def test_curatecli_makediff(tmp_path):
tmp_path = str(tmp_path) # Needed for python 3.5
filename1 = '6-31G_s_s-full.json.bz2'
filename2 = '6-31G-full.json.bz2'
file1 = os.path.join(curate_test_data_dir, filename1)
file2 = os.path.join(curate_test_data_dir, filename2)
tmpfile1 = os.path.join(tmp_path, filename1)
tmpfile2 = os.path.join(tmp_path, filename2)
shutil.copyfile(file1, tmpfile1)
shutil.copyfile(file2, tmpfile2)
_test_curatecli_cmd('make-diff -l {} -r {}'.format(tmpfile1, tmpfile2))
_test_curatecli_cmd('make-diff -l {} -r {}'.format(tmpfile2, tmpfile1))
diff1 = fileio.read_json_basis(tmpfile1 + '.diff')
diff2 = fileio.read_json_basis(tmpfile2 + '.diff')
assert len(diff1['elements']) == 36
assert len(diff2['elements']) == 0
reffilename = '6-31G_s_s-polarization.json.bz2'
reffile = os.path.join(curate_test_data_dir, reffilename)
refdata = fileio.read_json_basis(reffile)
assert curate.compare_basis(diff1, refdata, rel_tol=0.0)
def test_diff_json_files(tmp_path):
tmp_path = str(tmp_path) # Needed for python 3.5
filename1 = '6-31G_s_s-full.json.bz2'
filename2 = '6-31G-full.json.bz2'
file1 = os.path.join(test_data_dir, filename1)
file2 = os.path.join(test_data_dir, filename2)
tmpfile1 = os.path.join(tmp_path, filename1)
tmpfile2 = os.path.join(tmp_path, filename2)
shutil.copyfile(file1, tmpfile1)
shutil.copyfile(file2, tmpfile2)
curate.diff_json_files([tmpfile1], [tmpfile2])
curate.diff_json_files([tmpfile2], [tmpfile1])
diff1 = fileio.read_json_basis(tmpfile1 + '.diff')
diff2 = fileio.read_json_basis(tmpfile2 + '.diff')
assert len(diff1['elements']) == 36
assert len(diff2['elements']) == 0
reffilename = '6-31G_s_s-polarization.json.bz2'
reffile = os.path.join(test_data_dir, reffilename)
refdata = fileio.read_json_basis(reffile)
assert curate.compare_basis(diff1, refdata, rel_tol=0.0)
def test_read_write_basis(file_path):
# needed to be tested to make sure something isn't left
# out of the sort lists, etc
full_path = os.path.join(_data_dir, file_path)
full_path_new = full_path + '.new'
data = fileio.read_json_basis(full_path)
fileio.write_json_basis(full_path_new, data)
os.remove(full_path_new)
def test_diff_json_files_same(tmp_path):
tmp_path = str(tmp_path) # Needed for python 3.5
filename = 'def2-SV-base.1.json'
file1 = os.path.join(data_dir, 'ahlrichs', 'SV', filename)
tmpfile = os.path.join(tmp_path, filename)
shutil.copyfile(file1, tmpfile)
curate.diff_json_files([tmpfile], [tmpfile])
diff_file = tmpfile + '.diff'
assert os.path.isfile(diff_file)
diff_data = fileio.read_json_basis(diff_file)
assert len(diff_data['elements']) == 0
def test_add_basis(tmp_path):
tmp_path = str(tmp_path) # Needed for python 3.5
for sf, refs in _source_data.items():
sf_path = os.path.join(auth_data_dir, sf)
name = sf.split('.')[0]
curate.add_basis(sf_path, tmp_path, 'test_subdir', 'test_' + name,
'test_basis_' + name, 'test_family', 'orbital',
'Test Basis Description: ' + name, '1',
'Test Basis Revision Description', 'Test Source',
refs)
md = api.get_metadata(tmp_path)
assert len(md) == len(_source_data)
# Re-read
for sf in _source_data.keys():
name = name = sf.split('.')[0]
name = 'test_basis_' + name
bse_dict = api.get_basis(name, data_dir=tmp_path)
assert bse_dict['family'] == 'test_family'
# Compare against the file we created from
sf_path = os.path.join(auth_data_dir, sf)
assert curate.compare_basis_against_file(name,
sf_path,
data_dir=tmp_path)
# Check that all the files exist and contain the right elements
for fpath, elements in _expected_files.items():
fpath = os.path.join(tmp_path, fpath)
assert os.path.isfile(fpath)
fdata = fileio.read_json_basis(fpath)
expect_elements = set(misc.expand_elements(elements, True))
assert set(fdata['elements'].keys()) == expect_elements
# Validate the new data dir
validator.validate_data_dir(tmp_path)
#!/usr/bin/env python3
import re
import sys
import copy
from basis_set_exchange import fileio, lut, manip
base_data = fileio.read_json_basis('ANO-RCC.1.json')
with open('splitmap-ano-rcc.txt', 'r') as f:
split_lines = f.readlines()
all_names = [
'ANO-RCC-MB', 'ANO-RCC-VDZ', 'ANO-RCC-VDZP', 'ANO-RCC-VTZP',
'ANO-RCC-VQZP', 'ANO-RCC-VTZ'
]
split_data = {n: {} for n in all_names}
for l in split_lines:
name, cont = l.split()
el1, name1 = name.split('.')
el2, name2, _, _, cont, _ = cont.split('.')
assert el1 == el2
assert name2 == 'ANO-RCC'
assert name1 in all_names
el = lut.element_Z_from_sym(el1, as_str=True)
assert el not in split_data[name1]
cont = re.findall(r'\d+[a-z]+', cont)
split_data[name1][el] = cont
def test_print_table_basis(file_path):
full_path = os.path.join(data_dir, file_path)
tab = fileio.read_json_basis(full_path)
curate.print_table_basis(tab)
def test_print_elemental_basis(file_path):
full_path = os.path.join(data_dir, file_path)
el = fileio.read_json_basis(full_path)
curate.print_element_basis(el)
def test_print_component_basis(file_path):
full_path = os.path.join(data_dir, file_path)
comp = fileio.read_json_basis(full_path)
curate.print_component_basis(comp)
def test_print_component_basis(file_path):
full_path = os.path.join(data_dir, file_path)
comp = fileio.read_json_basis(full_path)
printing.component_basis_str(comp)
