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TST: Review _assert_within_tol positional arguments #15087

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merged 9 commits into from Dec 2, 2021
Merged

TST: Review _assert_within_tol positional arguments #15087

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7104f8f
TST: Review ``_assert_within_tol`` positional arguments
Kai-Striega Nov 23, 2021
192c768
STY: Fix whitespace around operators
Kai-Striega Nov 24, 2021
623f6f4
TST: Review test tolerances
Kai-Striega Nov 24, 2021
1bc855f
TST: Remove ``_asert_within_tol`` helper function
Kai-Striega Nov 25, 2021
3a6faa4
TST: Use atol for ``test_pdist_cosine_iris_*`` tests
Kai-Striega Dec 2, 2021
d3bdc48
Merge branch 'master' into fix_distance_verbosity_test
Kai-Striega Dec 2, 2021
c382bdf
TST: Remove `_assert_within_tol` from merge commit
Kai-Striega Dec 2, 2021
229b658
TST: Fix verbose_ argument
Kai-Striega Dec 2, 2021
abbfda5
TST: Revert to `atol` test_pdist_jensenshannon_iris
Kai-Striega Dec 2, 2021
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46 changes: 23 additions & 23 deletions scipy/spatial/tests/test_distance.py
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Expand Up @@ -439,24 +439,24 @@ def _my_metric(x, y, arg, kwarg=1, kwarg2=2):
arg=1.1, kwarg2=3.3), 5.4)

def test_cdist_euclidean_random_unicode(self):
eps = 1e-07
eps = 1e-15
X1 = eo['cdist-X1']
X2 = eo['cdist-X2']
Y1 = wcdist_no_const(X1, X2, 'euclidean')
Y2 = wcdist_no_const(X1, X2, 'test_euclidean')
_assert_within_tol(Y1, Y2, eps, verbose > 2)
_assert_within_tol(Y1, Y2, rtol=eps, verbose_=verbose > 2)

@pytest.mark.parametrize("p", [1.0, 1.23, 2.0, 3.8, 4.6, np.inf])
def test_cdist_minkowski_random(self, p):
eps = 1e-07
eps = 1e-15
X1 = eo['cdist-X1']
X2 = eo['cdist-X2']
Y1 = wcdist_no_const(X1, X2, 'minkowski', p=p)
Y2 = wcdist_no_const(X1, X2, 'test_minkowski', p=p)
_assert_within_tol(Y1, Y2, eps, verbose > 2)
_assert_within_tol(Y1, Y2, rtol=eps, verbose_=verbose > 2)

def test_cdist_cosine_random(self):
eps = 1e-07
eps = 1e-14
X1 = eo['cdist-X1']
X2 = eo['cdist-X2']
Y1 = wcdist(X1, X2, 'cosine')
Expand All @@ -467,7 +467,7 @@ def norms(X):

Y2 = 1 - np.dot((X1 / norms(X1)), (X2 / norms(X2)).T)

_assert_within_tol(Y1, Y2, eps, verbose > 2)
_assert_within_tol(Y1, Y2, rtol=eps, verbose_=verbose > 2)

def test_cdist_mahalanobis(self):
# 1-dimensional observations
Expand Down Expand Up @@ -575,11 +575,11 @@ def test_cdist_dtype_equivalence(self):
else:
for new_type in test[1]:
y2 = cdist(new_type(X1), new_type(X2), metric=metric)
_assert_within_tol(y1, y2, eps, verbose > 2)
_assert_within_tol(y1, y2, rtol=eps, verbose_=verbose > 2)
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Did you try tightening the eps in this test? It's still at 1e-07.


def test_cdist_out(self):
# Test that out parameter works properly
eps = 1e-07
eps = 1e-15
X1 = eo['cdist-X1']
X2 = eo['cdist-X2']
out_r, out_c = X1.shape[0], X2.shape[0]
Expand All @@ -592,7 +592,7 @@ def test_cdist_out(self):
Y1 = cdist(X1, X2, metric, **kwargs)
Y2 = cdist(X1, X2, metric, out=out1, **kwargs)
# test that output is numerically equivalent
_assert_within_tol(Y1, Y2, eps, verbose > 2)
_assert_within_tol(Y1, Y2, rtol=eps, verbose_=verbose > 2)
# test that Y_test1 and out1 are the same object
assert_(Y2 is out1)
# test for incorrect shape
Expand All @@ -616,7 +616,7 @@ def test_cdist_out(self):
def test_striding(self):
# test that striding is handled correct with calls to
# _copy_array_if_base_present
eps = 1e-07
eps = 1e-15
X1 = eo['cdist-X1'][::2, ::2]
X2 = eo['cdist-X2'][::2, ::2]
X1_copy = X1.copy()
Expand All @@ -638,7 +638,7 @@ def test_striding(self):
Y1 = cdist(X1, X2, metric, **kwargs)
Y2 = cdist(X1_copy, X2_copy, metric, **kwargs)
# test that output is numerically equivalent
_assert_within_tol(Y1, Y2, eps, verbose > 2)
_assert_within_tol(Y1, Y2, rtol=eps, verbose_=verbose > 2)

def test_cdist_refcount(self):
for metric in _METRICS_NAMES:
Expand Down Expand Up @@ -747,7 +747,7 @@ def test_pdist_euclidean_iris_float32(self):
X = np.float32(eo['iris'])
Y_right = eo['pdist-euclidean-iris']
Y_test1 = wpdist_no_const(X, 'euclidean')
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)
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Same here.


@pytest.mark.slow
def test_pdist_euclidean_iris_nonC(self):
Expand Down Expand Up @@ -846,7 +846,7 @@ def test_pdist_cosine_iris_float32(self):
X = np.float32(eo['iris'])
Y_right = eo['pdist-cosine-iris']
Y_test1 = wpdist(X, 'cosine')
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)
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... and here...


@pytest.mark.slow
def test_pdist_cosine_iris_nonC(self):
Expand Down Expand Up @@ -900,7 +900,7 @@ def test_pdist_cityblock_iris_float32(self):
X = np.float32(eo['iris'])
Y_right = eo['pdist-cityblock-iris']
Y_test1 = wpdist_no_const(X, 'cityblock')
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)

@pytest.mark.slow
def test_pdist_cityblock_iris_nonC(self):
Expand Down Expand Up @@ -947,7 +947,7 @@ def test_pdist_correlation_iris_float32(self):
X = eo['iris']
Y_right = np.float32(eo['pdist-correlation-iris'])
Y_test1 = wpdist(X, 'correlation')
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)

@pytest.mark.slow
def test_pdist_correlation_iris_nonC(self):
Expand Down Expand Up @@ -1024,7 +1024,7 @@ def test_pdist_minkowski_5_8_iris_float32(self):
X = np.float32(eo['iris'])
Y_right = eo['pdist-minkowski-5.8-iris']
Y_test1 = wpdist_no_const(X, 'minkowski', p=5.8)
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)

@pytest.mark.slow
def test_pdist_minkowski_5_8_iris_nonC(self):
Expand Down Expand Up @@ -1178,7 +1178,7 @@ def test_pdist_jensenshannon_iris_float32(self):
X = np.float32(eo['iris'])
Y_right = eo['pdist-jensenshannon-iris']
Y_test1 = pdist(X, 'jensenshannon')
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)

def test_pdist_jensenshannon_iris_nonC(self):
eps = 5e-12
Expand All @@ -1204,7 +1204,7 @@ def test_pdist_chebyshev_random_float32(self):
X = np.float32(eo['pdist-double-inp'])
Y_right = eo['pdist-chebyshev']
Y_test1 = pdist(X, 'chebyshev')
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)

def test_pdist_chebyshev_random_nonC(self):
eps = 1e-08
Expand All @@ -1225,7 +1225,7 @@ def test_pdist_chebyshev_iris_float32(self):
X = np.float32(eo['iris'])
Y_right = eo['pdist-chebyshev-iris']
Y_test1 = pdist(X, 'chebyshev')
_assert_within_tol(Y_test1, Y_right, eps, verbose > 2)
_assert_within_tol(Y_test1, Y_right, atol=eps, verbose_=verbose > 2)

def test_pdist_chebyshev_iris_nonC(self):
eps = 1e-15
Expand Down Expand Up @@ -1376,15 +1376,15 @@ def test_pdist_canberra_match(self):
eps = 1e-10
y1 = wpdist_no_const(D, "canberra")
y2 = wpdist_no_const(D, "test_canberra")
_assert_within_tol(y1, y2, eps, verbose > 2)
_assert_within_tol(y1, y2, atol=eps, verbose_=verbose > 2)

def test_pdist_canberra_ticket_711(self):
# Test pdist(X, 'canberra') to see if Canberra gives the right result
# as reported on gh-1238.
eps = 1e-8
pdist_y = wpdist_no_const(([3.3], [3.4]), "canberra")
right_y = 0.01492537
_assert_within_tol(pdist_y, right_y, eps, verbose > 2)
_assert_within_tol(pdist_y, right_y, atol=eps, verbose_=verbose > 2)

def test_pdist_custom_notdouble(self):
# tests that when using a custom metric the data type is not altered
Expand Down Expand Up @@ -1470,7 +1470,7 @@ def test_pdist_dtype_equivalence(self):
else:
for new_type in test[1]:
y2 = pdist(new_type(X1), metric=metric)
_assert_within_tol(y1, y2, eps, verbose > 2)
_assert_within_tol(y1, y2, rtol=eps, verbose_=verbose > 2)

def test_pdist_out(self):
# Test that out parameter works properly
Expand Down Expand Up @@ -1516,7 +1516,7 @@ def test_striding(self):
Y1 = pdist(X, metric, **kwargs)
Y2 = pdist(X_copy, metric, **kwargs)
# test that output is numerically equivalent
_assert_within_tol(Y1, Y2, eps, verbose > 2)
_assert_within_tol(Y1, Y2, rtol=eps, verbose_=verbose > 2)

class TestSomeDistanceFunctions:

Expand Down