dwhswenson/contact_map

File test_contact_map.py has 836 lines of code (exceeds 750 allowed). Consider refactoring.

Wontfix

import os
import collections
import mdtraj as md
import copy

TODO found

Open

    # TODO: add tests for ContactObject._check_consistency

• Exclude checks
  • Disable engine
  • Disable check

Identical blocks of code found in 3 locations. Consider refactoring.

Wontfix

traj_atom_contact_count = {
    frozenset([0, 8]): 1,
    frozenset([0, 9]): 1,
    frozenset([1, 4]): 4,
    frozenset([1, 5]): 1,

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Identical blocks of code found in 3 locations. Consider refactoring.

Wontfix

        expected_atom_count = {
            frozenset([0, 8]): -0.5,
            frozenset([0, 9]): -0.5,
            frozenset([1, 4]): 0.5 - 1.0,
            frozenset([1, 5]): 0.5,

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Identical blocks of code found in 3 locations. Consider refactoring.

Wontfix

        expected_atom_count = {
            frozenset([0, 8]): -1.0,
            frozenset([0, 9]): -1.0,
            frozenset([1, 4]): 0.75 - 1.0,
            frozenset([1, 5]): 0.25,

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    @pytest.mark.parametrize("intermediate", ["dict", "json"])
    def test_serialization_cycle(self, intermediate):
        serializer, deserializer = {
            'json': (self.map.to_json, ContactFrequency.from_json),
            'dict': (self.map.to_dict, ContactFrequency.from_dict)

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    def test_dict_serialization_cycle(self, idx):
        m = self.maps[idx]
        dct = m.to_dict()
        m2 = ContactFrequency.from_dict(dct)
        _contact_object_compare(m, m2)

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Similar blocks of code found in 2 locations. Consider refactoring.

Open

    def test_json_serialization_cycle(self, idx):
        m = self.maps[idx]
        json_str = m.to_json()
        m2 = ContactFrequency.from_json(json_str)
        _contact_object_compare(m, m2)

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Similar blocks of code found in 2 locations. Consider refactoring.

Wontfix

        for f in disabled_funcs:
            with pytest.raises(RuntimeError) as e:
                func = getattr(diff, f)
                # This should only trigger if f is not a property
                # (otherwise the previous line should raise)

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Similar blocks of code found in 2 locations. Consider refactoring.

Wontfix

        for f in disabled_funcs:
            with pytest.raises(RuntimeError) as e:
                func = getattr(diff, f)
                # This should only trigger if f is not a property
                # (otherwise the previous line should raise)

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Identical blocks of code found in 2 locations. Consider refactoring.

Open

            self.map4: [[0, 9], [0, 8], [1, 8], [1, 9], [1, 4], [8, 4],
                        [8, 5], [4, 6], [4, 7], [5, 6], [5, 7]]

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Similar blocks of code found in 3 locations. Consider refactoring.

Invalid

traj_residue_contact_count = {
    frozenset([0, 2]): 5,
    frozenset([0, 4]): 1,
    frozenset([2, 3]): 5,
    frozenset([2, 4]): 1

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Similar blocks of code found in 3 locations. Consider refactoring.

Invalid

        expected_residue_count = {
            frozenset([0, 2]): 0,
            frozenset([0, 4]): -0.5,
            frozenset([2, 3]): 0,
            frozenset([2, 4]): -0.5

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Similar blocks of code found in 3 locations. Consider refactoring.

Invalid

        expected_residue_count = {
            frozenset([0, 2]): 0.0,
            frozenset([0, 4]): -1.0,
            frozenset([2, 3]): 0.0,
            frozenset([2, 4]): -1.0

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Similar blocks of code found in 2 locations. Consider refactoring.

Wontfix

        expected_residue_contacts = {
            k: float(v) / self.expected_n_frames
            for (k, v) in self.expected_residue_contact_count.items()

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Similar blocks of code found in 2 locations. Consider refactoring.

Wontfix

        expected_atom_contacts = {
            k: float(v) / self.expected_n_frames
            for (k, v) in self.expected_atom_contact_count.items()

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