def test_hdf5():
"""Test HDF5 IO
"""
tempdir = _TempDir()
test_file = op.join(tempdir, "test.hdf5")
sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format="csc")
sp[2, 2] = 2
x = dict(
a=dict(b=np.zeros(3)),
c=np.zeros(2, np.complex128),
d=[dict(e=(1, -2.0, "hello", u"goodbyeu\u2764")), None],
f=sp,
)
write_hdf5(test_file, 1)
assert_equal(read_hdf5(test_file), 1)
assert_raises(IOError, write_hdf5, test_file, x) # file exists
write_hdf5(test_file, x, overwrite=True)
assert_raises(IOError, read_hdf5, test_file + "FOO") # not found
xx = read_hdf5(test_file)
assert_true(object_diff(x, xx) == "") # no assert_equal, ugly output
# bad title
assert_raises(ValueError, read_hdf5, test_file, title="nonexist")
assert_raises(ValueError, write_hdf5, test_file, x, overwrite=True, title=1)
assert_raises(ValueError, read_hdf5, test_file, title=1)
# unsupported objects
assert_raises(TypeError, write_hdf5, test_file, {1: "foo"}, overwrite=True)
assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)
def test_path_support():
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
write_hdf5(test_file, 1, title='first')
write_hdf5(test_file, 2, title='second/third', overwrite='update')
assert_raises(ValueError, read_hdf5, test_file, title='second')
assert_equal(read_hdf5(test_file, 'first'), 1)
assert_equal(read_hdf5(test_file, 'second/third'), 2)
def test_path_support():
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
write_hdf5(test_file, 1, title='first')
write_hdf5(test_file, 2, title='second/third', overwrite='update')
assert_raises(ValueError, read_hdf5, test_file, title='second')
assert_equal(read_hdf5(test_file, 'first'), 1)
assert_equal(read_hdf5(test_file, 'second/third'), 2)
def test_numpy_values():
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
for cast in [np.int8, np.int16, np.int32, np.int64, np.bool_,
np.float16, np.float32, np.float64]:
value = cast(1)
write_hdf5(test_file, value, title='first', overwrite='update')
assert_equal(read_hdf5(test_file, 'first'), value)
def test_multi_dim_array():
rng = np.random.RandomState(0)
traj = np.array([rng.randn(2, 1), rng.randn(3, 1)])
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
write_hdf5(test_file, traj, title='first', overwrite='update')
for traj_read, traj_sub in zip(read_hdf5(test_file, 'first'), traj):
assert (np.equal(traj_read, traj_sub).all())
traj_no_structure = np.array([rng.randn(2, 1, 1), rng.randn(3, 1, 2)])
pytest.raises(ValueError,
write_hdf5,
test_file,
traj_no_structure,
title='second',
overwrite='update')
def test_hdf5():
"""Test HDF5 IO
"""
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csc')
df = np.eye(3) if isinstance(DataFrame, type(None)) else DataFrame(
np.eye(3))
sr = np.eye(3) if isinstance(Series, type(None)) else Series(
np.random.randn(3))
sp[2, 2] = 2
x = dict(a=dict(b=np.zeros(3)),
c=np.zeros(2, np.complex128),
d=[dict(e=(1, -2., 'hello', u'goodbyeu\u2764')), None],
f=sp,
g=dict(dfa=df, srb=sr))
write_hdf5(test_file, 1)
assert_equal(read_hdf5(test_file), 1)
assert_raises(IOError, write_hdf5, test_file, x) # file exists
write_hdf5(test_file, x, overwrite=True)
assert_raises(IOError, read_hdf5, test_file + 'FOO') # not found
xx = read_hdf5(test_file)
assert_true(object_diff(x, xx) == '') # no assert_equal, ugly output
# bad title
assert_raises(ValueError, read_hdf5, test_file, title='nonexist')
assert_raises(ValueError,
write_hdf5,
test_file,
x,
overwrite=True,
title=1)
assert_raises(ValueError, read_hdf5, test_file, title=1)
# unsupported objects
assert_raises(TypeError, write_hdf5, test_file, {1: 'foo'}, overwrite=True)
assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)
write_hdf5(test_file, 1, title='first', overwrite=True)
write_hdf5(test_file, 2, title='second', overwrite='update')
assert_equal(read_hdf5(test_file, title='first'), 1)
assert_equal(read_hdf5(test_file, title='second'), 2)
assert_raises(IOError, write_hdf5, test_file, 3, title='second')
write_hdf5(test_file, 3, title='second', overwrite='update')
assert_equal(read_hdf5(test_file, title='second'), 3)
write_hdf5(test_file, 5, title='second', overwrite='update', compression=5)
assert_equal(read_hdf5(test_file, title='second'), 5)
def test_hdf5_use_json():
"""Test HDF5 IO
"""
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
splash_dict = {'first/second': {'one/more': 'value'}}
pytest.raises(ValueError,
write_hdf5,
test_file,
splash_dict,
overwrite=True,
slash='error',
use_json=True)
spec_dict = {'first/second': 'third'}
write_hdf5(test_file,
spec_dict,
overwrite=True,
slash='replace',
use_json=True)
assert_equal(
read_hdf5(test_file, slash='replace').keys(), spec_dict.keys())
in_keys = list(read_hdf5(test_file, slash='ignore').keys())
assert ('{FWDSLASH}' in in_keys[0])
comp_dict = {'first': [1, 2], 'second': 'str', 'third': {'a': 1}}
write_hdf5(test_file, comp_dict, overwrite=True, use_json=True)
assert_equal(sorted(read_hdf5(test_file, slash='replace').keys()),
sorted(comp_dict.keys()))
numpy_dict = {'first': np.array([1])}
write_hdf5(test_file, numpy_dict, overwrite=True, use_json=True)
assert_equal(
list(read_hdf5(test_file, slash='replace').values())[0],
list(numpy_dict.values())[0])
pytest.raises(ValueError, read_hdf5, test_file, slash='brains')
# Testing that title slashes aren't replaced
write_hdf5(test_file,
spec_dict,
title='one/two',
overwrite=True,
slash='replace',
use_json=True)
assert_equal(
read_hdf5(test_file, title='one/two', slash='replace').keys(),
spec_dict.keys())
def test_hdf5():
"""Test HDF5 IO
"""
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csc')
df = np.eye(3) if isinstance(DataFrame, type(None)) else DataFrame(
np.eye(3))
sr = np.eye(3) if isinstance(Series, type(None)) else Series(
np.random.randn(3))
sp[2, 2] = 2
x = dict(a=dict(b=np.zeros(3)), c=np.zeros(2, np.complex128),
d=[dict(e=(1, -2., 'hello', u'goodbyeu\u2764')), None], f=sp,
g=dict(dfa=df, srb=sr))
write_hdf5(test_file, 1)
assert_equal(read_hdf5(test_file), 1)
assert_raises(IOError, write_hdf5, test_file, x) # file exists
write_hdf5(test_file, x, overwrite=True)
assert_raises(IOError, read_hdf5, test_file + 'FOO') # not found
xx = read_hdf5(test_file)
assert_true(object_diff(x, xx) == '') # no assert_equal, ugly output
# bad title
assert_raises(ValueError, read_hdf5, test_file, title='nonexist')
assert_raises(ValueError, write_hdf5, test_file, x, overwrite=True,
title=1)
assert_raises(ValueError, read_hdf5, test_file, title=1)
# unsupported objects
assert_raises(TypeError, write_hdf5, test_file, {1: 'foo'},
overwrite=True)
assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)
write_hdf5(test_file, 1, title='first', overwrite=True)
write_hdf5(test_file, 2, title='second', overwrite='update')
assert_equal(read_hdf5(test_file, title='first'), 1)
assert_equal(read_hdf5(test_file, title='second'), 2)
assert_raises(IOError, write_hdf5, test_file, 3, title='second')
write_hdf5(test_file, 3, title='second', overwrite='update')
assert_equal(read_hdf5(test_file, title='second'), 3)
write_hdf5(test_file, 5, title='second', overwrite='update', compression=5)
assert_equal(read_hdf5(test_file, title='second'), 5)
def test_hdf5():
"""Test HDF5 IO
"""
tempdir = _TempDir()
test_file = op.join(tempdir, 'test.hdf5')
sp = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csc')
sp_csr = np.eye(3) if sparse is None else sparse.eye(3, 3, format='csr')
df = np.eye(3) if isinstance(DataFrame, type(None)) else DataFrame(
np.eye(3))
sr = np.eye(3) if isinstance(Series, type(None)) else Series(
np.random.randn(3))
sp[2, 2] = 2
sp_csr[2, 2] = 2
x = dict(a=dict(b=np.zeros(3)), c=np.zeros(2, np.complex128),
d=[dict(e=(1, -2., 'hello', u'goodbyeu\u2764')), None], f=sp,
g=dict(dfa=df, srb=sr), h=sp_csr, i=sr, j='hi')
write_hdf5(test_file, 1)
assert_equal(read_hdf5(test_file), 1)
assert_raises(IOError, write_hdf5, test_file, x) # file exists
write_hdf5(test_file, x, overwrite=True)
assert_raises(IOError, read_hdf5, test_file + 'FOO') # not found
xx = read_hdf5(test_file)
assert_true(object_diff(x, xx) == '') # no assert_equal, ugly output
list_file_contents(test_file) # Testing the h5 listing
assert_raises(TypeError, list_file_contents, sp) # Only string works
write_hdf5(test_file, np.bool_(True), overwrite=True)
assert_equal(read_hdf5(test_file), np.bool_(True))
# bad title
assert_raises(ValueError, read_hdf5, test_file, title='nonexist')
assert_raises(ValueError, write_hdf5, test_file, x, overwrite=True,
title=1)
assert_raises(ValueError, read_hdf5, test_file, title=1)
# unsupported objects
assert_raises(TypeError, write_hdf5, test_file, {1: 'foo'},
overwrite=True)
assert_raises(TypeError, write_hdf5, test_file, object, overwrite=True)
# special_chars
spec_dict = {'first/second': 'third'}
assert_raises(ValueError, write_hdf5, test_file, spec_dict, overwrite=True)
assert_raises(ValueError, write_hdf5, test_file, spec_dict, overwrite=True,
slash='brains')
write_hdf5(test_file, spec_dict, overwrite=True, slash='replace')
assert_equal(
read_hdf5(test_file, slash='replace').keys(), spec_dict.keys())
in_keys = list(read_hdf5(test_file, slash='ignore').keys())
assert_true('{FWDSLASH}' in in_keys[0])
assert_raises(ValueError, read_hdf5, test_file, slash='brains')
# Testing that title slashes aren't replaced
write_hdf5(
test_file, spec_dict, title='one/two', overwrite=True, slash='replace')
assert_equal(read_hdf5(test_file, title='one/two', slash='replace').keys(),
spec_dict.keys())
write_hdf5(test_file, 1, title='first', overwrite=True)
write_hdf5(test_file, 2, title='second', overwrite='update')
assert_equal(read_hdf5(test_file, title='first'), 1)
assert_equal(read_hdf5(test_file, title='second'), 2)
assert_raises(IOError, write_hdf5, test_file, 3, title='second')
write_hdf5(test_file, 3, title='second', overwrite='update')
assert_equal(read_hdf5(test_file, title='second'), 3)
write_hdf5(test_file, 5, title='second', overwrite='update', compression=5)
assert_equal(read_hdf5(test_file, title='second'), 5)