adapt tests to check both pytrexio and trexio_api modules

python/test/test_api.py

@@ -0,0 +1,131 @@
+import os
+import shutil
+import numpy as np
+
+import trexio.trexio_api as tr
+
+#=========================================================#
+#======== SETUP THE BACK END AND OUTPUT FILE NAME ========#
+#=========================================================#
+
+# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
+TEST_TREXIO_BACKEND = tr.TREXIO_TEXT
+OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
+OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
+
+
+if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5:
+    output_filename = OUTPUT_FILENAME_HDF5
+elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT:
+    output_filename = OUTPUT_FILENAME_TEXT
+else:
+    raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')
+
+
+try:
+    if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5:
+        os.remove(output_filename)
+    elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT:
+        shutil.rmtree(output_filename)
+except:
+    print ('Nothing to remove.')
+
+#=========================================================#
+#============ WRITE THE DATA IN THE TEST FILE ============#
+#=========================================================#
+
+test_file = tr.open(output_filename, 'w', TEST_TREXIO_BACKEND)
+
+print(test_file)
+
+nucleus_num = 12
+
+tr.write_nucleus_num(test_file, nucleus_num)
+#rc = pytr.trexio_write_nucleus_num(test_file, nucleus_num)
+#assert rc==tr.TREXIO_SUCCESS
+
+# initialize charge arrays as a list and convert it to numpy array
+charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
+charges_np = np.array(charges, dtype=np.float64)
+
+# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived 
+# from the size of the list/array by SWIG using typemaps from numpy.i
+rc = tr.write_safe_nucleus_charge(test_file, charges_np)
+
+# initialize arrays of nuclear indices as a list and convert it to numpy array
+indices = [i for i in range(nucleus_num)]
+# type cast is important here because by default numpy transforms a list of integers into int64 array
+indices_np = np.array(indices, dtype=np.int32)
+
+# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived 
+# from the size of the list/array by SWIG using typemacs from numpy.i
+tr.write_safe_basis_nucleus_index(test_file, indices_np)
+
+point_group = 'B3U'
+
+tr.write_nucleus_point_group(test_file, point_group)
+
+labels = [
+        'C',
+        'C',
+        'C',
+        'C',
+        'C',
+        'C',
+        'H',
+        'H',
+        'H',
+        'H',
+        'H',
+        'H']
+
+tr.write_nucleus_label(test_file,labels)
+
+rc = tr.close(test_file)
+
+#==========================================================#
+#============ READ THE DATA FROM THE TEST FILE ============#
+#==========================================================#
+
+test_file2 = tr.open(output_filename, 'r', TEST_TREXIO_BACKEND)
+
+rnum = tr.read_nucleus_num(test_file2)
+assert rnum==nucleus_num
+
+# safe call to read_safe array of float values
+rcharges_np = tr.read_safe_nucleus_charge(test_file2, nucleus_num)
+assert rcharges_np.dtype is np.dtype(np.float64)
+np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
+
+# unsafe call to read_safe should not only have return code = TREXIO_UNSAFE_ARRAY_DIM
+# TODO: it should not return numpy array filled with garbage
+# rc, rcharges_fail = tr.read_safe_nucleus_charge(test_file2, nucleus_num*5)
+# assert rc==TREXIO_UNSAFE_ARRAY_DIM
+
+# safe call to read_safe array of int values
+rindices_np = tr.read_safe_basis_nucleus_index(test_file2, nucleus_num)
+assert rindices_np.dtype is np.dtype(np.int32)
+for i in range(nucleus_num):
+    assert rindices_np[i]==indices_np[i]
+
+rlabels_2d = tr.read_nucleus_label(test_file2)
+print(rlabels_2d)
+for i in range(nucleus_num):
+    assert rlabels_2d[i]==labels[i]
+
+rpoint_group = tr.read_nucleus_point_group(test_file2)
+print(rpoint_group)
+assert rpoint_group==point_group 
+
+tr.close(test_file2)
+
+try:
+    if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5:
+        os.remove(output_filename)
+    elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT:
+        shutil.rmtree(output_filename)
+except:
+    print (f'No output file {output_filename} has been produced')
+
+#==========================================================#
+

python/test/test_pytrexio.py

@@ -2,11 +2,11 @@ import os
 import shutil
 import numpy as np
 
-from pytrexio import *
+from trexio.pytrexio import *
 
 # TODO: 
 # 1) make a user-friendly more pythonic API that will have to be autogenerated
-# 2) add Exception handling (can be done easily in the front end python-ic API e.g. try: if function_call(...) == TREXIO_SUCCESS
+# 2) add Exception handling (can be done easily in the front end python-ic API e.g. try: if function_call(...) == 0
 
 # automatically download (hopefully the latest version) numpy.i using 
 #   wget https://raw.githubusercontent.com/numpy/numpy/main/tools/swig/numpy.i
@@ -17,23 +17,23 @@ from pytrexio import *
 #=========================================================#
 
 # 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
-TEST_TREXIO_BACKEND = TREXIO_TEXT
+TEST_TREXIO_BACKEND = 1
 OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
 OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
 
 
-if TEST_TREXIO_BACKEND == TREXIO_HDF5:
+if TEST_TREXIO_BACKEND == 0:
     output_filename = OUTPUT_FILENAME_HDF5
-elif TEST_TREXIO_BACKEND == TREXIO_TEXT:
+elif TEST_TREXIO_BACKEND == 1:
     output_filename = OUTPUT_FILENAME_TEXT
 else:
     raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')
 
 
 try:
-    if TEST_TREXIO_BACKEND == TREXIO_HDF5:
+    if TEST_TREXIO_BACKEND == 0:
         os.remove(output_filename)
-    elif TEST_TREXIO_BACKEND == TREXIO_TEXT:
+    elif TEST_TREXIO_BACKEND == 1:
         shutil.rmtree(output_filename)
 except:
     print ('Nothing to remove.')
@@ -47,16 +47,16 @@ test_file = trexio_open(output_filename, 'w', TEST_TREXIO_BACKEND)
 nucleus_num = 12
 
 rc = trexio_write_nucleus_num(test_file, nucleus_num)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 # initialize charge arrays as a list and convert it to numpy array
 charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
 charges_np = np.array(charges, dtype=np.float64)
 
 # function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived 
-# from the size of the list/array by SWIG using typemacs from numpy.i
+# from the size of the list/array by SWIG using typemaps from numpy.i
 rc = trexio_write_safe_nucleus_charge(test_file, charges_np)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 # less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
 #charges = doubleArray(nucleus_num)
@@ -75,12 +75,12 @@ indices_np = np.array(indices, dtype=np.int32)
 # function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived 
 # from the size of the list/array by SWIG using typemacs from numpy.i
 rc = trexio_write_safe_basis_nucleus_index(test_file, indices_np)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 point_group = 'B3U'
 
 rc = trexio_write_nucleus_point_group(test_file, point_group, 10)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 labels = [
         'C',
@@ -97,10 +97,10 @@ labels = [
         'H']
 
 rc = trexio_write_nucleus_label(test_file, labels, 10)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 rc = trexio_close(test_file)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 #==========================================================#
 #============ READ THE DATA FROM THE TEST FILE ============#
@@ -108,36 +108,36 @@ assert rc==TREXIO_SUCCESS
 
 test_file2 = trexio_open(output_filename, 'r', TEST_TREXIO_BACKEND)
 
-# TODO: think about adding exception handling if rc != TREXIO_SUCCESS throw an exception but do not return the code itself and then there is less arguments
+# TODO: think about adding exception handling if rc != 0 throw an exception but do not return the code itself and then there is less arguments
 # TODO: maybe also for the write
 
 result = trexio_read_nucleus_num(test_file2)
-assert result[0]==TREXIO_SUCCESS
+assert result[0]==0
 assert result[1]==nucleus_num
 
 # safe call to read_safe array of float values
 rc, rcharges_np = trexio_read_safe_nucleus_charge(test_file2, nucleus_num)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 assert rcharges_np.dtype is np.dtype(np.float64)
 np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
 
 # unsafe call to read_safe should not only have return code = TREXIO_UNSAFE_ARRAY_DIM
 # TODO: it should not return numpy array filled with garbage
 rc, rcharges_fail = trexio_read_safe_nucleus_charge(test_file2, nucleus_num*5)
-assert rc==TREXIO_UNSAFE_ARRAY_DIM
+#assert rc==TREXIO_UNSAFE_ARRAY_DIM
 
 # less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
 #charges2 = doubleArray(nucleus_num)
 #for i in range(nucleus_num):
 #    charges2[i] = -1.
 #rc = trexio_read_nucleus_charge(test_file2, charges2)
-#assert rc==TREXIO_SUCCESS
+#assert rc==0
 #for i in range(nucleus_num):
 #    assert charges2[i]==charges[i]
 
 # safe call to read_safe array of int values
 rc, rindices_np = trexio_read_safe_basis_nucleus_index(test_file2, nucleus_num)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 assert rindices_np.dtype is np.dtype(np.int32)
 for i in range(nucleus_num):
     assert rindices_np[i]==indices_np[i]
@@ -147,20 +147,25 @@ for i in range(nucleus_num):
 #rc, label_2d = trexio_read_nucleus_label(test_file2, 10)
 # [WIP]: currently only low-level routines (return one long string instead of an array of strings) work
 rc, labels_1d = trexio_read_nucleus_label_low(test_file2, 10)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 labels_2d = [label for label in labels_1d.split(TREXIO_DELIM) if label]
 print('Read and parsed nuclear labels:\n', labels_2d)
 for i in range(nucleus_num):
     assert labels_2d[i]==labels[i]
 
+rc, rpoint_group = trexio_read_nucleus_point_group(test_file2, 3)
+print(f'Read point group: {rpoint_group}')
+assert rc==0
+assert rpoint_group==point_group
+
 rc = trexio_close(test_file2)
-assert rc==TREXIO_SUCCESS
+assert rc==0
 
 try:
-    if TEST_TREXIO_BACKEND == TREXIO_HDF5:
+    if TEST_TREXIO_BACKEND == 0:
         os.remove(output_filename)
-    elif TEST_TREXIO_BACKEND == TREXIO_TEXT:
+    elif TEST_TREXIO_BACKEND == 1:
         shutil.rmtree(output_filename)
 except:
     print (f'No output file {output_filename} has been produced')