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Copy pathtest_axis.py
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881 lines (763 loc) · 30.6 KB
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from __future__ import absolute_import, division, print_function
from unittest import TestCase
import pytest
import numpy as np
from larray.tests.common import assert_array_equal
from larray import Axis, AxisCollection, LGroup, IGroup
class TestAxis(TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_init(self):
sex_tuple = ('M', 'F')
sex_list = ['M', 'F']
sex_array = np.array(sex_list)
# wildcard axis
axis = Axis(10, 'axis')
assert len(axis) == 10
assert list(axis.labels) == list(range(10))
# tuple of strings
assert_array_equal(Axis(sex_tuple, 'sex').labels, sex_array)
# list of strings
assert_array_equal(Axis(sex_list, 'sex').labels, sex_array)
# array of strings
assert_array_equal(Axis(sex_array, 'sex').labels, sex_array)
# single string
assert_array_equal(Axis('sex=M,F').labels, sex_array)
# list of ints
assert_array_equal(Axis(range(116), 'age').labels, np.arange(116))
# range-string
axis = Axis('0..115', 'age')
assert_array_equal(axis.labels, np.arange(116))
# int-like labels with 0 padding
assert_array_equal(Axis('01..12', 'zero_padding').labels, [str(i).zfill(2) for i in range(1, 13)])
assert_array_equal(Axis('01,02,03,10,11,12', 'zero_padding').labels, ['01', '02', '03', '10', '11', '12'])
# another axis group
group = axis[:10]
group_axis = Axis(group)
assert_array_equal(group_axis.labels, np.arange(11))
assert_array_equal(group_axis.name, 'age')
# another axis as labels argument
other = Axis('other=0..10')
axis = Axis(other, 'age')
assert_array_equal(axis.labels, other.labels)
assert_array_equal(axis.name, 'age')
def test_equals(self):
self.assertTrue(Axis('sex=M,F').equals(Axis('sex=M,F')))
self.assertTrue(Axis('sex=M,F').equals(Axis(['M', 'F'], 'sex')))
self.assertFalse(Axis('sex=M,W').equals(Axis('sex=M,F')))
self.assertFalse(Axis('sex1=M,F').equals(Axis('sex2=M,F')))
self.assertFalse(Axis('sex1=M,W').equals(Axis('sex2=M,F')))
def test_getitem(self):
age = Axis('age=0..10')
# a tuple
a159 = age[1, 5, 9]
self.assertEqual(a159.key, [1, 5, 9])
self.assertIs(a159.name, None)
self.assertIs(a159.axis, age)
# a normal list
a159 = age[[1, 5, 9]]
self.assertEqual(a159.key, [1, 5, 9])
self.assertIs(a159.name, None)
self.assertIs(a159.axis, age)
# a string list
a159 = age['1,5,9']
self.assertEqual(a159.key, [1, 5, 9])
self.assertIs(a159.name, None)
self.assertIs(a159.axis, age)
# a normal slice
a10to20 = age[5:9]
self.assertEqual(a10to20.key, slice(5, 9))
self.assertIs(a10to20.axis, age)
# a string slice
a10to20 = age['5:9']
self.assertEqual(a10to20.key, slice(5, 9))
self.assertIs(a10to20.axis, age)
# with name
group = age[[1, 5, 9]] >> 'test'
self.assertEqual(group.key, [1, 5, 9])
self.assertEqual(group.name, 'test')
self.assertIs(group.axis, age)
# all
group = age[:] >> 'all'
self.assertEqual(group.key, slice(None))
self.assertIs(group.axis, age)
# an axis
age2 = Axis('age=0..5')
group = age[age2]
assert list(group.key) == list(age2.labels)
def test_translate(self):
# an axis with labels having the object dtype
a = Axis(np.array(["a0", "a1"], dtype=object), 'a')
self.assertEqual(a.index('a1'), 1)
self.assertEqual(a.index('a1 >> A1'), 1)
def test_getitem_lgroup_keys(self):
def group_equal(g1, g2):
return (g1.key == g2.key and g1.name == g2.name and
g1.axis is g2.axis)
age = Axis(range(100), 'age')
ages = [1, 5, 9]
val_only = LGroup(ages)
self.assertTrue(group_equal(age[val_only], LGroup(ages, axis=age)))
self.assertTrue(group_equal(age[val_only] >> 'a_name', LGroup(ages, 'a_name', axis=age)))
val_name = LGroup(ages, 'val_name')
self.assertTrue(group_equal(age[val_name], LGroup(ages, 'val_name', age)))
self.assertTrue(group_equal(age[val_name] >> 'a_name', LGroup(ages, 'a_name', age)))
val_axis = LGroup(ages, axis=age)
self.assertTrue(group_equal(age[val_axis], LGroup(ages, axis=age)))
self.assertTrue(group_equal(age[val_axis] >> 'a_name', LGroup(ages, 'a_name', axis=age)))
val_axis_name = LGroup(ages, 'val_axis_name', age)
self.assertTrue(group_equal(age[val_axis_name], LGroup(ages, 'val_axis_name', age)))
self.assertTrue(group_equal(age[val_axis_name] >> 'a_name', LGroup(ages, 'a_name', age)))
def test_getitem_group_keys(self):
a = Axis('a=a0..a2')
alt_a = Axis('a=a1..a3')
# a) key is a single LGroup
# -------------------------
# a.1) containing a scalar
key = a['a1']
# use it on the same axis
g = a[key]
self.assertEqual(g.key, 'a1')
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertEqual(g.key, 'a1')
self.assertIs(g.axis, alt_a)
# a.2) containing a slice
key = a['a1':'a2']
# use it on the same axis
g = a[key]
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, alt_a)
# a.3) containing a list
key = a[['a1', 'a2']]
# use it on the same axis
g = a[key]
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, alt_a)
# b) key is a single IGroup
# -------------------------
# b.1) containing a scalar
key = a.i[1]
# use it on the same axis
g = a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, 'a1')
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, 'a1')
self.assertIs(g.axis, alt_a)
# b.2) containing a slice
key = a.i[1:3]
# use it on the same axis
g = a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, alt_a)
# b.3) containing a list
key = a.i[[1, 2]]
# use it on the same axis
g = a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(list(g.key), ['a1', 'a2'])
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(list(g.key), ['a1', 'a2'])
self.assertIs(g.axis, alt_a)
# c) key is a slice
# -----------------
# c.1) with LGroup bounds
lg_a1 = a['a1']
lg_a2 = a['a2']
# use it on the same axis
g = a[lg_a1:lg_a2]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[lg_a1:lg_a2]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, alt_a)
# c.2) with IGroup bounds
pg_a1 = a.i[1]
pg_a2 = a.i[2]
# use it on the same axis
g = a[pg_a1:pg_a2]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[pg_a1:pg_a2]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, slice('a1', 'a2'))
self.assertIs(g.axis, alt_a)
# d) key is a list of scalar groups => create a single LGroup
# ---------------------------------
# d.1) with LGroup
key = [a['a1'], a['a2']]
# use it on the same axis
g = a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, alt_a)
# d.2) with IGroup
key = [a.i[1], a.i[2]]
# use it on the same axis
g = a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, alt_a)
# e) key is a list of non-scalar groups => retarget multiple groups to axis
# -------------------------------------
# e.1) with LGroup
key = [a['a1', 'a2'], a['a2', 'a1']]
# use it on the same axis => nothing happens
g = a[key]
self.assertIsInstance(g, list)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(g[0].key, ['a1', 'a2'])
self.assertEqual(g[1].key, ['a2', 'a1'])
self.assertIs(g[0].axis, a)
self.assertIs(g[1].axis, a)
# use it on a different axis => change axis
g = alt_a[key]
self.assertIsInstance(g, list)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(g[0].key, ['a1', 'a2'])
self.assertEqual(g[1].key, ['a2', 'a1'])
self.assertIs(g[0].axis, alt_a)
self.assertIs(g[1].axis, alt_a)
# e.2) with IGroup
key = (a.i[1, 2], a.i[2, 1])
# use it on the same axis => change to LGroup
g = a[key]
self.assertIsInstance(g, tuple)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(list(g[0].key), ['a1', 'a2'])
self.assertEqual(list(g[1].key), ['a2', 'a1'])
self.assertIs(g[0].axis, a)
self.assertIs(g[1].axis, a)
# use it on a different axis => retarget to axis
g = alt_a[key]
self.assertIsInstance(g, tuple)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(list(g[0].key), ['a1', 'a2'])
self.assertEqual(list(g[1].key), ['a2', 'a1'])
self.assertIs(g[0].axis, alt_a)
self.assertIs(g[1].axis, alt_a)
# f) key is a tuple of scalar groups => create a single LGroup
# ----------------------------------
# f.1) with LGroups
key = (a['a1'], a['a2'])
# use it on the same axis
g = a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, alt_a)
# f.2) with IGroup
key = (a.i[1], a.i[2])
# use it on the same axis
g = a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, LGroup)
self.assertEqual(g.key, ['a1', 'a2'])
self.assertIs(g.axis, alt_a)
# g) key is a tuple of non-scalar groups => retarget multiple groups to axis
# --------------------------------------
# g.1) with LGroups
key = (a['a1', 'a2'], a['a2', 'a1'])
# use it on the same axis
g = a[key]
self.assertIsInstance(g, tuple)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(g[0].key, ['a1', 'a2'])
self.assertEqual(g[1].key, ['a2', 'a1'])
self.assertIs(g[0].axis, a)
self.assertIs(g[1].axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, tuple)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(g[0].key, ['a1', 'a2'])
self.assertEqual(g[1].key, ['a2', 'a1'])
self.assertIs(g[0].axis, alt_a)
self.assertIs(g[1].axis, alt_a)
# g.2) with IGroup
key = (a.i[1, 2], a.i[2, 1])
# use it on the same axis
g = a[key]
self.assertIsInstance(g, tuple)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(list(g[0].key), ['a1', 'a2'])
self.assertEqual(list(g[1].key), ['a2', 'a1'])
self.assertIs(g[0].axis, a)
self.assertIs(g[1].axis, a)
# use it on a different axis
g = alt_a[key]
self.assertIsInstance(g, tuple)
self.assertIsInstance(g[0], LGroup)
self.assertIsInstance(g[1], LGroup)
self.assertEqual(list(g[0].key), ['a1', 'a2'])
self.assertEqual(list(g[1].key), ['a2', 'a1'])
self.assertIs(g[0].axis, alt_a)
self.assertIs(g[1].axis, alt_a)
def test_init_from_group(self):
code = Axis('code=C01..C03')
code_group = code[:'C02']
subset_axis = Axis(code_group, 'code_subset')
assert_array_equal(subset_axis.labels, ['C01', 'C02'])
def test_matching(self):
sutcode = Axis(['A23', 'A2301', 'A25', 'A2501'], 'sutcode')
self.assertEqual(sutcode.matching('^...$'), LGroup(['A23', 'A25']))
self.assertEqual(sutcode.startingwith('A23'), LGroup(['A23', 'A2301']))
self.assertEqual(sutcode.endingwith('01'), LGroup(['A2301', 'A2501']))
def test_iter(self):
sex = Axis('sex=M,F')
self.assertEqual(list(sex), [IGroup(0, axis=sex), IGroup(1, axis=sex)])
def test_positional(self):
age = Axis('age=0..115')
# these are NOT equivalent (not translated until used in an LArray
# self.assertEqual(age.i[:17], age[':17'])
key = age.i[:-1]
self.assertEqual(key.key, slice(None, -1))
self.assertIs(key.axis, age)
def test_contains(self):
# normal Axis
age = Axis('age=0..10')
age2 = age[2]
age2bis = age[(2,)]
age2ter = age[[2]]
age2qua = '2,'
age20 = LGroup('20')
age20bis = LGroup('20,')
age20ter = LGroup(['20'])
age20qua = '20,'
# TODO: move assert to another test
# self.assertEqual(age2bis, age2ter)
age247 = age['2,4,7']
age247bis = age[['2', '4', '7']]
age359 = age[['3', '5', '9']]
age468 = age['4,6,8'] >> 'even'
self.assertTrue(5 in age)
self.assertFalse('5' in age)
self.assertTrue(age2 in age)
# only single ticks are "contained" in the axis, not "collections"
self.assertFalse(age2bis in age)
self.assertFalse(age2ter in age)
self.assertFalse(age2qua in age)
self.assertFalse(age20 in age)
self.assertFalse(age20bis in age)
self.assertFalse(age20ter in age)
self.assertFalse(age20qua in age)
self.assertFalse(['3', '5', '9'] in age)
self.assertFalse('3,5,9' in age)
self.assertFalse('3:9' in age)
self.assertFalse(age247 in age)
self.assertFalse(age247bis in age)
self.assertFalse(age359 in age)
self.assertFalse(age468 in age)
# aggregated Axis
# FIXME: _to_tick(age2) == 2, but then np.asarray([2, '2,4,7', ...]) returns np.array(['2', '2,4,7'])
# instead of returning an object array
agg = Axis((age2, age247, age359, age468, '2,6', ['3', '5', '7'], ('6', '7', '9')), "agg")
# fails because of above FIXME
# self.assertTrue(age2 in agg)
self.assertFalse(age2bis in agg)
self.assertFalse(age2ter in agg)
self.assertFalse(age2qua in age)
self.assertTrue(age247 in agg)
self.assertTrue(age247bis in agg)
self.assertTrue('2,4,7' in agg)
self.assertTrue(['2', '4', '7'] in agg)
self.assertTrue(age359 in agg)
self.assertTrue('3,5,9' in agg)
self.assertTrue(['3', '5', '9'] in agg)
self.assertTrue(age468 in agg)
# no longer the case
# self.assertTrue('4,6,8' in agg)
# self.assertTrue(['4', '6', '8'] in agg)
self.assertTrue('even' in agg)
self.assertTrue('2,6' in agg)
self.assertTrue(['2', '6'] in agg)
self.assertTrue(age['2,6'] in agg)
self.assertTrue(age[['2', '6']] in agg)
self.assertTrue('3,5,7' in agg)
self.assertTrue(['3', '5', '7'] in agg)
self.assertTrue(age['3,5,7'] in agg)
self.assertTrue(age[['3', '5', '7']] in agg)
self.assertTrue('6,7,9' in agg)
self.assertTrue(['6', '7', '9'] in agg)
self.assertTrue(age['6,7,9'] in agg)
self.assertTrue(age[['6', '7', '9']] in agg)
self.assertFalse(5 in agg)
self.assertFalse('5' in agg)
self.assertFalse(age20 in agg)
self.assertFalse(age20bis in agg)
self.assertFalse(age20ter in agg)
self.assertFalse(age20qua in agg)
self.assertFalse('2,7' in agg)
self.assertFalse(['2', '7'] in agg)
self.assertFalse(age['2,7'] in agg)
self.assertFalse(age[['2', '7']] in agg)
class TestAxisCollection(TestCase):
def setUp(self):
self.lipro = Axis('lipro=P01..P04')
self.sex = Axis('sex=M,F')
self.sex2 = Axis('sex=F,M')
self.age = Axis('age=0..7')
self.geo = Axis('geo=A11,A12,A13')
self.value = Axis('value=0..10')
self.collection = AxisCollection((self.lipro, self.sex, self.age))
def test_init_from_group(self):
lipro_subset = self.lipro[:'P03']
col2 = AxisCollection((lipro_subset, self.sex))
self.assertEqual(col2.names, ['lipro', 'sex'])
assert_array_equal(col2.lipro.labels, ['P01', 'P02', 'P03'])
assert_array_equal(col2.sex.labels, ['M', 'F'])
def test_init_from_string(self):
col = AxisCollection('age=10;sex=M,F;year=2000..2017')
assert col.names == ['age', 'sex', 'year']
assert list(col.age.labels) == [10]
assert list(col.sex.labels) == ['M', 'F']
assert list(col.year.labels) == [y for y in range(2000, 2018)]
def test_eq(self):
col = self.collection
self.assertEqual(col, col)
self.assertEqual(col, AxisCollection((self.lipro, self.sex, self.age)))
self.assertEqual(col, (self.lipro, self.sex, self.age))
self.assertNotEqual(col, (self.lipro, self.age, self.sex))
def test_getitem_name(self):
col = self.collection
self.assert_axis_eq(col['lipro'], self.lipro)
self.assert_axis_eq(col['sex'], self.sex)
self.assert_axis_eq(col['age'], self.age)
def test_getitem_int(self):
col = self.collection
self.assert_axis_eq(col[0], self.lipro)
self.assert_axis_eq(col[-3], self.lipro)
self.assert_axis_eq(col[1], self.sex)
self.assert_axis_eq(col[-2], self.sex)
self.assert_axis_eq(col[2], self.age)
self.assert_axis_eq(col[-1], self.age)
def test_getitem_slice(self):
col = self.collection[:2]
self.assertEqual(len(col), 2)
self.assert_axis_eq(col[0], self.lipro)
self.assert_axis_eq(col[1], self.sex)
def test_setitem_name(self):
col = self.collection[:]
# replace an axis with one with another name
col['lipro'] = self.geo
self.assertEqual(len(col), 3)
self.assertEqual(col, [self.geo, self.sex, self.age])
# replace an axis with one with the same name
col['sex'] = self.sex2
self.assertEqual(col, [self.geo, self.sex2, self.age])
col['geo'] = self.lipro
self.assertEqual(col, [self.lipro, self.sex2, self.age])
col['age'] = self.geo
self.assertEqual(col, [self.lipro, self.sex2, self.geo])
col['sex'] = self.sex
col['geo'] = self.age
self.assertEqual(col, self.collection)
def test_setitem_name_axis_def(self):
col = self.collection[:]
# replace an axis with one with another name
col['lipro'] = 'geo=A11,A12,A13'
self.assertEqual(len(col), 3)
self.assertEqual(col, [self.geo, self.sex, self.age])
# replace an axis with one with the same name
col['sex'] = 'sex=F,M'
self.assertEqual(col, [self.geo, self.sex2, self.age])
col['geo'] = 'lipro=P01..P04'
self.assertEqual(col, [self.lipro, self.sex2, self.age])
col['age'] = 'geo=A11,A12,A13'
self.assertEqual(col, [self.lipro, self.sex2, self.geo])
col['sex'] = 'sex=M,F'
col['geo'] = 'age=0..7'
self.assertEqual(col, self.collection)
def test_setitem_int(self):
col = self.collection[:]
col[1] = self.geo
self.assertEqual(len(col), 3)
self.assertEqual(col, [self.lipro, self.geo, self.age])
col[2] = self.sex
self.assertEqual(col, [self.lipro, self.geo, self.sex])
col[-1] = self.age
self.assertEqual(col, [self.lipro, self.geo, self.age])
def test_setitem_list_replace(self):
col = self.collection[:]
col[['lipro', 'age']] = [self.geo, self.lipro]
self.assertEqual(col, [self.geo, self.sex, self.lipro])
def test_setitem_slice_replace(self):
col = self.collection[:]
# replace by list
col[1:] = [self.geo, self.sex]
self.assertEqual(col, [self.lipro, self.geo, self.sex])
# replace by collection
col[1:] = self.collection[1:]
self.assertEqual(col, self.collection)
def test_setitem_slice_insert(self):
col = self.collection[:]
col[1:1] = [self.geo]
self.assertEqual(col, [self.lipro, self.geo, self.sex, self.age])
def test_setitem_slice_delete(self):
col = self.collection[:]
col[1:2] = []
self.assertEqual(col, [self.lipro, self.age])
col[0:1] = []
self.assertEqual(col, [self.age])
def assert_axis_eq(self, axis1, axis2):
self.assertTrue(axis1.equals(axis2))
def test_delitem(self):
col = self.collection[:]
self.assertEqual(len(col), 3)
del col[0]
self.assertEqual(len(col), 2)
self.assert_axis_eq(col[0], self.sex)
self.assert_axis_eq(col[1], self.age)
del col['age']
self.assertEqual(len(col), 1)
self.assert_axis_eq(col[0], self.sex)
del col[self.sex]
self.assertEqual(len(col), 0)
def test_delitem_slice(self):
col = self.collection[:]
self.assertEqual(len(col), 3)
del col[0:2]
self.assertEqual(len(col), 1)
self.assertEqual(col, [self.age])
del col[:]
self.assertEqual(len(col), 0)
def test_pop(self):
col = self.collection[:]
lipro, sex, age = col
self.assertEqual(len(col), 3)
self.assertIs(col.pop(), age)
self.assertEqual(len(col), 2)
self.assertIs(col[0], lipro)
self.assertIs(col[1], sex)
self.assertIs(col.pop(), sex)
self.assertEqual(len(col), 1)
self.assertIs(col[0], lipro)
self.assertIs(col.pop(), lipro)
self.assertEqual(len(col), 0)
def test_replace(self):
col = self.collection[:]
newcol = col.replace('sex', self.geo)
# original collection is not modified
self.assertEqual(col, self.collection)
self.assertEqual(len(newcol), 3)
self.assertEqual(newcol.names, ['lipro', 'geo', 'age'])
self.assertEqual(newcol.shape, (4, 3, 8))
newcol = newcol.replace(self.geo, self.sex)
self.assertEqual(len(newcol), 3)
self.assertEqual(newcol.names, ['lipro', 'sex', 'age'])
self.assertEqual(newcol.shape, (4, 2, 8))
# from now on, reuse original collection
newcol = col.replace(self.sex, 3)
self.assertEqual(len(newcol), 3)
self.assertEqual(newcol.names, ['lipro', None, 'age'])
self.assertEqual(newcol.shape, (4, 3, 8))
newcol = col.replace(self.sex, ['a', 'b', 'c'])
self.assertEqual(len(newcol), 3)
self.assertEqual(newcol.names, ['lipro', None, 'age'])
self.assertEqual(newcol.shape, (4, 3, 8))
newcol = col.replace(self.sex, "letters=a,b,c")
self.assertEqual(len(newcol), 3)
self.assertEqual(newcol.names, ['lipro', 'letters', 'age'])
self.assertEqual(newcol.shape, (4, 3, 8))
def test_contains(self):
col = self.collection
self.assertTrue('lipro' in col)
self.assertFalse('nonexisting' in col)
self.assertTrue(0 in col)
self.assertTrue(1 in col)
self.assertTrue(2 in col)
self.assertTrue(-1 in col)
self.assertTrue(-2 in col)
self.assertTrue(-3 in col)
self.assertFalse(3 in col)
# objects actually in col
self.assertTrue(self.lipro in col)
self.assertTrue(self.sex in col)
self.assertTrue(self.age in col)
# other axis with the same name
self.assertTrue(self.sex2 in col)
self.assertFalse(self.geo in col)
self.assertFalse(self.value in col)
# test anonymous axes
anon = Axis([0, 1])
col.append(anon)
self.assertTrue(anon in col)
# different object, same values
anon2 = anon.copy()
self.assertTrue(anon2 in col)
# different values
anon3 = Axis([0, 2])
self.assertFalse(anon3 in col)
def test_index(self):
col = self.collection
self.assertEqual(col.index('lipro'), 0)
with self.assertRaises(ValueError):
col.index('nonexisting')
self.assertEqual(col.index(0), 0)
self.assertEqual(col.index(1), 1)
self.assertEqual(col.index(2), 2)
self.assertEqual(col.index(-1), -1)
self.assertEqual(col.index(-2), -2)
self.assertEqual(col.index(-3), -3)
with self.assertRaises(ValueError):
col.index(3)
# objects actually in col
self.assertEqual(col.index(self.lipro), 0)
self.assertEqual(col.index(self.sex), 1)
self.assertEqual(col.index(self.age), 2)
# other axis with the same name
self.assertEqual(col.index(self.sex2), 1)
# non existing
with self.assertRaises(ValueError):
col.index(self.geo)
with self.assertRaises(ValueError):
col.index(self.value)
# test anonymous axes
anon = Axis([0, 1])
col.append(anon)
self.assertEqual(col.index(anon), 3)
# different object, same values
anon2 = anon.copy()
self.assertEqual(col.index(anon2), 3)
# different values
anon3 = Axis([0, 2])
with self.assertRaises(ValueError):
col.index(anon3)
def test_get(self):
col = self.collection
self.assert_axis_eq(col.get('lipro'), self.lipro)
self.assertIsNone(col.get('nonexisting'))
self.assertIs(col.get('nonexisting', self.value), self.value)
def test_keys(self):
self.assertEqual(self.collection.keys(), ['lipro', 'sex', 'age'])
def test_getattr(self):
col = self.collection
self.assert_axis_eq(col.lipro, self.lipro)
self.assert_axis_eq(col.sex, self.sex)
self.assert_axis_eq(col.age, self.age)
def test_append(self):
col = self.collection
geo = Axis('geo=A11,A12,A13')
col.append(geo)
self.assertEqual(col, [self.lipro, self.sex, self.age, geo])
def test_extend(self):
col = self.collection
col.extend([self.geo, self.value])
self.assertEqual(col,
[self.lipro, self.sex, self.age, self.geo, self.value])
def test_insert(self):
col = self.collection
col.insert(1, self.geo)
self.assertEqual(col, [self.lipro, self.geo, self.sex, self.age])
def test_add(self):
col = self.collection.copy()
lipro, sex, age = self.lipro, self.sex, self.age
geo, value = self.geo, self.value
# 1) list
# a) no dupe
new = col + [self.geo, value]
self.assertEqual(new, [lipro, sex, age, geo, value])
# check the original has not been modified
self.assertEqual(col, self.collection)
# b) with compatible dupe
# the "new" age axis is ignored (because it is compatible)
new = col + [Axis('geo=A11,A12,A13'), Axis('age=0..7')]
self.assertEqual(new, [lipro, sex, age, geo])
# c) with incompatible dupe
# XXX: the "new" age axis is ignored. We might want to ignore it if it
# is the same but raise an exception if it is different
with self.assertRaises(ValueError):
col + [Axis('geo=A11,A12,A13'), Axis('age=0..6')]
# 2) other AxisCollection
new = col + AxisCollection([geo, value])
self.assertEqual(new, [lipro, sex, age, geo, value])
def test_combine(self):
col = self.collection.copy()
lipro, sex, age = self.lipro, self.sex, self.age
res = col.combine_axes((lipro, sex))
self.assertEqual(res.names, ['lipro_sex', 'age'])
self.assertEqual(res.size, col.size)
self.assertEqual(res.shape, (4 * 2, 8))
print(res.info)
assert_array_equal(res.lipro_sex.labels[0], 'P01_M')
res = col.combine_axes((lipro, age))
self.assertEqual(res.names, ['lipro_age', 'sex'])
self.assertEqual(res.size, col.size)
self.assertEqual(res.shape, (4 * 8, 2))
assert_array_equal(res.lipro_age.labels[0], 'P01_0')
res = col.combine_axes((sex, age))
self.assertEqual(res.names, ['lipro', 'sex_age'])
self.assertEqual(res.size, col.size)
self.assertEqual(res.shape, (4, 2 * 8))
assert_array_equal(res.sex_age.labels[0], 'M_0')
def test_info(self):
expected = """\
4 x 2 x 8
lipro [4]: 'P01' 'P02' 'P03' 'P04'
sex [2]: 'M' 'F'
age [8]: 0 1 2 ... 5 6 7"""
self.assertEqual(self.collection.info, expected)
def test_str(self):
self.assertEqual(str(self.collection), "{lipro, sex, age}")
def test_repr(self):
self.assertEqual(repr(self.collection), """AxisCollection([
Axis(['P01', 'P02', 'P03', 'P04'], 'lipro'),
Axis(['M', 'F'], 'sex'),
Axis([0, 1, 2, 3, 4, 5, 6, 7], 'age')
])""")
if __name__ == "__main__":
pytest.main()