def test_patterson_d(self):
aca = [[0, 2],
[2, 0],
[2, 0],
[1, 1],
[0, 0]]
acb = [[0, 2],
[0, 2],
[0, 2],
[1, 1],
[0, 2]]
acc = [[2, 0],
[2, 0],
[0, 2],
[1, 1],
[0, 2]]
acd = [[2, 0],
[0, 2],
[2, 0],
[1, 1],
[0, 2]]
num, den = allel.stats.patterson_d(aca, acb, acc, acd)
expect_num = [0., 1., -1., 0., np.nan]
expect_den = [0., 1., 1., 0.25, np.nan]
assert_array_nanclose(expect_num, num)
assert_array_nanclose(expect_den, den)
def test_patterson_d(self):
aca = [[0, 2],
[2, 0],
[2, 0],
[1, 1],
[0, 0]]
acb = [[0, 2],
[0, 2],
[0, 2],
[1, 1],
[0, 2]]
acc = [[2, 0],
[2, 0],
[0, 2],
[1, 1],
[0, 2]]
acd = [[2, 0],
[0, 2],
[2, 0],
[1, 1],
[0, 2]]
num, den = allel.patterson_d(aca, acb, acc, acd)
expect_num = [0., 1., -1., 0., np.nan]
expect_den = [0., 1., 1., 0.25, np.nan]
assert_array_nanclose(expect_num, num)
assert_array_nanclose(expect_den, den)
def test_nsl01_scan_int8_c():
h = np.array([[0, 0, 1], [0, 1, 1], [1, 1, 0], [1, 0, 0]], dtype='i1')
nsl0, nsl1 = nsl01_scan_int8(h)
expect_nsl0 = [1, np.nan, np.nan, 1]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [np.nan, 1, 1, np.nan]
assert_array_nanclose(expect_nsl1, nsl1)
def test_nsl01_scan_b():
h = np.array([[0, 0, 0, 1], [0, 0, 1, 0], [0, 1, 0, 0], [1, 0, 0, 0]])
nsl0, nsl1 = nsl01_scan(h)
expect_nsl0 = [1, 4 / 3, 4 / 3, 4 / 3]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_nsl1, nsl1)
def test_nsl01_scan_a():
h = np.array([[0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1]])
nsl0, nsl1 = nsl01_scan(h)
expect_nsl0 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl1, nsl1)
def test_nsl01_scan_int8_a():
h = np.array([[0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1]],
dtype='i1')
nsl0, nsl1 = nsl01_scan_int8(h)
expect_nsl0 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl1, nsl1)
def test_nsl01_scan_int8_a():
h = np.array([[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1]], dtype='i1')
nsl0, nsl1 = nsl01_scan_int8(h)
expect_nsl0 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl1, nsl1)
def test_nsl01_scan_int8_c():
h = np.array([[0, 0, 1],
[0, 1, 1],
[1, 1, 0],
[1, 0, 0]], dtype='i1')
nsl0, nsl1 = nsl01_scan_int8(h)
expect_nsl0 = [1, np.nan, np.nan, 1]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [np.nan, 1, 1, np.nan]
assert_array_nanclose(expect_nsl1, nsl1)
def test_patterson_f2(self):
aca = [[0, 2],
[2, 0],
[1, 1],
[0, 0]]
acb = [[0, 2],
[0, 2],
[0, 2],
[0, 2]]
expect = [0., 1., 0., np.nan]
actual = allel.stats.patterson_f2(aca, acb)
assert_array_nanclose(expect, actual)
def test_ihh_scan_d():
# edge case: start from 0 haplotype homozygosity
gaps = np.array([10], dtype='f8')
h = np.array([[0, 1], [1, 0]])
expect = [0, 0]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
expect = [0, 0]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
def test_patterson_f2(self):
aca = [[0, 2],
[2, 0],
[1, 1],
[0, 0]]
acb = [[0, 2],
[0, 2],
[0, 2],
[0, 2]]
expect = [0., 1., 0., np.nan]
actual = allel.patterson_f2(aca, acb)
assert_array_nanclose(expect, actual)
def test_ihh_scan_int8_d():
# edge case: start from 0 haplotype homozygosity
gaps = np.array([10], dtype='f8')
h = np.array([[0, 1],
[1, 0]], dtype='i1')
expect = [0, 0]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
expect = [0, 0]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
def test_ihh_scan_a():
# simple case: 1 haplotype pair, haplotype homozygosity over all variants
gaps = np.array([10, 10], dtype='f8')
h = np.array([[0, 0], [0, 0], [0, 0]])
# do not include edges
expect = [np.nan, np.nan, np.nan]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
# include edges
expect = [0, 10, 20]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
def test_ihh_scan_c():
# simple case: 1 haplotype pair, haplotype homozygosity decays
gaps = np.array([10, 10], dtype='f8')
h = np.array([[0, 1], [0, 0], [0, 0]])
# do not include edges
expect = [0, 5, 15]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
# include edges
expect = [0, 5, 15]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
def test_ihh_scan_b():
# 1 haplotype pair, haplotype homozygosity over all variants
# handling of large gap (encoded as -1)
gaps = np.array([10, -1], dtype='f8')
h = np.array([[0, 0], [0, 0], [0, 0]])
# do not include edges
expect = [np.nan, np.nan, np.nan]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
# include edges
expect = [0, 10, np.nan]
actual = ihh_scan(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
def test_ihh_scan_int8_c():
# simple case: 1 haplotype pair, haplotype homozygosity decays
gaps = np.array([10, 10], dtype='f8')
h = np.array([[0, 1],
[0, 0],
[0, 0]], dtype='i1')
# do not include edges
expect = [0, 5, 15]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
# include edges
expect = [0, 5, 15]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
def test_ihh_scan_int8_b():
# 1 haplotype pair, haplotype homozygosity over all variants
# handling of large gap (encoded as -1)
gaps = np.array([10, -1], dtype='f8')
h = np.array([[0, 0],
[0, 0],
[0, 0]], dtype='i1')
# do not include edges
expect = [np.nan, np.nan, np.nan]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
# include edges
expect = [0, 10, np.nan]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
def test_patterson_f3(self):
aca = [[0, 2],
[2, 0],
[0, 2],
[0, 2],
[0, 0]]
acb = [[2, 0],
[0, 2],
[0, 2],
[0, 2],
[0, 2]]
acc = [[1, 1],
[1, 1],
[0, 2],
[2, 0],
[1, 1]]
expect_f3 = [-.5, -.5, 0., 1., np.nan]
actual_f3, actual_hzc = allel.patterson_f3(acc, aca, acb)
assert_array_nanclose(expect_f3, actual_f3)
expect_hzc = [1., 1., 0., 0., 1.]
assert_array_nanclose(expect_hzc, actual_hzc)
def test_patterson_f3(self):
aca = [[0, 2],
[2, 0],
[0, 2],
[0, 2],
[0, 0]]
acb = [[2, 0],
[0, 2],
[0, 2],
[0, 2],
[0, 2]]
acc = [[1, 1],
[1, 1],
[0, 2],
[2, 0],
[1, 1]]
expect_f3 = [-.5, -.5, 0., 1., np.nan]
actual_f3, actual_hzc = allel.stats.patterson_f3(acc, aca, acb)
assert_array_nanclose(expect_f3, actual_f3)
expect_hzc = [1., 1., 0., 0., 1.]
assert_array_nanclose(expect_hzc, actual_hzc)
def test_ihh01_scan_a():
gaps = np.array([10, 10, 10], dtype='f8')
h = np.array([[0, 0, 1], [0, 1, 1], [1, 1, 0], [1, 0, 0]])
ihh0, ihh1 = ihh01_scan(h, gaps, min_ehh=0.05, include_edges=False)
expect_ihh0 = [np.nan, np.nan, np.nan, 5]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, 5, 5, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan(h, gaps, min_ehh=0, include_edges=True)
expect_ihh0 = [0, np.nan, np.nan, 5]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, 5, 5, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
def test_ihh01_scan_int8_c():
gaps = np.array([10, 10, 10], dtype='f8')
h = np.array([[0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1], [0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1]],
dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0.05)
expect_ihh0 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0, include_edges=True)
expect_ihh0 = [0, 10, 20, 30]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [0, 10, 20, 30]
assert_array_nanclose(expect_ihh1, ihh1)
def test_ihh01_scan_int8_c():
gaps = np.array([10, 10, 10], dtype='f8')
h = np.array([[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1]], dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0.05)
expect_ihh0 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0, include_edges=True)
expect_ihh0 = [0, 10, 20, 30]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [0, 10, 20, 30]
assert_array_nanclose(expect_ihh1, ihh1)
def test_ihh01_scan_int8_e():
# min_maf
gaps = np.array([10, 10], dtype='f8')
h = np.array([[0, 0, 1],
[0, 0, 1],
[0, 0, 1]], dtype='i1')
expect_ihh0 = [0, 10, 20]
expect_ihh1 = [np.nan, np.nan, np.nan]
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0,
min_maf=0, include_edges=True)
assert_array_nanclose(expect_ihh0, ihh0)
assert_array_nanclose(expect_ihh1, ihh1)
expect_ihh0 = [np.nan, np.nan, np.nan]
expect_ihh1 = [np.nan, np.nan, np.nan]
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0,
min_maf=0.4, include_edges=True)
assert_array_nanclose(expect_ihh0, ihh0)
assert_array_nanclose(expect_ihh1, ihh1)
def test_ihh01_scan_e():
# min_maf
gaps = np.array([10, 10], dtype='f8')
h = np.array([[0, 0, 1], [0, 0, 1], [0, 0, 1]])
expect_ihh0 = [0, 10, 20]
expect_ihh1 = [np.nan, np.nan, np.nan]
ihh0, ihh1 = ihh01_scan(h, gaps, min_ehh=0, min_maf=0, include_edges=True)
assert_array_nanclose(expect_ihh0, ihh0)
assert_array_nanclose(expect_ihh1, ihh1)
expect_ihh0 = [np.nan, np.nan, np.nan]
expect_ihh1 = [np.nan, np.nan, np.nan]
ihh0, ihh1 = ihh01_scan(h,
gaps,
min_ehh=0,
min_maf=0.4,
include_edges=True)
assert_array_nanclose(expect_ihh0, ihh0)
assert_array_nanclose(expect_ihh1, ihh1)
def test_ihh_scan_int8_e():
# edge case: start from haplotype homozygosity below min_ehh
gaps = np.array([10], dtype='f8')
h = np.array([[0, 0, 1], [0, 1, 0]], dtype='i1')
expect = [np.nan, 10 / 6]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=False)
assert_array_nanclose(expect, actual)
expect = [0, 10 / 6]
actual = ihh_scan_int8(h, gaps, min_ehh=0, include_edges=True)
assert_array_nanclose(expect, actual)
expect = [0, 0]
actual = ihh_scan_int8(h, gaps, min_ehh=0.5, include_edges=False)
assert_array_nanclose(expect, actual)
expect = [0, 0]
actual = ihh_scan_int8(h, gaps, min_ehh=0.5, include_edges=True)
assert_array_nanclose(expect, actual)
def test_ihh01_scan_int8(self):
from allel.opt.stats import ihh01_scan_int8
pos = [10, 20, 30, 40]
# case 1
h = np.array([[0, 0, 1],
[0, 1, 1],
[1, 1, 0],
[1, 0, 0]], dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=0.05)
expect_ihh0 = [np.nan, np.nan, np.nan, 0]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, 0, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=None)
expect_ihh0 = [0, np.nan, np.nan, 0]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, 0, 0, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
# case 2
h = np.array([[0, 0, 0, 1],
[0, 0, 1, 0],
[0, 1, 0, 0],
[1, 0, 0, 0]], dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=0.05)
expect_ihh0 = [np.nan, np.nan, np.nan, 10*2/3]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=None)
expect_ihh0 = [0, 10*2/3, 10*2/3, 10*2/3]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
# case 3
h = np.array([[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1]], dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=0.05)
expect_ihh0 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=None)
expect_ihh0 = [0, 10, 20, 30]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [0, 10, 20, 30]
assert_array_nanclose(expect_ihh1, ihh1)
# case 4
h = np.array([[0, 0, 1, 1, 1, 0],
[0, 1, 0, 1, 0, 1],
[1, 0, 0, 0, 1, 1],
[0, 0, 0, 1, 1, 1]], dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=0.05)
expect_ihh0 = [np.nan, np.nan, np.nan, 10*2/3]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, 10*2/3]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, pos, min_ehh=None)
expect_ihh0 = [0, 10*2/3, 10*2/3, 10*2/3]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [0, 10*2/3, 10*2/3, 10*2/3]
assert_array_nanclose(expect_ihh1, ihh1)
def test_ihh01_scan_d():
gaps = np.array([10, 10, 10], dtype='f8')
h = np.array([[0, 0, 1, 1, 1, 0], [0, 1, 0, 1, 0, 1], [1, 0, 0, 0, 1, 1],
[0, 0, 0, 1, 1, 1]])
ihh0, ihh1 = ihh01_scan(h, gaps, min_ehh=0.05)
x = (10 * (1 + 1 / 3) / 2) + (10 * (1 / 3 + 0) / 2)
expect_ihh0 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan(h, gaps, min_ehh=0)
expect_ihh0 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan(h, gaps, min_ehh=0, include_edges=True)
expect_ihh0 = [0, 10 * 2 / 3, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [0, 10 * 2 / 3, x, x]
assert_array_nanclose(expect_ihh1, ihh1)
def test_ihh01_scan_int8_d():
gaps = np.array([10, 10, 10], dtype='f8')
h = np.array([[0, 0, 1, 1, 1, 0],
[0, 1, 0, 1, 0, 1],
[1, 0, 0, 0, 1, 1],
[0, 0, 0, 1, 1, 1]], dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0.05)
x = (10 * (1 + 1 / 3) / 2) + (10 * (1 / 3 + 0) / 2)
expect_ihh0 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0)
expect_ihh0 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0, include_edges=True)
expect_ihh0 = [0, 10 * 2 / 3, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [0, 10 * 2 / 3, x, x]
assert_array_nanclose(expect_ihh1, ihh1)
def test_ssl01_scan_int8(self):
from allel.opt.stats import nsl01_scan_int8
h = np.array([[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1],
[0, 0, 0, 1, 1, 1]], dtype='i1')
nsl0, nsl1 = nsl01_scan_int8(h)
expect_nsl0 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [1, 2, 3, 4]
assert_array_nanclose(expect_nsl1, nsl1)
h = np.array([[0, 0, 0, 1],
[0, 0, 1, 0],
[0, 1, 0, 0],
[1, 0, 0, 0]], dtype='i1')
nsl0, nsl1 = nsl01_scan_int8(h)
expect_nsl0 = [1, 4/3, 4/3, 4/3]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_nsl1, nsl1)
h = np.array([[0, 0, 1],
[0, 1, 1],
[1, 1, 0],
[1, 0, 0]], dtype='i1')
nsl0, nsl1 = nsl01_scan_int8(h)
expect_nsl0 = [1, np.nan, np.nan, 1]
assert_array_nanclose(expect_nsl0, nsl0)
expect_nsl1 = [np.nan, 1, 1, np.nan]
assert_array_nanclose(expect_nsl1, nsl1)
def test_ihh01_scan_int8_b():
gaps = np.array([10, 10, 10], dtype='f8')
h = np.array([[0, 0, 0, 1], [0, 0, 1, 0], [0, 1, 0, 0], [1, 0, 0, 0]],
dtype='i1')
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0.05, include_edges=False)
x = (10 * (1 + 1 / 3) / 2) + (10 * (1 / 3 + 0) / 2)
expect_ihh0 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0, include_edges=False)
expect_ihh0 = [np.nan, np.nan, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)
ihh0, ihh1 = ihh01_scan_int8(h, gaps, min_ehh=0, include_edges=True)
expect_ihh0 = [0, 10 * (1 + 1 / 3) / 2, x, x]
assert_array_nanclose(expect_ihh0, ihh0)
expect_ihh1 = [np.nan, np.nan, np.nan, np.nan]
assert_array_nanclose(expect_ihh1, ihh1)