[med-svn] [ariba] 13/14: patch some upstream issues

[Sascha Steinbiss]

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satta pushed a commit to branch master
in repository ariba.

commit 96efe6abc1aa0d065a28952a0000abb1f912cb62
Author: Sascha Steinbiss <satta at debian.org>
Date:   Sun Jul 31 21:37:39 2016 +0000

    patch some upstream issues
---
 debian/patches/disable_spades_tests.patch | 17 +++++++++++++++++
 debian/patches/rename_test_input.patch    | 16 ++++++++++++++++
 debian/patches/series                     |  2 ++
 3 files changed, 35 insertions(+)

diff --git a/debian/patches/disable_spades_tests.patch b/debian/patches/disable_spades_tests.patch
new file mode 100644
index 0000000..924414c
--- /dev/null
+++ b/debian/patches/disable_spades_tests.patch
@@ -0,0 +1,17 @@
+Description: disable SPAdes specific test
+ This patch disables tests still requiring SPAdes support, as the
+ dependency on SPAdes has been dropped from 2.0.0+ds-1 on.
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/ariba/tests/assembly_test.py
++++ b/ariba/tests/assembly_test.py
+@@ -21,8 +21,8 @@
+         self.assertEqual(got, 42)
+ 
+ 
+-    def test_check_spades_log_file(self):
+-        '''test _check_spades_log_file'''
++    def _test_check_spades_log_file(self):
++        '''_test _check_spades_log_file'''
+         good_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.good')
+         bad_file = os.path.join(data_dir, 'assembly_test_check_spades_log_file.log.bad')
+         self.assertTrue(assembly.Assembly._check_spades_log_file(good_file))
diff --git a/debian/patches/rename_test_input.patch b/debian/patches/rename_test_input.patch
new file mode 100644
index 0000000..5d319db
--- /dev/null
+++ b/debian/patches/rename_test_input.patch
@@ -0,0 +1,16 @@
+Description: rename test input
+ This patch makes sure the correct file name is used for a
+ negative test targeting the fermi-lite extension. Trying to read a
+ nonexistent file leads to a failing assertion in fermi-lite's mrope.c.
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/ariba/tests/assembly_test.py
++++ b/ariba/tests/assembly_test.py
+@@ -47,7 +47,7 @@
+ 
+     def test_run_fermilite_fails(self):
+         '''test _run_fermilite when it fails'''
+-        reads = os.path.join(data_dir, 'assembly_run_fermilite_fails.reads.fq')
++        reads = os.path.join(data_dir, 'assembly_run_fermilite_fail.reads.fq')
+         tmp_fa = 'tmp.test_run_fermilite_fails.fa'
+         tmp_log = 'tmp.test_run_fermilite_fails.log'
+         expected_log = os.path.join(data_dir, 'assembly_run_fermilite_fails.expected.log')
diff --git a/debian/patches/series b/debian/patches/series
index 2fdf295..af2c346 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,4 @@
 rename-cdhit.patch
 use_debian_packaged_libs_for_extension.patch
+disable_spades_tests.patch
+rename_test_input.patch

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