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import sys
from typing import List, Set, Tuple, Union
import pytest
from cogent3.app.typing import (
AlignedSeqsType,
IdentifierType,
SeqsCollectionType,
SerialisableType,
TabularType,
UnalignedSeqsType,
get_constraint_names,
hints_from_strings,
type_tree,
)
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Gavin Huttley", "Nick Shahmaras"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Gavin Huttley"
__email__ = "Gavin.Huttley@anu.edu.au"
__status__ = "Production"
def test_get_constraint_names():
"""returns the correct names"""
from cogent3.core.alignment import (
Alignment,
ArrayAlignment,
SequenceCollection,
)
from cogent3.evolve.fast_distance import DistanceMatrix
from cogent3.util.dict_array import DictArray
from cogent3.util.table import Table
got = get_constraint_names(AlignedSeqsType)
assert got == {obj.__name__ for obj in (Alignment, ArrayAlignment)}
got = get_constraint_names(UnalignedSeqsType)
assert got == {SequenceCollection.__name__}
got = get_constraint_names(SeqsCollectionType)
assert got == {
obj.__name__ for obj in (Alignment, ArrayAlignment, SequenceCollection)
}
got = get_constraint_names(TabularType)
assert got == {obj.__name__ for obj in (Table, DictArray, DistanceMatrix)}
def test_get_constraint_names_builtins():
"""handles built-in types"""
got = get_constraint_names(Union[str, bytes])
assert got == {"str", "bytes"}
def test_get_constraint_names_serilisable():
"""SerialisableType does not define any compatible types"""
got = get_constraint_names(SerialisableType)
assert got == {"SerialisableType"}
def test_get_constraint_names_identifiertype():
"""IdentifierType does not define any compatible types"""
got = get_constraint_names(IdentifierType)
assert got == {"IdentifierType"}
def test_get_constraint_names_mixed_serilisable_identifiertype():
"""SerialisableType does not define any compatible types"""
got = get_constraint_names(Union[SerialisableType, IdentifierType, AlignedSeqsType])
assert got == {"SerialisableType", "IdentifierType", "Alignment", "ArrayAlignment"}
def test_hints_from_strings_invalid():
"""raise an exception if unknown string"""
with pytest.raises(ValueError):
hints_from_strings("abcde")
def test_hints_from_strings():
got = hints_from_strings("serialisable", "aligned")
assert got == [SerialisableType, AlignedSeqsType]
def test_hints_resolved_from_str():
got = get_constraint_names("DnaSequence")
assert got == {"DnaSequence"}
got = get_constraint_names(Union[SerialisableType, "DnaSequence"])
assert got == {"SerialisableType", "DnaSequence"}
@pytest.mark.parametrize("container", (List, Tuple, Set))
def test_hints_from_container_type(container):
got = get_constraint_names(container[AlignedSeqsType])
assert got == {"Alignment", "ArrayAlignment"}
@pytest.mark.skipif(
(sys.version_info.major, sys.version_info.minor) == (3, 8),
reason="type object subscripting supported in >= 3.9",
)
@pytest.mark.parametrize("container", (list, set, tuple))
def test_hints_from_container_type_obj(container):
got = get_constraint_names(container[AlignedSeqsType])
assert got == {"Alignment", "ArrayAlignment"}
def test_hint_inherited_class():
from collections.abc import MutableSequence
class dummy(MutableSequence):
...
got = get_constraint_names(dummy)
assert got == frozenset(["dummy"])
@pytest.mark.parametrize(
"hint,expect", ((int, 1), (Set[int], 2), (List[List[Set[float]]], 4))
)
def test_typing_tree_depth(hint, expect):
d, _ = type_tree(hint)
assert d == expect, (d, expect)
@pytest.mark.parametrize(
"hint,expect",
(
(int, int),
(Set[int], (set, (int,))),
(List[Set[int]], (list, (set, (int,)))),
),
)
def test_type_tree(hint, expect):
_, t = type_tree(hint)
assert t == expect, (t, expect)
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