Andreas Tille pushed to branch master at Debian Med / python-skbio
Commits: 27b8db6f by Andreas Tille at 2023-01-29T17:30:49+01:00 Fix some more numpy issues - - - - - b2462a75 by Andreas Tille at 2023-01-29T19:07:48+01:00 Temporary unavailable python-scipy-doc - - - - - ab3e3d2c by Andreas Tille at 2023-01-29T19:08:12+01:00 More numpy issues - - - - - 2 changed files: - debian/control - debian/patches/numpy-1.24.patch Changes: ===================================== debian/control ===================================== @@ -28,7 +28,7 @@ Build-Depends-Arch: python3-lockfile <!nocheck>, Build-Depends-Indep: python3-sphinx <!nodoc>, python3-sphinx-bootstrap-theme <!nodoc>, python3-doc <!nodoc>, - python-scipy-doc <!nodoc>, +# python-scipy-doc <!nodoc>, python-biom-format-doc <!nodoc>, python-pandas-doc <!nodoc> Standards-Version: 4.6.2 ===================================== debian/patches/numpy-1.24.patch ===================================== @@ -58,3 +58,72 @@ Forwarded: https://github.com/biocore/scikit-bio/issues/1839 except ValueError: raise QUALFormatError( "Could not convert quality scores to integers:\n%s" +--- a/skbio/metadata/_testing.py ++++ b/skbio/metadata/_testing.py +@@ -457,7 +457,7 @@ class PositionalMetadataMixinTests: + + def test_eq_from_different_source(self): + obj1 = self._positional_metadata_constructor_( +- 3, positional_metadata={'foo': np.array([1, 2, 3])}) ++ 3, positional_metadata={'foo': np.array([1, 2, 3], dtype=np.int64)}) + obj2 = self._positional_metadata_constructor_( + 3, positional_metadata=pd.DataFrame({'foo': [1, 2, 3]}, + index=['foo', 'bar', 'baz'])) +--- a/skbio/alignment/tests/test_tabular_msa.py ++++ b/skbio/alignment/tests/test_tabular_msa.py +@@ -1661,7 +1661,7 @@ class TestILoc(SharedPropertyIndexTests, + TabularMSA([a[0:0], b[0:0], c[0:0]], + metadata={3: 3}, + positional_metadata={3: np.array( +- [], dtype=int)})) ++ [], dtype=np.int64)})) + + def test_fancy_empty_both_axes(self): + a = DNA("ACGT", metadata={0: 0}, positional_metadata={0: [1, 2, 3, 4]}) +--- a/skbio/stats/_subsample.py ++++ b/skbio/stats/_subsample.py +@@ -226,7 +226,7 @@ def subsample_counts(counts, n, replace= + raise ValueError("n cannot be negative.") + + counts = np.asarray(counts) +- counts = counts.astype(int, casting='safe') ++ counts = counts.astype(np.int64, casting='safe') + + if counts.ndim != 1: + raise ValueError("Only 1-D vectors are supported.") +--- a/skbio/diversity/tests/test_driver.py ++++ b/skbio/diversity/tests/test_driver.py +@@ -157,7 +157,7 @@ class AlphaDiversityTests(TestCase): + + def test_empty(self): + # empty vector +- actual = alpha_diversity('observed_otus', np.array([], dtype=np.int64)) ++ actual = alpha_diversity('observed_otus', np.array([], dtype=np.int32)) + expected = pd.Series([0]) + assert_series_almost_equal(actual, expected) + +@@ -194,11 +194,11 @@ class AlphaDiversityTests(TestCase): + assert_series_almost_equal(actual, expected) + + def test_single_count_vector(self): +- actual = alpha_diversity('observed_otus', np.array([1, 0, 2])) ++ actual = alpha_diversity('observed_otus', np.array([1, 0, 2], np.int32)) + expected = pd.Series([2]) + assert_series_almost_equal(actual, expected) + +- actual = alpha_diversity('faith_pd', np.array([1, 3, 0, 1, 0]), ++ actual = alpha_diversity('faith_pd', np.array([1, 3, 0, 1, 0], np.int32), + tree=self.tree1, otu_ids=self.oids1) + self.assertAlmostEqual(actual[0], 4.5) + +@@ -252,6 +252,10 @@ class AlphaDiversityTests(TestCase): + def test_no_ids(self): + # expected values hand-calculated + expected = pd.Series([3, 3, 3, 3]) ++ # All this does not help ++ # expected = pd.Series(np.array([3, 3, 3, 3], int32)) ++ # actual = np.int64(alpha_diversity('observed_otus', self.table1)) ++ # actual = np.dtype('int64').type(alpha_diversity('observed_otus', self.table1)) + actual = alpha_diversity('observed_otus', self.table1) + assert_series_almost_equal(actual, expected) + View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/25c2f7dc92b4a683f456bceeb43f8c517a59595c...ab3e3d2cd2247f85503db43b49301d80472fa186 -- View it on GitLab: https://salsa.debian.org/med-team/python-skbio/-/compare/25c2f7dc92b4a683f456bceeb43f8c517a59595c...ab3e3d2cd2247f85503db43b49301d80472fa186 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit