[med-svn] [python-skbio] 01/04: Remove broken test

[Kevin Murray]

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

commit a54d7812c8211a33c66da96e21609c5b2b27641c
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Sun Feb 14 22:45:02 2016 -0800

    Remove broken test
---
 ...0005-Fix-test-failure-patch-from-upstream.patch |  1 -
 ...Remove-broken-test-on-upstream-suggestion.patch | 35 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 3 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch b/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch
index 8535817..886642c 100644
--- a/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch
+++ b/debian/patches/0005-Fix-test-failure-patch-from-upstream.patch
@@ -4,7 +4,6 @@ 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/debian/patches/0006-Remove-broken-test-on-upstream-suggestion.patch b/debian/patches/0006-Remove-broken-test-on-upstream-suggestion.patch
new file mode 100644
index 0000000..9f5d282
--- /dev/null
+++ b/debian/patches/0006-Remove-broken-test-on-upstream-suggestion.patch
@@ -0,0 +1,35 @@
+From: Kevin Murray <spam at kdmurray.id.au>
+Date: Sun, 14 Feb 2016 22:44:23 -0800
+Subject: Remove broken test on upstream suggestion
+
+---
+ skbio/io/format/tests/test_fastq.py | 16 +++++++++-------
+ 1 file changed, 9 insertions(+), 7 deletions(-)
+
+diff --git a/skbio/io/format/tests/test_fastq.py b/skbio/io/format/tests/test_fastq.py
+index cd7bab2..ae445bc 100644
+--- a/skbio/io/format/tests/test_fastq.py
++++ b/skbio/io/format/tests/test_fastq.py
+@@ -343,13 +343,15 @@ class TestReaders(unittest.TestCase):
+                                        'out of range \[0, 62\]'):
+                 list(_fastq_to_generator(fp, variant='illumina1.8'))
+ 
+-    def test_fastq_to_generator_solexa(self):
+-        # solexa support isn't implemented yet. should raise error even with
+-        # valid solexa file
+-        with self.assertRaises(NotImplementedError):
+-            list(_fastq_to_generator(
+-                get_data_path('solexa_full_range_original_solexa.fastq'),
+-                variant='solexa'))
++    # DEBIAN: This test hangs indefinately due to a Python bug. See
++    # https://github.com/biocore/scikit-bio/issues/1256
++    # def test_fastq_to_generator_solexa(self):
++    #     # solexa support isn't implemented yet. should raise error even with
++    #     # valid solexa file
++    #     with self.assertRaises(NotImplementedError):
++    #         list(_fastq_to_generator(
++    #             get_data_path('solexa_full_range_original_solexa.fastq'),
++    #             variant='solexa'))
+ 
+     def test_fastq_to_sequence(self):
+         for constructor in [Sequence, DNA, RNA, Protein]:
diff --git a/debian/patches/series b/debian/patches/series
index b43e709..a40c4be 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@
 0005-Set-mathjax-path-to-debian-s-copy.patch
 0004-Don-t-build-pdf-figures.patch
 0005-Fix-test-failure-patch-from-upstream.patch
+0006-Remove-broken-test-on-upstream-suggestion.patch

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