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Migrate tests/test_aamp_ostinato.py from npt.assert_almost_equal to npt.assert_allclose (#1182)
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Lines changed: 46 additions & 41 deletions

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‎tests/test_aamp_ostinato.py‎

Lines changed: 46 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -31,11 +31,11 @@ def test_random_ostinato(runs):
3131
Ts = [rng.RNG.rand(n) for n in [64, 128, 256]]
3232

3333
ref_radius, ref_Ts_idx, ref_subseq_idx = naive.aamp_ostinato(Ts, m)
34-
comp_radius, comp_Ts_idx, comp_subseq_idx = aamp_ostinato(Ts, m)
34+
cmp_radius, cmp_Ts_idx, cmp_subseq_idx = aamp_ostinato(Ts, m)
3535

36-
npt.assert_almost_equal(ref_radius, comp_radius)
37-
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
38-
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
36+
npt.assert_allclose(cmp_radius, ref_radius, atol=1.5e-07)
37+
npt.assert_allclose(cmp_Ts_idx, ref_Ts_idx, atol=1.5e-07)
38+
npt.assert_allclose(cmp_subseq_idx, ref_subseq_idx, atol=1.5e-07)
3939

4040

4141
@pytest.mark.parametrize("seed", [41, 88, 290, 292, 310, 328, 538, 556, 563, 570])
@@ -47,11 +47,11 @@ def test_deterministic_ostinato(seed):
4747

4848
for p in [1.0, 2.0, 3.0]:
4949
ref_radius, ref_Ts_idx, ref_subseq_idx = naive.aamp_ostinato(Ts, m, p=p)
50-
comp_radius, comp_Ts_idx, comp_subseq_idx = aamp_ostinato(Ts, m, p=p)
50+
cmp_radius, cmp_Ts_idx, cmp_subseq_idx = aamp_ostinato(Ts, m, p=p)
5151

52-
npt.assert_almost_equal(ref_radius, comp_radius)
53-
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
54-
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
52+
npt.assert_allclose(cmp_radius, ref_radius, atol=1.5e-07)
53+
npt.assert_allclose(cmp_Ts_idx, ref_Ts_idx, atol=1.5e-07)
54+
npt.assert_allclose(cmp_subseq_idx, ref_subseq_idx, atol=1.5e-07)
5555

5656

5757
@pytest.mark.parametrize("runs", range(25))
@@ -61,11 +61,11 @@ def test_random_ostinatoed(runs, dask_cluster):
6161
Ts = [rng.RNG.rand(n) for n in [64, 128, 256]]
6262

6363
ref_radius, ref_Ts_idx, ref_subseq_idx = naive.aamp_ostinato(Ts, m)
64-
comp_radius, comp_Ts_idx, comp_subseq_idx = aamp_ostinatoed(dask_client, Ts, m)
64+
cmp_radius, cmp_Ts_idx, cmp_subseq_idx = aamp_ostinatoed(dask_client, Ts, m)
6565

66-
npt.assert_almost_equal(ref_radius, comp_radius)
67-
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
68-
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
66+
npt.assert_allclose(cmp_radius, ref_radius, atol=1.5e-07)
67+
npt.assert_allclose(cmp_Ts_idx, ref_Ts_idx, atol=1.5e-07)
68+
npt.assert_allclose(cmp_subseq_idx, ref_subseq_idx, atol=1.5e-07)
6969

7070

7171
@pytest.mark.parametrize("seed", [41, 88, 290, 292, 310, 328, 538, 556, 563, 570])
@@ -78,13 +78,13 @@ def test_deterministic_ostinatoed(seed, dask_cluster):
7878

7979
for p in [1.0, 2.0, 3.0]:
8080
ref_radius, ref_Ts_idx, ref_subseq_idx = naive.aamp_ostinato(Ts, m, p=p)
81-
comp_radius, comp_Ts_idx, comp_subseq_idx = aamp_ostinatoed(
81+
cmp_radius, cmp_Ts_idx, cmp_subseq_idx = aamp_ostinatoed(
8282
dask_client, Ts, m, p=p
8383
)
8484

85-
npt.assert_almost_equal(ref_radius, comp_radius)
86-
npt.assert_almost_equal(ref_Ts_idx, comp_Ts_idx)
87-
npt.assert_almost_equal(ref_subseq_idx, comp_subseq_idx)
85+
npt.assert_allclose(cmp_radius, ref_radius, atol=1.5e-07)
86+
npt.assert_allclose(cmp_Ts_idx, ref_Ts_idx, atol=1.5e-07)
87+
npt.assert_allclose(cmp_subseq_idx, ref_subseq_idx, atol=1.5e-07)
8888

8989

9090
def test_input_not_overwritten_ostinato():
@@ -101,42 +101,46 @@ def test_input_not_overwritten_ostinato():
101101
aamp_ostinato(Ts_input, m)
102102
for i in range(len(Ts)):
103103
T_ref = Ts[i]
104-
T_comp = Ts_input[i]
105-
npt.assert_almost_equal(T_ref[np.isfinite(T_ref)], T_comp[np.isfinite(T_comp)])
104+
T_cmp = Ts_input[i]
105+
npt.assert_allclose(
106+
T_cmp[np.isfinite(T_cmp)], T_ref[np.isfinite(T_ref)], atol=1.5e-07
107+
)
106108

107109

108110
def test_extract_several_consensus_ostinato():
109111
# This test is to further ensure that the function `aamp_ostinato`
110112
# does not tamper with the original data.
111113
Ts = [rng.RNG.rand(n) for n in [256, 512, 1024]]
112114
Ts_ref = [T.copy() for T in Ts]
113-
Ts_comp = [T.copy() for T in Ts]
115+
Ts_cmp = [T.copy() for T in Ts]
114116

115117
m = 20
116118

117119
k = 5 # Get the first `k` consensus motifs
118120
for _ in range(k):
119-
# Find consensus motif and its NN in each time series in Ts_comp
120-
# Remove them from Ts_comp as well as Ts_ref, and assert that the
121+
# Find consensus motif and its NN in each time series in Ts_cmp
122+
# Remove them from Ts_cmp as well as Ts_ref, and assert that the
121123
# two time series are the same
122-
radius, Ts_idx, subseq_idx = aamp_ostinato(Ts_comp, m)
123-
consensus_motif = Ts_comp[Ts_idx][subseq_idx : subseq_idx + m].copy()
124-
for i in range(len(Ts_comp)):
124+
radius, Ts_idx, subseq_idx = aamp_ostinato(Ts_cmp, m)
125+
consensus_motif = Ts_cmp[Ts_idx][subseq_idx : subseq_idx + m].copy()
126+
for i in range(len(Ts_cmp)):
125127
if i == Ts_idx:
126128
query_idx = subseq_idx
127129
else:
128130
query_idx = None
129131

130132
idx = np.argmin(
131133
core.mass(
132-
consensus_motif, Ts_comp[i], normalize=False, query_idx=query_idx
134+
consensus_motif, Ts_cmp[i], normalize=False, query_idx=query_idx
133135
)
134136
)
135-
Ts_comp[i][idx : idx + m] = np.nan
137+
Ts_cmp[i][idx : idx + m] = np.nan
136138
Ts_ref[i][idx : idx + m] = np.nan
137139

138-
npt.assert_almost_equal(
139-
Ts_ref[i][np.isfinite(Ts_ref[i])], Ts_comp[i][np.isfinite(Ts_comp[i])]
140+
npt.assert_allclose(
141+
Ts_cmp[i][np.isfinite(Ts_cmp[i])],
142+
Ts_ref[i][np.isfinite(Ts_ref[i])],
143+
atol=1.5e-07,
140144
)
141145

142146

@@ -155,9 +159,9 @@ def test_input_not_overwritten_ostinatoed(dask_cluster):
155159
aamp_ostinatoed(dask_client, Ts_input, m)
156160
for i in range(len(Ts)):
157161
T_ref = Ts[i]
158-
T_comp = Ts_input[i]
159-
npt.assert_almost_equal(
160-
T_ref[np.isfinite(T_ref)], T_comp[np.isfinite(T_comp)]
162+
T_cmp = Ts_input[i]
163+
npt.assert_allclose(
164+
T_cmp[np.isfinite(T_cmp)], T_ref[np.isfinite(T_ref)], atol=1.5e-07
161165
)
162166

163167

@@ -166,19 +170,19 @@ def test_extract_several_consensus_ostinatoed(dask_cluster):
166170
# does not tamper with the original data.
167171
Ts = [rng.RNG.rand(n) for n in [256, 512, 1024]]
168172
Ts_ref = [T.copy() for T in Ts]
169-
Ts_comp = [T.copy() for T in Ts]
173+
Ts_cmp = [T.copy() for T in Ts]
170174

171175
m = 20
172176

173177
with Client(dask_cluster) as dask_client:
174178
k = 5 # Get the first `k` consensus motifs
175179
for _ in range(k):
176-
# Find consensus motif and its NN in each time series in Ts_comp
177-
# Remove them from Ts_comp as well as Ts_ref, and assert that the
180+
# Find consensus motif and its NN in each time series in Ts_cmp
181+
# Remove them from Ts_cmp as well as Ts_ref, and assert that the
178182
# two time series are the same
179-
radius, Ts_idx, subseq_idx = aamp_ostinatoed(dask_client, Ts_comp, m)
180-
consensus_motif = Ts_comp[Ts_idx][subseq_idx : subseq_idx + m].copy()
181-
for i in range(len(Ts_comp)):
183+
radius, Ts_idx, subseq_idx = aamp_ostinatoed(dask_client, Ts_cmp, m)
184+
consensus_motif = Ts_cmp[Ts_idx][subseq_idx : subseq_idx + m].copy()
185+
for i in range(len(Ts_cmp)):
182186
if i == Ts_idx:
183187
query_idx = subseq_idx
184188
else:
@@ -187,15 +191,16 @@ def test_extract_several_consensus_ostinatoed(dask_cluster):
187191
idx = np.argmin(
188192
core.mass(
189193
consensus_motif,
190-
Ts_comp[i],
194+
Ts_cmp[i],
191195
normalize=False,
192196
query_idx=query_idx,
193197
)
194198
)
195-
Ts_comp[i][idx : idx + m] = np.nan
199+
Ts_cmp[i][idx : idx + m] = np.nan
196200
Ts_ref[i][idx : idx + m] = np.nan
197201

198-
npt.assert_almost_equal(
202+
npt.assert_allclose(
203+
Ts_cmp[i][np.isfinite(Ts_cmp[i])],
199204
Ts_ref[i][np.isfinite(Ts_ref[i])],
200-
Ts_comp[i][np.isfinite(Ts_comp[i])],
205+
atol=1.5e-07,
201206
)

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