[med-svn] [python-skbio] 02/03: Patch broken test w/ upstream fix

[Kevin Murray]

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daube-guest pushed a commit to branch master
in repository python-skbio.

commit a7e9fae8604720de2c3c0b1f89e6cc51f4143318
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Sat Feb 13 18:30:15 2016 -0800

    Patch broken test w/ upstream fix
    
    (So autopkgtests pass)
---
 ...0005-Fix-test-failure-patch-from-upstream.patch | 35 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 2 files changed, 36 insertions(+)

diff --git a/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch b/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch
new file mode 100644
index 0000000..8535817
--- /dev/null
+++ b/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch
@@ -0,0 +1,35 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sat, 13 Feb 2016 18:46:48 -0800
+Subject: Fix test failure (patch from upstream)
+
+Remove when 0.5.0 is released, this patch extracted from upstream changes to
+allow autopkgtests to pass.
+
+---
+ skbio/stats/tests/test_composition.py | 6 +++---
+ 1 file changed, 3 insertions(+), 3 deletions(-)
+
+diff --git a/skbio/stats/tests/test_composition.py b/skbio/stats/tests/test_composition.py
+index 00e5ac1..ffdb236 100644
+--- a/skbio/stats/tests/test_composition.py
++++ b/skbio/stats/tests/test_composition.py
+@@ -622,8 +622,8 @@ class AncomTests(TestCase):
+         result = ancom(self.table1,
+                        self.cats1,
+                        multiple_comparisons_correction=None,
+-                       significance_test=scipy.stats.mannwhitneyu)
+-        exp = pd.DataFrame({'W': np.array([6, 6, 2, 2, 2, 2, 2]),
++                       significance_test=scipy.stats.ttest_ind)
++        exp = pd.DataFrame({'W': np.array([5, 5, 2, 2, 2, 2, 2]),
+                             'reject': np.array([True,  True, False, False,
+                                                 False, False, False],
+                                                dtype=bool)})
+@@ -633,7 +633,7 @@ class AncomTests(TestCase):
+         result = ancom(self.table2,
+                        self.cats2,
+                        multiple_comparisons_correction=None,
+-                       significance_test=scipy.stats.mannwhitneyu)
++                       significance_test=scipy.stats.ttest_ind)
+         exp = pd.DataFrame({'W': np.array([8, 8, 3, 3,
+                                            8, 3, 3, 3, 3]),
+                             'reject': np.array([True, True, False, False,
diff --git a/debian/patches/series b/debian/patches/series
index 40b52c0..b43e709 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@
 0004-Don-t-turn-sphinx-warnings-into-errors.patch
 0005-Set-mathjax-path-to-debian-s-copy.patch
 0004-Don-t-build-pdf-figures.patch
+0005-Fix-test-failure-patch-from-upstream.patch

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