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https://github.com/TREX-CoE/trexio.git
synced 2024-08-25 06:31:43 +02:00
add pattern matching for arrays of strings + comments
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12c2a3a014
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1f98604d58
@ -2,6 +2,7 @@
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/* Define SWIGWORDSIZE in order to properly align long integers on 64-bit system */
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#define SWIGWORDSIZE64
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%{
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#define SWIG_FILE_WITH_INIT
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/* Include the headers in the wrapper code */
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#include "trexio_s.h"
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#include "trexio.h"
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@ -9,7 +10,7 @@
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/* Include stdint to recognize types from stdint.h */
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%include <stdint.i>
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/* Include carrays to work with C-like arrays */
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/* Include carrays to work with C pointers to arrays */
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%include "carrays.i"
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/* Include classes that correspond to integer and float arrays */
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%array_class(double, doubleArray);
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@ -20,6 +21,7 @@
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Useful when working with C pointers
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*/
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%include typemaps.i
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/* Redefine the int32_t* and int64_t* num to be output
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Useful for TREXIO read_num functions where the
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num variable is modified by address
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@ -29,8 +31,14 @@
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/* Does not work for arrays (SIGSEGV)
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%apply double *OUTPUT { double* const dataset };
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*/
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/* TREXIO back ends and exit codes can be redefined in the SWIG target language using %ignore and further #define statements
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(instead of disabling the type cast in the trexio.h file)
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/* This enables access to trexio_[...]_read_dset_str_low set of functions
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in order to return one long string with TREXIO_DELIM delimeter as 2-nd argument of output tuple
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*/
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%include <cstring.i>
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%cstring_bounded_output(char* dset_out, 1024);
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/* [WIP] TREXIO back ends and exit codes can be redefined in the SWIG target language
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using %ignore and further #define statements (instead of disabling the type cast in the trexio.h file)
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*/
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/*
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%ignore TREXIO_HDF5; // Ignore a macro in the header file
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@ -38,8 +46,11 @@
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#define TREXIO_HDF5 0
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#define TREXIO_TEXT 0
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*/
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/* This tells SWIG to treat char ** as a special case */
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%typemap(in) char ** {
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/* This tells SWIG to treat char ** dset_in pattern as a special case
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Enables access to trexio_[...]_write_dset_str set of functions directly, i.e.
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by converting input list of strings from Python into char ** of C
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*/
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%typemap(in) char ** dset_in {
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/* Check if is a list */
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if (PyList_Check($input)) {
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int size = PyList_Size($input);
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@ -62,20 +73,51 @@
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}
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}
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/* This cleans up the char ** array we malloc-ed before */
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%typemap(freearg) char ** {
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%typemap(freearg) char ** dset_in {
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free((char *) $1);
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}
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/* Now a test function
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%inline %{
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int print_args(char ** argv) {
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int i = 0;
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while (argv[i]) {
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printf("argv[%d] = %s\n", i, argv[i]);
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i++;
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}
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return i;
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/* [WIP] This is an attempt to make SWIG treat char ** dset_out as a special case
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In order to return list of string to Python from C-native char ** dset_out,
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which is modified (but not allocated) within the trexio_[...}read_dset_str function
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*/
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%typemap(in, numinputs=0) char ** dset_out (char * temp) {
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/*temp = (char *) malloc(1028*sizeof(char));*/
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$1 = &temp;
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}
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%}*/
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%typemap(argout) char ** dset_out {
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Py_ssize_t i = 0;
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Py_ssize_t mysize = 12;
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PyObject *o_res = PyList_New(mysize);
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PyObject *o;
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for (i = 0; i < mysize; i++) {
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//printf("%s\n", $1[i]);
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o = PyString_FromString($1[i]);
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PyList_SetItem(o_res, i, o);
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}
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PyObject *o2, *o3;
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if ((!$result) || ($result == Py_None)) {
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$result = o_res;
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} else {
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if (!PyTuple_Check($result)) {
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PyObject *o2 = $result;
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$result = PyTuple_New(1);
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PyTuple_SetItem($result, 0, o2);
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}
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o3 = PyTuple_New(1);
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PyTuple_SetItem(o3, 0, o_res);
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o2 = $result;
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$result = PySequence_Concat(o2, o3);
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Py_DECREF(o2);
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Py_DECREF(o3);
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Py_DECREF(o_res);
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}
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}
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/* Parse the header files to generate wrappers */
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%include "trexio_s.h"
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%include "trexio.h"
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@ -1643,19 +1643,19 @@ trexio_read_chunk_ao_2e_int_eri_value_64(trexio_t* const file,
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#+begin_src c :tangle hrw_dset_str_front.h :exports none
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trexio_exit_code trexio_has_$group_dset$(trexio_t* const file);
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trexio_exit_code trexio_read_$group_dset$_low(trexio_t* const file, char* dset, const uint32_t max_str_len);
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trexio_exit_code trexio_write_$group_dset$_low(trexio_t* const file, const char* dset, const uint32_t max_str_len);
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trexio_exit_code trexio_read_$group_dset$(trexio_t* const file, char** dset, const uint32_t max_str_len);
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trexio_exit_code trexio_write_$group_dset$(trexio_t* const file, const char** dset, const uint32_t max_str_len);
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trexio_exit_code trexio_read_$group_dset$_low(trexio_t* const file, char* dset_out, const uint32_t max_str_len);
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trexio_exit_code trexio_write_$group_dset$_low(trexio_t* const file, const char* dset_in, const uint32_t max_str_len);
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trexio_exit_code trexio_read_$group_dset$(trexio_t* const file, char** dset_out, const uint32_t max_str_len);
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trexio_exit_code trexio_write_$group_dset$(trexio_t* const file, const char** dset_in, const uint32_t max_str_len);
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#+end_src
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#+begin_src c :tangle read_dset_str_front.c
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trexio_exit_code
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trexio_read_$group_dset$_low (trexio_t* const file, char* dset, const uint32_t max_str_len)
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trexio_read_$group_dset$_low (trexio_t* const file, char* dset_out, const uint32_t max_str_len)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (dset == NULL) return TREXIO_INVALID_ARG_2;
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if (dset_out == NULL) return TREXIO_INVALID_ARG_2;
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if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
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trexio_exit_code rc;
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@ -1673,15 +1673,15 @@ trexio_read_$group_dset$_low (trexio_t* const file, char* dset, const uint32_t m
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switch (file->back_end) {
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case TREXIO_TEXT:
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return trexio_text_read_$group_dset$(file, dset, rank, dims, max_str_len);
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return trexio_text_read_$group_dset$(file, dset_out, rank, dims, max_str_len);
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break;
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case TREXIO_HDF5:
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return trexio_hdf5_read_$group_dset$(file, dset, rank, dims, max_str_len);
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return trexio_hdf5_read_$group_dset$(file, dset_out, rank, dims, max_str_len);
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break;
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/*
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case TREXIO_JSON:
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rc = trexio_json_read_$group_dset$(file, dset, rank, dims);
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rc = trexio_json_read_$group_dset$(file, dset_out, rank, dims);
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break;
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,*/
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}
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@ -1690,11 +1690,11 @@ trexio_read_$group_dset$_low (trexio_t* const file, char* dset, const uint32_t m
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}
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trexio_exit_code
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trexio_read_$group_dset$ (trexio_t* const file, char** dset, const uint32_t max_str_len)
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trexio_read_$group_dset$ (trexio_t* const file, char** dset_out, const uint32_t max_str_len)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (dset == NULL) return TREXIO_INVALID_ARG_2;
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if (dset_out == NULL) return TREXIO_INVALID_ARG_2;
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if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
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assert(file->back_end < TREXIO_INVALID_BACK_END);
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@ -1725,8 +1725,8 @@ trexio_read_$group_dset$ (trexio_t* const file, char** dset, const uint32_t max_
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return TREXIO_FAILURE;
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}
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strcpy(dset[i], "");
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strcat(dset[i], pch);
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strcpy(dset_out[i], "");
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strcat(dset_out[i], pch);
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}
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@ -1738,11 +1738,11 @@ trexio_read_$group_dset$ (trexio_t* const file, char** dset, const uint32_t max_
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#+begin_src c :tangle write_dset_str_front.c
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trexio_exit_code
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trexio_write_$group_dset$_low (trexio_t* const file, const char* dset, const uint32_t max_str_len)
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trexio_write_$group_dset$_low (trexio_t* const file, const char* dset_in, const uint32_t max_str_len)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (dset == NULL) return TREXIO_INVALID_ARG_2;
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if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
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if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
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if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
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@ -1769,7 +1769,7 @@ trexio_write_$group_dset$_low (trexio_t* const file, const char* dset, const uin
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/* parse the string using strtok */
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for(uint64_t i=0; i<dims[0]; i++) {
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pch = i == 0 ? strtok( (char*) dset, TREXIO_DELIM) : strtok(NULL, TREXIO_DELIM) ;
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pch = i == 0 ? strtok( (char*) dset_in, TREXIO_DELIM) : strtok(NULL, TREXIO_DELIM) ;
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if (pch == NULL) {
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FREE(dset_str[0]);
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@ -1815,11 +1815,11 @@ trexio_write_$group_dset$_low (trexio_t* const file, const char* dset, const uin
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}
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trexio_exit_code
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trexio_write_$group_dset$ (trexio_t* const file, const char** dset, const uint32_t max_str_len)
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trexio_write_$group_dset$ (trexio_t* const file, const char** dset_in, const uint32_t max_str_len)
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{
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if (file == NULL) return TREXIO_INVALID_ARG_1;
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if (dset == NULL) return TREXIO_INVALID_ARG_2;
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if (dset_in == NULL) return TREXIO_INVALID_ARG_2;
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if (max_str_len <= 0) return TREXIO_INVALID_ARG_3;
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if (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) return TREXIO_DSET_ALREADY_EXISTS;
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@ -1838,7 +1838,7 @@ trexio_write_$group_dset$ (trexio_t* const file, const char** dset, const uint32
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strcpy(str_compiled, "");
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for (uint64_t i=0; i < dset_dim; i++) {
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strcat(str_compiled, dset[i]);
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strcat(str_compiled, dset_in[i]);
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strcat(str_compiled, TREXIO_DELIM);
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}
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15
src/test.py
15
src/test.py
@ -27,7 +27,7 @@ try:
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if TEST_TREXIO_BACKEND == 1:
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shutil.rmtree(output_filename)
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except:
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print (f'Test file {OUTPUT_FILENAME} does not exist')
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print (f'Test file {output_filename} does not exist')
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#=========================================================#
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#============ WRITE THE DATA IN THE TEST FILE ============#
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@ -95,13 +95,16 @@ assert rc==0
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for i in range(nucleus_num):
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assert charges2[i]==charges[i]
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labels2 = ['' for i in range(nucleus_num)]
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print(labels2)
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rc = trexio_read_nucleus_label(test_file2, labels2, 10)
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print(labels2)
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# [WIP]: ideally, the list of strings should be returned as below
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#rc, label_2d = trexio_read_nucleus_label(test_file2, 10)
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# [WIP]: currently only low-level routines (return one long string instead of an array of strings) work
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rc, labels_1d = trexio_read_nucleus_label_low(test_file2, 10)
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assert rc==0
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labels_2d = [label for label in labels_1d.split('\n') if label]
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print(labels_2d)
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for i in range(nucleus_num):
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assert labels2[i]==labels[i]
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assert labels_2d[i]==labels[i]
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rc = trexio_close(test_file2)
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assert rc==0
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