Andreas Tille pushed to branch master at Debian Med / unicycler
Commits: ca72ac59 by Andreas Tille at 2019-12-04T08:21:59Z Autopkgtest: Restrictions: skip-not-installable - - - - - c0e14aef by Andreas Tille at 2019-12-04T08:22:17Z Remove patches bowtie.patch that are missing from debian/patches/series. Fixes lintian: patch-file-present-but-not-mentioned-in-series See https://lintian.debian.org/tags/patch-file-present-but-not-mentioned-in-series.html for more details. - - - - - 62d02b79 by Andreas Tille at 2019-12-04T08:22:17Z Set upstream metadata fields: Repository-Browse. - - - - - 8c22dd06 by Andreas Tille at 2019-12-04T08:33:10Z Upload to unstable - - - - - 4 changed files: - debian/changelog - − debian/patches/bowtie.patch - debian/tests/control - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +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 <[email protected]> Wed, 04 Dec 2019 09:22:18 +0100 + unicycler (0.4.8+dfsg-1) unstable; urgency=medium [ Michael R. Crusoe ] ===================================== debian/patches/bowtie.patch deleted ===================================== @@ -1,38 +0,0 @@ -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 ===================================== @@ -1,3 +1,3 @@ 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 View it on GitLab: https://salsa.debian.org/med-team/unicycler/compare/5e0ac61653931fead4260da3c101cf3f82effc8c...8c22dd061ff0c4bff44216b4ebb8234ac55884b6 -- View it on GitLab: https://salsa.debian.org/med-team/unicycler/compare/5e0ac61653931fead4260da3c101cf3f82effc8c...8c22dd061ff0c4bff44216b4ebb8234ac55884b6 You're receiving this email because of your account on salsa.debian.org.
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