[med-svn] [Git][med-team/python-skbio][master] Add hack to get tests passing with np 1.24

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / python-skbio


Commits:
a83d97b4 by Nilesh Patra at 2023-01-25T20:55:34+05:30
Add hack to get tests passing with np 1.24

- - - - -


2 changed files:

- + debian/patches/numpy-1.24.patch
- debian/patches/series


Changes:

=====================================
debian/patches/numpy-1.24.patch
=====================================
@@ -0,0 +1,34 @@
+--- a/skbio/alignment/_indexing.py
++++ b/skbio/alignment/_indexing.py
+@@ -113,7 +113,10 @@
+         if isinstance(indexable, np.ndarray):
+             pass
+         elif hasattr(indexable, '__iter__'):
+-            indexable = np.asarray(list(indexable))
++            try:
++                indexable = np.asarray(list(indexable))
++            except:
++                indexable = np.asarray(list(indexable), dtype='object')
+         else:
+             return indexable
+ 
+--- a/skbio/sequence/tests/test_sequence.py
++++ b/skbio/sequence/tests/test_sequence.py
+@@ -459,7 +459,7 @@
+             Sequence(np.array([1, "23", 3]))
+         with self.assertRaises(TypeError):
+             # object
+-            Sequence(np.array([1, {}, ()]))
++            Sequence(np.array([1, {}, ()], dtype='object'))
+ 
+         # invalid input type (non-numpy.ndarray input)
+         with self.assertRaisesRegex(TypeError, r'tuple'):
+@@ -2212,7 +2212,7 @@
+                     yield i
+                 else:
+                     yield np.array([i], dtype=int)
+-        for c in (lambda x: x, list, tuple, lambda x: np.array(tuple(x)),
++        for c in (lambda x: x, list, tuple, lambda x: np.array(tuple(x), dtype='object'),
+                   lambda x: pd.Series(tuple(x))):
+             exp = np.arange(10, dtype=int)
+             obs = s._munge_to_index_array(c(mixed()))


=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ no_privacy_breach_logo.patch
 local_inventory
 older-scipy.patch
 modify-test.patch
+numpy-1.24.patch



View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/a83d97b4c1f37e3bb59df123d42fc4c1a4d07bf0

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View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/commit/a83d97b4c1f37e3bb59df123d42fc4c1a4d07bf0
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