 12:40:23 +01:00
c18a330eab
[WIP] working read/write of sparse data in the low-level (SWIG) Python API
...
TODO: top-level Python API with error handling and truncation of output arrays when EOF is encountered (low-level API fills the remaining elements with garbase)
2021-12-24 11:49:54 +01:00
0a8aa638f6
fix double deallocation in text back end
2021-12-23 18:49:00 +01:00
72897e4b5d
[WIP] read/write of sparse data in Python
2021-12-23 18:27:24 +01:00
c2376bf168
Fixed bug in text back-end when reading empt attributes
2021-12-23 18:21:17 +01:00
q-posev
31ccd27a0a
fix warnings on MacOS
2021-12-17 17:07:53 +01:00
2639b76a6e
optimize storage of indices depending on the size_max variable [TEXT]
2021-12-17 15:32:03 +01:00
daa5bdb3cc
(inout) buffer size instead if (out) [Fortran]
2021-12-17 13:33:27 +01:00
314beb58c9
refactoring done; moved common blocks into _hdf5_open_read_dset_sparse
2021-12-17 13:32:35 +01:00
1c49c81da8
[WIP] refactoring; write_dset_sparse done
2021-12-16 16:52:35 +01:00
fafb155228
return the number of read elements if read_sparse reached EOF
2021-12-16 11:05:57 +01:00
2e99a14b6e
read dim variable of sparse dset to compress storage of indices in HDF5
2021-12-14 18:03:51 +01:00
a8b251d820
write sparse values and compress int indices depending on the max num value
2021-12-14 18:02:58 +01:00
b90abcc307
fix memory leak in the Fortran test
2021-12-13 09:59:27 +01:00
070ef06818
better error handling for HDF5
2021-12-10 16:49:31 +01:00
1c16b75992
adapt HDF5 back end to be generated for an arbitrary number of indices
2021-12-10 16:02:38 +01:00
9f5ee463e1
only shift indices that have been read to the buffer (EOF case)
2021-12-10 14:02:05 +01:00
7afb53be49
implement shift of sparse indices to be one-based in Fortran
2021-12-10 11:34:37 +01:00
e00f3b106e
working HDF5 I/O for sparse indices
2021-12-09 16:13:28 +01:00
e774cb6852
add read_size function to HDF5 back end
2021-12-09 14:10:51 +01:00
d001844c2f
[WIP] working write_ for chunked extensible (sparse) datasets
2021-12-08 17:26:55 +01:00
e5bde10056
alternative way to check for EOF with fgets while reading
2021-12-03 19:23:01 +01:00
ed3bde973e
[WIP] more general templated variables for sparse data
...
+ renamed templated variables with std_dtype_in|out suffix into _format_scanf|printf for clarity
2021-12-03 15:42:40 +01:00
c520175cbe
use size_max values provided by the read_size functions
2021-12-03 11:48:51 +01:00
d2c95cd306
add functions to read the number of stored sparse elements
2021-12-02 17:28:37 +01:00
acdf982a94
fixed string length for file name + comments
2021-12-01 16:28:47 +01:00
7afce779a8
better error handling in TEXT back end
2021-12-01 16:11:40 +01:00
c30c3a532c
add Fortran interface for sparse data
2021-12-01 13:35:42 +01:00
83c926fd6b
replace offset_data arg with pointer arithmetics
2021-12-01 09:56:31 +01:00
d3ba8f3652
[WIP] working generator for sparse functions
...
+ remove trailing whitespaces
2021-11-30 16:30:36 +01:00
c1e1176400
[WIP] text back end
2021-11-24 17:44:54 +01:00
d44883f0ea
add search bar
...
close #40
2021-11-19 12:50:12 +01:00
527417cd8f
fix type conversion for 32-bit indices
2021-11-18 14:33:18 +01:00
72c355c7cc
Top-level CMakeLists with subdirectories
2021-11-17 14:00:35 +01:00
954ee4216c
add trexio_has_backend function to the C and Fortran APIs
2021-11-02 11:05:27 +01:00
7f3ee3cc18
reset back end values and add TREXIO_BACK_END_MISSING error
2021-11-02 10:32:00 +01:00
5504bc0fe6
wrap TREXIO_INVALID_BACK_END definition in preprocessor macro
2021-11-01 13:22:46 +01:00
d42dc7f449
optional HDF5 compilation
...
via configure script and pre-processor macros
2021-11-01 11:55:34 +01:00
1812deb9dd
Check return value of mkdtemp
2021-10-14 10:53:15 +02:00
5cf12131f1
Fix text back end for read-only directories (make distcheck in qmckl)
2021-10-13 17:43:15 +02:00
d017306706
Better error handling with open in text back end
2021-10-13 16:13:24 +02:00
954b26ccff
Update README
2021-10-13 14:24:54 +02:00
fb9c95bd61
add version attributes to the Fortran module
2021-10-08 13:55:56 +02:00
947a8a12f8
Fix bug due to PACKAGE_VERSION definition in trexio.h
2021-10-07 09:54:19 +02:00
68284161d3
downgrade numpy.i SWIG interface to numpy 1.17.3
2021-09-30 17:22:50 +02:00
2e2dac3982
modify rc_open only if it is not a NULL pointer
2021-09-24 12:23:59 +02:00
67b00efa9c
handle return error of trexio_open in the Python API
2021-09-22 16:40:55 +02:00
9457a826d2
return error code from trexio_open [C, Fortran]
2021-09-22 14:50:22 +02:00
14472cda48
better error handling in case of invalid dimensioning variable
2021-09-22 11:33:27 +02:00
389d265f7f
fix cppcheck warnings regarding redundant size_dset_str checks
2021-09-21 16:08:04 +02:00
d1a9af4185
remove blank spaces in front of pointers
2021-09-21 15:54:11 +02:00
788f7e666d
read single numerical attributes based on _isSet bool flag
2021-09-21 15:41:12 +02:00
d5405e700c
raise TREXIO_INVALID_ARG_2 also when writing zero as dimensioning variable
2021-09-21 14:35:29 +02:00
6459543afd
better front end documentation for numerical attributes
2021-09-21 10:58:07 +02:00
11a17c65d3
add attr_ prefix to the template file name for numerical attributes
2021-09-21 10:41:37 +02:00
c22e9d2925
put back sanity check that dimensioning variables are positive
2021-09-20 17:00:05 +02:00
ce0d98b984
add conversion of float-like attributes into an output tuple
2021-09-20 15:52:55 +02:00
4b9827048f
adapt the templates in back ends
2021-09-20 15:51:36 +02:00
261e7c8b84
modify front end for more general numerical attributes
2021-09-20 13:16:44 +02:00
11dadaab36
add tutorial HTML page to the main documentation
2021-09-15 13:43:57 +02:00
f251f0afba
remove unnecessary comments in the SWIG interface
2021-09-14 17:30:05 +02:00
d04106f72d
max_str_len should be int32_t to properly check for negative values
2021-09-13 13:35:45 +02:00
1589995775
do not use warnings for an attempt to overwrite in the Python API
2021-09-13 11:46:31 +02:00
2bd4ef9bfd
add has_ functions to the Python API
2021-09-13 11:29:00 +02:00
77e3f1ac11
print UserWarning instead of raising Error for an attempt to overwrite data
...
following suggestion of Vijay G.C.
2021-09-12 14:24:50 +02:00
d060808467
do not reveal paths to trexio (security concerns)
2021-09-12 13:36:24 +02:00
12dd1fd8dc
apply some suggestions from cppcheck
2021-09-12 13:25:03 +02:00
40d5fc31fc
check that the data object exists before reading it from the file
2021-09-10 09:38:26 +02:00
67e59f156c
explicitly provide __version__ attribute of the trexio module
2021-09-08 19:28:18 +02:00
96678fea2e
adapt write functions to receive multidimensional arrays or lists
2021-09-07 17:14:23 +02:00
3e82fd9ae8
FIX: a bug that was leading to Python and valgrind errors
2021-08-31 12:11:22 +03:00
74c69bb293
better Exception handling with custom exception class
2021-08-30 18:04:35 +03:00
5a2b4d96a7
reshape output arrays by default when reading from the file
2021-08-27 16:08:39 +03:00
7b5ebf6272
implement TREXIO File class and change import of pytrexio module
2021-08-26 17:01:53 +03:00
4c28a4cac8
add type converters for numerical arrays in read/write Python functions
2021-08-26 13:14:46 +03:00
1dcd32ef7d
add SWIG typemaps for safe API calls in single and double precision
2021-08-25 13:31:17 +03:00
ed7e3902e2
add memory-safe functions in single or double precision
2021-08-24 13:32:01 +03:00
2911e91941
make dim an optional argument in read_ functions
...
if dim is None - the function read all necessary dimensions from the TREXIO file
2021-08-24 12:51:43 +03:00
6f7c23aa11
add missing annotations
2021-08-21 13:13:55 +03:00
4fe86ee980
add Python docstrings for API functions
...
+ move definition of Fortran and Python back ends from Constant Prefixes to Back Ends section
2021-08-21 12:47:36 +03:00
5d5025ae1d
get rid of _safe suffix and add dimension to read_dset_str functions
2021-08-20 13:43:15 +03:00
831973fc8e
better python compilation
2021-08-18 16:28:43 +03:00
902147b45b
better structure of the python directory
2021-08-18 15:40:42 +03:00
9cc552409f
rename the front-end Python module
2021-08-18 13:30:03 +03:00
f0bccee32d
single top-level import of pytrexio resolves bug with caching
2021-08-18 13:28:37 +03:00
0b223b9d6e
return type cast of exit codes and back ends in C
...
add top-level string_of_error function in Python
2021-08-14 12:27:11 +03:00
721352cb89
add missing support for reading single string attributes
2021-08-11 16:01:36 +03:00
209f4506c8
update gitignore
2021-08-11 16:01:04 +03:00
2be1abd571
add Python front end
2021-08-11 15:59:58 +03:00
ec7a39f6c2
strict int types for DIM1 and arrays
2021-08-06 16:24:11 +03:00
808adc7cd8
add typemaps and tests for numpy int arrays
...
+ some cleaning in the Python test and SWIG interface files
2021-08-06 14:04:29 +03:00
1388ddef80
fix warnings produced during compilation of the Python extension module
2021-08-06 12:06:42 +03:00
d0c19e0ce0
pytrexio build and pip install working
2021-08-05 17:55:34 +03:00
60c28c1f3b
rename python test and add temporary TODO
2021-08-04 14:13:23 +03:00
9a28b8d4bc
Revert "create python directory and add TODO objectives"
...
This reverts commit 6ce91a6669
2021-08-04 12:07:27 +03:00
6ce91a6669
create python directory and add TODO objectives
2021-08-04 10:18:36 +03:00
e0162d4570
return double datasets as numpy arrays using numpy.i and safe API
2021-07-28 15:59:29 +02:00
ea0ea0ac38
move from distutils to setuptools
...
sdist and install arguments of setup.py work!
2021-07-28 15:57:42 +02:00
f3dbfc7be2
added License and install_requires in setup.py + cleaning
2021-07-28 10:33:33 +02:00
da5a990acc
add memory-safe API for numerical datasets
2021-07-28 10:19:00 +02:00
9f4176a8b6
resolve major compiler warnings produced by distutils
2021-07-27 11:06:06 +02:00
171cf1662b
ignore __pycache__
2021-07-26 19:28:56 +02:00
9bbae8fd7c
replace some integers with TREXIO-native constants
2021-07-26 19:27:45 +02:00
1f98604d58
add pattern matching for arrays of strings + comments
2021-07-26 18:49:26 +02:00
12c2a3a014
update gitignore
2021-07-26 18:43:49 +02:00
8c6289a8ba
build Python module using pythonic distutils
2021-07-26 18:43:15 +02:00
4faee98092
Merge branch 'master' into swig-python
2021-07-23 16:38:06 +02:00
578819afe7
do not propagate the local user name from config.h to trexio.h
2021-07-23 16:19:15 +02:00
2f876ef7cd
write TREXIO version in the file if not done yet
2021-07-23 15:55:16 +02:00
856412f06a
propagate package version and user name to trexio.h
2021-07-23 15:49:42 +02:00
836603fd32
do no wrap-up the code from back ends and private header
2021-07-20 14:22:54 +02:00
678f90f86a
add a note on alternative way to re-define ill-defined constants
2021-07-20 12:31:21 +02:00
46eec89774
remove unsafe and unused file_name field from trexio_hdf5_s
2021-07-20 12:08:18 +02:00
ac28110696
add include guard to the trexio_private.h file
2021-07-20 12:06:44 +02:00
88e777f68b
resolve complaint about undefined TREXIO_MAX_FILENAME_LENGTH and remove unused assert header
2021-07-20 11:36:23 +02:00
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
