How to use the dtaidistance.alignment.make_substitution_fn function in dtaidistance

def test_substitution_function():
    matrix = read_substitution_matrix(
        Path(__file__).parent / "rsrc" / "substitution.txt"
    )
    substitution = alignment.make_substitution_fn(matrix, gap=0.5)
    assert substitution('A', 'B') == (1, 0.5)
    assert substitution('A', 'A') == (-20.0, 0.5)
    assert substitution('A', 'C') == (3.0, 0.5)

    # test just changing gap function
    substitution2 = alignment.make_substitution_fn({}, gap=0.5)
    assert substitution2('A', 'A') == (-1, 0.5)
    assert substitution2('G', 'C') == (1, 0.5)
    assert alignment._default_substitution_fn('A', 'A') == (-1, 1)
    assert alignment._default_substitution_fn('G', 'C') == (1, 1)

def test_sequences_custom():

    matrix = read_substitution_matrix(
        Path(__file__).parent / "rsrc" / "substitution.txt"
    )
    substitution = alignment.make_substitution_fn(matrix)

    s1 = "CCAGG"
    s2 = "CCGA"

    value, matrix = alignment.needleman_wunsch(s1, s2)
    algn, s1a1, s2a1 = alignment.best_alignment(matrix, s1, s2, gap='-')
    algn_sol1 = [list("CCAGG"), list("CC-GA")]
    assert s1a1 == algn_sol1[0]
    assert s2a1 == algn_sol1[1]

    value, matrix = alignment.needleman_wunsch(s1, s2, substitution=substitution)
    algn, s1a2, s2a2 = alignment.best_alignment(matrix, s1, s2, gap='-')
    algn_sol2 = [list("CC-AGG"), list("CCGA--")]
    assert s1a2 == algn_sol2[0]
    assert s2a2 == algn_sol2[1]

def test_substitution_function():
    matrix = read_substitution_matrix(
        Path(__file__).parent / "rsrc" / "substitution.txt"
    )
    substitution = alignment.make_substitution_fn(matrix, gap=0.5)
    assert substitution('A', 'B') == (1, 0.5)
    assert substitution('A', 'A') == (-20.0, 0.5)
    assert substitution('A', 'C') == (3.0, 0.5)

    # test just changing gap function
    substitution2 = alignment.make_substitution_fn({}, gap=0.5)
    assert substitution2('A', 'A') == (-1, 0.5)
    assert substitution2('G', 'C') == (1, 0.5)
    assert alignment._default_substitution_fn('A', 'A') == (-1, 1)
    assert alignment._default_substitution_fn('G', 'C') == (1, 1)