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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/circlator">Debian Med / circlator</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/circlator/-/commit/77064f535de5c14476e4b940ecbf5b67f9f435ac">77064f53</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-10-25T03:44:39+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switch from nose -> pytest
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<strong><a href="https://salsa.debian.org/med-team/circlator/-/commit/d30b5789eb7d909f313b7e18e24d8589b9197de6">d30b5789</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-10-25T03:44:39+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#4f69e510f94ac966fba2b12f28de9cdd5b8933dd">
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+
debian/patches/switch-to-pytest.patch
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/circlator/-/compare/f5f1fb2324f59ad5d0416ad420533a02bada4b5f...d30b5789eb7d909f313b7e18e24d8589b9197de6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">circlator (1.5.6-6) 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"> * Team Upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Switch from nose -> pytest</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Mon, 25 Oct 2021 03:38:40 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">circlator (1.5.6-5) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Vagrant Cascadian ]</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/circlator/-/compare/f5f1fb2324f59ad5d0416ad420533a02bada4b5f...d30b5789eb7d909f313b7e18e24d8589b9197de6#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> python3-pysam,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> python3-pymummer,</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># Test-Depends:</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> python3-<span class="idiff left right">nose</span>,</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> python3-<span class="idiff left right">pytest</span>,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> spades,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> bwa (>= 0.7.12),</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> prodigal,</span>
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<a href="https://salsa.debian.org/med-team/circlator/-/compare/f5f1fb2324f59ad5d0416ad420533a02bada4b5f...d30b5789eb7d909f313b7e18e24d8589b9197de6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix_canu_detection.patch</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">switch-to-pytest.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/circlator/-/compare/f5f1fb2324f59ad5d0416ad420533a02bada4b5f...d30b5789eb7d909f313b7e18e24d8589b9197de6#4f69e510f94ac966fba2b12f28de9cdd5b8933dd"><strong>debian/patches/switch-to-pytest.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Switch from nose->pytest since the former is deprecated</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Nilesh Patra <nilesh@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Updated: 2021-10-25</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -15,8 +15,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> author_email='path-help@sanger.ac.uk',</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> url='https://github.com/sanger-pathogens/circlator',</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> scripts=glob.glob('scripts/*'),</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test_suite='nose.collector',</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tests_require=['nose >= 1.3'],</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ tests_require=['pytest'],</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> install_requires=[</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> 'openpyxl',</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> 'pyfastaq >= 3.12.1',</span></pre>
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<a href="https://salsa.debian.org/med-team/circlator/-/compare/f5f1fb2324f59ad5d0416ad420533a02bada4b5f...d30b5789eb7d909f313b7e18e24d8589b9197de6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -10,7 +10,7 @@ export LC_ALL=C.UTF-8</td>
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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">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> PYTHONPATH=$(CURDIR) <span class="idiff left">nose</span>test<span class="idiff">s</span>3 -v <span class="idiff right">--where=</span>circlator/tests</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> PYTHONPATH=$(CURDIR) <span class="idiff left">py</span>test<span class="idiff right">-</span>3 -v circlator/tests</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_installexamples:</span>
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<a href="https://salsa.debian.org/med-team/circlator/-/compare/f5f1fb2324f59ad5d0416ad420533a02bada4b5f...d30b5789eb7d909f313b7e18e24d8589b9197de6#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, python3-<span class="idiff left right">nose</span>, python3-all</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, python3-<span class="idiff left right">pytest</span>, python3-all</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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<a href="https://salsa.debian.org/med-team/circlator/-/compare/f5f1fb2324f59ad5d0416ad420533a02bada4b5f...d30b5789eb7d909f313b7e18e24d8589b9197de6#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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">...</td>
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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">@@ -17,4 +17,4 @@ cd "${AUTOPKGTEST_TMP}"</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar </span>xaf data.tar.xz</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s2" style="color: #d14;">"s/data_dir = os.path.join(modules_dir, 'tests', 'data')/data_dir = os.path.join(os.getcwd(), 'data')/"</span> <span class="k" style="font-weight: 600;">*</span>.py</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="idiff left">nose</span>test<span class="idiff">s3</span> <span class="nt" style="color: #000080;">-v</span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">.</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="idiff left">python3 </span><span class="nt" style="color: #000080;"><span class="idiff">-m</span></span><span class="idiff right"> py</span>test <span class="nt" style="color: #000080;">-v</span></span></pre>
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