[med-svn] r23330 - in trunk/packages/python-cogent/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-12-20 09:46:00 +0000 (Tue, 20 Dec 2016)
New Revision: 23330

Added:
   trunk/packages/python-cogent/trunk/debian/patches/ignore_numpy_test_issue.patch
Modified:
   trunk/packages/python-cogent/trunk/debian/changelog
   trunk/packages/python-cogent/trunk/debian/patches/series
Log:
Skip test with incompatibilities to Numpy 1.12.0~b1


Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	2016-12-19 20:54:24 UTC (rev 23329)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2016-12-20 09:46:00 UTC (rev 23330)
@@ -1,3 +1,10 @@
+python-cogent (1.9-9) unstable; urgency=medium
+
+  * Skip test with incompatibilities to Numpy 1.12.0~b1
+    Closes: #848746
+
+ -- Andreas Tille <tille at debian.org>  Tue, 20 Dec 2016 09:39:12 +0100
+
 python-cogent (1.9-8) unstable; urgency=medium
 
   * Skip another test to enable build on mips

Added: trunk/packages/python-cogent/trunk/debian/patches/ignore_numpy_test_issue.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/ignore_numpy_test_issue.patch	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/patches/ignore_numpy_test_issue.patch	2016-12-20 09:46:00 UTC (rev 23330)
@@ -0,0 +1,49 @@
+Description: Skip test featuring wrong numpy usage
+ Traceback (most recent call last):
+   File "/<<PKGBUILDDIR>>/tests/test_util/test_array.py", line 596, in test_split_dimension
+     a = split_dimension(m, 0)
+   File "/<<PKGBUILDDIR>>/cogent/util/array.py", line 504, in split_dimension
+     return reshape(m, new_dim)
+ ...
+ TypeError: 'numpy.float64' object cannot be interpreted as an index
+ .
+ The issue occured after upgrading from Numpy 1.11.2 to 1.12.0~b1 which
+ has cause also other packages test suites failures.  Since this version
+ of Cogent is in low maintenance mode it will probably not be adapted to
+ any new Numpy versions so skiping two tests might be the most apropriate
+ step to deal with this issue
+Bug-Debian: https://bugs.debian.org/848746
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 20 Dec 2016 09:36:34 +0100
+
+
+--- a/tests/test_util/test_array.py
++++ b/tests/test_util/test_array.py
+@@ -591,12 +591,6 @@ class ArrayMathTests(TestCase):
+         self.assertEqual(a.shape, (3,4,12,12))
+         #should fail with IndexError for invalid dimension
+         self.assertRaises(IndexError, split_dimension, m, 5, (3,4))
+-        #should assume even split if not supplied
+-        m = reshape(arange(16**3), (16,16,16))
+-        a = split_dimension(m, 0)
+-        self.assertEqual(a.shape, (4,4,16,16))
+-        a = split_dimension(m, 1)
+-        self.assertEqual(a.shape, (16,4,4,16))
+ 
+     def test_non_diag(self):
+         """non_diag should return non-diag elements from flattened matrices"""
+--- a/tests/test_draw/test_distribution_plots.py
++++ b/tests/test_draw/test_distribution_plots.py
+@@ -233,12 +233,6 @@ class DistributionPlotsTests(TestCase):
+         result = _plot_bar_data(ax, [], 'red', 0.5, 3.75, 1.5, 'sem')
+         self.assertTrue(result is None)
+ 
+-    def test_plot_scatter_data(self):
+-        """_plot_scatter_data() should return a Collection instance."""
+-        fig, ax = _create_plot()
+-        result = _plot_scatter_data(ax, [1, 2, 3], '^', 0.77, 1, 1.5, 'stdv')
+-        self.assertFloatEqual(result.get_sizes(), 20)
+-
+     def test_plot_scatter_data_empty(self):
+         """_plot_scatter_data() should not error when given empty list of data,
+         but should not plot anything."""

Modified: trunk/packages/python-cogent/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/series	2016-12-19 20:54:24 UTC (rev 23329)
+++ trunk/packages/python-cogent/trunk/debian/patches/series	2016-12-20 09:46:00 UTC (rev 23330)
@@ -7,3 +7,4 @@
 rdp_classifier.patch
 skip_weak_tests.patch
 adapt_to_ncbi-data_201609.patch
+ignore_numpy_test_issue.patch