def test_h5_io_lgroup(tmpdir):
fpath = os.path.join(str(tmpdir), 'lgroups.h5')
age.to_hdf(fpath)
named = age[':5'] >> 'age_05'
named_axis_not_in_file = lipro['P01,P03,P05'] >> 'P_odd'
anonymous = age[':5']
wildcard = age_wildcard[':5'] >> 'age_w_05'
string_group = Axis(['@!àéè&%µ$~', '/*-+_§()><', 'another label'],
'string_axis')[:] >> 'string_group'
# ---- default behavior ----
# named group
named.to_hdf(fpath)
named2 = read_hdf(fpath, key=named.name)
assert all(named == named2)
# anonymous group
with pytest.raises(
ValueError,
match=
"Argument key must be provided explicitly in case of anonymous group"
):
anonymous.to_hdf(fpath)
# wildcard group
wildcard.to_hdf(fpath)
wildcard2 = read_hdf(fpath, key=wildcard.name)
assert all(wildcard == wildcard2)
# associated axis not saved yet
named_axis_not_in_file.to_hdf(fpath)
named2 = read_hdf(fpath, key=named_axis_not_in_file.name)
assert all(named_axis_not_in_file == named2)
# string group
string_group.to_hdf(fpath)
string_group2 = read_hdf(fpath, key=string_group.name)
assert all(string_group == string_group2)
# ---- specific hdf group + key ----
hdf_group = 'my_groups'
# named group
key = hdf_group + '/named_group'
named.to_hdf(fpath, key)
named2 = read_hdf(fpath, key=key)
assert all(named == named2)
# anonymous group
key = hdf_group + '/anonymous_group'
anonymous.to_hdf(fpath, key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert all(anonymous == anonymous2)
# wildcard group
key = hdf_group + '/wildcard_group'
wildcard.to_hdf(fpath, key)
wildcard2 = read_hdf(fpath, key=key)
assert all(wildcard == wildcard2)
# associated axis not saved yet
key = hdf_group + '/named_group_axis_not_in_file'
named_axis_not_in_file.to_hdf(fpath, key=key)
named2 = read_hdf(fpath, key=key)
assert all(named_axis_not_in_file == named2)
# ---- specific axis_key ----
axis_key = 'axes/associated_axis_0'
# named group
named.to_hdf(fpath, axis_key=axis_key)
named2 = read_hdf(fpath, key=named.name)
assert all(named == named2)
# anonymous group
key = 'anonymous'
anonymous.to_hdf(fpath, key=key, axis_key=axis_key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert all(anonymous == anonymous2)
# wildcard group
wildcard.to_hdf(fpath, axis_key=axis_key)
wildcard2 = read_hdf(fpath, key=wildcard.name)
assert all(wildcard == wildcard2)
# associated axis not saved yet
axis_key = 'axes/associated_axis_1'
named_axis_not_in_file.to_hdf(fpath, axis_key=axis_key)
named2 = read_hdf(fpath, key=named_axis_not_in_file.name)
assert all(named_axis_not_in_file == named2)
def test_h5_io(tmpdir):
age = Axis('age=0..10')
lipro = Axis('lipro=P01..P05')
anonymous = Axis(range(3))
wildcard = Axis(3, 'wildcard')
string_axis = Axis(['@!àéè&%µ$~', '/*-+_§()><', 'another label'],
'string_axis')
fpath = os.path.join(str(tmpdir), 'axes.h5')
# ---- default behavior ----
# int axis
age.to_hdf(fpath)
age2 = read_hdf(fpath, key=age.name)
assert age.equals(age2)
# string axis
lipro.to_hdf(fpath)
lipro2 = read_hdf(fpath, key=lipro.name)
assert lipro.equals(lipro2)
# anonymous axis
with pytest.raises(
ValueError,
match=
"Argument key must be provided explicitly in case of anonymous axis"
):
anonymous.to_hdf(fpath)
# wildcard axis
wildcard.to_hdf(fpath)
wildcard2 = read_hdf(fpath, key=wildcard.name)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
# string axis
string_axis.to_hdf(fpath)
string_axis2 = read_hdf(fpath, string_axis.name)
assert string_axis.equals(string_axis2)
# ---- specific key ----
# int axis
key = 'axis_age'
age.to_hdf(fpath, key)
age2 = read_hdf(fpath, key=key)
assert age.equals(age2)
# string axis
key = 'axis_lipro'
lipro.to_hdf(fpath, key)
lipro2 = read_hdf(fpath, key=key)
assert lipro.equals(lipro2)
# anonymous axis
key = 'axis_anonymous'
anonymous.to_hdf(fpath, key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert_array_equal(anonymous.labels, anonymous2.labels)
# wildcard axis
key = 'axis_wildcard'
wildcard.to_hdf(fpath, key)
wildcard2 = read_hdf(fpath, key=key)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
# ---- specific hdf group + key ----
hdf_group = 'my_axes'
# int axis
key = hdf_group + '/axis_age'
age.to_hdf(fpath, key)
age2 = read_hdf(fpath, key=key)
assert age.equals(age2)
# string axis
key = hdf_group + '/axis_lipro'
lipro.to_hdf(fpath, key)
lipro2 = read_hdf(fpath, key=key)
assert lipro.equals(lipro2)
# anonymous axis
key = hdf_group + '/axis_anonymous'
anonymous.to_hdf(fpath, key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert_array_equal(anonymous.labels, anonymous2.labels)
# wildcard axis
key = hdf_group + '/axis_wildcard'
wildcard.to_hdf(fpath, key)
wildcard2 = read_hdf(fpath, key=key)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
def test_h5_io(tmpdir):
age = Axis('age=0..10')
lipro = Axis('lipro=P01..P05')
anonymous = Axis(range(3))
wildcard = Axis(3, 'wildcard')
fpath = os.path.join(str(tmpdir), 'axes.h5')
# ---- default behavior ----
# int axis
age.to_hdf(fpath)
age2 = read_hdf(fpath, key=age.name)
assert age.equals(age2)
# string axis
lipro.to_hdf(fpath)
lipro2 = read_hdf(fpath, key=lipro.name)
assert lipro.equals(lipro2)
# anonymous axis
with pytest.raises(ValueError, message="Argument key must be provided explicitly in case of anonymous axis"):
anonymous.to_hdf(fpath)
# wildcard axis
wildcard.to_hdf(fpath)
wildcard2 = read_hdf(fpath, key=wildcard.name)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
# ---- specific key ----
# int axis
key = 'axis_age'
age.to_hdf(fpath, key)
age2 = read_hdf(fpath, key=key)
assert age.equals(age2)
# string axis
key = 'axis_lipro'
lipro.to_hdf(fpath, key)
lipro2 = read_hdf(fpath, key=key)
assert lipro.equals(lipro2)
# anonymous axis
key = 'axis_anonymous'
anonymous.to_hdf(fpath, key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert_array_equal(anonymous.labels, anonymous2.labels)
# wildcard axis
key = 'axis_wildcard'
wildcard.to_hdf(fpath, key)
wildcard2 = read_hdf(fpath, key=key)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)
# ---- specific hdf group + key ----
hdf_group = 'my_axes'
# int axis
key = hdf_group + '/axis_age'
age.to_hdf(fpath, key)
age2 = read_hdf(fpath, key=key)
assert age.equals(age2)
# string axis
key = hdf_group + '/axis_lipro'
lipro.to_hdf(fpath, key)
lipro2 = read_hdf(fpath, key=key)
assert lipro.equals(lipro2)
# anonymous axis
key = hdf_group + '/axis_anonymous'
anonymous.to_hdf(fpath, key)
anonymous2 = read_hdf(fpath, key=key)
assert anonymous2.name is None
assert_array_equal(anonymous.labels, anonymous2.labels)
# wildcard axis
key = hdf_group + '/axis_wildcard'
wildcard.to_hdf(fpath, key)
wildcard2 = read_hdf(fpath, key=key)
assert wildcard2.iswildcard
assert wildcard.equals(wildcard2)