def _initialize_collection_and_read(aids):
'''initialize collection and read specified atoms files'''
my_col = AtomsCollection("Test", "tests/results")
data_path = 'tests/test_data/ni.p{0:s}.out'
for aid in aids:
my_col.read(data_path.format(aid),
28,
'lammps-dump-text',
rxid=r'ni.p(?P<aid>\d+).out')
return my_col
def test_read_empty_list(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# empty list
t1.read([],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 0 == len(t1)
shutil.rmtree("./tests/store")
def test_read_empty_dir_with_file(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# empty directory / directory and file
t1.read(["./tests/test_data/ni.p456.out", "./tests/test_data/empty"],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 1 == len(t1)
shutil.rmtree("./tests/store")
def test_read_directory(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# read directory
t1.read("./tests/test_data/sub1/",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 2 == len(t1)
shutil.rmtree("./tests/store")
def test_read_single_file(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# read single file
t1.read("./tests/test_data/ni.p455.out",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 1 == len(t1)
shutil.rmtree("./tests/store")
def test_aids(self):
t1 = AtomsCollection("Test_1", "./tests/test_paths")
t1.read(
["./tests/test_data/ni.p454.out", "./tests/test_data/ni.p453.out"],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out')
aid_list = t1.aids()
assert type(aid_list) is list
assert int(aid_list[0]) == int("453")
assert len(aid_list) is 2
def test_read_list(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# list of input files
t1.read(
["./tests/test_data/ni.p454.out", "./tests/test_data/ni.p453.out"],
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 2 == len(t1)
assert "test_454" == list(t1)[0]
shutil.rmtree("./tests/store")
def test_read_list_with_atomic_num_list(self):
t1 = AtomsCollection("Test_1", "./tests/store")
# list of input files with atomic num list (corresponding to one file)
t1.read(
["./tests/test_data/ni.p454.out", "./tests/test_data/ni.p453.out"],
[28, 28],
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 2 == len(t1)
assert "test_454" == list(t1)[0]
shutil.rmtree("./tests/store")
def test_read_nonexistent_directory(self):
# non-existent directory
t1 = AtomsCollection("Test_1", "./tests/store")
output = io.StringIO()
sys.stdout = output
t1.read("definitely_wrong",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert "Invalid file path, definitely_wrong was not read.\n" == output.getvalue(
)
shutil.rmtree("./tests/store")
def test_read_repeat_file(self):
# will not read previously read file
t1 = AtomsCollection("Test_1", "./tests/store")
t1.read("./tests/test_data/ni.p456.out",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
t1.read("./tests/test_data/ni.p456.out",
28,
"lammps-dump-text",
rxid=r'ni.p(?P<gbid>\d+).out',
prefix="TEST")
assert 1 == len(t1)
shutil.rmtree("./tests/store")