TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2024-12-23 04:43:57 +01:00
Code Issues Projects Releases Wiki Activity

BUG: trexio_open fails when test script is executed from outside the root test directory

Browse Source
This commit is contained in:
q-posev 2021-08-30 18:23:24 +03:00
parent 74c69bb293
commit ced8210ff0
3 changed files with 49 additions and 34 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
Makefile.am
View File

@ -191,7 +191,7 @@ setup_py = $(srcdir)/python/setup.py
setup_cfg = $(srcdir)/python/setup.cfg setup_cfg = $(srcdir)/python/setup.cfg
pytrexio_py = $(srcdir)/python/pytrexio/pytrexio.py pytrexio_py = $(srcdir)/python/pytrexio/pytrexio.py
trexio_py = $(srcdir)/python/trexio.py trexio_py = $(srcdir)/python/trexio.py
TEST_PY = $(srcdir)/python/test/test_api.py TEST_PY = python/test/test_api.py
pytrexio_c = $(srcdir)/src/pytrexio_wrap.c pytrexio_c = $(srcdir)/src/pytrexio_wrap.c
pytrexio_i = $(srcdir)/src/pytrexio.i pytrexio_i = $(srcdir)/src/pytrexio.i
numpy_i = $(srcdir)/src/numpy.i numpy_i = $(srcdir)/src/numpy.i

79
python/test/test_api.py
View File

@ -1,8 +1,10 @@
#!/usr/bin/env python3
import os import os
import shutil import shutil
import numpy as np import numpy as np
import trexio as tr import trexio
#=========================================================# #=========================================================#
#======== SETUP THE BACK END AND OUTPUT FILE NAME ========# #======== SETUP THE BACK END AND OUTPUT FILE NAME ========#
@ -15,9 +17,9 @@ OUTPUT_FILENAME_HDF5 = 'test_py_swig.h5'
# define TREXIO file name # define TREXIO file name
if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5: if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
output_filename = OUTPUT_FILENAME_HDF5 output_filename = OUTPUT_FILENAME_HDF5
elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT: elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
output_filename = OUTPUT_FILENAME_TEXT output_filename = OUTPUT_FILENAME_TEXT
else: else:
raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND') raise ValueError ('Specify one of the supported back ends as TEST_TREXIO_BACKEND')
@ -25,9 +27,9 @@ else:
# remove TREXIO file if exists in the current directory # remove TREXIO file if exists in the current directory
try: try:
if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5: if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
os.remove(output_filename) os.remove(output_filename)
elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT: elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
shutil.rmtree(output_filename) shutil.rmtree(output_filename)
except: except:
print ('Nothing to remove.') print ('Nothing to remove.')
@ -39,16 +41,29 @@ except:
# create TREXIO file and open it for writing # create TREXIO file and open it for writing
#test_file = tr.open(output_filename, 'w', TEST_TREXIO_BACKEND) #test_file = trexio.open(output_filename, 'w', TEST_TREXIO_BACKEND)
test_file = tr.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND) test_file = trexio.File(output_filename, mode='w', back_end=TEST_TREXIO_BACKEND)
# Print docstring of the tr.open function # Print docstring of the trexio.open function
#print(tr.open.__doc__) #print(trexio.open.__doc__)
nucleus_num = 12 nucleus_num = 12
try:
trexio.write_nucleus_num(test_file, -100)
except trexio.Error:
print("Writing negative nucleus_num: checked.")
# write nucleus_num in the file # write nucleus_num in the file
tr.write_nucleus_num(test_file, nucleus_num) try:
trexio.write_nucleus_num(test_file, nucleus_num)
except:
raise
try:
trexio.write_nucleus_num(test_file, nucleus_num*2)
except trexio.Error:
print("Attempt to overwrite nucleus_num: checked.")
# initialize charge arrays as a list and convert it to numpy array # 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 = [6., 6., 6., 6., 6., 6., 1., 1., 1., 1., 1., 1.]
@ -57,7 +72,7 @@ charges_np = np.array(charges, dtype=np.int32)
# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived # 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 # from the size of the list/array by SWIG using typemaps from numpy.i
tr.write_nucleus_charge(test_file, charges_np) trexio.write_nucleus_charge(test_file, charges_np)
# initialize arrays of nuclear indices as a list and convert it to numpy array # initialize arrays of nuclear indices as a list and convert it to numpy array
indices = [i for i in range(nucleus_num)] indices = [i for i in range(nucleus_num)]
@ -66,7 +81,7 @@ indices_np = np.array(indices, dtype=np.int64)
# function call below works with both lists and numpy arrays, dimension needed for memory-safety is derived # 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 typemacs from numpy.i
tr.write_basis_nucleus_index(test_file, indices_np) trexio.write_basis_nucleus_index(test_file, indices_np)
# initialize a list of nuclear coordinates # initialize a list of nuclear coordinates
coords = [ coords = [
@ -85,12 +100,12 @@ coords = [
] ]
# write coordinates in the file # write coordinates in the file
tr.write_nucleus_coord(test_file, coords) trexio.write_nucleus_coord(test_file, coords)
point_group = 'B3U' point_group = 'B3U'
# write nucleus_point_group in the file # write nucleus_point_group in the file
tr.write_nucleus_point_group(test_file, point_group) trexio.write_nucleus_point_group(test_file, point_group)
labels = [ labels = [
'C', 'C',
@ -107,13 +122,13 @@ labels = [
'H'] 'H']
# write nucleus_label in the file # write nucleus_label in the file
tr.write_nucleus_label(test_file,labels) trexio.write_nucleus_label(test_file,labels)
# close TREXIO file # close TREXIO file
# [TODO:] this functional call is no longer needed as we introduced TREXIO_File class which has a desctructor that closes the file # [TODO:] this functional call is no longer needed as we introduced TREXIO_File class which has a desctructor that closes the file
#tr.close(test_file) #trexio.close(test_file)
# [TODO:] without calling destructor on test_file the TREXIO_FILE is not getting created and the data is not written when using TEXT back end. This, the user still has to explicitly call destructor on test_file object instead # [TODO:] without calling destructor on test_file the TREXIO_FILE is not getting created and the data is not written when using TEXT back end. This, the user still has to explicitly call destructor on test_file object instead
# tr.close function. This is only an issue when the data is getting written and read in the same session (e.g. in Jupyter notebook) # trexio.close function. This is only an issue when the data is getting written and read in the same session (e.g. in Jupyter notebook)
del test_file del test_file
@ -123,68 +138,68 @@ del test_file
#==========================================================# #==========================================================#
# open previously created TREXIO file, now in 'read' mode # open previously created TREXIO file, now in 'read' mode
#test_file2 = tr.open(output_filename, 'r', TEST_TREXIO_BACKEND) #test_file2 = trexio.open(output_filename, 'r', TEST_TREXIO_BACKEND)
test_file2 = tr.File(output_filename, 'r', TEST_TREXIO_BACKEND) test_file2 = trexio.File(output_filename, 'r', TEST_TREXIO_BACKEND)
# read nucleus_num from file # read nucleus_num from file
rnum = tr.read_nucleus_num(test_file2) rnum = trexio.read_nucleus_num(test_file2)
assert rnum==nucleus_num assert rnum==nucleus_num
# safe call to read_nucleus_charge array of float values # safe call to read_nucleus_charge array of float values
rcharges_np = tr.read_nucleus_charge(test_file2, dim=nucleus_num) rcharges_np = trexio.read_nucleus_charge(test_file2, dim=nucleus_num)
assert rcharges_np.dtype is np.dtype(np.float64) assert rcharges_np.dtype is np.dtype(np.float64)
np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8) np.testing.assert_array_almost_equal(rcharges_np, charges_np, decimal=8)
# unsafe call to read_safe should fail with error message corresponding to TREXIO_UNSAFE_ARRAY_DIM # unsafe call to read_safe should fail with error message corresponding to TREXIO_UNSAFE_ARRAY_DIM
try: try:
rcharges_fail = tr.read_nucleus_charge(test_file2, dim=nucleus_num*5) rcharges_fail = trexio.read_nucleus_charge(test_file2, dim=nucleus_num*5)
except Exception: except Exception:
print("Unsafe call to safe API: checked") print("Unsafe call to safe API: checked")
# safe call to read array of int values (nuclear indices) # safe call to read array of int values (nuclear indices)
rindices_np_16 = tr.read_basis_nucleus_index(test_file2, dim=nucleus_num, dtype=np.int16) rindices_np_16 = trexio.read_basis_nucleus_index(test_file2, dim=nucleus_num, dtype=np.int16)
assert rindices_np_16.dtype is np.dtype(np.int16) assert rindices_np_16.dtype is np.dtype(np.int16)
for i in range(nucleus_num): for i in range(nucleus_num):
assert rindices_np_16[i]==indices_np[i] assert rindices_np_16[i]==indices_np[i]
rindices_np_32 = tr.read_basis_nucleus_index(test_file2, dim=nucleus_num, dtype=np.int32) rindices_np_32 = trexio.read_basis_nucleus_index(test_file2, dim=nucleus_num, dtype=np.int32)
assert rindices_np_32.dtype is np.dtype(np.int32) assert rindices_np_32.dtype is np.dtype(np.int32)
for i in range(nucleus_num): for i in range(nucleus_num):
assert rindices_np_32[i]==indices_np[i] assert rindices_np_32[i]==indices_np[i]
rindices_np_64 = tr.read_basis_nucleus_index(test_file2) rindices_np_64 = trexio.read_basis_nucleus_index(test_file2)
assert rindices_np_64.dtype is np.dtype(np.int64) assert rindices_np_64.dtype is np.dtype(np.int64)
assert rindices_np_64.size==nucleus_num assert rindices_np_64.size==nucleus_num
for i in range(nucleus_num): for i in range(nucleus_num):
assert rindices_np_64[i]==indices_np[i] assert rindices_np_64[i]==indices_np[i]
# read nuclear coordinates without providing optional argument dim # read nuclear coordinates without providing optional argument dim
rcoords_np = tr.read_nucleus_coord(test_file2) rcoords_np = trexio.read_nucleus_coord(test_file2)
assert rcoords_np.size==nucleus_num*3 assert rcoords_np.size==nucleus_num*3
np.testing.assert_array_almost_equal(rcoords_np, np.array(coords).reshape(nucleus_num,3), decimal=8) np.testing.assert_array_almost_equal(rcoords_np, np.array(coords).reshape(nucleus_num,3), decimal=8)
# set doReshape to False to get a flat 1D array (e.g. when reading matrices like nuclear coordinates) # set doReshape to False to get a flat 1D array (e.g. when reading matrices like nuclear coordinates)
#rcoords_reshaped_2 = tr.read_nucleus_coord(test_file2, doReshape=False) #rcoords_reshaped_2 = trexio.read_nucleus_coord(test_file2, doReshape=False)
# read array of nuclear labels # read array of nuclear labels
rlabels_2d = tr.read_nucleus_label(test_file2, dim=nucleus_num) rlabels_2d = trexio.read_nucleus_label(test_file2, dim=nucleus_num)
print(rlabels_2d) print(rlabels_2d)
for i in range(nucleus_num): for i in range(nucleus_num):
assert rlabels_2d[i]==labels[i] assert rlabels_2d[i]==labels[i]
# read a string corresponding to nuclear point group # read a string corresponding to nuclear point group
rpoint_group = tr.read_nucleus_point_group(test_file2) rpoint_group = trexio.read_nucleus_point_group(test_file2)
assert rpoint_group==point_group assert rpoint_group==point_group
# close TREXIO file # close TREXIO file
#tr.close(test_file2) #trexio.close(test_file2)
# cleaning (remove the TREXIO file) # cleaning (remove the TREXIO file)
try: try:
if TEST_TREXIO_BACKEND == tr.TREXIO_HDF5: if TEST_TREXIO_BACKEND == trexio.TREXIO_HDF5:
os.remove(output_filename) os.remove(output_filename)
elif TEST_TREXIO_BACKEND == tr.TREXIO_TEXT: elif TEST_TREXIO_BACKEND == trexio.TREXIO_TEXT:
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')

2
python/test/test_pytrexio.py
View File

@ -113,7 +113,7 @@ 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 # 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 # TODO: it should not return numpy array filled with garbage
rc, rcharges_fail = trexio_read_safe_nucleus_charge(test_file2, nucleus_num*5) rc, rcharges_fail = trexio_read_safe_nucleus_charge(test_file2, nucleus_num*5)
assert rc==TREXIO_UNSAFE_ARRAY_DIM assert rc==23
# less Python-ic way to read/write arrays using Array classes (probably more portable to other languages) # less Python-ic way to read/write arrays using Array classes (probably more portable to other languages)
#charges2 = doubleArray(nucleus_num) #charges2 = doubleArray(nucleus_num)