debian/changelog

+unicycler (0.4.8+dfsg-2) unstable; urgency=medium
+
+  * Autopkgtest: Restrictions: skip-not-installable
+    Closes: #945372
+  * Remove patches bowtie.patch that are missing from
+    debian/patches/series.
+  * Set upstream metadata fields: Repository-Browse.
+
+ -- Andreas Tille <tille@debian.org>  Wed, 04 Dec 2019 09:22:18 +0100
+
 unicycler (0.4.8+dfsg-1) unstable; urgency=medium
 
   [ Michael R. Crusoe ]

debian/patches/bowtie.patch

-Description: No idea how the test suite can be convinced to find the tools
-  Asked upstream for help in
-      https://github.com/rrwick/Unicycler/issues/114
-  This patch does not really help
-
---- a/unicycler/unicycler.py
-+++ b/unicycler/unicycler.py
-@@ -411,10 +411,10 @@ def get_arguments():
-                               help='Do not use Pilon to polish the final assembly (default: Pilon '
-                                    'is used)'
-                                    if show_all_args else argparse.SUPPRESS)
--    polish_group.add_argument('--bowtie2_path', type=str, default='bowtie2',
-+    polish_group.add_argument('--bowtie2_path', type=str, default='/usr/bin/bowtie2',
-                               help='Path to the bowtie2 executable'
-                                    if show_all_args else argparse.SUPPRESS)
--    polish_group.add_argument('--bowtie2_build_path', type=str, default='bowtie2-build',
-+    polish_group.add_argument('--bowtie2_build_path', type=str, default='/usr/bin/bowtie2-build',
-                               help='Path to the bowtie2_build executable'
-                                    if show_all_args else argparse.SUPPRESS)
-     polish_group.add_argument('--samtools_path', type=str, default='samtools',
---- a/test/test_dependencies.py
-+++ b/test/test_dependencies.py
-@@ -59,13 +59,13 @@ class TestDependencies(unittest.TestCase
-         self.assertEqual(ret_code, 1)
- 
-     def test_bowtie2_build_not_found(self):
--        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_build_path', 'not_a_real_path'])
-+        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_build_path', '/usr/bin'])
-         self.assertTrue(bool(re.search(r'bowtie2-build\s+not found', stdout)))
-         self.assertTrue('could not find bowtie2-build' in stderr)
-         self.assertEqual(ret_code, 1)
- 
-     def test_bowtie2_not_found(self):
--        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_path', 'not_a_real_path'])
-+        stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_path', '/usr/bin'])
-         self.assertTrue(bool(re.search(r'bowtie2\s+not found', stdout)))
-         self.assertTrue('could not find bowtie2' in stderr)
-         self.assertEqual(ret_code, 1)

debian/tests/control

 Tests: run-unit-test
 Depends: @, @builddeps@
-Restrictions: allow-stderr
+Restrictions: allow-stderr, skip-not-installable

debian/upstream/metadata

@@ -37,3 +37,4 @@ Registry:
 - Name: SciCrunch
   Entry: NA
 Repository: https://github.com/rrwick/Unicycler.git
+Repository-Browse: https://github.com/rrwick/Unicycler