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Fixed #1175 Migrate tests/test_aamp.py to npt.assert_allclose (#1178)
* Migrate tests/test_aamp.py from npt.assert_almost_equal to npt.assert_allclose npt.assert_almost_equal only checks a fixed absolute tolerance, and NumPy's docs recommend assert_allclose instead. Every comparison in this file is against `ref_mp`/`comp_mp` (or a column slice of it), which combine a float distance column with int index columns and so come back dtype=object - np.isclose can't handle that directly. Cast both sides to float64 before comparing instead of leaving these on the deprecated API; the values are always numeric so the cast is exact. rtol is left at its default rather than pinned to 0. First of a per-file split of #1175, per review feedback. * Addressed comments Flip npt.assert_allclose args so the stumpy-computed value is `actual` (1st) and naive is `desired` (2nd), and use a literal atol (1.5e-05) instead of a computed 1.5 * 10**-config.STUMPY_TEST_PRECISION expression for consistency. Also drops the now-unused config import. * Addressed comments Keep the reference to config.STUMPY_TEST_PRECISION instead of hardcoding its current value as a literal atol. * Addressed comments Rename comp_mp to cmp_mp so ref and cmp are both three letters.
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‎tests/test_aamp.py‎

Lines changed: 140 additions & 86 deletions
Original file line numberDiff line numberDiff line change
@@ -32,65 +32,83 @@ def test_aamp_self_join(T_A, T_B):
3232
m = 3
3333
for p in [1.0, 2.0, 3.0]:
3434
ref_mp = naive.aamp(T_B, m, p=p)
35-
comp_mp = aamp(T_B, m, p=p)
35+
cmp_mp = aamp(T_B, m, p=p)
3636
naive.replace_inf(ref_mp)
37-
naive.replace_inf(comp_mp)
38-
npt.assert_almost_equal(ref_mp, comp_mp)
37+
naive.replace_inf(cmp_mp)
38+
npt.assert_allclose(
39+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
40+
)
3941

40-
comp_mp = aamp(pd.Series(T_B), m, p=p)
41-
naive.replace_inf(comp_mp)
42-
npt.assert_almost_equal(ref_mp, comp_mp)
42+
cmp_mp = aamp(pd.Series(T_B), m, p=p)
43+
naive.replace_inf(cmp_mp)
44+
npt.assert_allclose(
45+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
46+
)
4347

4448

4549
@pytest.mark.parametrize("T_A, T_B", test_data)
4650
def test_aamp_A_B_join(T_A, T_B):
4751
m = 3
4852
for p in [1.0, 2.0, 3.0]:
4953
ref_mp = naive.aamp(T_A, m, T_B=T_B, p=p)
50-
comp_mp = aamp(T_A, m, T_B, ignore_trivial=False, p=p)
54+
cmp_mp = aamp(T_A, m, T_B, ignore_trivial=False, p=p)
5155
naive.replace_inf(ref_mp)
52-
naive.replace_inf(comp_mp)
53-
npt.assert_almost_equal(ref_mp, comp_mp)
56+
naive.replace_inf(cmp_mp)
57+
npt.assert_allclose(
58+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
59+
)
5460

55-
comp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False, p=p)
56-
naive.replace_inf(comp_mp)
57-
npt.assert_almost_equal(ref_mp, comp_mp)
61+
cmp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False, p=p)
62+
naive.replace_inf(cmp_mp)
63+
npt.assert_allclose(
64+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
65+
)
5866

5967

6068
def test_aamp_constant_subsequence_self_join():
6169
T_A = np.concatenate((np.zeros(20, dtype=np.float64), np.ones(5, dtype=np.float64)))
6270
m = 3
6371
ref_mp = naive.aamp(T_A, m)
64-
comp_mp = aamp(T_A, m, ignore_trivial=True)
72+
cmp_mp = aamp(T_A, m, ignore_trivial=True)
6573
naive.replace_inf(ref_mp)
66-
naive.replace_inf(comp_mp)
67-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
74+
naive.replace_inf(cmp_mp)
75+
npt.assert_allclose(
76+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
77+
) # ignore indices
6878

69-
comp_mp = aamp(pd.Series(T_A), m, ignore_trivial=True)
70-
naive.replace_inf(comp_mp)
71-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
79+
cmp_mp = aamp(pd.Series(T_A), m, ignore_trivial=True)
80+
naive.replace_inf(cmp_mp)
81+
npt.assert_allclose(
82+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
83+
) # ignore indices
7284

7385

7486
def test_aamp_one_constant_subsequence_A_B_join():
7587
T_A = rng.RNG.random(20)
7688
T_B = np.concatenate((np.zeros(20, dtype=np.float64), np.ones(5, dtype=np.float64)))
7789
m = 3
7890
ref_mp = naive.aamp(T_A, m, T_B=T_B)
79-
comp_mp = aamp(T_A, m, T_B, ignore_trivial=False)
91+
cmp_mp = aamp(T_A, m, T_B, ignore_trivial=False)
8092
naive.replace_inf(ref_mp)
81-
naive.replace_inf(comp_mp)
82-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
93+
naive.replace_inf(cmp_mp)
94+
npt.assert_allclose(
95+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
96+
) # ignore indices
8397

84-
comp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False)
85-
naive.replace_inf(comp_mp)
86-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
98+
cmp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False)
99+
naive.replace_inf(cmp_mp)
100+
npt.assert_allclose(
101+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
102+
) # ignore indices
87103

88104
# Swap inputs
89105
ref_mp = naive.aamp(T_B, m, T_B=T_A)
90-
comp_mp = aamp(T_B, m, T_A, ignore_trivial=False)
106+
cmp_mp = aamp(T_B, m, T_A, ignore_trivial=False)
91107
naive.replace_inf(ref_mp)
92-
naive.replace_inf(comp_mp)
93-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
108+
naive.replace_inf(cmp_mp)
109+
npt.assert_allclose(
110+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
111+
) # ignore indices
94112

95113

96114
def test_aamp_two_constant_subsequences_A_B_join():
@@ -100,25 +118,33 @@ def test_aamp_two_constant_subsequences_A_B_join():
100118
T_B = np.concatenate((np.zeros(20, dtype=np.float64), np.ones(5, dtype=np.float64)))
101119
m = 3
102120
ref_mp = naive.aamp(T_A, m, T_B=T_B)
103-
comp_mp = aamp(T_A, m, T_B, ignore_trivial=False)
121+
cmp_mp = aamp(T_A, m, T_B, ignore_trivial=False)
104122
naive.replace_inf(ref_mp)
105-
naive.replace_inf(comp_mp)
106-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
123+
naive.replace_inf(cmp_mp)
124+
npt.assert_allclose(
125+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
126+
) # ignore indices
107127

108-
comp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False)
109-
naive.replace_inf(comp_mp)
110-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
128+
cmp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False)
129+
naive.replace_inf(cmp_mp)
130+
npt.assert_allclose(
131+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
132+
) # ignore indices
111133

112134
# Swap inputs
113135
ref_mp = naive.aamp(T_B, m, T_B=T_A)
114-
comp_mp = aamp(T_B, m, T_A, ignore_trivial=False)
136+
cmp_mp = aamp(T_B, m, T_A, ignore_trivial=False)
115137
naive.replace_inf(ref_mp)
116-
naive.replace_inf(comp_mp)
117-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
138+
naive.replace_inf(cmp_mp)
139+
npt.assert_allclose(
140+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
141+
) # ignore indices
118142

119-
comp_mp = aamp(pd.Series(T_B), m, pd.Series(T_A), ignore_trivial=False)
120-
naive.replace_inf(comp_mp)
121-
npt.assert_almost_equal(ref_mp[:, 0], comp_mp[:, 0]) # ignore indices
143+
cmp_mp = aamp(pd.Series(T_B), m, pd.Series(T_A), ignore_trivial=False)
144+
naive.replace_inf(cmp_mp)
145+
npt.assert_allclose(
146+
cmp_mp[:, 0].astype(np.float64), ref_mp[:, 0].astype(np.float64), atol=1.5e-07
147+
) # ignore indices
122148

123149

124150
def test_aamp_identical_subsequence_self_join():
@@ -128,17 +154,21 @@ def test_aamp_identical_subsequence_self_join():
128154
T_A[11 : 11 + identical.shape[0]] = identical
129155
m = 3
130156
ref_mp = naive.aamp(T_A, m)
131-
comp_mp = aamp(T_A, m, ignore_trivial=True)
157+
cmp_mp = aamp(T_A, m, ignore_trivial=True)
132158
naive.replace_inf(ref_mp)
133-
naive.replace_inf(comp_mp)
134-
npt.assert_almost_equal(
135-
ref_mp[:, 0], comp_mp[:, 0], decimal=config.STUMPY_TEST_PRECISION
159+
naive.replace_inf(cmp_mp)
160+
npt.assert_allclose(
161+
cmp_mp[:, 0].astype(np.float64),
162+
ref_mp[:, 0].astype(np.float64),
163+
atol=1.5 * 10**-config.STUMPY_TEST_PRECISION,
136164
) # ignore indices
137165

138-
comp_mp = aamp(pd.Series(T_A), m, ignore_trivial=True)
139-
naive.replace_inf(comp_mp)
140-
npt.assert_almost_equal(
141-
ref_mp[:, 0], comp_mp[:, 0], decimal=config.STUMPY_TEST_PRECISION
166+
cmp_mp = aamp(pd.Series(T_A), m, ignore_trivial=True)
167+
naive.replace_inf(cmp_mp)
168+
npt.assert_allclose(
169+
cmp_mp[:, 0].astype(np.float64),
170+
ref_mp[:, 0].astype(np.float64),
171+
atol=1.5 * 10**-config.STUMPY_TEST_PRECISION,
142172
) # ignore indices
143173

144174

@@ -150,26 +180,32 @@ def test_aamp_identical_subsequence_A_B_join():
150180
T_B[11 : 11 + identical.shape[0]] = identical
151181
m = 3
152182
ref_mp = naive.aamp(T_A, m, T_B=T_B)
153-
comp_mp = aamp(T_A, m, T_B, ignore_trivial=False)
183+
cmp_mp = aamp(T_A, m, T_B, ignore_trivial=False)
154184
naive.replace_inf(ref_mp)
155-
naive.replace_inf(comp_mp)
156-
npt.assert_almost_equal(
157-
ref_mp[:, 0], comp_mp[:, 0], config.STUMPY_TEST_PRECISION
185+
naive.replace_inf(cmp_mp)
186+
npt.assert_allclose(
187+
cmp_mp[:, 0].astype(np.float64),
188+
ref_mp[:, 0].astype(np.float64),
189+
atol=1.5 * 10**-config.STUMPY_TEST_PRECISION,
158190
) # ignore indices
159191

160-
comp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False)
161-
naive.replace_inf(comp_mp)
162-
npt.assert_almost_equal(
163-
ref_mp[:, 0], comp_mp[:, 0], config.STUMPY_TEST_PRECISION
192+
cmp_mp = aamp(pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False)
193+
naive.replace_inf(cmp_mp)
194+
npt.assert_allclose(
195+
cmp_mp[:, 0].astype(np.float64),
196+
ref_mp[:, 0].astype(np.float64),
197+
atol=1.5 * 10**-config.STUMPY_TEST_PRECISION,
164198
) # ignore indices
165199

166200
# Swap inputs
167201
ref_mp = naive.aamp(T_B, m, T_B=T_A)
168-
comp_mp = aamp(T_B, m, T_A, ignore_trivial=False)
202+
cmp_mp = aamp(T_B, m, T_A, ignore_trivial=False)
169203
naive.replace_inf(ref_mp)
170-
naive.replace_inf(comp_mp)
171-
npt.assert_almost_equal(
172-
ref_mp[:, 0], comp_mp[:, 0], config.STUMPY_TEST_PRECISION
204+
naive.replace_inf(cmp_mp)
205+
npt.assert_allclose(
206+
cmp_mp[:, 0].astype(np.float64),
207+
ref_mp[:, 0].astype(np.float64),
208+
atol=1.5 * 10**-config.STUMPY_TEST_PRECISION,
173209
) # ignore indices
174210

175211

@@ -186,14 +222,18 @@ def test_aamp_nan_inf_self_join(T_A, T_B, substitute_B, substitution_locations):
186222
T_B_sub[substitution_location_B] = substitute_B
187223

188224
ref_mp = naive.aamp(T_B_sub, m)
189-
comp_mp = aamp(T_B_sub, m, ignore_trivial=True)
225+
cmp_mp = aamp(T_B_sub, m, ignore_trivial=True)
190226
naive.replace_inf(ref_mp)
191-
naive.replace_inf(comp_mp)
192-
npt.assert_almost_equal(ref_mp, comp_mp)
227+
naive.replace_inf(cmp_mp)
228+
npt.assert_allclose(
229+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
230+
)
193231

194-
comp_mp = aamp(pd.Series(T_B_sub), m, ignore_trivial=True)
195-
naive.replace_inf(comp_mp)
196-
npt.assert_almost_equal(ref_mp, comp_mp)
232+
cmp_mp = aamp(pd.Series(T_B_sub), m, ignore_trivial=True)
233+
naive.replace_inf(cmp_mp)
234+
npt.assert_allclose(
235+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
236+
)
197237

198238

199239
@pytest.mark.parametrize("T_A, T_B", test_data)
@@ -216,28 +256,34 @@ def test_aamp_nan_inf_A_B_join(
216256
T_B_sub[substitution_location_B] = substitute_B
217257

218258
ref_mp = naive.aamp(T_A_sub, m, T_B=T_B_sub)
219-
comp_mp = aamp(T_A_sub, m, T_B_sub, ignore_trivial=False)
259+
cmp_mp = aamp(T_A_sub, m, T_B_sub, ignore_trivial=False)
220260
naive.replace_inf(ref_mp)
221-
naive.replace_inf(comp_mp)
222-
npt.assert_almost_equal(ref_mp, comp_mp)
261+
naive.replace_inf(cmp_mp)
262+
npt.assert_allclose(
263+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
264+
)
223265

224-
comp_mp = aamp(
266+
cmp_mp = aamp(
225267
pd.Series(T_A_sub), m, pd.Series(T_B_sub), ignore_trivial=False
226268
)
227-
naive.replace_inf(comp_mp)
228-
npt.assert_almost_equal(ref_mp, comp_mp)
269+
naive.replace_inf(cmp_mp)
270+
npt.assert_allclose(
271+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
272+
)
229273

230274

231275
def test_aamp_nan_zero_mean_self_join():
232276
T = np.array([-1, 0, 1, np.inf, 1, 0, -1])
233277
m = 3
234278

235279
ref_mp = naive.aamp(T, m)
236-
comp_mp = aamp(T, m, ignore_trivial=True)
280+
cmp_mp = aamp(T, m, ignore_trivial=True)
237281

238282
naive.replace_inf(ref_mp)
239-
naive.replace_inf(comp_mp)
240-
npt.assert_almost_equal(ref_mp, comp_mp)
283+
naive.replace_inf(cmp_mp)
284+
npt.assert_allclose(
285+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
286+
)
241287

242288

243289
@pytest.mark.parametrize("T_A, T_B", test_data)
@@ -246,14 +292,18 @@ def test_aamp_self_join_KNN(T_A, T_B):
246292
for k in range(2, 4):
247293
for p in [1.0, 2.0, 3.0]:
248294
ref_mp = naive.aamp(T_B, m, p=p, k=k)
249-
comp_mp = aamp(T_B, m, p=p, k=k)
295+
cmp_mp = aamp(T_B, m, p=p, k=k)
250296
naive.replace_inf(ref_mp)
251-
naive.replace_inf(comp_mp)
252-
npt.assert_almost_equal(ref_mp, comp_mp)
297+
naive.replace_inf(cmp_mp)
298+
npt.assert_allclose(
299+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
300+
)
253301

254-
comp_mp = aamp(pd.Series(T_B), m, p=p, k=k)
255-
naive.replace_inf(comp_mp)
256-
npt.assert_almost_equal(ref_mp, comp_mp)
302+
cmp_mp = aamp(pd.Series(T_B), m, p=p, k=k)
303+
naive.replace_inf(cmp_mp)
304+
npt.assert_allclose(
305+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
306+
)
257307

258308

259309
@pytest.mark.parametrize("T_A, T_B", test_data)
@@ -262,13 +312,17 @@ def test_aamp_A_B_join_KNN(T_A, T_B):
262312
for k in range(2, 4):
263313
for p in [1.0, 2.0, 3.0]:
264314
ref_mp = naive.aamp(T_A, m, T_B=T_B, p=p, k=k)
265-
comp_mp = aamp(T_A, m, T_B, ignore_trivial=False, p=p, k=k)
315+
cmp_mp = aamp(T_A, m, T_B, ignore_trivial=False, p=p, k=k)
266316
naive.replace_inf(ref_mp)
267-
naive.replace_inf(comp_mp)
268-
npt.assert_almost_equal(ref_mp, comp_mp)
317+
naive.replace_inf(cmp_mp)
318+
npt.assert_allclose(
319+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
320+
)
269321

270-
comp_mp = aamp(
322+
cmp_mp = aamp(
271323
pd.Series(T_A), m, pd.Series(T_B), ignore_trivial=False, p=p, k=k
272324
)
273-
naive.replace_inf(comp_mp)
274-
npt.assert_almost_equal(ref_mp, comp_mp)
325+
naive.replace_inf(cmp_mp)
326+
npt.assert_allclose(
327+
cmp_mp.astype(np.float64), ref_mp.astype(np.float64), atol=1.5e-07
328+
)

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