c18a330eab
[WIP] working read/write of sparse data in the low-level (SWIG) Python API
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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
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+ 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
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+ 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
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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
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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
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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
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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
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+ 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
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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
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+ 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"
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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
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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
