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mirror of https://github.com/TREX-CoE/trexio.git synced 2024-12-22 20:35:44 +01:00

adapt tests to check both pytrexio and trexio_api modules

This commit is contained in:
q-posev 2021-08-18 13:40:27 +03:00
parent 9cc552409f
commit cb1e83ca57
2 changed files with 160 additions and 24 deletions

131
python/test/test_api.py Normal file
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@ -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')
#==========================================================#

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@ -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')