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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/unicycler">Debian Med / unicycler</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/ca72ac59165374ff16eaba2af7096f60e8fd9137">ca72ac59</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T08:21:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest: Restrictions: skip-not-installable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/c0e14aefdcd129c17046674d36b415cd84f576f6">c0e14aef</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T08:22:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">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.
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/62d02b7986c27c4b66ace199342d0b97260578c9">62d02b79</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T08:22:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Repository-Browse.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/8c22dd061ff0c4bff44216b4ebb8234ac55884b6">8c22dd06</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-04T08:33:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#ea165a50ce3f89ecc15bb42511c92bba65370fd4">
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−
debian/patches/bowtie.patch
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
debian/upstream/metadata
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/unicycler/compare/5e0ac61653931fead4260da3c101cf3f82effc8c...8c22dd061ff0c4bff44216b4ebb8234ac55884b6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">unicycler (0.4.8+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Autopkgtest: Restrictions: skip-not-installable</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #945372</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Remove patches bowtie.patch that are missing from</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> debian/patches/series.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Set upstream metadata fields: Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 04 Dec 2019 09:22:18 +0100</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">unicycler (0.4.8+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<li id="ea165a50ce3f89ecc15bb42511c92bba65370fd4">
<a href="https://salsa.debian.org/med-team/unicycler/compare/5e0ac61653931fead4260da3c101cf3f82effc8c...8c22dd061ff0c4bff44216b4ebb8234ac55884b6#ea165a50ce3f89ecc15bb42511c92bba65370fd4"><strong>debian/patches/bowtie.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: No idea how the test suite can be convinced to find the tools</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"> Asked upstream for help in</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> https://github.com/rrwick/Unicycler/issues/114</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"> This patch does not really help</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/unicycler/unicycler.py</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/unicycler/unicycler.py</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -411,10 +411,10 @@</span> def get_arguments():</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> help='Do not use Pilon to polish the final assembly (default: Pilon '</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> 'is used)'</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> if show_all_args else argparse.SUPPRESS)</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- polish_group.add_argument('--bowtie2_path', type=str, default='bowtie2',</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ polish_group.add_argument('--bowtie2_path', type=str, default='/usr/bin/bowtie2',</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> help='Path to the bowtie2 executable'</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> if show_all_args else argparse.SUPPRESS)</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- polish_group.add_argument('--bowtie2_build_path', type=str, default='bowtie2-build',</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ polish_group.add_argument('--bowtie2_build_path', type=str, default='/usr/bin/bowtie2-build',</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> help='Path to the bowtie2_build executable'</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> if show_all_args else argparse.SUPPRESS)</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> polish_group.add_argument('--samtools_path', type=str, default='samtools',</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/test_dependencies.py</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/test_dependencies.py</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="p">@@ -59,13 +59,13 @@</span> class TestDependencies(unittest.TestCase</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> self.assertEqual(ret_code, 1)</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> def test_bowtie2_build_not_found(self):</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_build_path', 'not_a_real_path'])</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_build_path', '/usr/bin'])</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> self.assertTrue(bool(re.search(r'bowtie2-build\s+not found', stdout)))</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> self.assertTrue('could not find bowtie2-build' in stderr)</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> self.assertEqual(ret_code, 1)</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> def test_bowtie2_not_found(self):</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_path', 'not_a_real_path'])</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ stdout, stderr, ret_code = self.run_unicycler(['--bowtie2_path', '/usr/bin'])</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"> self.assertTrue(bool(re.search(r'bowtie2\s+not found', stdout)))</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"> self.assertTrue('could not find bowtie2' in stderr)</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> self.assertEqual(ret_code, 1)</span></pre>
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<a href="https://salsa.debian.org/med-team/unicycler/compare/5e0ac61653931fead4260da3c101cf3f82effc8c...8c22dd061ff0c4bff44216b4ebb8234ac55884b6#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: @, @builddeps@</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr<span class="idiff left right">, skip-not-installable</span></span></pre>
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<a href="https://salsa.debian.org/med-team/unicycler/compare/5e0ac61653931fead4260da3c101cf3f82effc8c...8c22dd061ff0c4bff44216b4ebb8234ac55884b6#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,3 +37,4 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">- Name: SciCrunch</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> Entry: NA</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Repository: https://github.com/rrwick/Unicycler.git</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Repository-Browse: https://github.com/rrwick/Unicycler</span></pre>
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