def test_temporary_cd():
"""Test temporary_cd() context manager"""
initial_dir = os.getcwd()
temporary_dir = '/'
from openforcefield.utils import temporary_cd
with temporary_cd(temporary_dir):
assert os.getcwd() == temporary_dir
assert os.getcwd() == initial_dir
def run_script_file(file_path):
"""Run through the shell a python script."""
with tempfile.TemporaryDirectory() as tmp_dir:
with temporary_cd(tmp_dir):
cmd = ["python", file_path]
if "conformer_energies.py" in file_path:
cmd.append("--filename")
mol_file = get_data_file_path(
"molecules/ruxolitinib_conformers.sdf")
cmd.append(mol_file)
try:
subprocess.check_call(cmd)
except subprocess.CalledProcessError:
raise Exception(f"Example {file_path} failed")
def call(self, cmd, raise_err=True):
"""Helper function to execute direct CLI calls"""
if type(cmd) == str:
cmd = cmd.split()
with tempfile.TemporaryDirectory() as tmp_dir:
with temporary_cd(tmp_dir):
proc = subprocess.Popen(cmd,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
out, err = proc.communicate()
if err and raise_err:
raise Exception(err)
return out.decode(), err.decode()
def test_p_prefix(self, toolkit):
"""Ensure the output file has the -p prefix"""
registry = make_registry(toolkit)
ethanol = get_data_file_path("molecules/ethanol.sdf")
mols_out = generate_conformers(
molecule=ethanol,
forcefield="openff-1.0.0.offxml",
registry=registry,
prefix="test_ethanol",
)
with tempfile.TemporaryDirectory() as tmp_dir:
with temporary_cd(tmp_dir):
write_mols(
mols=mols_out,
toolkit_registry=registry,
molecule=ethanol,
prefix="test_ethanol",
)
assert pathlib.Path("test_ethanol_0.sdf").is_file()