diff --git a/python/test/test_api.py b/python/test/test_api.py new file mode 100644 index 0000000..f5bf278 --- /dev/null +++ b/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') + +#==========================================================# + diff --git a/python/test/test_py.py b/python/test/test_pytrexio.py similarity index 83% rename from python/test/test_py.py rename to python/test/test_pytrexio.py index b00da59..76c0e96 100644 --- a/python/test/test_py.py +++ b/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')