def test_launch_user_json(self, capsys):
"""Test launch with JSON topology file."""
args = self.args.copy()
args["lipid_jsons"] = [str(PATH_ROOT_DATA / "Berger_POPC.json")]
UI.launch(**args)
captured = capsys.readouterr().out
assert "Results written to OP_buildH.out" in captured
def test_main_output(self, capsys):
"""Test main with user defined output name."""
args = self.args.copy()
args["out_file"] = "text.txt"
UI.main(**args)
captured = capsys.readouterr().out
assert "Results written to text.txt" in captured
def test_main_subdef(self, capsys):
"""Test main with partial def file."""
args = self.args.copy()
args["def_file"] = str(PATH_DATA / "OP_def_HP_BergerPOPC.def")
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
def test_CLI_user_json(self, capsys):
"""Test working CLI with JSON topology file."""
sys.argv = (self.common_args + ["-l", "Berger_POPC"] +
["-lt", str(PATH_ROOT_DATA / "Berger_POPC.json")])
UI.entry_point()
captured = capsys.readouterr().out
assert "Results written to OP_buildH.out" in captured
def test_fails_launch_lipidtype(self, capsys):
"""Fail tests when passing a wrong lipid type."""
args = self.args.copy()
args["lipid_type"] = "PPHA"
with pytest.raises(BuildHError) as err:
UI.launch(**args)
assert err.type == BuildHError
assert "Lipid PPHA is not supported" in str(err.value)
def test_fails_CLI_lipidtype(self, capsys):
"""Fail tests when passing a wrong lipid type."""
sys.argv = self.common_args + ["-l", "PPHA"]
with pytest.raises(SystemExit) as err:
UI.entry_point()
# Make sur the exception is thrown
assert err.type == SystemExit
assert "Lipid PPHA is not supported" in capsys.readouterr().err
def test_main_traj(self, capsys):
"""Test main with trajectory."""
args = self.args.copy()
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
assert "Dealing with frame 10 at 10000.0 ps." in captured
def test_fail_main_coord_def_mismatch(self):
"""Test when coord file and def file doesn't match."""
args = self.args.copy()
args["def_file"] = str(PATH_DATA / "op_wrong1.def")
with pytest.raises(BuildHError) as err:
UI.main(**args)
assert f"Atoms defined in {args['def_file']} are missing in the structure" in str(
err.value)
def test_fail_launch_file(self):
"""Test fail launch with a non existant file."""
args = self.args.copy()
# Pass a string instead of a list
args["traj_file"] = "nofile.xtc"
with pytest.raises(FileNotFoundError) as err:
UI.launch(**args)
assert "nofile.xtc does not exist." in str(err.value)
def test_fail_launch_json(self):
"""Test fail launch with a wrong argument for JSON topology file."""
args = self.args.copy()
# Pass a string instead of a list
args["lipid_jsons"] = str(PATH_ROOT_DATA / "Berger_POPC.json")
with pytest.raises(TypeError) as err:
UI.launch(**args)
assert "a list is expected for argument 'lipid_jsons'" in str(
err.value)
def test_fail_main_subdef_traj(self, ):
"""Test main with partial def file and a output trajectory. Must fail."""
args = self.args.copy()
args["def_file"] = str(PATH_DATA / "OP_def_HP_BergerPOPC.def")
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
args["prefix_traj_ouput"] = "test"
with pytest.raises(BuildHError) as err:
UI.main(**args)
assert "Error on the number of H's to rebuild" in str(err.value)
def test_fails_CLI_slice(self, capsys):
"""Fail tests when passing a slice option without a trajectory."""
sys.argv = sys.argv = self.common_args + [
"-l", "Berger_POPC", "-e", "1000"
]
with pytest.raises(SystemExit) as err:
UI.entry_point()
assert err.type == SystemExit
assert "Slicing is only possible with a trajectory file." in capsys.readouterr(
).err
def test_main_traj_output(self, capsys):
"""Test main with trajectory and output trajectory."""
args = self.args.copy()
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
args["prefix_traj_ouput"] = "test"
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
assert "Writing new pdb with hydrogens." in captured
assert "Writing trajectory with hydrogens in xtc file." in captured
def test_main_traj_slice(self, capsys):
"""Test main with sliced trajectory."""
args = self.args.copy()
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
args["end"] = 3000
UI.main(**args)
captured = capsys.readouterr().out
assert self.stdout_output in captured
assert "Dealing with frame 3 at 3000.0 ps." in captured
# Make sure we stop at frame 3
assert "Dealing with frame 10 at 10000.0 ps." not in captured
def test_CLI_traj(self, capsys):
"""Test working CLI with all trajectory arguments."""
sys.argv = (self.common_args +
["-t", str(PATH_DATA / "2POPC.xtc")] +
["-l", "Berger_POPC"] + ["-o", "out.txt"] +
["-opx", "base"] + ["-b", "1000", "-e", "10000"])
UI.entry_point()
captured = capsys.readouterr().out
assert "Results written to out.txt" in captured
assert "Dealing with frame 10 at 10000.0 ps." in captured
assert "Writing new pdb with hydrogens." in captured
assert "Writing trajectory with hydrogens in xtc file." in captured
def test_fail_main_coord_topology_mismatch(self):
"""Test when coord file and topology doesn't match."""
args = self.args.copy()
lipids_tops = lipids.read_lipids_topH(
[lipids.PATH_JSON / "CHARMM36_POPC.json"])
dic_lipid = lipids_tops["CHARMM36_POPC"]
args["dic_lipid"] = dic_lipid
with pytest.raises(BuildHError) as err:
UI.main(**args)
assert "The topology chosen does not match the structure provided" in str(
err.value)
def test_launch_traj(self, capsys):
"""Test launch with all trajectory arguments."""
args = self.args.copy()
args["traj_file"] = str(PATH_DATA / "2POPC.xtc")
args["out_file"] = "out.txt"
args["prefix_traj_ouput"] = "basename"
args["begin"] = 0
args["end"] = 10000
UI.launch(**args)
captured = capsys.readouterr().out
assert "Results written to out.txt" in captured
assert "Dealing with frame 10 at 10000.0 ps." in captured
assert "Writing new pdb with hydrogens." in captured
assert "Writing trajectory with hydrogens in xtc file." in captured
def test_CLI_minimal(self, capsys):
"""Test working CLI with minimal arguments."""
sys.argv = self.common_args + ["-l", "Berger_POPC"]
UI.entry_point()
captured = capsys.readouterr().out
assert "Results written to OP_buildH.out" in captured
def test_launch_minimal(self, capsys):
"""Test launch with minimal arguments."""
UI.launch(**self.args)
captured = capsys.readouterr().out
assert "Results written to OP_buildH.out" in captured
def test_main_minimal(self, capsys):
"""Test main with minimal arguments."""
UI.main(**self.args)
captured = capsys.readouterr().out
assert self.stdout_output in captured