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https://github.com/TREX-CoE/trexio.git
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adapt tests to check both pytrexio and trexio_api modules
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python/test/test_api.py
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131
python/test/test_api.py
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@ -0,0 +1,131 @@
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import os
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import shutil
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import numpy as np
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import trexio.trexio_api as tr
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#=========================================================#
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#======== SETUP THE BACK END AND OUTPUT FILE NAME ========#
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#=========================================================#
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# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
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TEST_TREXIO_BACKEND = tr.TREXIO_TEXT
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OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
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OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
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if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5:
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output_filename = OUTPUT_FILENAME_HDF5
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elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT:
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output_filename = OUTPUT_FILENAME_TEXT
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else:
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raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')
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try:
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if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5:
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os.remove(output_filename)
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elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT:
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shutil.rmtree(output_filename)
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except:
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print ('Nothing to remove.')
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#=========================================================#
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#============ WRITE THE DATA IN THE TEST FILE ============#
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#=========================================================#
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test_file = tr.open(output_filename, 'w', TEST_TREXIO_BACKEND)
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print(test_file)
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nucleus_num = 12
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tr.write_nucleus_num(test_file, nucleus_num)
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#rc = pytr.trexio_write_nucleus_num(test_file, nucleus_num)
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#assert rc==tr.TREXIO_SUCCESS
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# initialize charge arrays as a list and convert it to numpy array
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charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
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charges_np = np.array(charges, dtype=np.float64)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemaps from numpy.i
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rc = tr.write_safe_nucleus_charge(test_file, charges_np)
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# initialize arrays of nuclear indices as a list and convert it to numpy array
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indices = [i for i in range(nucleus_num)]
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# type cast is important here because by default numpy transforms a list of integers into int64 array
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indices_np = np.array(indices, dtype=np.int32)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemacs from numpy.i
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tr.write_safe_basis_nucleus_index(test_file, indices_np)
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point_group = 'B3U'
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tr.write_nucleus_point_group(test_file, point_group)
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labels = [
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'C',
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'C',
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'C',
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'C',
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'C',
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'C',
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'H',
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'H',
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'H',
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'H',
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'H',
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'H']
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tr.write_nucleus_label(test_file,labels)
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rc = tr.close(test_file)
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#==========================================================#
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#============ READ THE DATA FROM THE TEST FILE ============#
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#==========================================================#
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test_file2 = tr.open(output_filename, 'r', TEST_TREXIO_BACKEND)
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rnum = tr.read_nucleus_num(test_file2)
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assert rnum==nucleus_num
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# safe call to read_safe array of float values
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rcharges_np = tr.read_safe_nucleus_charge(test_file2, nucleus_num)
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assert rcharges_np.dtype is np.dtype(np.float64)
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np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
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# unsafe call to read_safe should not only have return code = TREXIO_UNSAFE_ARRAY_DIM
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# TODO: it should not return numpy array filled with garbage
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# rc, rcharges_fail = tr.read_safe_nucleus_charge(test_file2, nucleus_num*5)
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# assert rc==TREXIO_UNSAFE_ARRAY_DIM
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# safe call to read_safe array of int values
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rindices_np = tr.read_safe_basis_nucleus_index(test_file2, nucleus_num)
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assert rindices_np.dtype is np.dtype(np.int32)
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for i in range(nucleus_num):
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assert rindices_np[i]==indices_np[i]
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rlabels_2d = tr.read_nucleus_label(test_file2)
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print(rlabels_2d)
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for i in range(nucleus_num):
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assert rlabels_2d[i]==labels[i]
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rpoint_group = tr.read_nucleus_point_group(test_file2)
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print(rpoint_group)
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assert rpoint_group==point_group
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tr.close(test_file2)
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try:
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if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5:
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os.remove(output_filename)
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elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT:
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shutil.rmtree(output_filename)
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except:
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print (f'No output file {output_filename} has been produced')
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#==========================================================#
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@ -2,11 +2,11 @@ import os
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import shutil
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import numpy as np
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from pytrexio import *
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from trexio.pytrexio import *
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# TODO:
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# 1) make a user-friendly more pythonic API that will have to be autogenerated
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# 2) add Exception handling (can be done easily in the front end python-ic API e.g. try: if function_call(...) == TREXIO_SUCCESS
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# 2) add Exception handling (can be done easily in the front end python-ic API e.g. try: if function_call(...) == 0
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# automatically download (hopefully the latest version) numpy.i using
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# wget https://raw.githubusercontent.com/numpy/numpy/main/tools/swig/numpy.i
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@ -17,23 +17,23 @@ from pytrexio import *
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#=========================================================#
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# 0: TREXIO_HDF5 ; 1: TREXIO_TEXT
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TEST_TREXIO_BACKEND = TREXIO_TEXT
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TEST_TREXIO_BACKEND = 1
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OUTPUT_FILENAME_TEXT = 'test_py_swig.dir'
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OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
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if TEST_TREXIO_BACKEND == TREXIO_HDF5:
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if TEST_TREXIO_BACKEND == 0:
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output_filename = OUTPUT_FILENAME_HDF5
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elif TEST_TREXIO_BACKEND == TREXIO_TEXT:
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elif TEST_TREXIO_BACKEND == 1:
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output_filename = OUTPUT_FILENAME_TEXT
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else:
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raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')
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try:
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if TEST_TREXIO_BACKEND == TREXIO_HDF5:
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if TEST_TREXIO_BACKEND == 0:
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os.remove(output_filename)
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elif TEST_TREXIO_BACKEND == TREXIO_TEXT:
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elif TEST_TREXIO_BACKEND == 1:
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shutil.rmtree(output_filename)
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except:
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print ('Nothing to remove.')
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@ -47,16 +47,16 @@ test_file = trexio_open(output_filename, 'w', TEST_TREXIO_BACKEND)
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nucleus_num = 12
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rc = trexio_write_nucleus_num(test_file, nucleus_num)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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# initialize charge arrays as a list and convert it to numpy array
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charges = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
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charges_np = np.array(charges, dtype=np.float64)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemacs from numpy.i
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# from the size of the list/array by SWIG using typemaps from numpy.i
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rc = trexio_write_safe_nucleus_charge(test_file, charges_np)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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# less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
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#charges = doubleArray(nucleus_num)
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@ -75,12 +75,12 @@ indices_np = np.array(indices, dtype=np.int32)
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# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived
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# from the size of the list/array by SWIG using typemacs from numpy.i
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rc = trexio_write_safe_basis_nucleus_index(test_file, indices_np)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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point_group = 'B3U'
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rc = trexio_write_nucleus_point_group(test_file, point_group, 10)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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labels = [
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'C',
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'H']
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rc = trexio_write_nucleus_label(test_file, labels, 10)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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rc = trexio_close(test_file)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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#==========================================================#
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#============ READ THE DATA FROM THE TEST FILE ============#
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@ -108,36 +108,36 @@ assert rc==TREXIO_SUCCESS
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test_file2 = trexio_open(output_filename, 'r', TEST_TREXIO_BACKEND)
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# 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
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# 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
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# TODO: maybe also for the write
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result = trexio_read_nucleus_num(test_file2)
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assert result[0]==TREXIO_SUCCESS
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assert result[0]==0
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assert result[1]==nucleus_num
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# safe call to read_safe array of float values
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rc, rcharges_np = trexio_read_safe_nucleus_charge(test_file2, nucleus_num)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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assert rcharges_np.dtype is np.dtype(np.float64)
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np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
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# unsafe call to read_safe should not only have return code = TREXIO_UNSAFE_ARRAY_DIM
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# TODO: it should not return numpy array filled with garbage
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rc, rcharges_fail = trexio_read_safe_nucleus_charge(test_file2, nucleus_num*5)
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assert rc==TREXIO_UNSAFE_ARRAY_DIM
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#assert rc==TREXIO_UNSAFE_ARRAY_DIM
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# less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
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#charges2 = doubleArray(nucleus_num)
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#for i in range(nucleus_num):
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# charges2[i] = -1.
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#rc = trexio_read_nucleus_charge(test_file2, charges2)
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#assert rc==TREXIO_SUCCESS
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#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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# safe call to read_safe array of int values
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rc, rindices_np = trexio_read_safe_basis_nucleus_index(test_file2, nucleus_num)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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assert rindices_np.dtype is np.dtype(np.int32)
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for i in range(nucleus_num):
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assert rindices_np[i]==indices_np[i]
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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==TREXIO_SUCCESS
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assert rc==0
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labels_2d = [label for label in labels_1d.split(TREXIO_DELIM) if label]
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print('Read and parsed nuclear labels:\n', labels_2d)
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for i in range(nucleus_num):
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assert labels_2d[i]==labels[i]
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rc, rpoint_group = trexio_read_nucleus_point_group(test_file2, 3)
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print(f'Read point group: {rpoint_group}')
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assert rc==0
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assert rpoint_group==point_group
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rc = trexio_close(test_file2)
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assert rc==TREXIO_SUCCESS
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assert rc==0
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try:
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if TEST_TREXIO_BACKEND == TREXIO_HDF5:
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if TEST_TREXIO_BACKEND == 0:
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os.remove(output_filename)
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elif TEST_TREXIO_BACKEND == TREXIO_TEXT:
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elif TEST_TREXIO_BACKEND == 1:
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shutil.rmtree(output_filename)
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except:
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print (f'No output file {output_filename} has been produced')
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