def test_new_id():
id1 = TrajectoryData.new_id()
assert id1 == str(uuid.UUID(id1))
id2 = TrajectoryData.new_id()
id3 = TrajectoryData.new_id('foo')
assert(id1 != id2 != id3)
id4 = TrajectoryData.new_id('foo')
assert(id3 == id4)
id5 = TrajectoryData.new_id('bar')
assert(id5 != id4)
def test_new_id():
id1 = TrajectoryData.new_id()
assert id1 == str(uuid.UUID(id1))
id2 = TrajectoryData.new_id()
id3 = TrajectoryData.new_id('foo')
assert (id1 != id2 != id3)
id4 = TrajectoryData.new_id('foo')
assert (id3 == id4)
id5 = TrajectoryData.new_id('bar')
assert (id5 != id4)
def test_from_qsd_data(traj1, datadir):
X1_file = join(datadir, 'traj1', 'X1.out')
X2_file = join(datadir, 'traj1', 'X2.out')
traj2 = TrajectoryData.from_qsd_data(
OrderedDict([('X2', X2_file), ('X1', X1_file)]), TRAJ1_SEED)
# traj1 and traj2 are the same except that the order of the operators is
# reversed => files are read in a differnt order
assert traj1.ID == traj2.ID
traj = traj1
md5sum = lambda f: hashlib.md5(open(f,'rb').read()).hexdigest()
md5 = "".join(sorted([md5sum(X1_file), md5sum(X2_file)]))
assert traj.ID == str(uuid.uuid3(TrajectoryData._uuid_namespace, md5))
assert traj.dt == 0.1
assert traj.nt == 51
assert traj.shape == (51, 9)
assert len(traj.record) == 1
assert list(traj.operators) == ['X1', 'X2']
for (id, (seed, n_traj, op_list)) in traj.record.items():
assert seed == TRAJ1_SEED
assert n_traj == 1
assert op_list == ['X1', 'X2']
assert traj.record_seeds == set([TRAJ1_SEED, ])
assert traj.record_IDs == set([traj.ID, ])
assert list(traj.table.keys()) == ['Re[<X1>]', 'Im[<X1>]', 'Re[var(X1)]',
'Im[var(X1)]', 'Re[<X2>]', 'Im[<X2>]', 'Re[var(X2)]',
'Im[var(X2)]']
fname = join(datadir, 'traj1', 'X1.out')
(tgrid, re_exp, im_exp, re_var, im_var) \
= np.genfromtxt(fname, dtype=np.float64, skip_header=1, unpack=True)
assert np.max(np.abs(re_exp - traj.table['Re[<X1>]'])) < 1.0e-15
assert np.max(np.abs(im_exp - traj.table['Im[<X1>]'])) < 1.0e-15
assert np.max(np.abs(re_var - traj.table['Re[var(X1)]'])) < 1.0e-15
assert np.max(np.abs(im_var - traj.table['Im[var(X1)]'])) < 1.0e-15
def proto_fixture(datadir):
operators = OrderedDict()
datafiles = sorted(glob(os.path.join(datadir, folder, '*.out')))
assert len(datafiles) > 0, "No files *.out in %s" % folder
for file in datafiles:
op_name = os.path.splitext(os.path.split(file)[1])[0]
operators[op_name] = file
return TrajectoryData.from_qsd_data(operators, seed=seed)
def test_parse_header_line():
line = '# t Re[<X1>] Im[<X1>] Re[var(X1)] Im[var(X1)] Re[<X2>] Im[<X2>] Re[var(X2)] Im[var(X2)]'
fields = TrajectoryData._parse_header_line(line)
assert fields == [
'# t', ' Re[<X1>]', ' Im[<X1>]', ' Re[var(X1)]',
' Im[var(X1)]', ' Re[<X2>]', ' Im[<X2>]', ' Re[var(X2)]',
' Im[var(X2)]'
]
fields = TrajectoryData._parse_header_line(line, strip=True)
assert fields == [
'# t', 'Re[<X1>]', 'Im[<X1>]', 'Re[var(X1)]', 'Im[var(X1)]',
'Re[<X2>]', 'Im[<X2>]', 'Re[var(X2)]', 'Im[var(X2)]'
]
line = '#tRe[<X1>]Im[<X1>]'
fields = TrajectoryData._parse_header_line(line)
assert fields == ['#t', 'Re[<X1>]', 'Im[<X1>]']
line = '# t Re[<A[1]>] Im[<A[1]>]'
fields = TrajectoryData._parse_header_line(line, strip=True)
assert fields == ['# t', 'Re[<A[1]>]', 'Im[<A[1]>]']
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<A]>] Im[<A]>]'
fields = TrajectoryData._parse_header_line(line, strip=True)
assert "unbalanced brackets" in str(excinfo.value)
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<A[1]>] Im[<A[1]>] X1 X2'
fields = TrajectoryData._parse_header_line(line, strip=True)
assert "trailing characters" in str(excinfo.value)
def test_get_op_names_from_header_line(traj1):
# use of traj1 is arbitrary, we just need some instance
line = '# t Re[<X1>] Im[<X1>] Re[var(X1)] Im[var(X1)] Re[<X2>] Im[<X2>] Re[var(X2)] Im[var(X2)]'
ops = traj1._get_op_names_from_header_line(line)
assert ops == ['X1', 'X2']
op = 'X'*20
line = '# t '+" ".join(TrajectoryData._operator_cols(op))
ops = traj1._get_op_names_from_header_line(line)
assert ops == [op, ]
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<X1>] Im[<X1>] Re[var(X1)]'
ops = traj1._get_op_names_from_header_line(line)
assert "Unexpected number of columns" in str(excinfo.value)
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<X\t2>]'
ops = traj1._get_op_names_from_header_line(line)
assert "contains invalid characters" in str(excinfo.value)
def test_get_op_names_from_header_line(traj1):
# use of traj1 is arbitrary, we just need some instance
line = '# t Re[<X1>] Im[<X1>] Re[var(X1)] Im[var(X1)] Re[<X2>] Im[<X2>] Re[var(X2)] Im[var(X2)]'
ops = traj1._get_op_names_from_header_line(line)
assert ops == ['X1', 'X2']
op = 'X' * 20
line = '# t ' + " ".join(TrajectoryData._operator_cols(op))
ops = traj1._get_op_names_from_header_line(line)
assert ops == [
op,
]
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<X1>] Im[<X1>] Re[var(X1)]'
ops = traj1._get_op_names_from_header_line(line)
assert "Unexpected number of columns" in str(excinfo.value)
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<X\t2>]'
ops = traj1._get_op_names_from_header_line(line)
assert "contains invalid characters" in str(excinfo.value)
def test_from_qsd_data(traj1, datadir):
X1_file = join(datadir, 'traj1', 'X1.out')
X2_file = join(datadir, 'traj1', 'X2.out')
traj2 = TrajectoryData.from_qsd_data(
OrderedDict([('X2', X2_file), ('X1', X1_file)]), TRAJ1_SEED)
# traj1 and traj2 are the same except that the order of the operators is
# reversed => files are read in a differnt order
assert traj1.ID == traj2.ID
traj = traj1
md5sum = lambda f: hashlib.md5(open(f, 'rb').read()).hexdigest()
md5 = "".join(sorted([md5sum(X1_file), md5sum(X2_file)]))
assert traj.ID == str(uuid.uuid3(TrajectoryData._uuid_namespace, md5))
assert traj.dt == 0.1
assert traj.nt == 51
assert traj.shape == (51, 9)
assert len(traj.record) == 1
assert list(traj.operators) == ['X1', 'X2']
for (id, (seed, n_traj, op_list)) in traj.record.items():
assert seed == TRAJ1_SEED
assert n_traj == 1
assert op_list == ['X1', 'X2']
assert traj.record_seeds == set([
TRAJ1_SEED,
])
assert traj.record_IDs == set([
traj.ID,
])
assert list(traj.table.keys()) == [
'Re[<X1>]', 'Im[<X1>]', 'Re[var(X1)]', 'Im[var(X1)]', 'Re[<X2>]',
'Im[<X2>]', 'Re[var(X2)]', 'Im[var(X2)]'
]
fname = join(datadir, 'traj1', 'X1.out')
(tgrid, re_exp, im_exp, re_var, im_var) \
= np.genfromtxt(fname, dtype=np.float64, skip_header=1, unpack=True)
assert np.max(np.abs(re_exp - traj.table['Re[<X1>]'])) < 1.0e-15
assert np.max(np.abs(im_exp - traj.table['Im[<X1>]'])) < 1.0e-15
assert np.max(np.abs(re_var - traj.table['Re[var(X1)]'])) < 1.0e-15
assert np.max(np.abs(im_var - traj.table['Im[var(X1)]'])) < 1.0e-15
def test_parse_header_line():
line = '# t Re[<X1>] Im[<X1>] Re[var(X1)] Im[var(X1)] Re[<X2>] Im[<X2>] Re[var(X2)] Im[var(X2)]'
fields = TrajectoryData._parse_header_line(line)
assert fields == ['# t', ' Re[<X1>]', ' Im[<X1>]',
' Re[var(X1)]', ' Im[var(X1)]', ' Re[<X2>]',
' Im[<X2>]', ' Re[var(X2)]', ' Im[var(X2)]']
fields = TrajectoryData._parse_header_line(line, strip=True)
assert fields == ['# t', 'Re[<X1>]', 'Im[<X1>]',
'Re[var(X1)]', 'Im[var(X1)]', 'Re[<X2>]',
'Im[<X2>]', 'Re[var(X2)]', 'Im[var(X2)]']
line = '#tRe[<X1>]Im[<X1>]'
fields = TrajectoryData._parse_header_line(line)
assert fields == ['#t', 'Re[<X1>]', 'Im[<X1>]']
line = '# t Re[<A[1]>] Im[<A[1]>]'
fields = TrajectoryData._parse_header_line(line, strip=True)
assert fields == ['# t', 'Re[<A[1]>]', 'Im[<A[1]>]']
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<A]>] Im[<A]>]'
fields = TrajectoryData._parse_header_line(line, strip=True)
assert "unbalanced brackets" in str(excinfo.value)
with pytest.raises(TrajectoryParserError) as excinfo:
line = '# t Re[<A[1]>] Im[<A[1]>] X1 X2'
fields = TrajectoryData._parse_header_line(line, strip=True)
assert "trailing characters" in str(excinfo.value)
def test_read(datadir, tmpdir, traj1, traj2_10, traj11_20):
filename = join(datadir, 'read_input_files', 'good.dat')
traj = TrajectoryData.read(filename)
file_str = open(filename).read()
assert str(traj) == file_str.rstrip()
filename = str(tmpdir.join("traj1.dat"))
traj1.write(filename)
traj_r = TrajectoryData.read(filename)
assert str(traj_r) == str(traj1)
filename = str(tmpdir.join("traj1-20.dat"))
traj = traj11_20 + traj2_10 + traj1
traj.col_width = 12
traj.write(filename)
traj_r = TrajectoryData.read(filename)
assert str(traj_r) == str(traj)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_header.dat')
traj = TrajectoryData.read(filename)
assert "does not define an ID" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_record.dat')
traj = TrajectoryData.read(filename)
assert "does not contain a record" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_col_labels.dat')
traj = TrajectoryData.read(filename)
assert "does not contain a header" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_data.dat')
traj = TrajectoryData.read(filename)
assert "contains no data" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'empty.dat')
traj = TrajectoryData.read(filename)
assert "does not define an ID" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'wrong_col_labels.dat')
traj = TrajectoryData.read(filename)
assert "Malformed header" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'wrong_col_labels2.dat')
traj = TrajectoryData.read(filename)
assert "Invalid header line" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_tgrid.dat')
traj = TrajectoryData.read(filename)
assert "missing time grid" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'missing_im.dat')
traj = TrajectoryData.read(filename)
assert "Unexpected number of columns" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'header_data_mismatch.dat')
traj = TrajectoryData.read(filename)
assert "number of data columns differs from the number indicated in "\
"the header" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'single_row.dat')
traj = TrajectoryData.read(filename)
assert "Too few rows" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'truncated.dat')
traj = TrajectoryData.read(filename)
assert "Wrong number of columns at line 3" in str(exc_info.value)
def test_init_validation():
dt_ok = 0.1
ID_ok = 'd9831647-f2e7-3793-8b24-7c49c5c101a7'
data_ok = OrderedDict([
('X', (np.zeros(3), np.zeros(3), np.zeros(3), np.zeros(3))),
('Y', (np.zeros(3), np.zeros(3), np.zeros(3), np.zeros(3)))
])
TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data_ok)
with pytest.raises(ValueError) as excinfo:
TrajectoryData(ID='1232',
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data_ok)
assert 'badly formed hexadecimal UUID string' in str(excinfo.value)
with pytest.raises(ValueError) as excinfo:
TrajectoryData(ID=ID_ok,
dt=0.0,
seed=None,
n_trajectories=None,
data=data_ok)
assert 'dt must be a value >0' in str(excinfo.value)
with pytest.raises(ValueError) as excinfo:
TrajectoryData(ID=ID_ok,
dt="bla",
seed=None,
n_trajectories=None,
data=data_ok)
assert 'could not convert string' in str(excinfo.value)
with pytest.raises(ValueError) as excinfo:
TrajectoryData(ID=ID_ok,
dt=None,
seed=None,
n_trajectories=None,
data=data_ok)
assert 'dt must be a float with value >0' in str(excinfo.value)
with pytest.raises(AttributeError) as excinfo:
TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=None)
with pytest.raises(ValueError) as excinfo:
data = OrderedDict([('X', (np.zeros(3), np.zeros(3), np.zeros(3))),
('Y', (np.zeros(3), np.zeros(3), np.zeros(3)))])
TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data)
assert 'need more than 3 values to unpack' in str(excinfo.value)
with pytest.raises(ValueError) as excinfo:
data = OrderedDict([('X', ("a", "b", "c", "d")),
('Y', ("a", "b", "c", "d"))])
TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data)
assert 'could not convert string to float' in str(excinfo.value)
assert TrajectoryData.col_width == 25
data = OrderedDict([
('Y' * 20, data_ok['X']),
])
traj = TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data)
assert traj.col_width == 20 + TrajectoryData._col_padding
with pytest.raises(ValueError) as excinfo:
data = OrderedDict([
('a\tb', data_ok['X']),
])
TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data)
assert 'contains invalid characters' in str(excinfo.value)
with pytest.raises(ValueError) as excinfo:
data = OrderedDict([
('A[[2]', data_ok['X']),
])
TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data)
assert 'contains unbalanced brackets' in str(excinfo.value)
with pytest.raises(ValueError) as excinfo:
data = OrderedDict([
('A]', data_ok['X']),
])
TrajectoryData(ID=ID_ok,
dt=dt_ok,
seed=None,
n_trajectories=None,
data=data)
assert 'contains unbalanced brackets' in str(excinfo.value)
def test_read(datadir, tmpdir, traj1, traj2_10, traj11_20):
filename = join(datadir, 'read_input_files', 'good.dat')
traj = TrajectoryData.read(filename)
file_str = open(filename).read()
assert str(traj) == file_str.rstrip()
filename = str(tmpdir.join("traj1.dat"))
traj1.write(filename)
traj_r = TrajectoryData.read(filename)
assert str(traj_r) == str(traj1)
filename = str(tmpdir.join("traj1-20.dat"))
traj = traj11_20 + traj2_10 + traj1
traj.col_width = 12
traj.write(filename)
traj_r = TrajectoryData.read(filename)
assert str(traj_r) == str(traj)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_header.dat')
traj = TrajectoryData.read(filename)
assert "does not define an ID" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_record.dat')
traj = TrajectoryData.read(filename)
assert "does not contain a record" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_col_labels.dat')
traj = TrajectoryData.read(filename)
assert "does not contain a header" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_data.dat')
traj = TrajectoryData.read(filename)
assert "contains no data" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'empty.dat')
traj = TrajectoryData.read(filename)
assert "does not define an ID" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'wrong_col_labels.dat')
traj = TrajectoryData.read(filename)
assert "Malformed header" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'wrong_col_labels2.dat')
traj = TrajectoryData.read(filename)
assert "Invalid header line" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'no_tgrid.dat')
traj = TrajectoryData.read(filename)
assert "missing time grid" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'missing_im.dat')
traj = TrajectoryData.read(filename)
assert "Unexpected number of columns" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files',
'header_data_mismatch.dat')
traj = TrajectoryData.read(filename)
assert "number of data columns differs from the number indicated in "\
"the header" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'single_row.dat')
traj = TrajectoryData.read(filename)
assert "Too few rows" in str(exc_info.value)
with pytest.raises(TrajectoryParserError) as exc_info:
filename = join(datadir, 'read_input_files', 'truncated.dat')
traj = TrajectoryData.read(filename)
assert "Wrong number of columns at line 3" in str(exc_info.value)
