larray/larray/tests/test_group.py at 11a1c6f78d4162906622edecffe13926275bb73e · alixdamman/larray

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# -*- coding: utf8 -*-

from __future__ import absolute_import, division, print_function

import pytest

import os.path

import numpy as np

from larray.tests.common import assert_array_equal

from larray import Axis, IGroup, LGroup, LSet, ndtest, read_hdf

from larray.util.oset import OrderedSet

age = Axis('age=0..10')

lipro = Axis('lipro=P01..P05')

anonymous = Axis(range(3))

age_wildcard = Axis(10, 'wildcard')

def test_equals():

a = Axis('a=a0..a2')

# keys are single value

assert a['a0'].equals(a['a0'])

# keys are arrays

assert a[np.array(['a0', 'a2'])].equals(a[np.array(['a0', 'a2'])])

# axis names

anonymous_axis = Axis('a0..a2')

assert anonymous_axis['a0:a2'].equals(anonymous_axis['a0:a2'])

assert not a['a0:a2'].equals(anonymous_axis['a0:a2'])

assert not a['a0:a2'].equals(a.rename('other_name')['a0:a2'])

# list of labels

a02 = a['a0,a1,a2'] >> 'group'

assert a02.equals(a02)

a02_unamed = a['a0,a1,a2']

assert not a02.equals(a02_unamed)

a13 = a['a1,a2,a3'] >> 'group'

assert not a02.equals(a13)

a02_other_axis_name = a.rename('other_name')['a0,a1,a2'] >> 'group'

assert not a02.equals(a02_other_axis_name)

# ################## #

# LGroup #

# ################## #

@pytest.fixture

def lgroups():

class TestLGroup():

def __init__(self):

self.slice_both_named_wh_named_axis = LGroup('1:5', "full", age)

self.slice_both_named = LGroup('1:5', "named")

self.slice_both = LGroup('1:5')

self.slice_start = LGroup('1:')

self.slice_stop = LGroup(':5')

self.slice_none_no_axis = LGroup(':')

self.slice_none_wh_named_axis = LGroup(':', axis=lipro)

self.slice_none_wh_anonymous_axis = LGroup(':', axis=anonymous)

self.single_value = LGroup('P03')

self.list = LGroup('P01,P03,P04')

self.list_named = LGroup('P01,P03,P04', "P134")

return TestLGroup()

def test_init_lgroup(lgroups):

assert lgroups.slice_both_named_wh_named_axis.name == "full"

assert lgroups.slice_both_named_wh_named_axis.key == slice(1, 5, None)

assert lgroups.slice_both_named_wh_named_axis.axis is age

assert lgroups.slice_both_named.name == "named"

assert lgroups.slice_both_named.key == slice(1, 5, None)

assert lgroups.slice_both.key == slice(1, 5, None)

assert lgroups.slice_start.key == slice(1, None, None)

assert lgroups.slice_stop.key == slice(None, 5, None)

assert lgroups.slice_none_no_axis.key == slice(None, None, None)

assert lgroups.slice_none_wh_named_axis.axis is lipro

assert lgroups.slice_none_wh_anonymous_axis.axis is anonymous

assert lgroups.single_value.key == 'P03'

assert lgroups.list.key == ['P01', 'P03', 'P04']

group = LGroup('1:5', age, age)

assert group.name == age.name

group = age['1:5'] >> age

assert group.name == age.name

group2 = LGroup('1', axis=age)

group = LGroup('1', group2, axis=age)

assert group.name == '1'

group = age['1'] >> group2

assert group.name == '1'

group2 = LGroup('1:5', 'age', age)

group = LGroup('1:5', group2, axis=age)

assert group.name == group2.name

group = age['1:5'] >> group2

assert group.name == group2.name

axis = Axis('axis=a,a0..a3,b,b0..b3,c,c0..c3')

for code in axis.matching(regex='^.$'):

group = axis.startingwith(code) >> code

assert group.equals(axis.startingwith(code) >> str(code))

def test_eq_lgroup(lgroups):

# with axis vs no axis do not compare equal

# lgroups.slice_both == lgroups.slice_both_named_wh_named_axis

assert lgroups.slice_both == lgroups.slice_both_named

res = lgroups.slice_both_named_wh_named_axis == age[1:5]

assert isinstance(res, np.ndarray)

assert res.shape == (5,)

assert res.all()

assert lgroups.slice_both == LGroup(slice(1, 5))

assert lgroups.slice_start == LGroup(slice(1, None))

assert lgroups.slice_stop == LGroup(slice(5))

assert lgroups.slice_none_no_axis == LGroup(slice(None))

assert lgroups.single_value == LGroup('P03')

assert lgroups.list == LGroup(['P01', 'P03', 'P04'])

assert lgroups.list_named == LGroup(['P01', 'P03', 'P04'])

assert lgroups.slice_both == slice(1, 5)

assert lgroups.slice_start == slice(1, None)

assert lgroups.slice_stop == slice(5)

assert lgroups.slice_none_no_axis == slice(None)

assert lgroups.single_value == 'P03'

assert lgroups.list == ['P01', 'P03', 'P04']

assert lgroups.list_named == ['P01', 'P03', 'P04']

def test_getitem_lgroup():

axis = Axis("a=a0,a1")

assert axis['a0'][0] == 'a'

assert axis['a0'][1] == '0'

assert axis['a0':'a1'][1] == 'a1'

assert axis[:][1] == 'a1'

assert list(axis[:][0:2]) == ['a0', 'a1']

assert list((axis[:][[1, 0]])) == ['a1', 'a0']

assert axis[['a0', 'a1', 'a0']][2] == 'a0'

assert axis[('a0', 'a1', 'a0')][2] == 'a0'

assert axis[ndtest("a=a0,a1,a0")][2] == 2

def test_sorted_lgroup():

assert sorted(LGroup(['c', 'd', 'a', 'b'])) == [LGroup('a'), LGroup('b'), LGroup('c'), LGroup('d')]

def test_asarray_lgroup(lgroups):

assert_array_equal(np.asarray(lgroups.slice_both_named_wh_named_axis), np.array([1, 2, 3, 4, 5]))

assert_array_equal(np.asarray(lgroups.slice_none_wh_named_axis), np.array(['P01', 'P02', 'P03', 'P04', 'P05']))

def test_hash_lgroup(lgroups):

# this test is a lot less important than what it used to, because we cannot have Group ticks on an axis anymore

d = {lgroups.slice_both: 1, lgroups.single_value: 2, lgroups.list_named: 3}

assert d.get(lgroups.slice_both) == 1

assert d.get(lgroups.single_value) == 2

assert d.get(lgroups.list) == 3

assert d.get(lgroups.list_named) == 3

def test_repr_lgroup(lgroups):

assert repr(lgroups.slice_both_named_wh_named_axis) == "age[1:5] >> 'full'"

assert repr(lgroups.slice_both_named) == "LGroup(slice(1, 5, None)) >> 'named'"

assert repr(lgroups.slice_both) == "LGroup(slice(1, 5, None))"

assert repr(lgroups.list) == "LGroup(['P01', 'P03', 'P04'])"

assert repr(lgroups.slice_none_no_axis) == "LGroup(slice(None, None, None))"

assert repr(lgroups.slice_none_wh_named_axis) == "lipro[:]"

assert repr(lgroups.slice_none_wh_anonymous_axis) == "LGroup(slice(None, None, None), axis=Axis([0, 1, 2], None))"

def test_to_int_lgroup():

a = Axis(['42'], 'a')

assert int(a['42']) == 42

def test_to_float_lgroup():

a = Axis(['42'], 'a')

assert float(a['42']) == 42.0

def test_to_lset_lgroup():

alpha = Axis('alpha=a,b,c,d')

# list key

lg = LGroup(['a', 'a', 'c'], axis=alpha)

res = lg.set()

assert isinstance(res, LSet)

assert res.axis is alpha

assert res.key == OrderedSet(['a', 'c'])

# scalar key

lg = LGroup('c', axis=alpha)

res = lg.set()

assert isinstance(res, LSet)

assert res.axis is alpha

assert res.key == OrderedSet(['c'])

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)

# ################## #

# LSet #

# ################## #

def test_or_lset():

# without axis

assert LSet(['a', 'b']) | LSet(['c', 'd']) == LSet(['a', 'b', 'c', 'd'])

assert LSet(['a', 'b', 'c']) | LSet(['c', 'd']) == LSet(['a', 'b', 'c', 'd'])

alpha = Axis('alpha=a,b,c,d')

res = alpha['a', 'b'].set() | alpha['c', 'd'].set()

assert res.axis is alpha

assert res == alpha['a', 'b', 'c', 'd'].set()

assert alpha['a', 'b', 'c'].set() | alpha['c', 'd'].set() == alpha['a', 'b', 'c', 'd'].set()

alpha = Axis('alpha=a,b,c,d')

res = alpha['a', 'b'].set() | alpha['c', 'd']

assert res.axis is alpha

assert res == alpha['a', 'b', 'c', 'd'].set()

assert alpha['a', 'b', 'c'].set() | alpha['c', 'd'] == alpha['a', 'b', 'c', 'd'].set()

alpha = Axis('alpha=a,b,c,d')

res = alpha['a', 'b'].set().named('ab') | alpha['c', 'd'].set().named('cd')

assert res.axis is alpha

assert res.name == 'ab | cd'

assert res == alpha['a', 'b', 'c', 'd'].set()

assert alpha['a', 'b', 'c'].set() | alpha['c', 'd'] == alpha['a', 'b', 'c', 'd'].set()

num = Axis(range(10), 'num')

assert num[1, 5, 3].set() | 4 == num[1, 5, 3, 4].set()

assert num[1, 5, 3].set() | num[4] == num[1, 5, 3, 4].set()

assert num[4].set() | num[1, 5, 3] == num[4, 1, 5, 3].set()

assert num[:2].set() | num[8:] == num[0, 1, 2, 8, 9].set()

assert num[:2].set() | num[5] == num[0, 1, 2, 5].set()

def test_and_lset():

# without axis

assert LSet(['a', 'b', 'c']) & LSet(['c', 'd']) == LSet(['c'])

alpha = Axis('alpha=a,b,c,d')

res = alpha['a', 'b', 'c'].named('abc').set() & alpha['c', 'd'].named('cd')

assert res.axis is alpha

assert res.name == 'abc & cd'

assert res == alpha[['c']].set()

def test_sub_lset():

assert LSet(['a', 'b', 'c']) - LSet(['c', 'd']) == LSet(['a', 'b'])

assert LSet(['a', 'b', 'c']) - ['c', 'd'] == LSet(['a', 'b'])

assert LSet(['a', 'b', 'c']) - 'b' == LSet(['a', 'c'])

assert LSet([1, 2, 3]) - 4 == LSet([1, 2, 3])

assert LSet([1, 2, 3]) - 2 == LSet([1, 3])

# ################## #

# IGroup #

# ################## #

@pytest.fixture

def igroups():

class TestIGroup():

def __init__(self):

self.code_axis = Axis('code=a0..a4')

self.slice_both_named = self.code_axis.i[1:4] >> 'a123'

self.slice_both = self.code_axis.i[1:4]

self.slice_start = self.code_axis.i[1:]

self.slice_stop = self.code_axis.i[:4]

self.slice_none = self.code_axis.i[:]

self.first_value = self.code_axis.i[0]

self.last_value = self.code_axis.i[-1]

self.list = self.code_axis.i[[0, 1, -2, -1]]

self.tuple = self.code_axis.i[0, 1, -2, -1]

return TestIGroup()

def _assert_array_equal_is_true_array(a, b):

res = a == b

assert isinstance(res, np.ndarray)

assert res.shape == np.asarray(b).shape

assert res.all()

def test_asarray_igroup(igroups):

assert_array_equal(np.asarray(igroups.slice_both), np.array(['a1', 'a2', 'a3']))

def test_eq_igroup(igroups):

_assert_array_equal_is_true_array(igroups.slice_both, ['a1', 'a2', 'a3'])

_assert_array_equal_is_true_array(igroups.slice_both_named, ['a1', 'a2', 'a3'])

_assert_array_equal_is_true_array(igroups.slice_both, igroups.slice_both_named)

_assert_array_equal_is_true_array(igroups.slice_both_named, igroups.slice_both)

_assert_array_equal_is_true_array(igroups.slice_start, ['a1', 'a2', 'a3', 'a4'])

_assert_array_equal_is_true_array(igroups.slice_stop, ['a0', 'a1', 'a2', 'a3'])

_assert_array_equal_is_true_array(igroups.slice_none, ['a0', 'a1', 'a2', 'a3', 'a4'])

assert igroups.first_value == 'a0'

assert igroups.last_value == 'a4'

_assert_array_equal_is_true_array(igroups.list, ['a0', 'a1', 'a3', 'a4'])

_assert_array_equal_is_true_array(igroups.tuple, ['a0', 'a1', 'a3', 'a4'])

def test_getitem_igroup():

axis = Axis("a=a0,a1")

assert axis.i[0][0] == 'a'

assert axis.i[0][1] == '0'

assert axis.i[0:1][1] == 'a1'

assert axis.i[:][1] == 'a1'

assert list(axis.i[:][0:2]) == ['a0', 'a1']

assert list((axis.i[:][[1, 0]])) == ['a1', 'a0']

assert axis.i[[0, 1, 0]][2] == 'a0'

assert axis.i[(0, 1, 0)][2] == 'a0'

def test_getattr_igroup():

agg = Axis(['a1:a2', ':a2', 'a1:'], 'agg')

assert agg.i[0].split(':') == ['a1', 'a2']

assert agg.i[1].split(':') == ['', 'a2']

assert agg.i[2].split(':') == ['a1', '']

def test_dir_igroup():

agg = Axis(['a', 1], 'agg')

assert 'split' in dir(agg.i[0])

assert 'strip' in dir(agg.i[0])

def test_repr_igroup(igroups):

assert repr(igroups.slice_both_named) == "code.i[1:4] >> 'a123'"

assert repr(igroups.slice_both) == "code.i[1:4]"

assert repr(igroups.slice_start) == "code.i[1:]"

assert repr(igroups.slice_stop) == "code.i[:4]"

assert repr(igroups.slice_none) == "code.i[:]"

assert repr(igroups.first_value) == "code.i[0]"

assert repr(igroups.last_value) == "code.i[-1]"

assert repr(igroups.list) == "code.i[0, 1, -2, -1]"

assert repr(igroups.tuple) == "code.i[0, 1, -2, -1]"

def test_to_int_igroup():

a = Axis(['42'], 'a')

assert int(a.i[0]) == 42

def test_to_float_igroup():

a = Axis(['42'], 'a')

assert float(a.i[0]) == 42.0

def test_to_lset_igroup():

alpha = Axis('alpha=a,b,c,d')

# list key

ig = IGroup([0, 0, 2], axis=alpha)

res = ig.set()

assert isinstance(res, LSet)

assert res.axis is alpha

assert res.key == OrderedSet(['a', 'c'])

# scalar key

ig = IGroup(2, axis=alpha)

res = ig.set()

assert isinstance(res, LSet)

assert res.axis is alpha

assert res.key == OrderedSet(['c'])

def test_h5_io_igroup(tmpdir):

fpath = os.path.join(str(tmpdir), 'igroups.h5')

age.to_hdf(fpath)

named = age.i[:6] >> 'age_05'

named_axis_not_in_file = lipro.i[1::2] >> 'P_odd'

anonymous = age.i[:6]

wildcard = age_wildcard.i[:6] >> 'age_w_05'

# ---- 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)

# ---- 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)

if __name__ == "__main__":

pytest.main()

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