tests.model.test_taxonomy.TestFind.test_root_leaf() - Code Metrics - dmyersturnbull/mandos - Measure and Improve Code Quality continuously with Scrutinizer

TestFind.test_root_leaf() A
last analyzed 2021-01-25 23:07 UTC

↳ Parent: tests.model.test_taxonomy

Complexity

Conditions

Size

Total Lines	6
Code Lines	6

Duplication

Lines	0
Ratio	0 %

Importance

Changes

Metric	Value
cc	1
eloc	6
nop	1
dl	0
loc	6
rs	10
c	0
b	0
f	0

import pytest


from mandos import MandosResources
from mandos.model.caches import TaxonomyFactories
from mandos.model.taxonomy import Taxon, Taxonomy, _Taxon


class TestFind:

    def test_find(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        tax = TaxonomyFactories.from_vertebrata().load(7742)
        assert len(tax) == 100670
        assert tax.roots == [Taxon(7742, "Vertebrata", None, set())]
        assert len(tax.roots[0].descendents) == 100669
        assert tax[7742] is not None
        assert tax[7742].name == "Vertebrata"
        assert tax[7742].parent is None
        assert tax[117571].id == 117571
        assert tax[117571].name == "Euteleostomi"
        assert tax[10116].name == "Rattus norvegicus"
        assert 117571 in tax
        assert [c.id for c in tax[117571].children] == [7898, 8287]
        with pytest.raises(KeyError):
            assert tax[3343463643446436347457475]
        assert tax.get(3343463643446436347457475) is None
        assert tax.get(117571).id == 117571
        assert 117571 in tax
        assert 13745754745745 not in tax

    def test_empty(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        tax = Taxonomy({})
        assert len(tax) == 0
        assert tax.roots == []

    def test_root_leaf(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        taxon = Taxon(1, "abc", None, set())
        tax = Taxonomy.from_list([taxon])
        assert len(tax) == 1
        assert tax.roots == [taxon]
        assert tax.leaves == [taxon]

    def test_double(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        a = _Taxon(1, "a", None, set())

        b = _Taxon(2, "b", a, set())

        a.add_child(b)
        tax = Taxonomy.from_list([a, b])
        assert len(tax) == 2
        assert tax.roots == [a]
        assert tax.leaves == [b]
        assert set(tax.taxa) == {a, b}
        under = tax.subtree(1)
        assert len(under) == 2
        assert under[1] == a
        assert under[2] == b
        under = tax.subtree(2)
        assert len(under) == 1
        assert under[2] == b

    def test_sort(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        a = _Taxon(10, "z", None, set())

        b = _Taxon(2, "a", a, set())

        c = _Taxon(4, "b", a, set())

        assert b < c, f"{b} vs {c}"
        assert b < c < a, f"{a} vs {b} vs {c}"

    def test_real(self):
class Foo:
    def some_method(self, x, y):
        return x + y;
        path = MandosResources.path("7742.tab.gz")
        tax = Taxonomy.from_path(path)
        assert len(tax) == 100670
        tax = tax.subtree(117571)
        # number from https://www.uniprot.org/taxonomy/117571
        assert len(tax) == 97993


if __name__ == "__main__":
    pytest.main()


1			import pytest
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing module docstring Loading history... introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Unable to import 'pytest' Loading history...
2
3			from mandos import MandosResources
4			from mandos.model.caches import TaxonomyFactories
5			from mandos.model.taxonomy import Taxon, Taxonomy, _Taxon
6
7
8			class TestFind:
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing class docstring Loading history...
9			def test_find(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
10			tax = TaxonomyFactories.from_vertebrata().load(7742)
11			assert len(tax) == 100670
12			assert tax.roots == [Taxon(7742, "Vertebrata", None, set())]
13			assert len(tax.roots[0].descendents) == 100669
14			assert tax[7742] is not None
15			assert tax[7742].name == "Vertebrata"
16			assert tax[7742].parent is None
17			assert tax[117571].id == 117571
18			assert tax[117571].name == "Euteleostomi"
19			assert tax[10116].name == "Rattus norvegicus"
20			assert 117571 in tax
21			assert [c.id for c in tax[117571].children] == [7898, 8287]
22			with pytest.raises(KeyError):
23			assert tax[3343463643446436347457475]
24			assert tax.get(3343463643446436347457475) is None
25			assert tax.get(117571).id == 117571
26			assert 117571 in tax
27			assert 13745754745745 not in tax
28
29			def test_empty(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
30			tax = Taxonomy({})
31			assert len(tax) == 0
32			assert tax.roots == []
33
34			def test_root_leaf(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
35			taxon = Taxon(1, "abc", None, set())
36			tax = Taxonomy.from_list([taxon])
37			assert len(tax) == 1
38			assert tax.roots == [taxon]
39			assert tax.leaves == [taxon]
40
41			def test_double(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
42			a = _Taxon(1, "a", None, set())
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "a" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
43			b = _Taxon(2, "b", a, set())
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "b" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
44			a.add_child(b)
45			tax = Taxonomy.from_list([a, b])
46			assert len(tax) == 2
47			assert tax.roots == [a]
48			assert tax.leaves == [b]
49			assert set(tax.taxa) == {a, b}
50			under = tax.subtree(1)
51			assert len(under) == 2
52			assert under[1] == a
53			assert under[2] == b
54			under = tax.subtree(2)
55			assert len(under) == 1
56			assert under[2] == b
57
58			def test_sort(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
59			a = _Taxon(10, "z", None, set())
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "a" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
60			b = _Taxon(2, "a", a, set())
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "b" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
61			c = _Taxon(4, "b", a, set())
			0 ignored issues – show Coding Style Naming introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Variable name "c" doesn't conform to snake_case naming style ('([^\\W\\dA-Z][^\\WA-Z]2,\|_[^\\WA-Z]*\|__[^\\WA-Z\\d_][^\\WA-Z]+__)$' pattern) This check looks for invalid names for a range of different identifiers. You can set regular expressions to which the identifiers must conform if the defaults do not match your requirements. If your project includes a Pylint configuration file, the settings contained in that file take precedence. To find out more about Pylint, please refer to their site. Loading history...
62			assert b < c, f"{b} vs {c}"
63			assert b < c < a, f"{a} vs {b} vs {c}"
64
65			def test_real(self):
			0 ignored issues – show introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report Missing function or method docstring Loading history... Coding Style introduced 2021-01-25 23:06 UTC by Report Bug Copy Issue Report This method could be written as a function/class method. If a method does not access any attributes of the class, it could also be implemented as a function or static method. This can help improve readability. For example class Foo: def some_method(self, x, y): return x + y; could be written as class Foo: @classmethod def some_method(cls, x, y): return x + y; Loading history...
66			path = MandosResources.path("7742.tab.gz")
67			tax = Taxonomy.from_path(path)
68			assert len(tax) == 100670
69			tax = tax.subtree(117571)
70			# number from https://www.uniprot.org/taxonomy/117571
71			assert len(tax) == 97993
72
73
74			if __name__ == "__main__":
75			pytest.main()
76

dmyersturnbull / mandos

TestFind.test_root_leaf() A last analyzed 2021-01-25 23:07 UTC

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TestFind.test_root_leaf() A
last analyzed 2021-01-25 23:07 UTC