[WIP] read/write of sparse data in Python

python/test/test_pytrexio.py

@@ -83,6 +83,17 @@ assert rc==0
 rc = trexio_write_safe_basis_nucleus_index(test_file, indices_np)
 assert rc==0
 
+# test writing of sparse data
+rc = trexio_write_mo_num(test_file, 600)
+assert rc==0
+
+indices = [i for i in range(400)]
+values  = [(3.14 + float(i)) for i in range(100)]
+
+rc = trexio_write_mo_2e_int_eri_safe(test_file, 0, 100, indices, values)
+assert rc==0
+
+
 point_group = 'B3U'
 
 rc = trexio_write_nucleus_point_group(test_file, point_group, 10)
@@ -172,16 +183,20 @@ print(f'Read point group: {rpoint_group}')
 assert rc==0
 assert rpoint_group==point_group
 
+num = 100
+ret_tuple = trexio_read_mo_2e_int_eri_safe(test_file2, 0, num)
+print(ret_tuple)
+assert ret_tuple[0]==0
+
 rc = trexio_close(test_file2)
 assert rc==0
 
-try:
+#try:
-    if TEST_TREXIO_BACKEND == 0:
+#    if TEST_TREXIO_BACKEND == 0:
-        os.remove(output_filename)
+#        os.remove(output_filename)
-    elif TEST_TREXIO_BACKEND == 1:
+#    elif TEST_TREXIO_BACKEND == 1:
-        shutil.rmtree(output_filename)
+#        shutil.rmtree(output_filename)
-except:
+#except:
-    print (f'No output file {output_filename} has been produced')
+#    print (f'No output file {output_filename} has been produced')
 
 #==========================================================#
-

src/pytrexio.i

@@ -33,11 +33,17 @@
    Useful for TREXIO read_num functions where the
    num variable is modified by address
 */
+/* Return num variables as part of the output tuple */
 %apply int *OUTPUT { int32_t* const num};
 %apply int *OUTPUT { int64_t* const num};
 %apply float *OUTPUT { float* const num};
 %apply float *OUTPUT { double* const num};
+/* Return TREXIO exit code from trexio_open as part of the output tuple */
 %apply int *OUTPUT { trexio_exit_code* const rc_open};
+/* Return number of sparse data points stored in the file as part of the output tuple */
+%apply int *OUTPUT { int64_t* const size_max};
+/* Return number of sparse data points read from the file as part of the output tuple */
+/* %apply int *INOUT { int64_t* const buffer_size_read}; */
 
 /* Does not work for arrays (SIGSEGV) */
 
@@ -81,6 +87,12 @@ import_array();
 /* Enable write|read_safe functions to convert numpy arrays from/to int64 arrays */
 %apply (int64_t* ARGOUT_ARRAY1, int64_t DIM1) {(int64_t* const dset_out, const int64_t dim_out)};
 %apply (int64_t* IN_ARRAY1, int64_t DIM1) {(const int64_t* dset_in, const int64_t dim_in)};
+/* Enable write|read_safe functions to convert numpy arrays from/to sparse arrays */
+%apply (double* IN_ARRAY1, int64_t DIM1) {(const double* value_sparse, const int64_t size_value_write)};
+%apply (int32_t* IN_ARRAY1, int64_t DIM1) {(const int32_t* index_sparse, const int64_t size_index_write)};
+
+%apply (int32_t* ARGOUT_ARRAY1, int DIM1) {(int32_t* const index_sparse_read, const int64_t size_index_read)};
+%apply (double* ARGOUT_ARRAY1, int DIM1) {(double* const value_sparse_read, const int64_t size_value_read)};
 
 /* This tells SWIG to treat char ** dset_in pattern as a special case
    Enables access to trexio_[...]_write_dset_str set of functions directly, i.e.
@@ -116,4 +128,3 @@ import_array();
 /* Parse the header files to generate wrappers */
 %include "trexio_s.h"
 %include "trexio.h"
-