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_sub():
col = AxisCollection('a0,a1;b0,b1,b2')
res = col - Axis(2)
assert res == AxisCollection('b0,b1,b2')
res = col - Axis(3)
assert res == AxisCollection('a0,a1')
col = AxisCollection('a0,a1;b0,b1')
# when several axes are compatible, remove first
res = col - Axis(2)
assert res == AxisCollection('b0,b1')
# when no axis is compatible, do not remove any
res = col - Axis(3)
assert res == col
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_add(col):
col2 = col.copy()
new = col2 + [geo, value]
assert new == [lipro, sex, age, geo, value]
assert col2 == col
new = col2 + [Axis('geo=A11,A12,A13'), Axis('age=0..7')]
assert new == [lipro, sex, age, geo]
with pytest.raises(ValueError):
col2 + [Axis('geo=A11,A12,A13'), Axis('age=0..6')]
# 2) other AxisCollection
new = col2 + AxisCollection([geo, value])
assert new == [lipro, sex, age, geo, value]
def test_eq(col):
assert col == col
assert col == AxisCollection((lipro, sex, age))
assert col == (lipro, sex, age)
assert col != (lipro, age, sex)
def test_init_from_string():
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_init_from_group():
lipro_subset = lipro[:'P03']
col2 = AxisCollection((lipro_subset, sex))
assert col2.names == ['lipro', 'sex']
assert_array_equal(col2.lipro.labels, ['P01', 'P02', 'P03'])
assert_array_equal(col2.sex.labels, ['M', 'F'])
def col():
return AxisCollection((lipro, sex, age))
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))
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')
])""")
def test_create_checkedsession_instance(meta):
# As of v1.0 of pydantic all fields with annotations (whether annotation-only or with a default value)
# will precede all fields without an annotation. Within their respective groups, fields remain in the
# order they were defined.
# See https://pydantic-docs.helpmanual.io/usage/models/#field-ordering
declared_variable_keys = ['a', 'a2', 'a01', 'c', 'e', 'g', 'f', 'h', 'b', 'b024', 'anonymous', 'ano01', 'd']
# setting variables without default values
cs = TestCheckedSession(a, a01, a2=a2, e=e, f=f, g=g, h=h)
assert list(cs.keys()) == declared_variable_keys
assert cs.b.equals(b)
assert cs.b024.equals(b024)
assert cs.a.equals(a)
assert cs.a2.equals(a2)
assert cs.anonymous.equals(anonymous)
assert cs.a01.equals(a01)
assert cs.ano01.equals(ano01)
assert cs.c == c
assert cs.d == d
assert cs.e.equals(e)
assert cs.g.equals(g)
assert cs.f.equals(f)
assert cs.h.equals(h)
# metadata
cs = TestCheckedSession(a, a01, a2=a2, e=e, f=f, g=g, h=h, meta=meta)
assert cs.meta == meta
# override default value
b_alt = Axis('b=b0..b4')
cs = TestCheckedSession(a, a01, b=b_alt, a2=a2, e=e, f=f, g=g, h=h)
assert cs.b is b_alt
# test for "NOT_LOADED" variables
with must_warn(UserWarning, msg="No value passed for the declared variable 'a'", check_file=False):
TestCheckedSession(a01=a01, a2=a2, e=e, f=f, g=g, h=h)
cs = TestCheckedSession()
assert list(cs.keys()) == declared_variable_keys
# --- variables with default values ---
assert cs.b.equals(b)
assert cs.b024.equals(b024)
assert cs.anonymous.equals(anonymous)
assert cs.ano01.equals(ano01)
assert cs.c == c
assert cs.d == d
# --- variables without default values ---
assert isinstance(cs.a, NotLoaded)
assert isinstance(cs.a2, NotLoaded)
assert isinstance(cs.a01, NotLoaded)
assert isinstance(cs.e, NotLoaded)
assert isinstance(cs.g, NotLoaded)
assert isinstance(cs.f, NotLoaded)
assert isinstance(cs.h, NotLoaded)
# passing a scalar to set all elements a CheckedArray
cs = TestCheckedSession(a, a01, a2=a2, e=e, f=f, g=g, h=5)
assert cs.h.axes == AxisCollection((a3, b2))
assert cs.h.equals(full(axes=(a3, b2), fill_value=5))
# add the undeclared variable 'i'
with must_warn(UserWarning, f"'i' is not declared in '{cs.__class__.__name__}'", check_file=False):
cs = TestCheckedSession(a, a01, a2=a2, i=5, e=e, f=f, g=g, h=h)
assert list(cs.keys()) == declared_variable_keys + ['i']
# test inheritance between checked sessions
class TestInheritance(TestCheckedSession):
# override variables
b = b2
c: int = 5
f: CheckedArray((a3, b2), dtype=int)
h: CheckedArray((Axis(3), Axis(2)))
# new variables
n0 = 'first new var'
n1: str
declared_variable_keys += ['n1', 'n0']
cs = TestInheritance(a, a01, a2=a2, e=e, f=h, g=g, h=f, n1='second new var')
assert list(cs.keys()) == declared_variable_keys
# --- overriden variables ---
assert cs.b.equals(b2)
assert cs.c == 5
assert cs.f.equals(h)
assert cs.h.equals(f)
# --- new variables ---
assert cs.n0 == 'first new var'
assert cs.n1 == 'second new var'
# --- variables declared in the base class ---
assert cs.b024.equals(b024)
assert cs.a.equals(a)
assert cs.a2.equals(a2)
assert cs.anonymous.equals(anonymous)
assert cs.a01.equals(a01)
assert cs.ano01.equals(ano01)
assert cs.d == d
assert cs.e.equals(e)
assert cs.g.equals(g)