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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/q2-sample-classifier">Debian Med / q2-sample-classifier</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/341a19e5f0454279e758d2b10d9273d0f557d52e">341a19e5</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-25T02:29:39+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: Add depends on python3-distutils, q2-types, q2-feature-table
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<strong><a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/d2b7f845e808c2a52ad0425d3f4e624734382b5e">d2b7f845</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-25T02:29:50+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
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<strong><a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/commit/b2266ad700082dc1640bfb9db1eb7df594360f7e">b2266ad7</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-25T02:30:53+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
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<h4>5 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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debian/tests/control
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/compare/51f1dbc957466f837f2b3d37337782904627211d...b2266ad700082dc1640bfb9db1eb7df594360f7e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-sample-classifier (2020.11.1-2) UNRELEASED; 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"> * d/control: Add depends on python3-distutils,</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> q2-types, q2-feature-table</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add autopkgtests</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"> -- Nilesh Patra <nilesh@debian.org> Sun, 25 Jul 2021 02:30:21 +0530</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">q2-sample-classifier (2020.11.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/compare/51f1dbc957466f837f2b3d37337782904627211d...b2266ad700082dc1640bfb9db1eb7df594360f7e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" 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="22" 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">@@ -22,6 +22,9 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">python3</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">2020.11.0</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">distutils</span><span class="p">,</span></span>
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<td class="new_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">feature</span><span class="p">-</span><span class="n" style="color: #333;">table</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">plugin</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">machine</span> <span class="n" style="color: #333;">learning</span> <span class="n" style="color: #333;">prediction</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">sample</span> <span class="n" style="color: #333;">data</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span><span class="p">,</span> <span class="n" style="color: #333;">extensible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">decentralized</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">focus</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">transparency</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">enables</span></span>
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<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/compare/51f1dbc957466f837f2b3d37337782904627211d...b2266ad700082dc1640bfb9db1eb7df594360f7e#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">@@ -13,11 +13,11 @@ override_dh_auto_install:</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> rm -rf debian/q2-sample-classifier/usr/lib/python3.9/site-packages/q2_sample_classifier/__pycache__/</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> rm -rf debian/q2-sample-classifier/usr/lib/python3.9/site-packages/q2_sample_classifier/tests/__pycache__/</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">#<span class="idiff left"> </span>FIXME:<span class="idiff right"> modules cannot be registered at build time - ignoring build tests for now</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">#FIXME:</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"><span class="idiff left right">#</span>ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> <span class="idiff left">dh_</span>auto<span class="idiff">_</span>test<span class="idiff right"> || true</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"><span class="idiff left right">#</span>endif</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> <span class="idiff left">echo "I: Delaying true testing to </span>auto<span class="idiff">pkg</span>test<span class="idiff right">s since QIIME2 module cannot be registered at build time"</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> dh_auto_clean</span>
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<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/compare/51f1dbc957466f837f2b3d37337782904627211d...b2266ad700082dc1640bfb9db1eb7df594360f7e#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-pytest-cov</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr, skip-not-installable</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-sample-classifier/-/compare/51f1dbc957466f837f2b3d37337782904627211d...b2266ad700082dc1640bfb9db1eb7df594360f7e#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>q2_sample_classifier</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/lib/python3/dist-packages/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}*</span>/tests <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">ls</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> /usr/lib/python3/dist-packages/pytest_cov/__init__.py <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please install package python3-pytest-cov to run this script"</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run build-time tests</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">py.test-3 <span class="nt" style="color: #000080;">--cov</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span></span></pre>
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