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Merged
ganow merged 2 commits into from
May 29, 2026
Merged

Use tolerant assertions for floating-point tests #130

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18c406c
fix: replace strict float assertions with assert_allclose in tests
KenyaOtsuka May 26, 2026
7970919
fix: replace assertTrue(np.allclose) with assert_allclose in test_met…
KenyaOtsuka May 28, 2026
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57 changes: 27 additions & 30 deletions tests/evals/test_metrics.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -18,9 +18,9 @@ def test_profile_correlation(self):
for i in range(n)
]])

self.assertTrue(np.allclose(
profile_correlation(x, y), r
))
np.testing.assert_allclose(
profile_correlation(x, y), r, rtol=1e-12, atol=1e-12
)
self.assertEqual(profile_correlation(x, y).shape, (1, n))

# Multi-d array
Expand All @@ -34,9 +34,9 @@ def test_profile_correlation(self):
]])
r = r.reshape(1, 4, 3, 2)

self.assertTrue(np.allclose(
profile_correlation(x, y), r
))
np.testing.assert_allclose(
profile_correlation(x, y), r, rtol=1e-12, atol=1e-12
)
self.assertEqual(profile_correlation(x, y).shape, (1, 4, 3, 2))

def test_pattern_correlation(self):
Expand All @@ -48,9 +48,9 @@ def test_pattern_correlation(self):
for i in range(10)
])

self.assertTrue(np.allclose(
pattern_correlation(x, y), r
))
np.testing.assert_allclose(
pattern_correlation(x, y), r, rtol=1e-12, atol=1e-12
)
self.assertEqual(pattern_correlation(x, y).shape, (10,))

# Multi-d array
Expand All @@ -63,26 +63,23 @@ def test_pattern_correlation(self):
for i in range(10)
])

self.assertTrue(np.allclose(
pattern_correlation(x, y), r
))
np.testing.assert_allclose(
pattern_correlation(x, y), r, rtol=1e-12, atol=1e-12
)
self.assertEqual(pattern_correlation(x, y).shape, (10,))

def test_2d(self):
with open('tests/data/testdata-2d.pkl.gz', 'rb') as f:
d = pickle.load(f)
self.assertTrue(np.allclose(
profile_correlation(d['x'], d['y']),
d['r_prof']
))
self.assertTrue(np.allclose(
pattern_correlation(d['x'], d['y']),
d['r_patt']
))
self.assertTrue(np.allclose(
pairwise_identification(d['x'], d['y']),
d['ident_acc']
))
np.testing.assert_allclose(
profile_correlation(d['x'], d['y']), d['r_prof'], rtol=1e-12, atol=1e-12
)
np.testing.assert_allclose(
pattern_correlation(d['x'], d['y']), d['r_patt'], rtol=1e-12, atol=1e-12
)
np.testing.assert_allclose(
pairwise_identification(d['x'], d['y']), d['ident_acc'], rtol=1e-12, atol=1e-12
)

def test_2d_nan(self):
with open('tests/data/testdata-2d-nan.pkl.gz', 'rb') as f:
Expand All @@ -91,14 +88,14 @@ def test_2d_nan(self):
# profile_correlation(d['x'], d['y']),
# d['r_prof']
# ))
self.assertTrue(np.allclose(
np.testing.assert_allclose(
pattern_correlation(d['x'], d['y'], remove_nan=True),
d['r_patt'],
))
self.assertTrue(np.allclose(
d['r_patt'], rtol=1e-12, atol=1e-12
)
np.testing.assert_allclose(
pairwise_identification(d['x'], d['y'], remove_nan=True),
d['ident_acc'],
))
d['ident_acc'], rtol=1e-12, atol=1e-12
)

if __name__ == '__main__':
unittest.main()
24 changes: 12 additions & 12 deletions tests/feature/test_feature.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ def test_normalize_feature_1d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (channel-wise) + SD (all)
feat_valid = ((feat - feat_mean_ch) / feat_std_all) * feat_std0 + feat_mean0
Expand All @@ -35,7 +35,7 @@ def test_normalize_feature_1d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (all) + SD (channel-wise)
feat_valid = ((feat - feat_mean_all) / feat_std_ch) * feat_std0 + feat_mean0
Expand All @@ -44,7 +44,7 @@ def test_normalize_feature_1d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (all) + SD (all)
feat_valid = ((feat - feat_mean_all) / feat_std_all) * feat_std0 + feat_mean0
Expand All @@ -53,7 +53,7 @@ def test_normalize_feature_1d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (channel-wise) + SD (channel-wise), self-mean shift
feat_valid = ((feat - feat_mean_ch) / feat_std_ch) * feat_std0 + feat_mean_ch
Expand All @@ -62,7 +62,7 @@ def test_normalize_feature_1d(self):
shift='self', scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (channel-wise) + SD (channel-wise), self-mean shift and self-SD scale
feat_valid = ((feat - feat_mean_ch) / feat_std_ch) * feat_std_ch + feat_mean_ch
Expand All @@ -71,7 +71,7 @@ def test_normalize_feature_1d(self):
shift='self', scale='self',
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

def test_normalize_feature_3d(self):
feat = np.random.rand(64, 16, 16)
Expand All @@ -94,7 +94,7 @@ def test_normalize_feature_3d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (channel-wise) + SD (all)
feat_valid = ((feat - feat_mean_ch) / feat_std_all) * feat_std0 + feat_mean0
Expand All @@ -103,7 +103,7 @@ def test_normalize_feature_3d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (all) + SD (channel-wise)
feat_valid = ((feat - feat_mean_all) / feat_std_ch) * feat_std0 + feat_mean0
Expand All @@ -112,7 +112,7 @@ def test_normalize_feature_3d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (all) + SD (all)
feat_valid = ((feat - feat_mean_all) / feat_std_all) * feat_std0 + feat_mean0
Expand All @@ -121,7 +121,7 @@ def test_normalize_feature_3d(self):
shift=feat_mean0, scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (channel-wise) + SD (channel-wise), self-mean shift
feat_valid = ((feat - feat_mean_ch) / feat_std_ch) * feat_std0 + feat_mean_ch
Expand All @@ -130,7 +130,7 @@ def test_normalize_feature_3d(self):
shift='self', scale=feat_std0,
std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)

# Mean (channel-wise) + SD (channel-wise), self-mean shift and self-SD scale
feat_valid = ((feat - feat_mean_ch) / feat_std_ch) * feat_std_ch + feat_mean_ch
Expand All @@ -146,7 +146,7 @@ def test_normalize_feature_3d(self):
channel_wise_std=False,
scale=feat_std0, std_ddof=1)

np.testing.assert_array_equal(feat_test, feat_valid)
np.testing.assert_allclose(feat_test, feat_valid, rtol=1e-12, atol=1e-12)


if __name__ == '__main__':
Expand Down
8 changes: 4 additions & 4 deletions tests/preproc/test_interface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ def test_average_sample(cls):
test_output_x, test_output_ind = interface.average_sample(
x, group, verbose=True)

np.testing.assert_array_equal(test_output_x, exp_output_x)
np.testing.assert_allclose(test_output_x, exp_output_x, rtol=1e-12, atol=1e-12)
np.testing.assert_array_equal(test_output_ind, exp_output_ind)

@classmethod
Expand All @@ -43,7 +43,7 @@ def test_detrend_sample_default(cls):

test_output = interface.detrend_sample(x, group, verbose=True)

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

@classmethod
def test_detrend_sample_nokeepmean(cls):
Expand All @@ -59,7 +59,7 @@ def test_detrend_sample_nokeepmean(cls):
test_output = interface.detrend_sample(
x, group, keep_mean=False, verbose=True)

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

@classmethod
def test_normalize_sample(cls):
Expand All @@ -77,7 +77,7 @@ def test_normalize_sample(cls):

test_output = interface.normalize_sample(x, group, verbose=True)

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

@classmethod
def test_shift_sample_singlegroup(cls):
Expand Down
5 changes: 3 additions & 2 deletions tests/recon/torch/modules/test_optimizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ def test_build_optimizer_factory(self):
latent_next,
latent_next_expected,
rtol=1e-6,
atol=1e-8,
err_msg="Optimizer does not update the latent variable correctly.",
)

Expand Down Expand Up @@ -92,10 +93,10 @@ def test_build_scheduler_factory(self):
loss.backward()
optimizer.step()
scheduler.step()
self.assertEqual(
self.assertAlmostEqual(
optimizer.param_groups[0]["lr"],
0.1 * 0.1,
"Scheduler does not update the learning rate correctly.",
msg="Scheduler does not update the learning rate correctly.",
)

# check if reference to the optimizer is kept during re-initialization
Expand Down
10 changes: 5 additions & 5 deletions tests/test_stats.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ def test_corrcoef_matrix_matrix_default(self):

test_output = bdst.corrcoef(x, y)

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

def test_corrcoef_matrix_matrix_varcol(self):
'''Test for corrcoef (matrix and matrix, var=col)'''
Expand All @@ -33,7 +33,7 @@ def test_corrcoef_matrix_matrix_varcol(self):

test_output = bdst.corrcoef(x, y, var='col')

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

def test_corrcoef_vector_vector(self):
'''Test for corrcoef (vector and vector)'''
Expand All @@ -45,7 +45,7 @@ def test_corrcoef_vector_vector(self):

test_output = bdst.corrcoef(x, y)

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

def test_corrcoef_hvector_hvector(self):
'''Test for corrcoef (horizontal vector and horizontal vector)'''
Expand All @@ -57,7 +57,7 @@ def test_corrcoef_hvector_hvector(self):

test_output = bdst.corrcoef(x, y)

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

def test_corrcoef_vvector_vvector(self):
'''Test for corrcoef (vertical vector and vertical vector)'''
Expand All @@ -69,7 +69,7 @@ def test_corrcoef_vvector_vvector(self):

test_output = bdst.corrcoef(x, y)

np.testing.assert_array_equal(test_output, exp_output)
np.testing.assert_allclose(test_output, exp_output, rtol=1e-12, atol=1e-12)

def test_corrcoef_matrix_vector_varrow(self):
'''Test for corrcoef (matrix and vector, var=row)'''
Expand Down
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